[ { "text": "Quantum-chemistry-aided identification, synthesis and experimental\n validation of model systems for conformationally controlled reaction studies:\n Separation of the conformers of 2,3-dibromobuta-1,3-diene in the gas phase: The Diels-Alder cycloaddition, in which a diene reacts with a dienophile to\nform a cyclic compound, counts among the most important tools in organic\nsynthesis. Achieving a precise understanding of its mechanistic details on the\nquantum level requires new experimental and theoretical methods. Here, we\npresent an experimental approach that separates different diene conformers in a\nmolecular beam as a prerequisite for the investigation of their individual\ncycloaddition reaction kinetics and dynamics under single-collision conditions\nin the gas phase. A low- and high-level quantum-chemistry-based screening of\nmore than one hundred dienes identified 2,3-dibromobutadiene (DBB) as an\noptimal candidate for efficient separation of its gauche and s-trans conformers\nby electrostatic deflection. A preparation method for DBB was developed which\nenabled the generation of dense molecular beams of this compound. The\ntheoretical predictions of the molecular properties of DBB were validated by\nthe successful separation of the conformers in the molecular beam. A marked\ndifference in photofragment ion yields of the two conformers upon\nfemtosecond-laser pulse ionization was observed, pointing at a pronounced\nconformer-specific fragmentation dynamics of ionized DBB. Our work sets the\nstage for a rigorous examination of mechanistic models of cycloaddition\nreactions under controlled conditions in the gas phase.", "category": "physics_chem-ph" }, { "text": "Resonant diffusion of normal alkanes in zeolites: Effect of the zeolite\n structure and alkane molecule vibrations: Diffusion of normal alkanes in one-dimensional zeolites is theoretically\nstudied on the basis of the stochastic equation formalism. The calculated\ndiffusion coefficient accounts for the vibrations of the diffusing molecule and\nzeolite framework, molecule-zeolite interaction, and specific structure of the\nzeolite. It is shown that when the interaction potential is predominantly\ndetermined by the zeolite pore structure, the diffusion coefficient varies\nperiodically with the number of carbon atoms of the alkane molecule, a\nphenomenon called resonant diffusion. A criterion for observable resonance is\nobtained from the balance between the interaction potentials of the molecule\ndue to the atomic and pore structures of the zeolite. It shows that the\ndiffusion is not resonant in zeolites without pore structure, such as ZSM-12.\nMoreover, even in zeolites with developed pore structure no resonant dependence\nof the diffusion constant can be detected if the pore structure energy barriers\nare not at least three times higher than the atomic structure energy barriers.\nThe role of the alkane molecule vibrations is examined as well and a surprising\neffect of suppression of the diffusion in comparison with the case of a rigid\nmolecule is observed. This effect is explained with the balance between the\nstatic and dynamic interaction of the molecule and zeolite.", "category": "physics_chem-ph" }, { "text": "Near-exact treatment of seniority-zero ground and excited states with a\n Richardson-Gaudin mean-field: Eigenvectors of the reduced Bardeen-Cooper-Schrieffer Hamiltonian,\nRichardson-Gaudin (RG) states, are used as a variational wavefunction Ansatz\nfor strongly-correlated electronic systems. These states are geminal products\nwhose coefficients are solutions of non-linear equations. Previous results\nshowed un-physical behaviour but in this contribution it is shown that with\nonly the variational solution for the ground state, all the seniority-zero\nstates are quite well approximated. The difficulty is in choosing the correct\nRG state. The systems studied showed a clear choice and we expect it should\nalways be possible to reason physically which state to choose.", "category": "physics_chem-ph" }, { "text": "Associated Legendre Polynomials and Spherical Harmonics Computation for\n Chemistry Applications: Associated Legendre polynomials and spherical harmonics are central to\ncalculations in many fields of science and mathematics - not only chemistry but\ncomputer graphics, magnetic, seismology and geodesy. There are a number of\nalgorithms for these functions published since 1960 but none of them satisfy\nour requirements. In this paper, we present a comprehensive review of\nalgorithms in the literature and, based on them, propose an efficient and\naccurate code for quantum chemistry. Our requirements are to efficiently\ncalculate these functions for all non-negative integer degrees and orders up to\na given number (<=1000) and the absolute or the relative error of each\ncalculated value should not exceed 10E-10. We achieve this by normalizing the\npolynomials, employing efficient and stable recurrence relations, and\nprecomputing coefficients. The algorithm presented here is straightforward and\nmay be used in other areas of science.", "category": "physics_chem-ph" }, { "text": "Ab initio atom-atom potentials using CamCASP: Many-body potentials for\n the pyridine dimer: In Part I of this two-part investigation we described a methodology for the\ndevelopment of robust, analytic, many-body atom-atom potentials for small\norganic molecules from first principles and demonstrated how the CamCASP\nprogram can be used to derive the damped, distributed multipole models for\npyridine. Here we demonstrate how the theoretical ideas for the short-range\nmodels described in Part I, which are implemented in the CamCASP suite of\nprograms, can be used to develop a series of many-body potentials for the\npyridine system. Even the simplest of these potentials exhibit r.m.s. errors of\nonly about 0.6kJ mol-1 for the low-energy pyridine dimers, significantly\nsurpassing the best empirical potentials. Our best model is shown to support\neight stable minima, four of which have not been reported in the literature\nbefore. Further, the functional form can be made systematically more elaborate\nso as to improve the accuracy without a significant increase in the human-time\nspent in their generation. We investigate the effects of anisotropy, rank of\nmultipoles, and choice of polarizability and dispersion models.", "category": "physics_chem-ph" }, { "text": "Time-dependent optimized coupled-cluster method for multielectron\n dynamics IV: Approximate consideration of the triple excitation amplitudes: We present a cost-effective treatment of the triple excitation amplitudes in\nthe time-dependent optimized coupled-cluster (TD-OCC) framework called\nTD-OCCDT(4) for studying intense laser-driven multielectron dynamics. It\nconsiders triple excitation amplitudes correct up to fourth-order in many-body\nperturbation theory and achieves a computational scaling of O(N7), with N being\nthe number of active orbital functions. This method is applied to the electron\ndynamics in Ne and Ar atoms exposed to an intense near-infrared laser pulse\nwith various intensities. We benchmark our results against the time-dependent\ncomplete-active-space self-consistent field (TD-CASSCF), time-dependent\noptimized coupled-cluster with double and triple excitations (TD-OCCDT),\ntime-dependent optimized coupled-cluster with double excitations (TD-OCCD), and\nthe time-dependent Hartree-Fock (TDHF) methods to understand how this\napproximate scheme performs in describing nonperturbatively nonlinear\nphenomena, such as field-induced ionization and high-harmonic generation. We\nfind that the TD-OCCDT(4) method performs equally well as the TD-OCCDT method,\nalmost perfectly reproducing the results of fully-correlated TD-CASSCF with a\nmore favorable computational scaling.", "category": "physics_chem-ph" }, { "text": "Interplay of Fluorescence and Phosphorescence in Organic Biluminescent\n Emitters: Biluminescent organic emitters show simultaneous fluorescence and\nphosphorescence at room temperature. So far, the optimization of the room\ntemperature phosphorescence (RTP) in these materials has drawn the attention of\nresearch. However, the continuous wave operation of these emitters will\nconsequently turn them into systems with vastly imbalanced singlet and triplet\npopulations, which is due to the respective excited state lifetimes. This study\nreports on the exciton dynamics of the biluminophore NPB\n(N,N-di(1-naphthyl)-N,N-diphenyl-(1,1-biphenyl)-4,4-diamine). In the extreme\ncase, the singlet and triplet exciton lifetimes stretch from 3 ns to 300 ms,\nrespectively. Through sample engineering and oxygen quenching experiments, the\ntriplet exciton density can be controlled over several orders of magnitude\nallowing to studying exciton interactions between singlet and triplet\nmanifolds. The results show, that singlet-triplet annihilation reduces the\noverall biluminescence efficiency already at moderate excitation levels.\nAdditionally, the presented system represents an illustrative role model to\nstudy excitonic effects in organic materials.", "category": "physics_chem-ph" }, { "text": "Can disorder enhance incoherent exciton diffusion?: Recent experiments aimed at probing the dynamics of excitons have revealed\nthat semiconducting films composed of disordered molecular subunits, unlike\nexpectations for their perfectly ordered counterparts, can exhibit a\ntime-dependent diffusivity in which the effective early time diffusion constant\nis larger than that of the steady state. This observation has led to\nspeculation about what role, if any, microscopic disorder may play in enhancing\nexciton transport properties. In this article, we present the results of a\nmodel study aimed at addressing this point. Specifically, we present a general\nmodel, based upon F\\\"orster theory, for incoherent exciton diffusion in a\nmaterial composed of independent molecular subunits with static energetic\ndisorder. Energetic disorder leads to heterogeneity in molecule-to-molecule\ntransition rates which we demonstrate has two important consequences related to\nexciton transport. First, the distribution of local site-specific diffusivity\nis broadened in a manner that results in a decrease in average exciton\ndiffusivity relative to that in a perfectly ordered film. Second, since\nexcitons prefer to make transitions that are downhill in energy, the steady\nstate distribution of exciton energies is biased towards low energy molecular\nsubunits, those that exhibit reduced diffusivity relative to a perfectly\nordered film. These effects combine to reduce the net diffusivity in a manner\nthat is time dependent and grows more pronounced as disorder is increased.\nNotably, however, we demonstrate that the presence of energetic disorder can\ngive rise to a population of molecular subunits with exciton transfer rates\nexceeding that of subunits in an energetically uniform material. Such\nenhancements may play an important role in processes that are sensitive to\nmolecular-scale fluctuations in exciton density field.", "category": "physics_chem-ph" }, { "text": "Robust Parahydrogen-Induced Polarization at High Concentrations: Parahydrogen-Induced Polarization (PHIP) is a potent technique for generating\ntarget molecules with high nuclear spin polarization. The PHIP process involves\na chemical reaction between parahydrogen and a target molecule, followed by the\ntransformation of nuclear singlet spin order into magnetization of a designated\nnucleus through magnetic field manipulations. Although the\nsinglet-to-magnetization polarization transfer process works effectively at\nmoderate concentrations, it is observed to become much less efficient at high\nmolar polarization, defined as the product of polarization and concentration.\nThis strong dependence on the molar polarization is attributed to interference\nfrom the field produced by the sample's magnetization during polarization\ntransfer, which leads to complex dynamics and can severely impact the\nscalability of the technique. We address this challenge with a pulse sequence\nthat negates the influence of the distant dipolar field, while simultaneously\nachieving singlet-to-magnetization polarization transfer to the desired target\nspins, free from restrictions on the molar polarization.", "category": "physics_chem-ph" }, { "text": "On the thermodynamic derivation of Nernst relation: What is the maximum voltage of a cell with a given electrochemical reaction?\nThe answer to this question has been given more than a century ago by Walther\nNernst and bears his name. Unfortunately, the assumptions behind the answer\nhave been forgotten by many authors, which leads to wrong forms of the Nernst\nrelation. Such mistakes can be overcome by applying a correct thermodynamic\nderivation independently of the form in which the reaction is written. The\ncorrect form of Nernst relation is important for instance in modelling of\nvanadium redox flow batteries or zinc-air batteries. In particular, the\npresence of corrosion can impact the OCV in the case of zinc-air batteries.", "category": "physics_chem-ph" }, { "text": "Model of Charge Transfer Collisions Between $C_{60}$ and Slow Ions: A semi-classical model describing the charge transfer collisions of $C_{60}$\nfullerene with different slow ions has been developed to explain available\nexperimental data. This data reveals multiple Breit-Wigner like peaks in the\ncross sections, with subsequent peaks of reactive cross sections decreasing in\nmagnitude. Calculations of the charge transfer probabilities and cross sections\nfor quasi-resonant and reactive collisions have been performed using\nsemi-empirical potentials of interaction between fullerenes and ion\nprojectiles. All computations have been carried out with realistic wave\nfunctions for $C_{60}$'s valence electrons derived from the simplified jellium\nmodel. The quality of these electron wave functions have been successfully\nverified by comparing theoretical calculations and experimental data on the\nsmall angle cross sections of resonant $C_{60}+ C_{60}^+$ collisions. Using the\nsemi-empirical potentials to describe resonant scattering phenomena in $C_{60}$\ncollisions with ions and Landau-Zener charge transfer theory, we calculated\ntheoretical cross sections for various $C_{60}$ charge transfer and\nfragmentation reactions which agree with experiments.", "category": "physics_chem-ph" }, { "text": "Blackbody radiation and thermal effects on chemical reactions and phase\n transitions in cavities: An important question in polariton chemistry is whether reacting molecules\nare in thermal equilibrium with their surroundings. If not, can experimental\nchanges observed in reaction rates of molecules in a cavity (even without\noptical pumping) be attributed to a higher/lower temperature inside the cavity?\nIn this work, we address this question by computing temperature differences\nbetween reacting molecules inside a cavity and the air outside. We find this\ntemperature difference to be negligible for most reactions. On the other hand,\nfor phase transitions inside cavities, as the temperature of the material is\nactively maintained by a heating/cooling source in experiments, we show\ncavities can modify observed transition temperatures when mirrors and cavity\nwindows are ideal (non-absorbing); however, this modification vanishes when\nreal mirrors and windows are used. Finally, we find substantial differences in\nblackbody spectral energy density between free space and infrared cavities,\nwhich reveal resonance effects and could potentially play a role in explaining\nchanges in chemical reactivity in the dark.", "category": "physics_chem-ph" }, { "text": "Measurements of trap dynamics of cold OH molecules using resonance\n enhanced multiphoton ionization: Trapping cold, chemically important molecules with electromagnetic fields is\na useful technique to study small molecules and their interactions. Traps\nprovide long interaction times that are needed to precisely examine these low\ndensity molecular samples. However, the trapping fields lead to non-uniform\nmolecular density distributions in these systems. Therefore, it is important to\nbe able to experimentally characterize the spatial density distribution in the\ntrap. Ionizing molecules in different locations in the trap using resonance\nenhanced multiphoton ionization (REMPI) and detecting the resulting ions can be\nused to probe the density distribution even with the low density present in\nthese experiments because of the extremely high efficiency of detection. Until\nrecently, one of the most chemically important molecules, OH, did not have a\nconvenient REMPI scheme. Here, we use a newly developed 1 + 1' REMPI scheme to\ndetect trapped cold OH molecules. We use this capability to measure trap\ndynamics of the central density of the cloud and the density distribution.\nThese types of measurements can be used to optimize loading of molecules into\ntraps, as well as to help characterize the energy distribution, which is\ncritical knowledge for interpreting molecular collision experiments.", "category": "physics_chem-ph" }, { "text": "Why the traditional concept of local hardness does not work: Finding a proper local measure of chemical hardness has been a long-standing\naim of density functional theory. The traditional approach to defining a local\nhardness index, by the derivative of the chemical potential with respect to the\nelectron density subject to the constraint of a fixed external potential, has\nraised several questions, and its chemical applicability has proved to be\nlimited. Here, we point out that the only actual possibility to obtain a local\nhardness measure in the traditional approach emerges if the external potential\nconstraint is dropped; consequently, utilizing the ambiguity of a restricted\nchemical potential derivative is not an option to gain alternative definitions\nof local hardness. At the same time, however, the arising local hardness\nconcept turns out to be fatally undermined by its inherent connection with the\nasymptotic value of the second derivative of the universal density functional.\nThe only other local hardness concept one may deduce from the traditional\ndefinition is the one that gives a constant value, the global hardness itself,\nthroughout an electron system in its ground state. Consequently, the\ntraditional approach is in principle incapable of delivering a local hardness\nindicator. The parallel case of defining a local version of the chemical\npotential itself is also outlined, arriving at a similar conclusion. Namely,\nthe only local chemical potential concept that can be gained from a definition\ndE[n]/dn(r)|v is the one that gives a constant, mu itself, for electron systems\nin their ground state.", "category": "physics_chem-ph" }, { "text": "Understanding and eliminating spurious modes in variational Monte Carlo\n using collective variables: The use of neural network parametrizations to represent the ground state in\nvariational Monte Carlo (VMC) calculations has generated intense interest in\nrecent years. However, as we demonstrate in the context of the periodic\nHeisenberg spin chain, this approach can produce unreliable wave function\napproximations. One of the most obvious signs of failure is the occurrence of\nrandom, persistent spikes in the energy estimate during training. These energy\nspikes are caused by regions of configuration space that are over-represented\nby the wave function density, which are called ``spurious modes'' in the\nmachine learning literature. After exploring these spurious modes in detail, we\ndemonstrate that a collective-variable-based penalization yields a\nsubstantially more robust training procedure, preventing the formation of\nspurious modes and improving the accuracy of energy estimates. Because the\npenalization scheme is cheap to implement and is not specific to the particular\nmodel studied here, it can be extended to other applications of VMC where a\nreasonable choice of collective variable is available.", "category": "physics_chem-ph" }, { "text": "The structure of the density-potential mapping. Part II: Including\n magnetic fields: The Hohenberg-Kohn theorem of density-functional theory (DFT) is broadly\nconsidered the conceptual basis for a full characterization of an electronic\nsystem in its ground state by just the one-body particle density. In this\nPart~II of a series of two articles, we aim at clarifying the status of this\ntheorem within different extensions of DFT including magnetic fields. We will\nin particular discuss current-density-functional theory (CDFT) and review the\ndifferent formulations known in the literature, including the conventional\nparamagnetic CDFT and some non-standard alternatives. For the former, it is\nknown that the Hohenberg-Kohn theorem is no longer valid due to\ncounterexamples. Nonetheless, paramagnetic CDFT has the mathematical framework\nclosest to standard DFT and, just like in standard DFT, non-differentiability\nof the density functional can be mitigated through Moreau-Yosida\nregularization. Interesting insights can be drawn from both\nMaxwell-Schr\\\"odinger DFT and quantum-electrodynamical DFT, which are also\ndiscussed here.", "category": "physics_chem-ph" }, { "text": "Resonant multiphoton ionisation probe of the photodissociation dynamics\n of ammonia: The dissociation dynamics of the $\\tilde{A}$-state of ammonia have been\nstudied using a resonant multiphoton ionisation probe in a photoelectron\nspectroscopy experiment. The use of a resonant intermediate in the multiphoton\nionisation process changes the ionisation propensity, allowing access to\ndifferent ion states when compared with equivalent single photon ionisation\nexperiments. Ionisation through the $E'$ $^1$A$_1'$ Rydberg intermediate means\nwe maintain overlap with the ion state for an extended period allowing us to\nmonitor the excited state population for several hundred femtoseconds. The\nvibrational states in the photoelectron spectrum show two distinct timescales,\n200 fs and 320 fs, that we assign to the non-adiabatic and adiabatic\ndissociation processes respectively. The different timescales derive from\ndifferences in the wavepacket trajectories for the two dissociation pathways\nthat resonantly excite different vibrational states in the intermediate Rydberg\nstate. The timescales are similar to those obtained from time resolved ion\nkinetic energy release measurements, suggesting we can measure the different\ntrajectories taken out to the region of conical intersection.", "category": "physics_chem-ph" }, { "text": "Quantum simulations of neutral water clusters and singly-charged water\n cluster anions: We report a computational study of the structural and energetic properties of\nwater clustersand singly-charged water cluster anions containing from 20 to 573\nwater molecules. We have used both a classical and a quantum description of the\nmolecular degrees of freedom. Water intra and inter-molecular interactions have\nbeen modelled through the SPC/F model, while the water-excess electron\ninteraction has been described via the well-known Turi-Borgis potential. We\nfind that in general the quantum effects of the water degrees of freedom are\nsmall, but they do influence the cluster-size at which the excess electron\nstabilises inside the cluster, which occurs at smaller cluster sizes when\nquantum effects are taken into consideration.", "category": "physics_chem-ph" }, { "text": "Robust and Bright Photoluminescence from Colloidal Nanocrystal /\n Al$_2$O$_3$ Composite Films fabricated by Atomic Layer Deposition: Colloidal nanocrystals are a promising fluorescent class of materials, whose\nspontaneous emission features can be tuned over a broad spectral range via\ntheir composition, geometry and size. However, towards embedding nanocrystals\nfilms in elaborated device geometries, one significant drawback is the\nsensitivity of their emission properties on further fabrication processes like\nlithography, metal or oxide deposition, etc. In this work, we demonstrate how\nbright emitting and robust thin films can be obtained by combining nanocrystal\ndeposition from solutions via spin2 coating with subsequent atomic layer\ndeposition of alumina. For the resulting composite films, the layer thickness\ncan be controlled on the nanoscale, and their refractive index can be finely\ntuned by the amount of deposited alumina. Ellipsometry is used to measure the\nreal and imaginary part of the dielectric permittivity, which gives direct\naccess to the wavelength dependent refractive index absorbance of the film.\nDetailed analysis of the photophysics of thin films of core-shell nanocrystal\nwith different shape and different shell thickness allow to correlate the\nbehavior of the photoluminescence and of the decay life time to the changes in\nthe non-radiative rate that are induced by the alumina deposition. We show that\nthe photoemission properties of such composite films are stable in wavelength\nand intensity over several months, and that the photoluminescence completely\nrecovers from heating processes up to 240$^\\circ$C. The latter is particularly\ninteresting, since it demonstrates robustness to the typical heat treatment\nthat is needed in several process steps like resist-based lithography and\ndeposition by thermal or electron beam evaporation of metals or oxides.", "category": "physics_chem-ph" }, { "text": "Computer simulation study of surface wave dynamics at the crystal--melt\n interface: We study, by means of computer simulations, the crystal-melt interface of\nthree different systems: hard-spheres, Lennard Jones and the TIP4P/2005 water\nmodel. In particular, we focus on the dynamics of surface waves. We observe\nthat the processes involved in the relaxation of surface waves are\ncharacterized by distinct time scales: a slow one related to the continuous\nrecrystallization and melting, that is governed by capillary forces; and a fast\none which we suggest to be due to a combination of processes that quickly cause\nsmall perturbations to the shape of the interface (like e. g. Rayleigh waves,\nsubdiffusion, or attachment/detachment of particles to/from the crystal). The\nrelaxation of surface waves becomes dominated by the slow process as the\nwavelength increases. Moreover, we see that the slow relaxation is not\ninfluenced by the details of the microscopic dynamics. In a time scale\ncharacteristic for the diffusion of the liquid phase, the relaxation dynamics\nof the crystal-melt interface of water is around one order of magnitude slower\nthan that of Lennard Jones or hard spheres, which we ascribe to the presence of\norientational degrees of freedom in the water molecule. Finally, we estimate\nthe rate of crystal growth from our analysis of the capillary wave dynamics and\ncompare it with previous simulation studies and with experiments for the case\nof water.", "category": "physics_chem-ph" }, { "text": "Chemical Bonding in Many Electron Molecules: Chemical bonding is the stabilization of a composite molecular system caused\nby different interactions in and between the subsystems, among the strong kinds\nof bonding is covalent bonding especially important. Characteristic for\ncovalent bonding are small atom groups with short distances between the\ninvolved atoms, indicating that covalent bonding is essentially a local effect,\naccording to Lewis, this is caused by shared electron pairs. However, the\nenergetic stabilization is an approximately additive one-electron effect, as\nwas shown by Ruedenberg and coworkers. In systems composed of many-electron\nsubsystems, the fermionic character of the electrons determines the structure\nof the electron distribution in a subsystem, and it is decisive for the local\ninteractions between the subsystems. Especially important is the Pauli\nexclusion principle (PEP), which directs the relative positions of identical\nelectrons. Spin and charge rearrangements are of utmost importance for chemical\nbonding. Quantum chemical methods like CASSCF (complete active space SCF), also\ncalled FORS (fully optimized reaction space), are made to cover all such\nprocesses. The standard building blocks of CASSCF wave functions are\ndelocalized molecular orbitals, which cannot display local effects. OVB\n(orthogonal valence bond) is a method to analyze CASSCF wave functions and to\nreveal local processes that are responsible for both the energetic aspects of\nbonding and the spatial structure of the stabilized system. This is shown by\nanalyzing dissociation of ethene, disilene, and silaethene, and the\ncorresponding reverse reactions. Aspects of diabaticity of the reactions and\nentanglement of subsystems are discussed.", "category": "physics_chem-ph" }, { "text": "Solvation and Transport of Lithium Ions in Deep Eutectic Solvents: Lithium based deep eutectic solvents (DESs) are excellent candidates for\neco-friendly electrolytes in lithium ion batteries. While some of these DES\nhave shown promising results, a clear mechanism of lithium ion transport in\nDESs is not yet established. This work reports the study on the solvation and\ntransport of lithium in a DES made from lithium perchlorate and acetamide using\nMolecular Dynamics (MD) simulation and neutron scattering techniques. Based on\nhydrogen bonding (H-bonding) of acetamide with neighbouring molecules/ions, two\nstates are largely prevalent: 1) acetamide molecules which are H-bonded to\nlithium ions (~ 36 %) and 2) acetamide molecules that are entirely free (~\n58%). Analysing their stochastic dynamics independently, it is observed that\nthe long-range diffusion of the former is significantly slower than the latter\none. This is also validated from the neutron scattering experiment on the same\nDES system. Further, the analysis the lithium dynamics shows that the diffusion\nof acetamide molecules in the first category is strongly coupled to that of\nlithium ions. On an average the lithium ions are H-bonded to ~ 3.2 acetamide\nmolecules in their first solvation. These observations are further bolstered\nthrough the analysis of the H-bond correlation function between acetamide and\nlithium ions, which show that ~ 90% of lithium ionic transport is achieved by\nvehicular motion where the ions diffuse along with its first solvation shell.\nThe findings of this work are an important advancement in understanding\nsolvation and transport of lithium ion in DES.", "category": "physics_chem-ph" }, { "text": "Relativistic short-range exchange energy functionals beyond the\n local-density approximation: We develop relativistic short-range exchange energy functionals for\nfour-component relativistic range-separated density-functional theory using a\nDirac-Coulomb Hamiltonian in the no-pair approximation. We show how to improve\nthe short-range local-density approximation exchange functional for large\nrange-separation parameters by using the on-top exchange pair density as a new\nvariable. We also develop a relativistic short-range generalized-gradient\napproximation exchange functional which further increases the accuracy for\nsmall range-separation parameters. Tests on the helium, beryllium, neon, and\nargon isoelectronic series up to high nuclear charges show that this latter\nfunctional gives exchange energies with a maximal relative percentage error of\n3 %. The development of this exchange functional represents a step forward for\nthe application of four-component relativistic range-separated\ndensity-functional theory to chemical compounds with heavy elements.", "category": "physics_chem-ph" }, { "text": "A perspective on the microscopic pressure (stress) tensor: history,\n current understanding, and future challenges: The pressure tensor (equivalent to the negative stress tensor) at both\nmicroscopic and macroscopic levels is fundamental to many aspects of\nengineering and science, including fluid dynamics, solid mechanics, biophysics,\nand thermodynamics. In this perspective paper, we review methods to calculate\nthe microscopic pressure tensor. Connections between different pressure forms\nfor equilibrium and non-equilibrium systems are established. We also point out\nseveral challenges in the field, including the historical controversies over\nthe definition of the microscopic pressure tensor; the difficulties with\nmany-body and long-range potentials; the insufficiency of software and\ncomputational tools; and the lack of experimental routes to probe the pressure\ntensor at the nanoscale. Possible future directions are suggested.", "category": "physics_chem-ph" }, { "text": "Machine learning frontier orbital energies of nanodiamonds: Nanodiamonds have a wide range of applications including catalysis, sensing,\ntribology and biomedicine. To leverage nanodiamond design via machine learning,\nwe introduce the new dataset ND5k, consisting of 5,089 diamondoid and\nnanodiamond structures and their frontier orbital energies. ND5k structures are\noptimized via tight-binding density functional theory (DFTB) and their frontier\norbital energies are computed using density functional theory (DFT) with the\nPBE0 hybrid functional. We also compare recent machine learning models for\npredicting frontier orbital energies for similar structures as they have been\ntrained on (interpolation on ND5k), and we test their abilities to extrapolate\npredictions to larger structures. For both the interpolation and extrapolation\ntask, we find best performance using the equivariant graph neural network\nPaiNN. The second best results are achieved with a message passing neural\nnetwork using a tailored set of atomic descriptors proposed here.", "category": "physics_chem-ph" }, { "text": "Low-energy spectrum of iron-sulfur clusters directly from many-particle\n quantum mechanics: FeS clusters are a universal biological motif. They carry out electron\ntransfer, redox chemistry, and even oxygen sensing, in diverse processes\nincluding nitrogen fixation, respiration, and photosynthesis. The low-lying\nelectronic states are key to their remarkable reactivity, but cannot be\ndirectly observed. Here we present the first ever quantum calculation of the\nelectronic levels of [2Fe-2S] and [4Fe-4S] clusters free from any model\nassumptions. Our results highlight limitations of long-standing models of their\nelectronic structure. In particular, we demonstrate that the widely used\nHeisenberg-Double-Exchange model underestimates the number of states by 1-2\norders of magnitude, which can conclusively be traced to the absence of Fe\nd$\\rightarrow$d excitations, thought to be important in these clusters.\nFurther, the electronic energy levels of even the same spin are dense on the\nscale of vibrational fluctuations, and this provides a natural explanation for\nthe ubiquity of these clusters in nature for catalyzing reactions.", "category": "physics_chem-ph" }, { "text": "Ultrafast charge transfer processes accompanying KLL Auger decay in\n aqueous KCl solution: X-ray photoelectron spectroscopy (XPS) and KLL Auger spectra of aqueous KCl\nsolution were measured for the K$^+$ and Cl$^-$ edges. While the XPS spectra of\npotassium and chloride have similar structures, both exhibiting only weak\nsatellite structures near the main line, the Auger spectra of these\nisoelectronic ions differ dramatically. A very strong satellite peak was found\nin the K$^+$ KLL Auger spectrum at the low kinetic energy side of the $^1$D\nstate. Using equivalent core models and ab initio calculations this spectral\nstructure was assigned to electron transfer processes from solvent water\nmolecules to the solvated K$^+$ cation. Contrary to the potassium case, no\nextra peak was found in the KLL Auger spectrum of solvated Cl$^-$ indicating on\na strong dependence of the underlying processes on ionic charge. The observed\ncharge transfer processes are suggested to play an important role in charge\nredistribution following single and multiple core-hole creation in atomic and\nmolecular systems placed into an environment.", "category": "physics_chem-ph" }, { "text": "Dramatic changes in electronic structure revealed by fractionally\n charged nuclei: Discontinuous changes in the electronic structure upon infinitesimal changes\nto the Hamiltonian are demonstrated. Remarkably, these are revealed in one and\ntwo electron molecular systems if the realm of the nuclear charge is extended\nto be fractional. Dramatic changes in the electron density from full\nconfiguration interaction are observed in real space illustrating key\nintricacies of electronic structure including the transfer, hopping and removal\nof electrons. Physically, this is due to the particle nature of electrons and\nmanifests itself theoretically as a diverging linear density response function\nor an energy derivative discontinuity that occurs at constant number of\nelectrons. This is essential to correctly describe real physical processes,\nfrom chemical reactions to electron transport and metal-insulator transitions.\nThe dramatic errors of DFT are seen in real space as this physics is missing\nfrom currently used approximations and poses a great challenge for the\ndevelopment of new electronic structure methods.", "category": "physics_chem-ph" }, { "text": "Impact of Electron-Withdrawing Groups on Ion Transport and Structure in\n Lithium Borate Ionic Liquids: Among the distinctive structural features of lithium ionic liquids (LILs), a\nnovel class of single-component electrolytes, the variation of the\nelectron-withdrawing group stands out as a key factor in determining their\ndynamics. To understand this phenomenon, we conducted molecular dynamics (MD)\nsimulations for LILs based on hexafluoro-2-propanoxy (LIL2),\nhexafluoro-2-methyl-2-propanoxy (LIL4), and trifluoro-2-propanoxy (LIL6)\nderivatives. Results revealed that correlated ion dynamics govern the general\ntransport characteristics in LILs, while the electron-withdrawing group\nregulates the Li transport mechanism. Upon saturation by fluorine atoms, LILs\nexhibit higher inhomogeneity in their transport and structure properties.\nStrong coordination along the ethoxide group promotes jumps of Li across\npositive domains, while in fluorine-poor LILs, stronger coordination in\nproximity to boron atoms carries the anion along Li transport. Understanding\nthe results of MD simulation will aid the further design and widespread use of\nthis class of electrolytes in production of the energy storage and conversion\ndevices", "category": "physics_chem-ph" }, { "text": "Attosecond-resolved photoionization of chiral molecules: Chiral light-matter interactions have been investigated for two centuries,\nleading to the discovery of many chiroptical processes used for discrimination\nof enantiomers. Whereas most chiroptical effects result from a response of\nbound electrons, photoionization can produce much stronger chiral signals that\nmanifest as asymmetries in the angular distribution of the photoelectrons along\nthe light propagation axis. Here we implement a self-referenced attosecond\nphotoelectron interferometry to measure the temporal profile of the forward and\nbackward electron wavepackets emitted upon photoionization of camphor by\ncircularly polarized laser pulses. We found a delay between electrons ejected\nforward and backward, which depends on the ejection angle and reaches 24\nattoseconds. The asymmetric temporal shape of electron wavepackets emitted\nthrough an autoionizing state further reveals the chiral character of\nstrongly-correlated electronic dynamics.", "category": "physics_chem-ph" }, { "text": "Electron paramagnetic resonance g-tensors from state interaction\n spin-orbit coupling density matrix renormalization group: We present a state interaction spin-orbit coupling method to calculate\nelectron paramagnetic resonance (EPR) $g$-tensors from density matrix\nrenormalization group wavefunctions. We apply the technique to compute\n$g$-tensors for the \\ce{TiF3} and \\ce{CuCl4^2-} complexes, a [2Fe-2S] model of\nthe active center of ferredoxins, and a \\ce{Mn4CaO5} model of the S2 state of\nthe oxygen evolving complex. These calculations raise the prospects of\ndetermining $g$-tensors in multireference calculations with a large number of\nopen shells.", "category": "physics_chem-ph" }, { "text": "PAH chemistry at eV internal energies. 2. Ring alteration and\n dissociation: Recognized as important interstellar constituents, polycyclic aromatic\nhydrocarbons (PAHs) have been intensively studied in astrochemistry and their\nspectroscopy, thermodynamics, dynamics, and fragmentations are now amply\ndocumented. There exists typical alternatives to the ground-state regular\nplanar structures of PAHs, as long as they bear internal energies in the range\n1-10 eV. Resulting from intramolecular rearrangements, such high-lying minima\non the potential- energy surfaces should be taken into consideration in the\nstudies of PAH processing in astrophysical conditions. Resting upon DFT\ncalculations mainly performed on two emblematic PAH representatives, coronene\nand pyrene, in their neutral and mono and multi-cationic states, this second\nsurvey addresses the following alternatives: (1) opened forms containing\nethynyl or 2- butynyl groups, (2) vinylidene isomers, in which phenanthrene\npatterns are reorganized into dibenzofulvene ones, (3) twisted forms, where\nexternal CH=CH bonds can be partly twisted, and (4) bicyclobutane forms, in\nwhich the latter are integrated in saturated bicyclic forms. A few scenarios\nfor elimination of fragments H, H2, C2H2 and C2H4 are explored. As far as\npossible, familiar concepts of organic chemistry, such as aromaticity or Clar's\nrules, are invoked for interpretations.", "category": "physics_chem-ph" }, { "text": "Predicting acoustic relaxation absorption in gas mixtures for extraction\n of composition relaxation contributions: The existing molecular relaxation models based on both parallel relaxation\ntheory and series relaxation theory cannot extract the contributions of gas\ncompositions to acoustic relaxation absorption in mixtures. In this paper, we\npropose an analytical model to predict acoustic relaxation absorption and\nclarify composition relaxation contributions based on the rate-determining\nenergy transfer processes in molecular relaxation in excitable gases. By\ncombining parallel and series relaxation theory, the proposed model suggests\nthat the vibration-translation process of the lowest vibrational mode in each\ncomposition provides the primary deexcitation path of the relaxation energy,\nand the rate-determining vibration-vibration processes between the lowest mode\nand others dominate the coupling energy transfer between different modes. Thus,\neach gas composition contributes directly one single relaxation process to the\nmolecular relaxation in mixture, which can be illustrated by the decomposed\nacoustic relaxation absorption spectrum of the single relaxation process. The\nproposed model is validated by simulation results in good agreement with\nexperimental data such as $\\mathrm{N_2}$, $\\mathrm{O_2}$, $\\mathrm{CO_2}$,\n$\\mathrm{CH_4}$ and their mixtures.", "category": "physics_chem-ph" }, { "text": "Reactions between cold methyl halide molecules and alkali-metal atoms: We investigate the potential energy surfaces and activation energies for\nreactions between methyl halide molecules CH$_{3}X$ ($X$ = F, Cl, Br, I) and\nalkali-metal atoms $A$ ($A$ = Li, Na, K, Rb) using high-level {\\it ab initio}\ncalculations. We examine the anisotropy of each intermolecular potential energy\nsurface (PES) and the mechanism and energetics of the only available exothermic\nreaction pathway, ${\\rm CH}_{3}X+A\\rightarrow{\\rm CH}_{3}+AX$. The region of\nthe transition state is explored using two-dimensional PES cuts and estimates\nof the activation energies are inferred. Nearly all combinations of methyl\nhalide and alkali-metal atom have positive barrier heights, indicating that\nreactions at low temperatures will be slow.", "category": "physics_chem-ph" }, { "text": "A comprehensive guide for measuring total vanadium concentration and\n state of charge of vanadium electrolytes using UV-Visible spectroscopy: This paper presents an exhaustive how-to guide on measuring the total\nvanadium concentration and state of charge of vanadium electrolytes using\nUV-Visible spectroscopy. The study is provided with an open-access database\n(https://github.com/AngeAM/SOC_Vanadium_Spectra_2023.git) that supports the\nmethods and procedures and facilitates access to the calibration data. The\nstudy covers the three types of electrolyte solutions relevant to vanadium\nredox flow batteries, namely the anolyte $V^{II}/V^{III}$, the catholyte\n$V^{IV}V^V$, and the $V^{III}/V^{IV}$ commercial electrolyte, meant to be\npreconditioned to either $V^{III}$ or $V^{IV}$ before battery operation.\nAnalytical expressions to calculate the concentration of different vanadium\nspecies in the electrolyte solutions are provided based on either empirical\ncorrelations or spectral deconvolution methods. The paper also examines the\nlimitations of the measurement technique and provides insightful\nrecommendations for future research. The open-access database provided by the\nauthors is expected to serve as a valuable repository for scholars and\nscientists working in the field of vanadium redox flow batteries.", "category": "physics_chem-ph" }, { "text": "Practical Phase-Space Electronic Hamiltonians for Ab Initio Dynamics: Modern electronic structure theory is built around the Born-Oppenheimer\napproximation and the construction of an electronic Hamiltonian H_{el}(X) that\ndepends on the nuclear position X (and not the nuclear momentum P). In this\narticle, using the well-known theory of electron translation (Gamma') and\nrotational (Gamma'') factors to couple electronic transitions to nuclear\nmotion, we construct a practical phase-space electronic Hamiltonian that\ndepends on both nuclear position and momentum, H_{PS}(X,P). While classical\nBorn-Oppenheimer dynamics that run along the eigensurfaces of the operator\nH_{el}(X) can recover many nuclear properties correctly, we present some\nevidence that motion along the eigensurfaces of H_{PS}(X,P) can better capture\nboth nuclear and electronic properties (including the elusive electronic\nmomentum studied by Nafie). Moreover, only the latter (as opposed to the\nformer) conserves the total linear and angular momentum in general.", "category": "physics_chem-ph" }, { "text": "Search for the Parity-Violating Effects between D- and L-alanine: The contribution of parity-violating effects to the phase transition of the\nD-/L-alanine crystals was confirmed by 1H CRAMPS solid state NMR, DC-magnetic\nsusceptibilities and ultrasonic measurements. It was found that the spin\nrelaxation mechanism of alpha-H nucleus of D-alanine molecule is different from\nL-alanine and the effect is stronger than that of L-alanine. In addition,\nD-alanine undergoes a magnetic phase transition at a field of 1.0T, which is\nconfirmed by a peak-form ultrasonic attenuation curve. DC-magnetic\nsusceptibilities measurements of L-alanine also indicate abnormal magnetic\nproperties, which is accompanied by a step-form ultrasonic attenuation jump and\nits mechanism seems different from that of D-alanine. The phase transition is\nconsidered to act as a cooperating amplification mechanism of the P-odd effects\nat the molecular level.", "category": "physics_chem-ph" }, { "text": "Graphene-based sponges for electrochemical degradation of persistent\n organic contaminants: Graphene-based sponges doped with atomic nitrogen and boron were applied for\nthe electrochemical degradation of persistent organic contaminants in one-pass,\nflow-through mode, and in a low-conductivity supporting electrolyte. The\nB-doped anode and N-doped cathode was capable of >90% contaminant removal at\nthe geometric anodic current density of 173 A m2. The electrochemical\ndegradation of contaminants was achieved via the direct electron transfer, the\nanodically formed O3, and by the OH radicals formed by the decomposition of\nH2O2 produced at the cathode. The identified transformation products of\niopromide show that the anodic cleavage of all three C-I bonds at the aromatic\nring was preferential over scissions at the alkyl side chains, suggesting a\ndetermining role of the pi-pi interactions with the graphene surface. In the\npresence of 20 mM sodium chloride (NaCl), the current efficiency for chlorine\nproduction was <0.04%, and there was no chlorate and perchlorate formation,\ndemonstrating a very low electrocatalytic activity of the graphene-based sponge\nanode towards chloride. Graphene-based sponges were produced using a low-cost,\nbottom-up method that allows easy introduction of dopants and functionalization\nof the reduced graphene oxide coating, and thus tailoring of the material for\nthe removal of specific contaminants.", "category": "physics_chem-ph" }, { "text": "Efficient Site-specific Low-energy Electron Production via Interatomic\n Coulombic Decay Following Resonant Auger Decay: We identified interatomic Coulombic decay (ICD) channels in argon dimers\nafter spectator-type resonant Auger decay $2p^{-1}~3d \\to 3p^{-2}3d, 4d$ in one\nof the atoms, using momentum resolved electron-ion-ion coincidence. The results\nillustrate that the resonant core excitation is a very efficient way of\nproducing slow electrons at a specific site, which may cause localized\nradiation damage. We find also that ICD rate for $3p^{-2}4d$ is significantly\nlower than that for $3p^{-2}3d$.", "category": "physics_chem-ph" }, { "text": "Revisiting Gauge-Independent Kinetic Energy Densities in Meta-GGAs and\n Local Hybrid Calculations of Magnetizabilities: In a recent study [J. Chem. Theory Comput. 2021, 17, 1457-1468], some of us\nexamined the accuracy of magnetizabilities calculated with density functionals\nrepresenting the local density approximation (LDA), generalized gradient\napproximation (GGA), meta-GGA (mGGA) as well as global hybrid (GH) and\nrange-separated (RS) hybrid functionals by assessment against accurate\nreference values obtained with coupled-cluster theory with singles, doubles and\nperturbative triples [CCSD(T)]. Our study was later extended to local-hybrid\n(LH) functionals by Holzer et al. [J. Chem. Theory Comput. 2021, 17,\n2928-2947]; in this work, we examine a larger selection of LH functionals, also\nincluding range-separated LH (RSLH) functionals and strong-correlation LH\n(scLH) functionals. Holzer et al also studied the importance of the physically\ncorrect handling of the magnetic gauge dependence of the kinetic energy density\n$(\\tau)$ in mGGA calculations by comparing the Maximoff--Scuseria formulation\nof $\\tau$ used in our aforementioned study to the more physical current-density\nextension derived by Dobson. In this work, we also revisit this comparison with\na larger selection of mGGA functionals. We find that the newly tested LH, RSLH\nand scLH functionals outperform all the functionals considered in the previous\nstudies. The various LH functionals afford the seven lowest mean absolute\nerrors, while also showing remarkably small standard deviations and mean\nerrors. Most strikingly, the best two functionals are scLHs that also perform\nremarkably well in cases with significant multiconfigurational character such\nas the ozone molecule, which is traditionally excluded from the statistical\nerror evaluation due to its large errors with common density functionals.", "category": "physics_chem-ph" }, { "text": "Hierarchy of protein loop-lock structures: a new server for the\n decomposition of a protein structure into a set of closed loops: HoPLLS (Hierarchy of protein loop-lock structures)\n(http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that\nidentifies closed loops - a structural basis for protein domain hierarchy. The\nserver is based on the loop-and-lock theory for structural organisation of\nnatural proteins. We describe this web server, the algorithms for the\ndecomposition of a 3D protein into loops and the results of scientific\ninvestigations into a structural \"alphabet\" of loops and locks.", "category": "physics_chem-ph" }, { "text": "Shake-Rattle-and-Roll: A Model of Dynamic Structural Disorder in\n Supported Nanoscale Catalysts: We investigate the effects of \"dynamic structural disorder\" (DSD) on the\nbehavior of supported nano-scale catalysts. DSD refers to the intrinsic\nfluctuating, inhomogeneous structure of such nano-scale systems. In contrast to\nbulk materials, nano-scale systems exhibit substantial fluctuations in energy,\ncharge, and other extensive quantities as well as large surface effects. The\nDSD is driven by the stochastic librational motion of the center of mass and\nfluxional bonding at the nanoparticle surface due to thermal coupling with the\nsubstrate. Our approach for calculating DSD is based on a combination of\nstatistical mechanics, transient coupled-oscillator models, and real-time\nDFT/MD simulations. This approach treats thermal and dynamic effects over\nmultiple time-scales, including bond-stretching and -bending vibrations, DSD,\nand transient tethering to the substrate at longer ps time-scales. Model\ncalculations of molecule-cluster interactions and molecular dissociation\nreaction paths are presented in which the reactant molecules are adsorbed on\nthe surface of dynamically sampled clusters. This model suggests that DSD\naffects both the prefactors and distribution of energy barriers in reaction\nrates, and thus can strongly affect catalytic activity at the nano-scale.", "category": "physics_chem-ph" }, { "text": "Thermodynamics of supercooled water: We review the available experimental information on the thermodynamic\nproperties of supercooled ordinary and heavy water and demonstrate the\npossibility of modeling these thermodynamic properties on a theoretical basis.\nWe show that by assuming the existence of a liquid-liquid critical point in\nsupercooled water, the theory of critical phenomena can give an accurate\naccount of the experimental thermodynamic-property data up to a pressure of 150\nMPa. In addition, we show that a phenomenological extension of the theoretical\nmodel can account for all currently available experimental data in the\nsupercooled region, up to 400 MPa. The stability limit of the liquid state and\npossible coupling between crystallization and liquid-liquid separation are\ndiscussed. It is concluded that critical-point thermodynamics describes the\navailable thermodynamic data for supercooled water within experimental\naccuracy, thus establishing a benchmark for further developments in this area.", "category": "physics_chem-ph" }, { "text": "MultiDK: A Multiple Descriptor Multiple Kernel Approach for Molecular\n Discovery and Its Application to The Discovery of Organic Flow Battery\n Electrolytes: We propose a multiple descriptor multiple kernel (MultiDK) method for\nefficient molecular discovery using machine learning. We show that the MultiDK\nmethod improves both the speed and the accuracy of molecular property\nprediction. We apply the method to the discovery of electrolyte molecules for\naqueous redox flow batteries. Using \\emph{multiple-type - as opposed to\nsingle-type - descriptors}, more relevant features for machine learning can be\nobtained. Following the principle of the 'wisdom of the crowds', the\ncombination of multiple-type descriptors significantly boosts prediction\nperformance. Moreover, MultiDK can exploit irregularities between molecular\nstructure and property relations better than the linear regression method by\nemploying multiple kernels - more than one kernel functions for a set of the\ninput descriptors. The multiple kernels consist of the Tanimoto similarity\nfunction and a linear kernel for a set of binary descriptors and a set of\nnon-binary descriptors, respectively. Using MultiDK, we achieve average\nperformance of $r^2 = 0.92$ with a set of molecules for solubility prediction.\nWe also extend MultiDK to predict pH-dependent solubility and apply it to\nsolubility estimation of quinone molecules with ionizable functional groups as\nstrong candidates of flow battery electrolytes.", "category": "physics_chem-ph" }, { "text": "Probing Charge Transfer Dynamics in a Single Iron Tetraphenylporphyrin\n Dyad Adsorbed on an Insulating Surface: Although the dynamics of charge transfer (CT) processes can be probed with\nultimate lifetime resolution, the helplessness to control CT at the nanoscale\nconstitutes one of the most important road-blocks to revealing some of its deep\nfundamental aspects. In this work, we present an investigation of CT dynamics\nin a single iron tetraphenylporphyrin (Fe-TPP) donor/acceptor dyad adsorbed on\na CaF2/Si(100) insulating surface. The tip of a scanning tunneling microscope\n(STM) is used to create local ionic states in one fragment of the dyad. The CT\nprocess is monitored by imaging subsequent changes in the neighbor acceptor\nmolecule and its efficiency is mapped revealing the influence of the initial\nexcited state in the donor molecule. In validation of the experiments,\nsimulations based on density functional theory show that holes have a higher\ndonor-acceptor CT rate compared to electrons and highlight a noticeable initial\nstate dependence on the CT process. We leverage the unprecedented spatial\nresolution achieved in our experiments to show that the CT process in the dyad\nis governed via molecule-molecule coherent tunneling with negligible\nsurface-mediated character.", "category": "physics_chem-ph" }, { "text": "EMReact: A Tool for Modelling Electromagnetic Field Induced Effects in\n Chemical Reactions by Solving the Discrete Stochastic Master Equation: The effects of electromagnetic fields (EMF) have been widely debated\nconcerning their role in chemical reactions. Reactions usually took hours or\ndays to complete, and have been shown to happen a thousand times faster using\nEMF radiations. This work develops a formalism and a computer program to\nevaluate and quantify the EMF effects in chemical reactions. The master\nequation employed in this program solves the internal energy of the reaction\nunder EMFs while including collisional effects. Multiphoton absorption and\nemission are made possible with the transitioning energy close to the EMF and\nare influenced by the dielectric properties of the system. Dimethyl Sulfoxide\nand Benzyl Chloride are simulated under different EMF intensities. The results\nshow that EMF absorption is closely related to the collisional redistribution\nof energy in molecules. The EMF effect can be interpreted as a shift of the\nthermodynamic equilibrium. Under such nonequilibrium energy distribution, the\n\"temperature\" is not a reliable quantity for defining the state of the system.", "category": "physics_chem-ph" }, { "text": "Unravelling the stereodynamics of cold HD-H2 collisions: Measuring inelastic rates with partial wave resolution requires temperatures\nclose to a Kelvin or below, even for the lightest molecule. In a recent\nexperiment Perreault et al. [1] studied collisional relaxation of excited HD\nmolecules in the v = 1, j = 2 state by para- and ortho-H2 at a temperature of\nabout 1 K, extracting the angular distribution of scattered HD in the v = 1,j =\n0 state. By state-preparation of the HD molecules, control of the angular\ndistribution of scattered HD was demonstrated. Here, we report a\nfirst-principles simulation of that experiment which enables us to attribute\nthe main features of the observed angular distribution to a single L = 2\npartial-wave shape resonance. Our results demonstrate important stereodynamical\ninsights that can be gained when numerically-exact quantum scattering\ncalculations are combined with experimental results in the few-partial-wave\nregime.", "category": "physics_chem-ph" }, { "text": "Supercell convergence of charge-transfer energies in pentacene molecular\n crystals from constrained DFT: Singlet fission (SF) is a multi-exciton generation process that could be\nharnessed to improve the efficiency of photovoltaic devices. Experimentally,\nsystems derived from the pentacene molecule have been shown to exhibit\nultrafast SF with high yields. Charge-transfer (CT) configurations are likely\nto play an important role as intermediates in the SF process in these systems.\nIn molecular crystals, electrostatic screening effects and band formation can\nbe significant in lowering the energy of CT states, enhancing their potential\nto effectively participate in SF. In order to simulate these, it desirable to\nadopt a computational approach which is acceptably accurate, relatively\ninexpensive, which and scales well to larger systems, thus enabling the study\nof screening effects. We propose a novel, electrostatically-corrected\nconstrained Density Functional Theory (cDFT) approach as a low-cost solution to\nthe calculation of CT energies in molecular crystals such as pentacene. Here we\nconsider an implementation in the context of the ONETEP linear-scaling DFT\ncode, but our electrostatic correction method is in principle applicable in\ncombination with any constrained DFT implementation, also outside the\nlinear-scaling framework. Our newly developed method allows us to estimate CT\nenergies in the infinite crystal limit, and with these to validate the accuracy\nof the cluster approximation.", "category": "physics_chem-ph" }, { "text": "A Markov theoretic description of stacking disordered aperiodic crystals\n including ice and opaline silica: We review the Markov theoretic description of 1D aperiodic crystals,\ndescribing the stacking-faulted crystal polytype as a special case of an\naperiodic crystal. Under this description we generalise the centrosymmetric\nunit cell underlying a topologically centrosymmetric crystal to a reversible\nMarkov chain underlying a reversible aperiodic crystal. We show that for the\nclose-packed structure, almost all stackings are irreversible when the\ninteraction reichweite is greater than 4. Moreover, we present an analytic\nexpression of the scattering cross section of a large class of stacking\ndisordered aperiodic crystals, lacking translational symmetry of their layers,\nincluding ice and opaline silica (opal CT). We then relate the observed\nstackings and their underlying reichweite to the physics of various nucleation\nand growth processes of disordered ice.", "category": "physics_chem-ph" }, { "text": "Optical response of small carbon clusters: We apply the time-dependent local density approximation (TDLDA) to calculate\ndipole excitations in small carbon clusters. A strong low-frequency mode is\nfound which agrees well with observation for clusters C_n with n in the range\n7-15. The size dependence of the mode may be understood simply as the classical\nresonance of electrons in a conducting needle. For a ring geometry, the lowest\ncollective mode occurs at about twice the frequency of the collective mode in\nthe linear chain, and this may also be understood in simple terms.", "category": "physics_chem-ph" }, { "text": "Thermodynamics and kinetics of binary nucleation in ideal-gas mixtures: The nonisothermal single-component theory of droplet nucleation\n(Alekseechkin, 2014) is extended to binary case; the droplet volume V,\ncomposition x, and temperature T are the variables of the theory. An approach\nbased on macroscopic kinetics (in contrast to the standard microscopic model of\nnucleation operating with the probabilities of monomer attachment and\ndetachment) is developed for the droplet evolution and results in the derived\ndroplet motion equations in the space (V,x,T) - equations for V_dot, x_dot, and\nT_dot. The work W(V,x,T) of the droplet formation is calculated; it is obtained\nin the vicinity of the saddle point as a quadratic form with diagonal matrix.\nAlso the problem of generalizing the single-component Kelvin equation for the\nequilibrium vapor pressure to binary case is solved; it is presented here as a\nproblem of integrability of a Pfaffian equation. The equation for is shown to\nbe the first law of thermodynamics for the droplet, which is a consequence of\nOnsagers reciprocal relations and the linked-fluxes concept. As an example of\nideal solution for demonstrative numerical calculations, the o-xylene-m-xylene\nsystem is employed. Both nonisothermal and enrichment effects are shown to\nexist; the mean steady-state overheat of droplets and their mean steady-state\nenrichment are calculated with the help of the 3D distribution function. The\nqualitative peculiarities of the nucleation thermodynamics and kinetics in the\nwater-sulfuric acid system are considered in the model of regular solution. It\nis shown that there is a small kinetic parameter in the theory due to the small\namount of the acid in the vapor and, as a consequence, the nucleation process\nis isothermal.", "category": "physics_chem-ph" }, { "text": "Accelerating Pythonic coupled cluster implementations: a comparison\n between CPUs and GPUs: We scrutinize how to accelerate the bottleneck operations of Pythonic coupled\ncluster implementations performed on a \\texttt{NVIDIA} Tesla V100S PCIe 32GB\n(rev 1a) Graphics Processing Unit (GPU). The \\texttt{NVIDIA} Compute Unified\nDevice Architecture (CUDA) API is interacted with via \\texttt{CuPy}, an\nopen-source library for Python, designed as a \\texttt{NumPy} drop-in\nreplacement for GPUs. The implementation uses the Cholesky linear algebra\ndomain and is done in {PyBEST}, the Pythonic Black-box Electronic Structure\nTool -- a fully-fledged modern electronic structure software package. Due to\nthe limitations of Video Memory (VRAM), the GPU calculations must be performed\nbatch-wise. Timing results of some contractions containing large tensors are\npresented. The \\texttt{CuPy} implementation leads to factor 10 speed-up\ncompared to calculations on 36 CPUs. Furthermore, we benchmark several Pythonic\nroutines for time and memory requirements to identify the optimal choice of the\ntensor contraction operations available. Finally, we compare an example CCSD\nand pCCD-LCCSD calculation performed solely on CPUs to their CPU--GPU hybrid\nimplementation. Our results indicate a significant speed-up (up to a factor of\n16 regarding the bottleneck operations) when offloading specific contractions\nto the GPU using \\texttt{CuPy}.", "category": "physics_chem-ph" }, { "text": "Mixed quantum-classical approach to model non-adiabatic electron-nuclear\n dynamics: Detailed balance and improved surface hopping method: We develop a density matrix formalism to describe coupled electron-nuclear\ndynamics. To this end we introduce an effective Hamiltonian formalism that\ndescribes electronic transitions and small (quantum) nuclear fluctuations along\na classical trajectory of the nuclei. Using this Hamiltonian we derive\nequations of motion for the electronic occupation numbers and for the nuclear\ncoordinates and momenta. We show that in the limit when the number of nuclear\ndegrees of freedom coupled to a given electronic transition is sufficiently\nhigh (i.e., the strong decoherence limit), the equations of motion for the\nelectronic occupation numbers become Markovian. Furthermore the transition\nrates in these (rate) equations are asymmetric with respect to the\nlower-to-higher energy transitions and vice versa. In thermal equilibrium such\nasymmetry corresponds to the detailed balance condition. We also study the\nequations for the electronic occupations in non-Markovian regime and develop a\nsurface hopping algorithm based on our formalism. To treat the decoherence\neffects we introduce additional \"virtual\" nuclear wavepackets whose\ninterference with the \"real\" (physical) wavepackets leads to the reduction in\ncoupling between the electronic states (i.e., decoherence) as well as to the\nphase shifts that improve the accuracy of the numerical approach. Remarkably,\nthe same phase shifts lead to the detailed balance condition in the strong\ndecoherence limit.", "category": "physics_chem-ph" }, { "text": "A Method for Measurement of Spin-Spin Couplings with sub-mHz Precision\n Using Zero- to Ultralow-Field Nuclear Magnetic Resonance: We present a method which allows for the extraction of physical quantities\ndirectly from zero- to ultralow-field nuclear magnetic resonance (ZULF NMR)\ndata. A numerical density matrix evolution is used to simulate ZULF NMR spectra\nof several molecules in order to fit experimental data. The method is utilized\nto determine the indirect spin-spin couplings ($J$-couplings) in these, which\nis achieved with precision of $10^{-2}$--$10^{-4}$ Hz. The simulated and\nmeasured spectra are compared to earlier research. Agreement and precision\nimprovement for most of the $J$-coupling estimates are achieved. The\navailability of an efficient, flexible fitting method for ZULF NMR enables a\nnew generation of precision-measurement experiments for spin-dependent\ninteractions and physics beyond the Standard Model.", "category": "physics_chem-ph" }, { "text": "The phase diagram of ice: a quasi-harmonic study based on a flexible\n water model: The phase diagram of ice is studied by a quasi-harmonic approximation. The\nfree energy of all experimentally known ice phases has been calculated with the\nflexible q-TIP4P/F model of water. The only exception is the high pressure ice\nX, in which the presence of symmetric O-H-O bonds prevents its modeling with\nthis empirical interatomic potential. The simplicity of our approach allows us\nto study ice phases at state points of the T-P plane that have been omitted in\nprevious simulations using free energy methods based on thermodynamic\nintegration. The effect in the phase diagram of averaging the proton disorder\nthat appears in several ice phases has been studied. It is found particularly\nrelevant for ice III, at least for cell sizes typically used in phase\ncoexistence simulations. New insight into the capability of the employed water\nmodel to describe the coexistence of ice phases is presented. We find that the\nH-ordered ices IX and XIV, as well as the H-disordered ice XII, are\nparticularly stable for this water model. This fact disagrees with experimental\ndata. The unexpected large stability of ice IX is a property related to the\nTIP4P-character of the water model. Only after omission of these three stable\nice phases, the calculated phase diagram becomes in reasonable qualitative\nagreement to the experimental one in the T-P region corresponding to ice Ih,\nII, III, V, and VI. The calculation of the phase diagram in the quantum and\nclassical limits shows that the most important quantum effect is the\nstabilization of ice II due to its lower zero-point energy when compared to\nthat one of ices Ih, III, and V.", "category": "physics_chem-ph" }, { "text": "Hydrogen storage with titanium-functionalized graphene: We report on hydrogen adsorption and desorption on titanium-covered graphene\nin order to test theoretical proposals to use of graphene functionalized with\nmetal atoms for hydrogen storage. At room temperature titanium islands grow\nwith an average diameter of about 10 nm. Samples were then loaded with\nhydrogen, and its desorption kinetics was studied by thermal desorption\nspectroscopy. We observe the desorption of hydrogen in the temperature range\nbetween 400K and 700 K. Our results demonstrate the stability of hydrogen\nbinding at room temperature and show that hydrogen desorbs at moderate\ntemperatures in line with what required for practical hydrogen-storage\napplications.", "category": "physics_chem-ph" }, { "text": "Deep Learning Collective Variables from Transition Path Ensemble: The study of the rare transitions that take place between long lived\nmetastable states is a major challenge in molecular dynamics simulations. Many\nof the methods suggested to address this problem rely on the identification of\nthe slow modes of the system which are referred to as collective variables.\nRecently machine learning methods have been used to learn the collective\nvariables as functions of a large number of physical descriptors. Among many\nsuch methods Deep Targeted Discriminant Analysis has proven to be useful. This\ncollective variable is built from data harvested in short unbiased simulation\nin the two basins. Here we enrich the set of data on which the Deep Targeted\nDiscriminant Analysis collective variable is built by adding data coming from\nthe transition path ensemble. These are collected from a number of reactive\ntrajectories obtained using the On-the-fly Probability Enhanced Sampling\nFlooding method. The collective variables thus trained, lead to a more accurate\nsampling and faster convergence. The performance of these new collective\nvariables is tested on a number of representative examples.", "category": "physics_chem-ph" }, { "text": "Electron dynamics method using a locally projected group diabatic Fock\n matrix for molecules and aggregates: We propose a method using reduced size of Hilbert space to describe an\nelectron dynamics in molecule and aggregate based on our previous theoretical\nscheme [ T. Yonehara and T. Nakajima, J. Chem. Phys. \\textbf{147}, 074110\n(2017) ]. The real-time time-dependent density functional theory is combined\nwith newly introduced projected group diabatic Fock matrix. First, this\nprojection method is applied to a test donor--acceptor dimer, namely, a\nnaphthalene--tetracyanoethylene with and without initial local excitations and\nlight fields. Secondly, we calculate an absorption spectrum of\nfive-unit-polythiophene monomer. The importance of feedback of instantaneous\ndensity to Fock matrix is also clarified. In all cases, half of the orbitals\nwere safely reduced without loss of accuracy in descriptions of properties. The\npresent scheme provides one possible way to investigate and analyze a complex\nexcited electron dynamics in molecular aggregates within a moderate\ncomputational cost.", "category": "physics_chem-ph" }, { "text": "X-ray induced desorption and photochemistry in CO ice: We report an investigation of X-ray induced desorption of neutrals, cations\nand anions from CO ice. The desorption of neutral CO, by far the most abundant,\nis quantified and discussed within the context of its application to\nastrochemistry. The desorption of many different cations, including large\ncations up to the mass limit of the spectrometer, are observed. In contrast,\nthe only desorbing anions detected are O$^-$ and C$^-$. The desorption\nmechanisms of all these species are discussed with the aid of their\nphotodesorption spectrum. The evolution of the X-ray absorption spectrum shows\nsignificant chemical modifications of the ice upon irradiation, which along\nwith the desorption of large cations gives a new insight into X-ray induced\nphotochemistry in CO ice.", "category": "physics_chem-ph" }, { "text": "Meridional composite pulses for low-field magnetic resonance: We discuss procedures for error-tolerant spin control in environments that\npermit transient, large-angle reorientation of magnetic bias field. Short\nsequences of pulsed, non-resonant magnetic field pulses in a laboratory-frame\nmeridional plane are derived. These are shown to have band-pass excitation\nproperties comparable to established amplitude-modulated, resonant pulses used\nin high, static-field magnetic resonance. Using these meridional pulses, we\ndemonstrate robust $z$ inversion in proton ($^{1}$H) nuclear magnetic resonance\nnear earth's field.", "category": "physics_chem-ph" }, { "text": "Crystallization Mechanism of Hard Sphere Glasses: In supercooled liquids, vitrification generally suppresses crystallization.\nYet some glasses can still crystallize despite the arrest of diffusive motion.\nThis ill-understood process may limit the stability of glasses, but its\nmicroscopic mechanism is not yet known. Here we present extensive computer\nsimulations addressing the crystallization of monodisperse hard-sphere glasses\nat constant volume (as in a colloid experiment). Multiple crystalline patches\nappear without particles having to diffuse more than one diameter. As these\npatches grow, the mobility in neighbouring areas is enhanced, creating dynamic\nheterogeneity with positive feedback. The future crystallization pattern cannot\nbe predicted from the coordinates alone: crystallization proceeds by a sequence\nof stochastic micro-nucleation events, correlated in space by emergent dynamic\nheterogeneity.", "category": "physics_chem-ph" }, { "text": "What Makes a Good Descriptor for Heterogeneous Ice Nucleation on\n OH-Patterned Surfaces: Freezing of water is arguably one of the most common phase transitions on\nEarth and almost always happens heterogeneously. Despite its importance, we\nlack a fundamental understanding of what makes substrates efficient ice\nnucleators. Here we address this by computing the ice nucleation (IN) ability\nof numerous model hydroxylated substrates with diverse surface hydroxyl (OH)\ngroup arrangements. Overall, for the substrates considered, we find that\nneither the symmetry of the OH patterns nor the similarity between a substrate\nand ice correlate well with the IN ability. Instead, we find that the OH\ndensity and the substrate-water interaction strength are useful descriptors of\na material's IN ability. This insight allows the rationalization of ice\nnucleation ability across a wide range of materials, and can aid the search and\ndesign of novel potent ice nucleators in the future.", "category": "physics_chem-ph" }, { "text": "Quantum mechanical and quasiclassical investigation of the time domain\n nonadiabatic dynamics of NO2 close to the bottom of the X2A1-A2B2 conical\n intersection: We use the effective Hamiltonian that we recently fitted against the first\n306 experimentally observed vibronic transitions of NO2 [J. Chem. Phys. 119,\n5923 (2003)] to investigate the time domain nonadiabatic dynamics of this\nmolecule on the coupled X2A1 and A2B2 electronic states, using both quantum\nmechanical and quasiclassical techniques. From the quantum mechanical point of\nview, we show that the transfer of population to the electronic ground state\noriginating from a wave packet launched on the excited state occurs in a\nstepwise fashion. The evolution of wave packets launched on the electronic\nground state is instead more complex because the crossing seam is located close\nto the bottom of the electronic excited state. We next use the mapping\nformalism, which replaces the discrete electronic degrees of freedom by\ncontinuous ones, to obtain a classical description of the coupled electronic\nstates. We propagate gaussian swarms of trajectories to show that this approach\ncan be used to calculate the populations in each electronic state. We finally\npropose a very simple trajectory surface hopping model, which assumes that\ntrajectories have a constant probability to jump onto the other state in a\nparticular region of the phase space and a null hopping probability outside\nfrom this region. Quasiclassical calculations show that this model enables a\nprecise estimation of complex quantities, like for example the projection of\nthe instantaneous probability density on given planes.", "category": "physics_chem-ph" }, { "text": "Water Agglomerates on Fe3O4(001): Determining the structure of water adsorbed on solid surfaces is a\nnotoriously difficult task, and pushes the limits of experimental and\ntheoretical techniques. Here, we follow the evolution of water agglomerates on\nFe3O4(001); a complex mineral surface relevant in both modern technology and\nthe natural environment. Strong OH-H2O bonds drive the formation of\npartially-dissociated water dimers at low coverage, but a surface\nreconstruction restricts the density of such species to one per unit cell. The\ndimers act as an anchor for further water molecules as the coverage increases,\nleading first to partially-dissociated water trimers, and then to a ring-like,\nhydrogen-bonded network that covers the entire surface. Unraveling this\ncomplexity requires the concerted application of several state-of-the-art\nmethods. Quantitative temperature programmed desorption (TPD) reveals the\ncoverage of stable structures, monochromatic x-ray photoelectron spectroscopy\n(XPS) shows the extent of partial dissociation, and non-contact Atomic Force\nMicroscopy (AFM) using a CO-functionalized tip provides a direct view of the\nagglomerate structure. Together, these data provide a stringent test of the\nminimum energy configurations determined via a van der Waals density functional\ntheory (DFT)-based genetic search.", "category": "physics_chem-ph" }, { "text": "Deciphering the Rotational Spectrum of the First Excited Torsional State\n of Propylene Oxide: The first excited torsional state of the chiral molecule propylene oxide,\n$\\mathrm{CH_{3}C_{2}H_{3}O}$, is investigated from millimeter up to\nsub-millimeter wavelengths (75-950 GHz). The first excited vibrational mode of\npropylene oxide, $\\upsilon_{24}$, is analysed using the programs ERHAM and\nXIAM. Rotational constants and tunneling parameters are provided, and a\ndescription of the A-E splittings due to internal rotation is given.\nFurthermore, the potential barrier height to internal rotation $V_{3}$ is\ndetermined to be $V_{3} = 894.5079(259) \\mathrm{cm^{-1}}$ . Our results are\ncompared with quantum chemical calculations and literature values. We present a\nline list of the dense spectrum of the first excited torsional state of\npropylene oxide in the (sub-)millimeter range. Our results will be useful for\nfurther studies of chiral molecules in vibrationally excited states, and will\nenable astronomers to search for rotational transitions originating from\n$\\upsilon_{24}$ of propylene oxide in interstellar space.", "category": "physics_chem-ph" }, { "text": "Using Azobenzene Photocontrol to Set Proteins in Motion: Controlling the activity of proteins with azobenzene photoswitches is a\npotent tool for manipulating their biological function. With the help of light,\none can change e.g. binding affinities, control allostery or temper with\ncomplex biological processes. Additionally, due to their intrinsically fast\nphotoisomerisation, azobenzene photoswitches can serve as triggers to initiate\nout-of-equilibrium processes. Such switching of the activity, therefore,\ninitiates a cascade of conformational events, which can only be accessed with\ntime-resolved methods. In this Review, we will show how combining the potency\nof azobenzene photoswitching with transient spectroscopic techniques helps to\ndisclose the order of events and provide an experimental observation of\nbiomolecular interactions in real-time. This will ultimately help us to\nunderstand how proteins accommodate, adapt and readjust their structure to\nanswer an incoming signal and it will complete our knowledge of the dynamical\ncharacter of proteins.", "category": "physics_chem-ph" }, { "text": "High-order geometric integrators for representation-free Ehrenfest\n dynamics: Ehrenfest dynamics is a useful approximation for ab initio mixed\nquantum-classical molecular dynamics that can treat electronically nonadiabatic\neffects. Although a severe approximation to the exact solution of the molecular\ntime-dependent Schr\\\"odinger equation, Ehrenfest dynamics is symplectic,\ntime-reversible, and conserves exactly the total molecular energy as well as\nthe norm of the electronic wavefunction. Here, we surpass apparent\ncomplications due to the coupling of classical nuclear and quantum electronic\nmotions and present efficient geometric integrators for \"representation-free\"\nEhrenfest dynamics, which do not rely on a diabatic or adiabatic representation\nof electronic states and are of arbitrary even orders of accuracy in the time\nstep. These numerical integrators, obtained by symmetrically composing the\nsecond-order splitting method and exactly solving the kinetic and potential\npropagation steps, are norm-conserving, symplectic, and time-reversible\nregardless of the time step used. Using a nonadiabatic simulation in the region\nof a conical intersection as an example, we demonstrate that these integrators\npreserve the geometric properties exactly and, if highly accurate solutions are\ndesired, can be even more efficient than the most popular non-geometric\nintegrators.", "category": "physics_chem-ph" }, { "text": "ipie: A Python-based Auxiliary-Field Quantum Monte Carlo Program with\n Flexibility and Efficiency on CPUs and GPUs: We report the development of a python-based auxiliary-field quantum Monte\nCarlo (AFQMC) program, ipie, with preliminary timing benchmarks and new AFQMC\nresults on the isomerization of [Cu$_2$O$_2$$]^{2+}$. We demonstrate how\nimplementations for both central and graphical processing units (CPUs and GPUs)\nare achieved in ipie. We show an interface of ipie with PySCF as well as a\nstraightforward template for adding new estimators to ipie. Our timing\nbenchmarks against other C++ codes, QMCPACK and Dice, suggest that ipie is\nfaster or similarly performing for all chemical systems considered on both CPUs\nand GPUs. Our results on [Cu$_2$O$_2$$]^{2+}$ using selected configuration\ninteraction trials show that it is possible to converge the ph-AFQMC\nisomerization energy between bis($\\mu$-oxo) and $\\mu$-$\\eta^2$:$\\eta^2$ peroxo\nconfigurations to the exact known results for small basis sets with $10^5$ to\n$10^6$ determinants. We also report the isomerization energy with a\nquadruple-zeta basis set with an estimated error less than a kcal/mol, which\ninvolved 52 electrons and 290 orbitals with $10^6$ determinants in the trial\nwavefunction. These results highlight the utility of ph-AFQMC and ipie for\nsystems with modest strong correlation and large-scale dynamic correlation.", "category": "physics_chem-ph" }, { "text": "First-principles molecular quantum electrodynamics theory at all\n coupling strengths: The ever-growing intersection of quantum electrodynamics (QED) and molecular\nprocesses has shown remarkable and unanticipated advancements in altering\nmolecular properties and reactivity by exploiting light-matter couplings. In\nrecent years, multiple ab initio methods have been developed to compute the\neigenstates of molecular systems strongly coupled to cavities, ranging from the\nmean-field to quantum many-body methods. The quantum many-body methods, such as\ncoupled-cluster theories, usually rely on the quality of mean-field reference\nwavefunctions. Hence, developing efficient and physically reliable mean-filed\napproaches for molecular quantum electrodynamics problems is crucial. The\ncurrent widely used methods, such as QED Hartree-Fock and the self-consistent\ncounterpart, are limited to specific coupling regimes. In this work, we\ndeveloped a variational transformation-based molecular quantum electrodynamics\nmean-field method, namely VT-QEDHF, for light-matter interaction at arbitrary\ncoupling strength. The numerical benchmark demonstrates that the VT-QEDHF\nmethod naturally connects both QEDHF and self-consistent QEDHF methods at the\ntwo limits, showcasing the advantage of VT-QEHDF across all coupling strengths.", "category": "physics_chem-ph" }, { "text": "Elementary conjugated fragments in acyclic polyenes with heteroatoms: The study is aimed at revealing the most important substructures (fragments)\nof polyenes with heteroatoms determining the alteration in the conjugation\nenergy of the whole compound due to substitution and the relevant charge\nredistribution. The systems are modelled as sets of weakly-interacting\nformally-double bonds, where the formally-single bonds represent the\ninteraction. Expressions for total energies and populations of basis orbitals\nare then derived in the form of power series with respect to two small\nparameters. Analysis of these series shows that conjugated substructures\nconsisting of two connected formally-double bonds and containing at least s\nsingle heteroatom play the role of fragments being sought. Nine potential\nfragments of this type are considered separately that differ one from another\nin the number of heteroatoms and/or their relative positions inside and are\ncalled elementary conjugated fragments.", "category": "physics_chem-ph" }, { "text": "Strong Field Molecular Ionization in the Impulsive Limit: Freezing\n Vibrations with Short Pulses: We study strong-field molecular ionization as a function of pulse duration.\nExperimental measurements of the photoelectron yield for a number of molecules\nreveal competition between different ionization continua (cationic states)\nwhich depends strongly on pulse duration. Surprisingly, in the limit of short\npulse duration, we find that a single ionic continuum dominates the yield,\nwhereas multiple continua are produced for longer pulses. Using calculations\nwhich take vibrational dynamics into account, we interpret our results in terms\nof nuclear motion and non-adiabatic dynamics during the ionization process.", "category": "physics_chem-ph" }, { "text": "Computational investigation on the thermodynamics of H2CO + NH2 NH2CHO +\n H on interstellar water ice surfaces: Formamide has a key role in prebiotic chemistry as it is the simplest\nmolecule containing the four most important atoms from a biological point of\nview: hydrogen, carbon, nitrogen and oxygen. Due to its importance, the\nformation of this molecule has been studied and different pathways have been\nconsidered both in gas-phase and on ices of dust grains since it was first\ndetected. In the present work, the thermodynamics of the formation route of\nformamide starting from NH2 and H2CO, a reaction channel proposed to occur in\nthe gas phase, has been theoretically investigated in the scenario taking place\non icy dust grains modelled by both a cluster and a periodic approach.\nDifferent DFT functionals have been employed to obtain accurate energy values\nfor the mechanistic steps involved in the reaction.", "category": "physics_chem-ph" }, { "text": "Molecular dynamics-driven global tetra-atomic potential energy surfaces:\n Application to the AlF dimer: In this work, we present a general machine learning approach for\nfull-dimensional potential energy surfaces for tetra-atomic systems. Our method\nemploys an active learning scheme trained on {\\it ab initio} points, which size\ngrows based on the accuracy required. The training points are selected based on\nmolecular dynamics simulations, choosing the most suitable configurations for\ndifferent collision energy and mapping the most relevant part of the potential\nenergy landscape of the system. The present approach does not require\nlong-range information and is entirely general. As an example, we provide the\nfull-dimensional AlF-AlF potential energy surface, requiring $\\lesssim 0.1\\%$\nof the configurations to be calculated {\\it ab initio}. Furthermore, we analyze\nthe general properties of the AlF-AlF system, finding key difference with other\nreported results on CaF or bi-alkali dimers.", "category": "physics_chem-ph" }, { "text": "Anomalous pH-gradient in Ampholyte Solution: A mathematical model describing a steady pH-gradient in the solution of\nampholytes in water has been studied with the use of analytical, asymptotic,\nand numerical methods. We show that at the large values of an electric current\na concentration distribution takes the form of a piecewise constant function\nthat is drastically different from a classical Gaussian form. The correspondent\npH-gradient takes a stepwise form, instead of being a linear function. A\ndiscovered anomalous pH-gradient can crucially affect the understanding of an\nisoelectric focusing process.", "category": "physics_chem-ph" }, { "text": "Ultra-Fast Relaxation, Decoherence and Localization of Photoexcited\n States in $\u03c0$-Conjugated Polymers: A TEBD Study: The exciton relaxation dynamics of photoexcited electronic states in\npoly($p$-phenylenevinylene) (PPV) are theoretically investigated within a\ncoarse-grained model, in which both the exciton and nuclear degrees of freedom\nare treated quantum mechanically. The Frenkel-Holstein Hamiltonian is used to\ndescribe the strong exciton-phonon coupling present in the system, while\nexternal damping of the internal nuclear degrees of freedom are accounted for\nby a Lindblad master equation. Numerically, the dynamics are computed using the\ntime evolving block decimation (TEBD) and quantum jump trajectory techniques.\nThe values of the model parameters physically relevant to polymer systems\nnaturally lead to a separation of time scales, with the ultra-fast dynamics\ncorresponding to energy transfer from the exciton to the internal phonon modes\n(i.e., the C-C bond oscillations), while the longer time dynamics correspond to\ndamping of these phonon modes by the external dissipation. Associated with\nthese time scales, we investigate the following processes that are indicative\nof the system relaxing onto the emissive chromophores of the polymer: 1)\nExciton-polaron formation occurs on an ultra-fast time scale, with the\nassociated exciton-phonon correlations present within half a vibrational time\nperiod of the C-C bond oscillations. 2) Exciton decoherence is driven by the\ndecay in the vibrational overlaps associated with exciton-polaron formation,\noccurring on the same time scale. 3) Exciton density localization is driven by\nthe external dissipation, arising from `wavefunction collapse' occurring as a\nresult of the system-environment interactions. Finally, we show how\nfluorescence anisotropy measurements can be used to investigate the exciton\ndecoherence process during the relaxation dynamics.", "category": "physics_chem-ph" }, { "text": "Deuteron and triton magnetic moments from NMR spectra of the hydrogen\n molecule: We present a theory and calculations of the nuclear magnetic shielding with\nfinite nuclear mass effects and determine magnetic moments of deuteron and\ntriton using the known NMR spectra of HD and HT molecules. The results $\\mu_d =\n0.857\\,438\\,234\\,6(53)\\;\\mu_N$ and $\\mu_t = 2.978\\,962\\,471(10)\\;\\mu_N$ are\nmore accurate and in a good agreement with the currently accepted values.", "category": "physics_chem-ph" }, { "text": "Anisotropic coarse-grained statistical potentials improve the ability to\n identify native-like protein structures: We present a new method to extract distance and orientation dependent\npotentials between amino acid side chains using a database of protein\nstructures and the standard Boltzmann device. The importance of orientation\ndependent interactions is first established by computing orientational order\nparameters for proteins with alpha-helical and beta-sheet architecture.\nExtraction of the anisotropic interactions requires defining local reference\nframes for each amino acid that uniquely determine the coordinates of the\nneighboring residues. Using the local reference frames and histograms of the\nradial and angular correlation functions for a standard set of non-homologue\nprotein structures, we construct the anisotropic pair potentials. The\nperformance of the orientation dependent potentials was studied using a large\ndatabase of decoy proteins. The results demonstrate that the new distance and\norientation dependent residue-residue potentials present a significantly\nimproved ability to recognize native folds from a set of native and decoy\nprotein structures.", "category": "physics_chem-ph" }, { "text": "Relaxation of Chemical Reactions to Stationary States in the Chemical\n Affinities Space: Using the mass balance equations for chemical reactions, we show how the\nsystem relaxes towards a steady state in and out of the Onsager region. In the\nchemical affinities space, after fast transients, the relaxation process is a\nstraight line when operating in the Onsager region, while out of this regime,\nthe evolution of the system is such that the projections of the evolution\nequations for the forces and the shortest path on the flows coincide. For\nspatially-extended systems, similar results are valid for the evolution of the\nthermodynamic mode (i.e., the mode with wave-number k = 0). These results allow\nus to obtain the expression for the affine connection of the space covered by\nthe thermodynamic forces, close to the steady states. Through the affine\nconnection, the nonlinear closure equations are derived.", "category": "physics_chem-ph" }, { "text": "Relativistic configuration interaction calculation on the ground and\n excited states of iridium monoxide: We present the fully relativistic multi-reference configuration interaction\ncalculations of the ground and low-lying excited electronic states of IrO for\nindividual spin-orbit component. The lowest states for four spin-orbit\ncomponents 1/2, 3/2, 5/2, and 7/2 are calculated intensively to clarify the\nground state of IrO. Our calculation suggests that the ground state is of 1/2\nspin-orbit component, which is highly mixed with $^4\\Sigma^-$ and $^2\\Pi$\nstates in $\\Lambda-S$ notation. The two low-lying states of the 5/2 and 7/2\nspin-orbit components are nearly degenerate with the ground state and locate\nonly 234 and 260 cm$^{-1}$ above, respectively. The equilibrium bond length\n1.712 \\AA \\ and harmonic vibrational frequency 903 cm$^{-1}$ of the 5/2\nspin-orbit component are close to the experimental measurement of 1.724 \\AA \\\nand 909 cm$^{-1}$, which suggests the 5/2 state should be the low-lying state\ncontributed to spectra in experimental study. Moreover, the electronic states\nthat give rise to the observed transition bands are assigned in terms of the\nexcited energies and oscillator strengths obtained for the 5/2 and 7/2\nspin-orbit components.", "category": "physics_chem-ph" }, { "text": "Communication: Curing basis set overcompleteness with pivoted Cholesky\n decompositions: The description of weakly bound electronic states is especially difficult\nwith atomic orbital basis sets. The diffuse atomic basis functions that are\nnecessary to describe the extended electronic state generate significant linear\ndependencies in the molecular basis set, which may make the electronic\nstructure calculations ill-convergent. We propose a method where the\nover-complete molecular basis set is pruned by a pivoted Cholesky decomposition\nof the overlap matrix, yielding an optimal low-rank approximation that is\nnumerically stable; the pivot indices determining a reduced basis set that is\ncomplete enough to describe all the basis functions in the original\nover-complete basis. The method can be implemented either by a simple\nmodification to the usual canonical orthogonalization procedure, which hides\nthe excess functions and yields fewer efficiency benefits, or by generating\ncustom basis sets for all the atoms in the system, yielding significant cost\nreductions in electronic structure calculations. The pruned basis sets from the\nlatter choice allow accurate calculations to be performed at a lower cost even\nat the self-consistent field level, as illustrated on a solvated (H2O)24-\nanion. Our results indicate that the Cholesky procedure allows one to perform\ncalculations with accuracies close to standard augmented basis sets with cost\nsavings which increase with the size of the basis set, ranging from 9% fewer\nfunctions in single-{\\zeta} basis sets to 28% fewer functions in triple-{\\zeta}\nbasis sets.", "category": "physics_chem-ph" }, { "text": "Large barrier behaviour of the rate constant from the diffusion equation: Many processes in chemistry, physics, and biology depend on thermally\nactivated events in which the system changes its state by surmounting an\nactivation barrier. Examples range from chemical reactions, protein folding,\nand nucleation events. Parameterized forms of the mean-field potential are\noften employed in the stochastic modeling of activated processes. In this\ncontribution, we explore the alternative of employing parameterized forms of\nthe equilibrium distribution by means of the symmetric linear combination of\ntwo gaussian functions. Such a procedure leads to flexible and convenient\nmodels for the landscape and the energy barrier whose features are controlled\nby the second moments of the gaussian functions. The rate constants are\nexamined through the solution of the corresponding diffusion problem, that is\nthe Fokker-Planck-Smoluchowski equation specified according to the\nparameterized equilibrium distribution. The numerical calculations clearly show\nthat the asymptotic limit of large barriers does not agree with the results of\nthe Kramers theory. The underlying reason is that the linear scaling of the\npotential, the procedure justifying the Kramers theory, cannot be applied when\ndealing with parameterized forms of the equilibrium distribution. A different\nkind of asymptotic analysis is then required and we introduce the appropriate\ntheory when the equilibrium distribution is represented as a symmetric linear\ncombination of two gaussian functions, first in the one-dimensional case and\nafterward in the multi-dimensional diffusion model.", "category": "physics_chem-ph" }, { "text": "The origin of the E/Z isomer ratio of imines in the interstellar medium: Recent astronomical observations of both isomers E and Z of imines such as\ncyanomethanimine, ethanimine and 2-propyn-1-imine, have revealed that the\nabundances in the ISM of these isomers differ by factors of ~3-10. Several\ntheories have been proposed to explain the observed behavior, but none of them\nsuccessfully explains the [E]/[Z] ratios. In this work we present a detailed\nstudy of the kinetics of the one-step E-Z isomerization reactions of\ncyanomethanimine, ethanimine and 2-propyn-1-imine under interstellar conditions\n(in the 10-400 K temperature range). This reaction was previously thought to be\nnon-viable in the ISM due to its associated high-energy barrier (about 13,000\nK). In this Letter, we show that considering the multidimensional small\ncurvature tunneling approximation, the tunneling effect enables the\nisomerization even at low temperatures. This is due to the fact that the\nrepresentative tunneling energy lies in the vibrational ground state of the\nleast stable isomer up to approximately 150 K, making the reaction constants of\nthe isomerization from the least stable to the most stable isomer basically\nconstant. The predicted [E]/[Z] ratios are almost the same as those reported\nfrom the astronomical observations for all imines observed. This study\ndemonstrates that the [E]/[Z] ratio of imines in the ISM strongly depends on\ntheir relative stability.", "category": "physics_chem-ph" }, { "text": "Density functional theory calculations and vibrational spectroscopy on\n iron spin-crossover compounds: Iron complexes with a suitable ligand field undergo spin-crossover (SCO),\nwhich can be induced reversibly by temperature, pressure or even light.\nTherefore, these compounds are highly interesting candidates for optical\ninformation storage, for display devices and pressure sensors. The SCO\nphenomenon can be conveniently studied by spectroscopic techniques like Raman\nand infrared spectroscopy as well as nuclear inelastic scattering, a technique\nwhich makes use of the M\\\"ossbauer effect. This review covers new developments\nwhich have evolved during the last years like, e.g. picosecond infrared\nspectroscopy and thin film studies but also gives an overviewon newtechniques\nfor the theoretical calculation of spin transition phenomena and vibrational\nspectroscopic data of SCO complexes.", "category": "physics_chem-ph" }, { "text": "Excited rotational states of molecules in a superfluid: We combine experimental and theoretical approaches to explore excited\nrotational states of molecules embedded in helium nanodroplets using CS$_2$ and\nI$_2$ as examples. Laser-induced nonadiabatic molecular alignment is employed\nto measure spectral lines for rotational states extending beyond those\ninitially populated at the 0.37 K droplet temperature. We construct a simple\nquantum mechanical model, based on a linear rotor coupled to a single-mode\nbosonic bath, to determine the rotational energy structure in its entirety. The\ncalculated and measured spectral lines are in good agreement. We show that the\neffect of the surrounding superfluid on molecular rotation can be rationalized\nby a single quantity -- the angular momentum, transferred from the molecule to\nthe droplet.", "category": "physics_chem-ph" }, { "text": "Long-run in-operando NMR to investigate the evolution and degradation of\n battery cells: Nuclear magnetic resonance (NMR) investigations of electrochemical systems\nrequire gas-tight and non-metallic cell housings. This contribution reports on\nthe development and evaluation of a cylindrical battery container in\ncombination with a numerically optimized saddle coil that is suitable for NMR\ninvestigations of battery cells over hundreds of charge-discharge cycles. The\nreliability of the new cell container design and its long-time gas-tight\nsealing are shown by rate capability comparisons to standard housings with\nLiCoO$_{2}$ (LCO) vs. Li-metal electrodes as well as a charge-discharge\nexperiment of a LCO vs. graphite batteries over more than 2000 hours. To\ndemonstrate the performance of the entire NMR setup, long-run in-operando\nmeasurements on a Li-metal vs. graphite cell are presented. The NMR data reveal\nthe formation and evolution of mossy and dendritic Li microstructures over a\nperiod of 1000 h. Analyzing the measured rate of microstructure growth could\nhelp to identify dendrite mitigation strategies, such as enhanced cell pressure\nor additives, and could enable a method for battery lifetime prediction.", "category": "physics_chem-ph" }, { "text": "The Need, Benefits, and Demonstration of a Minimization Principle for\n Excited States: It is shown that the standard methods of computing excited states in\ntruncated spaces must yield wave functions that, beyond truncation, are in\nprinciple veered away from the exact, and a remedy is demonstrated via a\npresented functional, F$_n$, obeying a minimization principle for excited\nstates. It is further demonstrated that near avoided crossings, between two\nMCSCF 'flipped roots' the wave function that leads to the excited state has the\nlowest F$_n$.", "category": "physics_chem-ph" }, { "text": "Accurate description of charged excitations in molecular solids from\n embedded many-body perturbation theory: We present a novel hybrid quantum/classical (QM/MM) approach to the\ncalculation of charged excitations in molecular solids based on the many-body\nGreen's function $GW$ formalism. Molecules described at the $GW$ level are\nembedded into the crystalline environment modeled with an accurate classical\npolarizable scheme. This allows the calculation of electron addition and\nremoval energies in the bulk and at crystal surfaces where charged excitations\nare probed in photoelectron experiments. By considering the paradigmatic case\nof pentacene and perfluoropentacene crystals, we discuss the different\ncontributions from intermolecular interactions to electronic energy levels,\ndistinguishing between polarization, which is accounted for combining quantum\nand classical polarizabilities, and crystal field effects, that can impact\nenergy levels by up to $\\pm0.6$ eV. After introducing band dispersion, we\nachieve quantitative agreement (within 0.2 eV) on the ionization potential and\nelectron affinity measured at pentacene and perfluoropentacene crystal surfaces\ncharacterized by standing molecules.", "category": "physics_chem-ph" }, { "text": "Corresponding Active Orbital Spaces along Chemical Reaction Paths: The accuracy of reaction energy profiles calculated with\nmulti-configurational electronic structure methods and corrected by\nmulti-reference perturbation theory depends crucially on consistent active\norbital spaces selected along the reaction path. However, it has been\nchallenging to choose molecular orbitals that can be considered corresponding\nin different molecular structures. Here, we demonstrate how active orbital\nspaces can be selected consistently along reaction coordinates in a fully\nautomated way. The approach requires no structure interpolation between\nreactants and products. Instead, it emerges from a synergy of the Direct\nOrbital Selection orbital mapping ansatz combined with our fully automated\nactive space selection algorithm autoCAS. We demonstrate our algorithm for the\npotential energy profile of the homolytic carbon-carbon bond dissociation and\nrotation around the double bond of 1-pentene in the electronic ground state.\nHowever, our algorithm also applies to electronically excited Born-Oppenheimer\nsurfaces.", "category": "physics_chem-ph" }, { "text": "Reduced variance analysis of molecular dynamics simulations by linear\n combination of estimators: Building upon recent developments of force-based estimators with a reduced\nvariance for the computation of densities, radial distribution functions or\nlocal transport properties from molecular simulations, we show that the\nvariance can be further reduced by considering optimal linear combinations of\nsuch estimators. This control variates approach, well known in Statistics and\nalready used in other branches of computational Physics, has been comparatively\nmuch less exploited in molecular simulations. We illustrate this idea on the\nradial distribution function and the one-dimensional density of a bulk and\nconfined Lennard-Jones fluid, where the optimal combination of estimators is\ndetermined for each distance or position, respectively. In addition to reducing\nthe variance everywhere at virtually no additional cost, this approach cures an\nartefact of the initial force-based estimators, namely small but non-zero\nvalues of the quantities in regions where they should vanish. Beyond the\nexamples considered here, the present work highlights more generally the\nunderexplored potential of control variates to estimate observables from\nmolecular simulations.", "category": "physics_chem-ph" }, { "text": "Analytical evaluation of relativistic molecular integrals. III.\n Computation and results for molecular auxiliary functions: This work describes the fully analytical method for calculation of the\nmolecular integrals over Slater-type orbitals with non-integer principal\nquantum numbers. These integrals are expressed through relativistic molecular\nauxiliary functions derived in our previous paper [Phys. Rev. E 91, 023303\n(2015)]. The procedure for computation of the molecular auxiliary functions is\ndetailed. It applies both in relativistic and non-relativistic electronic\nstructure theory. It is capable of yielding highly accurate molecular integrals\nfor all ranges of orbital parameters and quantum numbers.", "category": "physics_chem-ph" }, { "text": "Attosecond timing of electron emission from a molecular shape resonance: Shape resonances in physics and chemistry arise from the spatial confinement\nof a particle by a potential barrier. In molecular photoionization, these\nbarriers prevent the electron from escaping instantaneously, so that nuclei may\nmove and modify the potential, thereby affecting the ionization process. By\nusing an attosecond two-color interferometric approach in combination with high\nspectral resolution, we have captured the changes induced by the nuclear motion\non the centrifugal barrier that sustains the well-known shape resonance in\nvalence-ionized N$_2$. We show that despite the nuclear motion altering the\nbond length by only $2\\%$, which leads to tiny changes in the potential\nbarrier, the corresponding change in the ionization time can be as large as\n$200$ attoseconds. This result poses limits to the concept of instantaneous\nelectronic transitions in molecules, which is at the basis of the Franck-Condon\nprinciple of molecular spectroscopy.", "category": "physics_chem-ph" }, { "text": "Global Natural Orbital Functional: Towards the Complete Description of\n the Electron Correlation: The current work presents a natural orbital functional (NOF) for electronic\nsystems with any spin value independent of the external potential being\nconsidered, that is, a global NOF (GNOF). It is based on a new two-index\nreconstruction of the two-particle reduced density matrix for spin multiplets.\nThe emergent functional describes the complete intrapair electron correlation,\nand the correlation between orbitals that make up both the pairs and the\nindividual electrons. The interorbital correlation is composed of static and\ndynamic terms. The concept of dynamic part of the occupation numbers is\nintroduced. To evaluate the accuracy achieved with GNOF, calculation of a\nvariety of properties is presented. They include the total energies and energy\ndifferences between the ground state and the lowest-lying excited state with\ndifferent spin of atoms from H to Ne, ionization potentials of the first-row\ntransition-metal atoms (Sc-Zn), and the total energies of a selected set of 55\nmolecular systems in different spin states. GNOF is also applied to the\nhomolytic dissociation of selected diatomic molecules in different spin states\nand to the rotation barrier of ethylene, both paradigmatic cases of systems\nwith significant multi-configurational character. The values obtained agree\nwith those reported at high level of theory and experimental data.", "category": "physics_chem-ph" }, { "text": "Numerical methods for a Kohn-Sham density functional model based on\n optimal transport: In this paper, we study numerical discretizations to solve density functional\nmodels in the \"strictly correlated electrons\" (SCE) framework. Unlike previous\nstudies our work is not restricted to radially symmetric densities. In the SCE\nframework, the exchange-correlation functional encodes the effects of the\nstrong correlation regime by minimizing the pairwise Coulomb repulsion,\nresulting in an optimal transport problem. We give a mathematical derivation of\nthe self-consistent Kohn-Sham-SCE equations, construct an efficient numerical\ndiscretization for this type of problem for N = 2 electrons, and apply it to\nthe H2 molecule in its dissociating limit. Moreover, we prove that the SCE\ndensity functional model is correct for the H2 molecule in its dissociating\nlimit.", "category": "physics_chem-ph" }, { "text": "Models and corrections: range separation for electronic interaction --\n lessons from density functional theory: Model Hamiltonians with long-range interaction yield energies that are\ncorrected taking into account the universal behavior of the electron-electron\ninteraction at short range. Although the intention of the paper is to explore\nthe foundations of using density functionals combined with range separation,\nthe approximations presented can be used without them, as illustrated by a\ncalculation on Harmonium. In the regime when the model system approaches the\nCoulomb system, they allow the calculation of ground states, excited states,\nand properties, without making use of the Hohenberg-Kohn theorem.\nAsymptotically, the technique is improvable, allows for error estimates that\ncan validate the results. Some considerations for correcting the errors of\nfinite basis sets in this spirit are also presented. Being related to the\npresent understanding of density functional approximations, the results are\ncomparable to those obtained with the latter, as long as these are accurate.", "category": "physics_chem-ph" }, { "text": "Geometry, supertransfer, and optimality in the light harvesting of\n purple bacteria: The remarkable rotational symmetry of the photosynthetic antenna complexes of\npurple bacteria has long been thought to enhance their light harvesting and\nexcitation energy transport. We study the role of symmetry by modeling\nhypothetical antennas whose symmetry is broken by altering the orientations of\nthe bacteriochlorophyll pigments. We find that in both LH2 and LH1 complexes,\nsymmetry increases energy transfer rates by enabling the cooperative, coherent\nprocess of supertransfer. The enhancement is particularly pronounced in the LH1\ncomplex, whose natural geometry outperforms the average randomized geometry by\n5.5 standard deviations, the most significant coherence-related enhancement\nfound in a photosynthetic complex.", "category": "physics_chem-ph" }, { "text": "Aggregation of ferromagnetic and paramagnetic atoms at edges of\n graphenes and graphite: In this work, we report that when ferromagnetic metals (Fe, Co and Ni) are\nthermally evaporated onto n-layer graphenes and graphite, a metal nanowire and\nadjacent nanogaps can be found along the edges regardless of its zigzag or\narmchair structure. Similar features can also be observed for paramagnetic\nmetals, such as Mn, Al and Pd. Meanwhile, metal nanowires and adjacent nanogaps\ncan not be found for diamagnetic metals (Au and Ag). An external magnetic field\nduring the evaporation of metals can make these unique features disappear for\nferromagnetic and paramagnetic metal; and the morphologies of diamagnetic metal\ndo not change after the application of an external magnetic field. We discuss\nthe possible reasons for these novel and interesting results, which include\npossible one dimensional ferromagnets along the edge and edge-related binding\nenergy.", "category": "physics_chem-ph" }, { "text": "Ground-state correlation energy of beryllium dimer by the Bethe-Salpeter\n equation: Since the '30s the interatomic potential of the beryllium dimer Be$_2$ has\nbeen both an experimental and a theoretical challenge. Calculating the\nground-state correlation energy of Be$_2$ along its dissociation path is a\ndifficult problem for theory. We present ab initio many-body perturbation\ntheory calculations of the Be$_2$ interatomic potential using the GW\napproximation and the Bethe-Salpeter equation (BSE). The ground-state\ncorrelation energy is calculated by the trace formula with checks against the\nadiabatic-connection fluctuation-dissipation theorem formula. We show that\ninclusion of GW corrections already improves the energy even at the level of\nthe random-phase approximation. At the level of the BSE on top of the GW\napproximation, our calculation is in surprising agreement with the most\naccurate theories and with experiment. It even reproduces an experimentally\nobserved flattening of the interatomic potential due to a delicate correlations\nbalance from a competition between covalent and van der Waals bonding.", "category": "physics_chem-ph" }, { "text": "The Differential Virial Theorem with Gradient Formulas for the Operators: A gradient dependent formula is derived for the spinless one-particle\ndensity-matrix operator z from the differential virial theorem. A gradient\ndependent formula is also derived for a spinless one-particle density-matrix\noperator that can replace the two operators of the differential virial theorem\nthat arise from the kinetic energy operator. Other operators are also derived\nthat can replace the operators mentioned above in the differential virial\ntheorem; these operators depend on the real part of spinless one-particle\ndensity-matrix.", "category": "physics_chem-ph" }, { "text": "Evaporation of water in a microfluidic channel under magnetic field: The evaporation of drops of water placed at the center of long poly(methyl\nmethacrylate) microfluidic channels with a rectangular cross section of 0.38\nmm2 is studied by simultaneously monitoring the shapes of two samples, one is\nin a 300 mT magnetic field, the other is in no field. A magnetic enhancement of\nthe evaporation rate of up to 140 % is observed, which can be understood by\ntreating the ortho and para nuclear isomers of water vapor as quasi-independent\ngasses with an ortho:para ratio in fresh vapor close to 2:3. It would take much\nlonger than the 2 - 4 h duration of an experiment in the channel, for the ratio\nto approach the 3:1 equilibrium value. Magnetic field influences evaporation\nrate by equalizing the isomeric populations in the vapor phase. The atmosphere\nin the channel is saturated with water vapor yet the evaporation rate far\nexceeds that in open beakers.", "category": "physics_chem-ph" }, { "text": "Analytic gradients for natural orbital functional theory: The analytic energy gradients with respect to nuclear motion are derived for\nnatural orbital functional (NOF) theory. The resulting equations do not require\nto resort to linear-response theory, so the computation of NOF energy gradients\nis analogous to gradient calculations at the Hartree-Fock level of theory. The\nstructures of 15 spin-compensated systems, composed by first- and second-row\natoms, are optimized employing the conjugate gradient algorithm. As\nfunctionals, two orbital-pairing approaches were used, namely, the fifth and\nsixth Piris NOFs (PNOF5 and PNOF6). For the latter, the obtained equilibrium\ngeometries are compared with coupled cluster singles and doubles (CCSD)\ncalculations and accurate empirical data.", "category": "physics_chem-ph" }, { "text": "Quasi-chemical Theories of Associated Liquids: It is shown how traditional development of theories of fluids based upon the\nconcept of physical clustering can be adapted to an alternative local\nclustering definition. The alternative definition can preserve a detailed\nvalence description of the interactions between a solution species and its\nnear-neighbors, i.e., cooperativity and saturation of coordination for strong\nassociation. These clusters remain finite even for condensed phases. The\nsimplest theory to which these developments lead is analogous to quasi-chemical\ntheories of cooperative phenomena. The present quasi-chemical theories require\nadditional consideration of packing issues because they don't impose lattice\ndiscretizations on the continuous problem. These quasi-chemical theories do not\nrequire pair decomposable interaction potential energy models. Since\ncalculations may be required only for moderately sized clusters, we suggest\nthat these quasi-chemical theories could be implemented with computational\ntools of current electronic structure theory. This can avoid an intermediate\nstep of approximate force field generation.", "category": "physics_chem-ph" }, { "text": "The quest to simulate excited-state dynamics of transition metal\n complexes: This Perspective describes current computational efforts in the field of\nsimulating photodynamics of transition metal complexes. We present the typical\nworkflows and feature the strengths and limitations of the different\ncontemporary approaches. From electronic structure methods suitable to describe\ntransition metal complexes to approaches able to simulate their nuclear\ndynamics under the effect of light, we lay particular attention to build a\nbridge between theory and experiment by critically discussing the different\nmodels commonly adopted in the interpretation of spectroscopic experiments and\nthe simulation of particular observables. Thereby, we review all the studies of\nexcited state dynamics on transition metal complexes, both in gas phase and in\nsolution from reduced to full dimensionality", "category": "physics_chem-ph" }, { "text": "Tuning the stability of Electrochemical Interfaces by Electron Transfer\n reactions: The morphology of interfaces is known to play fundamental role on the\nefficiency of energy-related applications, such light harvesting or ion\nintercalation. Altering the morphology on demand, however, is a very difficult\ntask. Here, we show ways the morphology of interfaces can be tuned by driven\nelectron transfer reactions. By using non-equilibrium thermodynamic stability\ntheory, we uncover the operating conditions that alter the interfacial\nmorphology. We apply the theory to ion intercalation and surface growth where\nelectrochemical reactions are described using Butler-Volmer or coupled\nion-electron transfer kinetics. The latter connects microscopic/quantum\nmechanical concepts with the morphology of electrochemical interfaces. Finally,\nwe construct non-equilibrium phase diagrams in terms of the applied driving\nforce (current/voltage) and discuss the importance of engineering the density\nof states of the electron donor in applications related to energy harvesting\nand storage, electrocatalysis and photocatalysis.", "category": "physics_chem-ph" }, { "text": "Kinetics of solubilization with Triton X-100 of egg-yolk lecithin\n bilayers containing cholesterol: The titration solubilization of multilamellar egg-yolk lecithin liposomes\n(MLV-EYL) with Triton X-100 was studied by rectangular optical diffusimetric\nmeasurements as a function of cholesterol (Chol) concentration. It was\ndeterminated the variation of optic percentage diffu-sion (per mmol\nsurfactant), DDif%/mmol TX-100, in the course of solubilization of MLV-EYL-Chol\nsystem with TX-100 10mM. The statistical analysis of the titration curves can\nreveal the contribution of cholesterol to the stability of phospholipid bilayer\nmembranes. The solubilization of the lecithin-cholesterol mixtures, with a high\ncholesterol content, much more bile salt requires.", "category": "physics_chem-ph" }, { "text": "Signatures of classical bifurcations in the quantum scattering\n resonances of dissociating molecules: A study is reported of the quantum scattering resonances of dissociating\nmolecules using a semiclassical approach based on periodic-orbit theory. The\ndynamics takes place on a potential energy surface with an energy barrier\nseparating two channels of dissociation. Above the barrier, the unstable\nsymmetric-stretch periodic orbit may undergo a supercritical pitchfork\nbifurcation, leading to a classically chaotic regime. Signatures of the\nbifurcation appear in the spectrum of resonances, which have a shorter lifetime\nthan classically expected. A method is proposed to evaluate semiclassically the\nenergy and lifetime of the quantum resonances in this intermediate regime.", "category": "physics_chem-ph" }, { "text": "Quantum-classical nonadiabatic dynamics of Floquet driven systems: We develop a trajectory-based approach for excited-state molecular dynamics\nsimulations of systems subject to an external periodic drive. We combine the\nexact-factorization formalism, allowing to treat electron-nuclear systems in\nnonadiabatic regimes, with the Floquet formalism for time-periodic processes.\nThe theory is developed starting with the molecular time-dependent Schroedinger\nequation with inclusion of an external periodic drive that couples to the\nsystem dipole moment. With the support of the Floquet formalism, quantum\ndynamics is approximated by combining classical-like, trajectory-based, nuclear\nevolution with electronic dynamics represented in the Floquet basis. The\nresulting algorithm, which is an extension of the coupled-trajectory mixed\nquantum-classical scheme for periodically driven systems, is applied to a model\nstudy, exactly solvable, with different field intensities.", "category": "physics_chem-ph" }, { "text": "Language models in molecular discovery: The success of language models, especially transformer-based architectures,\nhas trickled into other domains giving rise to \"scientific language models\"\nthat operate on small molecules, proteins or polymers. In chemistry, language\nmodels contribute to accelerating the molecule discovery cycle as evidenced by\npromising recent findings in early-stage drug discovery. Here, we review the\nrole of language models in molecular discovery, underlining their strength in\nde novo drug design, property prediction and reaction chemistry. We highlight\nvaluable open-source software assets thus lowering the entry barrier to the\nfield of scientific language modeling. Last, we sketch a vision for future\nmolecular design that combines a chatbot interface with access to computational\nchemistry tools. Our contribution serves as a valuable resource for\nresearchers, chemists, and AI enthusiasts interested in understanding how\nlanguage models can and will be used to accelerate chemical discovery.", "category": "physics_chem-ph" }, { "text": "Nuclear spin relaxation in cold atom-molecule collisions: We explore the quantum dynamics of nuclear spin relaxation in cold collisions\nof $^1\\Sigma^+$ molecules with structureless atoms in an external magnetic\nfield. To this end, we develop a rigorous coupled-channel methodology, which\naccounts for rotational and nuclear spin degrees of freedom of $^1\\Sigma^+$\nmolecules, their interaction with an external magnetic field, as well as for\nanisotropic atom-molecule interactions. We apply the methodology to study\ncollisional relaxation of the nuclear spin sublevels of $^{13}$CO molecules\nimmersed in a cold buffer gas of $^4$He atoms. We find that nuclear spin\nrelaxation in the ground rotational manifold of CO occurs extremely slowly due\nto the absence of direct couplings between the nuclear spin sublevels. The\nrates of collisional transitions between the $N=1$ nuclear spin states of CO\nare generally much higher due to the direct nuclear spin-rotation coupling\nbetween the states. These transitions obey selection rules, which depend on the\nvalues of space-fixed projections of rotational and nuclear spin angular\nmomenta for the initial and final molecular states. For some initial states, we\nalso observe a strong magnetic field dependence, which can be understood using\nthe first Born approximation. We use our calculated nuclear spin relaxation\nrates to investigate the thermalization of a single nuclear spin state of\nCO$(N=0)$ immersed in a cold buffer gas of He. The calculated nuclear spin\nrelaxation times ($T_1\\simeq 0.5$ s at $T=1$ K) display a steep temperature\ndependence decreasing rapidly at elevated temperatures due to the increased\npopulation of rotationally excited states, which undergo nuclear spin\nrelaxation at a much faster rate. Thus, long relaxation times of $N=0$ nuclear\nspin states in cold collisions with buffer gas atoms can only be maintained at\nsufficiently low temperatures ($kT\\ll 2B_e$), where $B_e$ is the rotational\nconstant.", "category": "physics_chem-ph" }, { "text": "A photo-mechanical coupling theory for photoisomerization hydrogel\n considering the distribution state of molecular chains: Owing to the possibility of controlling its specific mechanical behaviors up\ntaken by irradiated by light at particular wavelengths, the photoisomerization\nhydrogels have a broad range of potential applications. A theory connecting the\noptical excitation to mechanical behavior is essential to precisely control the\nphoto-mechanical behaviors of the hydrogel. In this work, a photo-mechanical\ncoupling theory is developed to describe the photo-mechanical responses of\nphotoisomerization hydrogels within the framework of finite deformation\ncontinuum thermodynamics. In the model, the deformation gradient is decomposed\ninto two parts to effectively model the light induced deformation and the\nelastic one. To consider the effect of the optical excitation on mechanical\nbehaviors, we first investigate the transporting mechanism of light in\nhydrogel, as well as the photochemical reaction process; and we then explore\nthe disturbance of light irradiation on the equilibrium of the thermodynamic\nsystem of hydrogel, as well as the relationship of conformational entropy of\nhydrogel network with the photochemical reaction; finally, based on the entropy\nelasticity theory, we propose a new free energy function of the photosensitive\nhydrogel to consider the effect of molecular chain distribution evolution on\nthe stiffness of the hydrogel network. With the implementation of the proposed\nmodel, we study the photo-mechanical behaviors and mechanical properties of\nphotoisomerization hydrogels. The present research is helpful for understanding\nthe multi-field coupling behaviors of the photosensitive hydrogel, and then\nproviding guidelines for the application of photoisomerization hydrogel.", "category": "physics_chem-ph" }, { "text": "First principles correction scheme for linear-response time-dependent\n density functional theory calculations of core electronic states: Linear-response time-dependent density functional theory (LR-TDDFT) for core\nlevel spectroscopy using standard local functionals suffers from\nself-interaction error and a lack of orbital relaxation upon creation of the\ncore hole. As a result, LR-TDDFT calculated X-ray absorption near edge\nstructure (XANES) spectra need to be shifted along the energy axis to match\nexperimental data. We propose a correction scheme based on many body\nperturbation theory to calculate the shift from first principles. The\nionization potential of the core donor state is first computed and then\nsubstituted for the corresponding Kohn--Sham orbital energy, thus emulating\nKoopmans' condition. Both self-interaction error and orbital relaxation are\ntaken into account. The method exploits the localized nature of core states for\nefficiency and integrates seamlessly in our previous implementation of core\nlevel LR-TDDFT, yielding corrected spectra in a single calculation. We\nbenchmark the correction scheme on molecules at the K- and L-edges as well as\nfor core binding energies and report accuracies comparable to higher order\nmethods. We also demonstrate applicability in large and extended systems and\ndiscuss efficient approximations.", "category": "physics_chem-ph" }, { "text": "Using symmetry-adapted optimized sum-of-products basis functions to\n calculate vibrational spectra: Vibrational spectra can be computed without storing full-dimensional vectors\nby using low-rank sum-of-products (SOP) basis functions. We introduce symmetry\nconstraints in the SOP basis functions to make it possible to separately\ncalculate states in different symmetry subgroups. This is done using a power\nmethod to compute eigenvalues and an alternating least squares method to\noptimize basis functions. Owing to the fact that the power method favours the\nconvergence of the lowest states, one must be careful not to exclude basis\nfunctions of some symmetries. Exploiting symmetry facilitates making\nassignments and improves the accuracy. The method is applied to the\nacetonitrile molecule.", "category": "physics_chem-ph" }, { "text": "Accuracy of reaction coordinate based rate theories for modelling\n chemical reactions: insights from the thermal isomerization in retinal: Modern potential energy surfaces have shifted attention to molecular\nsimulations of chemical reactions. While various methods can estimate rate\nconstants for conformational transitions in molecular dynamics simulations,\ntheir applicability to studying chemical reactions remains uncertain due to the\nhigh and sharp energy barriers and complex reaction coordinates involved. This\nstudy focuses on the thermal cis-trans isomerization in retinal, employing\nmolecular simulations and comparing rate constant estimates based on\none-dimensional rate theories with those based on sampling transitions and\ngrid-based models for low-dimensional collective variable spaces. Even though\neach individual method to estimate the rate passes its quality tests, the rate\nconstant estimates exhibit disparities of up to four orders of magnitude. Rate\nconstant estimates based on one-dimensional reaction coordinates prove\nchallenging to converge, even if the reaction coordinate is optimized. However,\nconsistent estimates of the rate constant are achieved by sampling transitions\nand by multi-dimensional grid-based models.", "category": "physics_chem-ph" }, { "text": "Predicting long timescale kinetics under variable experimental\n conditions with Kinetica.jl: Predicting the degradation processes of molecules over long timescales is a\nkey aspect of industrial materials design. However, it is made computationally\nchallenging by the need to construct large networks of chemical reactions that\nare relevant to the experimental conditions that kinetic models must mirror,\nwith every reaction requiring accurate kinetic data. Here we showcase\nKinetica.jl, a new software package for constructing large-scale chemical\nreaction networks in a fully-automated fashion by exploring chemical reaction\nspace with a kinetics-driven algorithm; coupled to efficient machine-learning\nmodels of activation energies for sampled elementary reactions, we show how\nthis approach readily enables generation and kinetic characterization of\nnetworks containing $\\sim10^{3}$ chemical species and $10^{4}$ - $10^{5}$\nreactions. Symbolic-numeric modelling of the generated reaction networks is\nused to allow for flexible, efficient computation of kinetic profiles under\nexperimentally-realizable conditions such as continuously-variable temperature\nregimes, enabling direct connection between bottom-up reaction networks and\nexperimental observations. Highly efficient propagation of long-timescale\nkinetic profiles is required for automated reaction network refinement and is\nenabled here by a new discrete kinetic approximation. The resulting Kinetica.jl\nsimulation package therefore enables automated generation, characterization,\nand long-timescale modelling of complex chemical reaction systems. We\ndemonstrate this for hydrocarbon pyrolysis simulated over timescales of\nseconds, using transient temperature profiles representing those of tubular\nflow reactor experiments.", "category": "physics_chem-ph" }, { "text": "A deterministic projector configuration interaction approach for the\n ground state of quantum many-body systems: In this work we propose a novel approach to solve the Schr\\\"{o}dinger\nequation which combines projection onto the ground state with a path-filtering\ntruncation scheme. The resulting projector configuration interaction (PCI)\napproach realizes a deterministic version of the full configuration interaction\nquantum Monte Carlo (FCIQMC) method [Booth, G. H.; Thom, A. J. W.; Alavi, A. J.\nChem. Phys. 2009, 131, 054106]. To improve upon the linearized imaginary-time\npropagator, we develop an optimal projector scheme based on an exponential\nChebyshev expansion in the limit of an infinite imaginary time step. After\nwriting the exact projector as a path integral in determinant space, we\nintroduce a path filtering procedure that truncates the size of the\ndeterminantal basis and approximates the Hamiltonian. The path filtering\nprocedure is controlled by one real threshold that determines the accuracy of\nthe PCI energy and is not biased towards any determinant. Therefore, the PCI\napproach can equally well describe static and dynamic electron correlation.\nThis point is illustrated in benchmark computation on N$_2$ at both equilibrium\nand stretched geometries. In both cases, the PCI achieves chemical accuracy\nwith wave functions that contain less than 0.5% of the full CI space. We also\nreport computations on the ground state of C$_2$ with up to quaduple-$\\zeta$\nbasis sets and wave functions as large as 200 million determinants, which allow\na direct comparison of the PCI, FCIQMC, and density matrix renormalization\ngroup (DMRG) methods. The size of the PCI wave function grows modestly with the\nnumber of unoccupied orbitals and its accuracy may be tuned to match that of\nFCIQMC and DMRG.", "category": "physics_chem-ph" }, { "text": "The Saturated and Supercritical Stirling Cycle Thermodynamic Heat Engine\n Cycle: On the assumption that experimentally validated tabulated thermodynamic\nproperties of saturated fluids published by the National Institute of Standards\nand Technology are accurate, a theoretical thermodynamic cycle can be\ndemonstrated that produces a net-negative entropy generation to the universe.\nThe experimental data on the internal energy can also be used to obtain a\nsimple, empirical equation for the change in internal energy of a real fluid\nundergoing isothermal expansion and compression. This demonstration provides\nexperimental evidence to the theory that temperature-dependent intermolecular\nattractive forces can be an entropic force that can enhance the thermodynamic\nefficiency of a real-fluid macroscopic heat engine to exceed that of the Carnot\nefficiency.", "category": "physics_chem-ph" }, { "text": "Gas temperature dependent sticking of hydrogen on cold amorphous water\n ice surfaces of interstellar interest: Using the King & Wells method, we present experimental data on the dependence\nof the sticking of molecular hydrogen and deuterium on the beam temperature\nonto non- porous amorphous solid water (ASW) ice surfaces of interstellar\ninterest. A statistical model that explains the isotopic effect and the beam\ntemperature behavior of our data is proposed. This model gives an understanding\nof the discrepancy between all known experimental results on the sticking of\nmolecular hydrogen. Moreover it is able to fit the theoretical results of V.\nBuch et al. [Astrophys. J. (1991), 379, 647] on atomic hydrogen and deuterium.\nFor astrophysical applications, an analytical formula for the sticking\ncoefficients of H, D, H2, D2 and HD in the case of a gas phase at thermal\nequilibrium is also provided at the end of the article.", "category": "physics_chem-ph" }, { "text": "Efficient and accurate modeling of electron photoemission in\n nanostructures with TDDFT: We review different computational methods for the calculation of\nphotoelectron spectra and angular distributions of atoms and molecules when\nexcited by laser pulses using time-dependent density-functional theory (TDDFT)\nthat are suitable for the description of electron emission in compact spatial\nregions. We derive and extend the time-dependent surface-flux method introduced\nin Reference [Tao L and Scrinzi A 2012 New Journal of Physics 14 013021] within\na TDDFT formalism and compare its performance to other existing methods. We\nillustrate the performance of the new method by simulating strong-field\nionization of C$_{60}$ fullerene and discuss final state effects in the orbital\nreconstruction of planar organic molecules.", "category": "physics_chem-ph" }, { "text": "$G_0W_0$ Ionization Potentials of First-Row Transition Metal Aqua Ions: We report computations of the vertical ionization potentials within the $GW$\napproximation of the near-complete series of first-row transition metal (V-Cu)\naqua ions in their most common oxidation states, i.e. V$^{3+}$, Cr$^{3+}$,\nCr$^{2+}$, Mn$^{2+}$, Fe$^{3+}$, Fe$^{2+}$, Co$^{2+}$, Ni$^{2+}$, and\nCu$^{2+}$. The $d$-orbital occupancy of these systems spans a broad range from\n$d^2$ to $d^9$. All the structures were first optimized at the density\nfunctional theory level using a large cluster of explicit water molecules that\nare embedded in a continuum solvation model. Vertical ionization potentials\nwere computed with the one-shot $G_0W_0$ approach on a range of transition\nmetal ion clusters (6, 18, 40, and 60 explicit water molecules) wherein the\nconvergence with respect to the basis set size was evaluated using the systems\nwith 40 water molecules. We assess the results using three different density\nfunctional approximations as starting points for the vertical ionization\npotential calculations, namely $G_0W_0$@PBE, $G_0W_0$@PBE0, and\n$G_0W_0$@r$^2$SCAN. While the predicted ground-state structures are similar\nwith all three exchange-correlation functionals, the vertical ionization\npotentials were in closer agreement with the experiment when using the\n$G_0W_0$@PBE0 and $G_0W_0$@r$^2$SCAN approaches, with the r2SCAN based\ncalculations being significantly less expensive. Computed bond distances and\nvertical ionization potentials for all structures were compared with available\nexperimental data and are in good agreement.", "category": "physics_chem-ph" }, { "text": "Statistical Analysis of Submicron X-Ray Tomography Data on Polymer\n Imbibition into Arrays of Cylindrical Nanopores: Frozen transient imbibition states in arrays of straight cylindrical pores\n400 nm in diameter were imaged by phase-contrast X-ray computed tomography with\nsingle-pore resolution. A semi-automatic algorithm yielding brightness profiles\nalong all pores identified within the probed sample volume is described.\nImbibition front positions are determined by descriptive statistics. A first\napproach involves the evaluation of frequency densities of single-pore\nimbibition lengths, a second one the evaluation of the statistical brightness\ndispersion within the probed volume as a function of the distance from the pore\nmouths. We plotted average imbibition front positions against systematically\nvaried powers of the imbibition time and determined the optimal exponent of the\nimbibition time by considering the correlation coefficients of the\ncorresponding linear fits. Thus, slight deviations from the proportionality of\nthe average imbibition front position to the square root of the imbibition time\npredicted by the Lucas-Washburn theory were found. A meaningful preexponential\nfactor in the power law relating imbibition front position and imbibition time\nmay only be determined after ambiguities regarding the exponent of the\nimbibition time are resolved. The dispersion of peaks representing the\nimbibition front in frequency densities of single-pore imbibition lengths and\nin brightness dispersion profiles plotted against the pore depth is suggested\nas measure of the imbibition front width. Phase-contrast X-ray computed\ntomography allows the evaluation of a large number of infiltrated submicron\npores taking advantage of phase-contrast imaging; artifacts related to sample\ndamage by tomography requiring physical ablation of sample material are\navoided.", "category": "physics_chem-ph" }, { "text": "A Theory of Pitch for the Hydrodynamic Properties of Molecules, Helices,\n and Achiral Swimmers at Low Reynolds Number: We present a theory for pitch, a matrix property which is linked to the\ncoupling of rotational and translational motion of rigid bodies at low Reynolds\nnumber. The pitch matrix is a geometric property of objects in contact with a\nsurrounding fluid, and it can be decomposed into three principal axes of pitch\nand their associated \\textit{moments of pitch}. The moments of pitch predict\nthe translational motion in a direction parallel to each pitch axis when the\nobject is rotated around that axis, and can be used to explain translational\ndrift, particularly for rotating helices. We also provide a symmetrized\nboundary element model for blocks of the resistance tensor, allowing\ncalculation of the pitch matrix for arbitrary rigid bodies. We analyze a range\nof chiral objects, including chiral molecules and helices. Chiral objects with\na $C_n$ symmetry axis with $n > 2$ show additional symmetries in their pitch\nmatrices. We also show that some achiral objects have non-vanishing pitch\nmatrices, and use this result to explain recent observations of achiral\nmicroswimmers. We also discuss the small, but non-zero pitch of Lord Kelvin's\nisotropic helicoid.", "category": "physics_chem-ph" }, { "text": "Predicting polymerization reactions via transfer learning using chemical\n language models: Polymers are candidate materials for a wide range of sustainability\napplications such as carbon capture and energy storage. However, computational\npolymer discovery lacks automated analysis of reaction pathways and stability\nassessment through retro-synthesis. Here, we report the first extension of\ntransformer-based language models to polymerization reactions for both forward\nand retrosynthesis tasks. To that end, we have curated a polymerization dataset\nfor vinyl polymers covering reactions and retrosynthesis for representative\nhomo-polymers and co-polymers. Overall, we obtain a forward model Top-4\naccuracy of 80% and a backward model Top-4 accuracy of 60%. We further analyze\nthe model performance with representative polymerization and retro-synthesis\nexamples and evaluate its prediction quality from a materials science\nperspective.", "category": "physics_chem-ph" }, { "text": "Enhanced Hydrogen Evolution Catalysis of Pentlandite due to the\n Increases in Coordination Number and Sulfur Vacancy during Cubic-Hexagonal\n Phase Transition: The search for new phases is an important direction in materials science. The\nphase transition of sulfides results in significant changes in catalytic\nperformance, such as MoS2 and WS2. Cubic pentlandite [cPn, (Fe, Ni)9S8] can be\na functional material in batteries, solar cells, and catalytic fields. However,\nno report about the material properties of other phases of pentlandite exists.\nIn this study, the unit-cell parameters of a new phase of pentlandite,\nsulfur-vacancy enriched hexagonal pentlandite (hPn), and the phase boundary\nbetween cPn and hPn were determined for the first time. Compared to cPn, the\nhPn shows a high coordination number, more sulfur vacancies, and high\nconductivity, which result in significantly higher hydrogen evolution\nperformance of hPn than that of cPn and make the non-nano rock catalyst hPn\nsuperior to other most known nanosulfide catalysts. The increase of sulfur\nvacancies during phase transition provides a new approach to designing\nfunctional materials.", "category": "physics_chem-ph" }, { "text": "Improving the Accuracy of Variational Quantum Eigensolvers With Fewer\n Qubits Using Orbital Optimization: Near-term quantum computers will be limited in the number of qubits on which\nthey can process information as well as the depth of the circuits that they can\ncoherently carry out. To-date, experimental demonstrations of algorithms such\nas the Variational Quantum Eigensolver (VQE) have been limited to small\nmolecules using minimal basis sets for this reason. In this work we propose\nincorporating an orbital optimization scheme into quantum eigensolvers wherein\na parameterized partial unitary transformation is applied to the basis\nfunctions set in order to reduce the number of qubits required for a given\nproblem. The optimal transformation is found by minimizing the ground state\nenergy with respect to this partial unitary matrix. Through numerical\nsimulations of small molecules up to 16 spin orbitals, we demonstrate that this\nmethod has the ability to greatly extend the capabilities of near-term quantum\ncomputers with regard to the electronic structure problem. We find that VQE\npaired with orbital optimization consistently achieves lower ground state\nenergies than traditional VQE when using the same number of qubits and even\nfrequently achieves lower ground state energies than VQE methods using more\nqubits.", "category": "physics_chem-ph" }, { "text": "Collision Cross Section of the J = 2 <- 1 Rotational Transition of\n CF3CCH due to Higher Order Interactions: The collision cross section of the rotational transition J = 2 <- 1 of\n3,3,3-trifluoropropyne, CF3CCH, caused by rare gas perturbers has been\ndetermined by investigating transient emission signals of molecular gas\nsamples. From analysis of the pressure dependence of the width of the\nrotational line J = 2<-1 pressure broadening parameters have been derived for\nthe pure gas and for mixtures with the rare gases He, Ne, Ar, Kr and Xe. The\npressure shift parameter for the pure gas sigmas/p = 29.03(12) kHz/Pa also has\nbeen obtained. Calculations based on the Anderson-Tsao-Curnutte theory using\ninduction and dispersion interactions for the description of collisions of\nCF3CCH with He, Ne, Ar, Kr and Xe, respectively, are in qualitative agreement\nwith the experimental results.", "category": "physics_chem-ph" }, { "text": "Transferable Water Potentials Using Equivariant Neural Networks: Machine learning interatomic potentials (MLIPs) are an emerging modeling\ntechnique that promises to provide electronic structure theory accuracy for a\nfraction of its cost, however, the transferability of MLIPs is a largely\nunknown factor. Recently, it has been proposed (J. Chem. Phys., 2023, 158,\n084111) that MLIPs trained on solely liquid water data cannot describe\nvapor-liquid equilibrium while recovering the many-body decomposition analysis\nof gas-phase water clusters, as MLIPs do not directly learn the physically\ncorrect interactions of water molecules, limiting transferability. In this\nwork, we show that MLIPs based on an equivariant neural network architecture\ntrained on only 3,200 bulk liquid water structures reproduces liquid-phase\nwater properties (e.g., density within 0.003 g/cm3 between 230 and 365 K),\nvapor-liquid equilibrium properties up to 550 K, the many-body decomposition\nanalysis of gas-phase water cluster up to six-body interactions, and the\nrelative energy and the vibrational density of states of ice phases. This study\nhighlights that state-of-the-art MLIPs have the potential to develop\ntransferable models for arbitrary phases of water that remain stable in\nnanosecond-long simulations.", "category": "physics_chem-ph" }, { "text": "Delayed Ultrafast X-ray Auger Probing (DUXAP) of Nucleobase Ultraviolet\n Photoprotection: We present a new method for ultrafast spectroscopy of molecular photoexcited\ndynamics. The technique uses a pair of femtosecond pulses: a photoexcitation\npulse initiating excited state dynamics followed by a soft x-ray (SXR) probe\npulse that core ionizes certain atoms inside the molecule. We observe the Auger\ndecay of the core hole as a function of delay between the photoexcitation and\nSXR pulses. The core hole decay is particularly sensitive to the local valence\nelectrons near the core and shows new types of propensity rules, compared to\ndipole selection rules in SXR absorption or emission spectroscopy. We apply the\ndelayed ultrafast x-ray Auger probing (DUXAP) method to the specific problem of\nnucleobase photoprotection to demonstrate its potential. The ultraviolet\nphotoexcited \\pi\\pi* states of nucleobases are prone to chemical reactions with\nneighboring bases. To avoid this, the single molecules funnel the \\pi\\pi*\npopulation to lower lying electronic states on an ultrafast timescale under\nviolation of the Born-Oppenheimer approximation. The new type of propensity\nrule, which is confirmed by Auger decay simulations, allows us to have\nincreased sensitivity on the direct relaxation from the \\pi\\pi* state to the\nvibrationally hot electronic ground state. For the nucleobase thymine, we\nmeasure a decay constant of 300 fs in agreement with previous quantum chemical\nsimulations.", "category": "physics_chem-ph" }, { "text": "Predicting the Electronic Density Response of Condensed-Phase Systems to\n Electric Field Perturbations: We present a local and transferable machine learning approach capable of\npredicting the real-space density response of both molecules and periodic\nsystems to external homogeneous electric fields. The new method, SALTER, builds\non the Symmetry-Adapted Gaussian Process Regression SALTED framework. SALTER\nrequires only a small, but necessary, modification to the descriptors used to\nrepresent the atomic environments. We present the performance of the method on\nisolated water molecules, bulk water and a naphthalene crystal. Root mean\nsquare errors of the predicted density response lie at or below 10% with barely\nmore than 100 training structures. Derived quantities, such as polarizability\ntensors and even Raman spectra further derived from these tensors show a good\nagreement with those calculated directly from quantum mechanical methods.\nTherefore, SALTER shows excellent performance when predicting derived\nquantities, while retaining all of the information contained in the full\nelectronic response. This method is thus capable of learning vector fields in a\nchemical context and serves as a landmark for further developments.", "category": "physics_chem-ph" }, { "text": "Dielectric Anomalies in Crystalline Ice: Indirect Evidence of the\n Existence of a Liquid-Liquid Critical Point in H2O: The phase diagram of H2O is extremely complex, in particular, it is believed\nthat a second critical point exists deep below the supercooled water (SCW)\nregion where two liquids of different densities coexist. The problem however,\nis that SCW freezes at temperatures just above this hypothesized liquid-liquid\ncritical point (LLCP) so direct experimental verification of its existence has\nyet to be realized. Here, we report two anomalies in the complex dielectric\nconstant during warming in the form of a peak anomaly near Tp=203 K and a sharp\nminimum near Tm=212 K from ice samples prepared from SCW under hydrostatic\npressures up to 760 MPa. The same features were observed about 4 K higher in\nheavy ice. Tp is believed to be associated to the nucleation process of\nmetastable cubic ice Ic and Tm the transitioning of ice Ic to either ices Ih or\nII depending on pressure. Given that Tp and Tm are nearly isothermal and\npresent up to at least 620 MPa and ending as a critical point near 33-50 MPa,\nit is deduced that two types of SCW with different density concentrations\nexists which affects the surface energy of ice Ic nuclei in the \"no man's land\"\nregion of the phase diagram. Our results are consistent with the LLCP theory\nand suggest that a metastable critical point exists in the region of 33-50 MPa\nand Tc > 212 K.", "category": "physics_chem-ph" }, { "text": "Quantum-Mechanical Force Balance Between Multipolar Dispersion and Pauli\n Repulsion in Atomic van der Waals Dimers: The structure and stability of atomic and molecular systems with van der\nWaals (vdW) bonding are often determined by the interplay between attractive\ndispersion interactions and repulsive interactions caused by electron\nconfinement. Arising due to different mechanisms -- electron correlation for\ndispersion and the Pauli exclusion principle for exchange-repulsion -- these\ninteractions do not appear to have a straightforward connection. In this paper,\nwe use a coarse-grained approach for evaluating the exchange energy for two\ncoupled quantum Drude oscillators and investigate the mutual compensation of\nthe attractive and repulsive forces at the equilibrium distance within the\nmultipole expansion of the Coulomb potential. This compensation yields a\ncompact formula relating the vdW radius of an atom to its multipole\npolarizabilities, $R_{\\rm vdW} = A_l^{\\,}\\, \\alpha_l^{{2}/{7(l+1)}}$, where $l$\nis the multipole rank and $A_l$ is a conversion factor. Such a relation is\ncompelling because it connects an electronic property of an isolated atom\n(atomic polarizability) with an equilibrium distance in a dimer composed of two\nclosed-shell atoms. We assess the accuracy of the revealed formula for\nnoble-gas, alkaline-earth, and alkali atoms and show that the $A_l$ can be\nassumed to be universal constants. Besides a seamless definition of vdW radii,\nthe proposed relation can also be used for the efficient determination of\natomic multipole polarizabilities solely based on the corresponding dipole\npolarizability and the vdW radius. Finally, our work provides a basis for the\nconstruction of efficient and minimally-empirical interatomic potentials by\ncombining multipolar interatomic exchange and dispersion forces on an equal\nfooting.", "category": "physics_chem-ph" }, { "text": "Exploring the magnetic properties of the largest single molecule magnets: The giant $\\{ \\mathrm{Mn}_{70} \\}$ and $\\{ \\mathrm{Mn}_{84} \\}$ wheels are\nthe largest nuclearity single-molecule magnets synthesized to date and\nunderstanding their magnetic properties poses a challenge to theory. Starting\nfrom first principles calculations, we explore the magnetic properties and\nexcitations in these wheels using effective spin Hamiltonians. We find that the\nunusual geometry of the superexchange pathways leads to weakly coupled $\\{\n\\mathrm{Mn}_{7} \\}$ subunits carrying an effective $S=2$ spin. The spectrum\nexhibits a hierarchy of energy scales and massive degeneracies, with the lowest\nenergy excitations arising from Heisenberg-ring-like excitations of the $\\{\n\\mathrm{Mn}_{7} \\}$ subunits around the wheel, at energies consistent with the\nobserved temperature dependence of the magnetic susceptibility. We further\nsuggest an important role for weak longer-range couplings in selecting the\nprecise spin ground-state of the $\\mathrm{Mn}$ wheels out of the nearly\ndegenerate ground-state band.", "category": "physics_chem-ph" }, { "text": "The consistent behavior of negative Poissons ratio with interlayer\n interactions: Negative Poissons ratio (NPR) is of great interest due to the novel\napplications in lots of fields. Films are the most commonly used form in\npractical applications, which involves multiple layers. However, the effect of\ninterlayer interactions on the NPR is still unclear. In this study, based on\nfirst principles calculations, we systematically investigate the effect of\ninterlayer interactions on the NPR by comparably studying single-layer\ngraphene, few-layer graphene, h-BN, and graphene-BN heterostructure. It is\nfound that they almost have the same geometry-strain response. Consequently,\nthe NPR in bilayer graphene, triple-layer graphene, and graphene-BN\nheterostructure are consistent with that in single-layer graphene and h-BN. The\nfundamental mechanism lies in that the response to strain of the orbital\ncoupling are consistent under the effect of interlayer interactions. The deep\nunderstanding of the NPR with the effect of interlayer interactions as achieved\nin this study is beneficial for the future design and development of\nmicro-/nanoscale electromechanical devices with novel functions based on\nnanostructures.", "category": "physics_chem-ph" }, { "text": "High-Resolution Adiabatic Calorimetry of Supercooled Water: Liquid water exhibits anomalous behavior in the supercooled region. A popular\nhypothesis to explain supercooled water's anomalies is the existence of a\nmetastable liquid-liquid transition terminating at a critical point.\n The hypothesized phase transition is not directly accessible in a bulk\nexperiment because it is expected to occur in \"no-man's\" region below the\nkinetic stability limit of the liquid phase at about 235 K, the temperature of\nhomogeneous ice formation. Therefore, verifications of this hypothesis are\nusually based on extrapolations from the experimentally accessible region.\n In this work, we present the results of high-resolution adiabatic calorimetry\nmeasurements of cold and supercooled liquid water in the range from 294 to 244\nK, the lowest temperature of water's supercooling achieved so far in a bulk\nadiabatic-calorimetry experiment. The resolution of the measurements is also\nrecord-high, with the average statistical (random) error of about 0.1 %. The\ndata are consistent with adiabatic-calorimetry measurements of supercooled\nwater earlier reported by Tombari et al. [Chem. Phys Lett., Vol. 300, P. 749\n(1999)] but significantly deviate from differential-scanning calorimetry\nmeasurements in emulsified water reported by Angell et al. [J. Phys. Chem.,\nVol. 86, P. 998 (1982)] and by Archer and Carter [J. Phys. Chem B., Vol. 104,\nP. 8563 (2000)]. Consequences of the new heat-capacity data in interpretation\nof the nature of water's anomalies are discussed.", "category": "physics_chem-ph" }, { "text": "Rotational-state-selected Carbon Astrochemistry: The addition of individual quanta of rotational excitation to a molecule has\nbeen shown to markedly change its reactivity by significantly modifying the\nintermolecular interactions. So far, it has only been possible to observe these\nrotational effects in a very limited number of systems due to lack of\nrotational selectivity in chemical reaction experiments. The recent development\nof rotationally controlled molecular beams now makes such investigations\npossible for a wide range of systems. This is particularly crucial in order to\nunderstand the chemistry occurring in the interstellar medium, such as\nexploring the formation of carbon-based astrochemical molecules and the\nemergence of molecular complexity in interstellar space from the reaction of\nsmall atomic and molecular fragments.", "category": "physics_chem-ph" }, { "text": "Systematic Improvement of Empirical Energy Functions in the Era of\n Machine Learning: The impact of targeted replacement of individual terms in empirical force\nfields is quantitatively assessed for pure water, dichloromethane (DCM), and\nsolvated K$^+$ and Cl$^-$ ions. For the electrostatics, point charges (PCs) and\nmachine learning (ML)based minimally distributed charges (MDCM) fitted to the\nmolecular electrostatic potential are evaluated together with electrostatics\nbased on the Coulomb integral. The impact of explicitly including second-order\nterms is investigated by adding a fragment molecular orbital (FMO)-derived\npolarization energy to an existing force field, in this case CHARMM. It is\ndemonstrated that anisotropic electrostatics reduce the RMSE for water (by 1.6\nkcal/mol), DCM (by 0.8 kcal/mol) and for solvated Cl$^-$ clusters (by 0.4\nkcal/mol). An additional polarization term can be neglected for DCM but notably\nimproves errors in pure water (by 1.1 kcal/mol) and in Cl$^-$ clusters (by 0.4\nkcal/mol) and is key to describing solvated K$^+$, reducing the RMSE by 2.3\nkcal/mol. A 12-6 Lennard-Jones functional form is found to perform\nsatisfactorily with PC and MDCM electrostatics, but is not appropriate for\ndescriptions that account for the electrostatic penetration energy. The\nimportance of many-body contributions is assessed by comparing a strictly\n2-body approach with self-consistent reference data. DCM can be approximated\nwell with a 2-body potential while water and solvated K$^+$ and Cl$^-$ ions\nrequire explicit many-body corrections. The present work systematically\nquantifies which terms improve the performance of an existing force field and\nwhat reference data to use for parametrizing these terms in a tractable fashion\nfor ML fitting of pure and heterogeneous systems.", "category": "physics_chem-ph" }, { "text": "Exciton transport in thin-film cyanine dye J-aggregates: We present a theoretical model for the study of exciton dynamics in\nJ-aggregated monolayers of fluorescent dyes. The excitonic evolution is\ndescribed by a Monte-Carlo wave function approach which allows for a unified\ndescription of the quantum (ballistic) and classical (diffusive) propagation of\nan exciton on a lattice in different parameter regimes. The transition between\nthe ballistic and diffusive regime is controlled by static and dynamic\ndisorder. As an example, the model is applied to three cyanine dye\nJ-aggregates: TC, TDBC, and U3. Each of the molecule-specific structure and\nexcitation parameters are estimated using time-dependent density functional\ntheory. The exciton diffusion coefficients are calculated and analyzed for\ndifferent degrees of film disorder and are correlated to the physical\nproperties and the structural arrangement of molecules in the aggregates.\nFurther, exciton transport is anisotropic and dependent on the initial exciton\nenergy. The upper-bound estimation of the exciton diffusion length in the TDBC\nthin-film J-aggregate is of the order of hundreds of nanometers, which is in\ngood qualitative agreement with the diffusion length estimated from\nexperiments.", "category": "physics_chem-ph" }, { "text": "Dynamics and decay rates of a time-dependent two-saddle system: The framework of transition state theory (TST) provides a powerful way for\nanalyzing the dynamics of physical and chemical reactions. While TST has\nalready been successfully used to obtain reaction rates for systems with a\nsingle time-dependent saddle point, multiple driven saddles have proven\nchallenging because of their fractal-like phase space structure. This paper\npresents the construction of an approximately recrossing-free dividing surface\nbased on the normally hyperbolic invariant manifold in a time-dependent\ntwo-saddle model system. Based on this, multiple methods for obtaining\ninstantaneous (time-resolved) decay rates of the underlying activated complex\nare presented and their results discussed.", "category": "physics_chem-ph" }, { "text": "Novel \u03bb^3-Iodane Based Functionalization of Synthetic Carbon\n Allotropes (SCAs) - Common Concepts and Quantification of the Degree of\n Addition: The covalent functionalization of carbon allotropes represents a main topic\nin the growing field of nano materials. However, the development of functional\narchitectures is impeded by the intrinsic polydispersibility of the respective\nstarting material, the unequivocal characterization of the introduced\nfunctional moieties and the exact determination of the degree of\nfunctionalization. Based on a novel carbon allotrope functionalization\nreaction, utilizing {\\lambda}^3-iodanes as radical precursor systems, we were\nable to demonstrate the feasibility to separate and to quantify thermally\ndetached functional groups, formerly covalently linked to carbon nanotubes and\ngraphene via TG-GC/MS.", "category": "physics_chem-ph" }, { "text": "Explicitly correlated Helium wave function and hyperspherical\n coordinates: Wave functions of a new functional kind have been proposed for Helium-like\natoms in this work . These functions explicitly depend on interelectronic and\nhyperspherical coordinates. The best ground state energy for the Helium atom $\n-2.903724376677 a.u.$ has been calculated with variational method with basis\nset of simple functions with a single exponential parameter. To the author's\nknowledge, this is the best result with use of hyperspherical coordinates so\nfar. Comparable result has been obtained for the hydrogen anion. For Helium\natom, our best wave functions matched the Kato cusp conditions within the\naccuracy below $6.10^{-4} $. An important feature of proposed wave functions is\nthe inclusion of negative powers of $R=\\sqrt(r^{2}_{1}+r^{2}_{2})$ in\ncombination with positive powers of $r_{12}$ into the wave function. We showed\nthat this is necessary condition for proposed wave function to be a formal\nsolution of Schr\\\"odinger equation.", "category": "physics_chem-ph" }, { "text": "Magnetic dipolar interaction between correlated triplets created by\n singlet fission in tetracene crystals: Singlet fission (SF) can potentially break the Shockley-Queisser efficiency\nlimit in single-junction solar cells by splitting one photo-excited singlet\nexciton (S1) into two triplets (2T1) in organic semiconductors. A dark\nmulti-exciton (ME) state has been proposed as the intermediate connecting S1 to\n2T1. However, the exact nature of this ME state, especially how the\ndoubly-excited triplets interact, remains elusive. Here, we report a\nquantitative study on the magnetic dipolar interaction between SF-induced\ncorrelated triplets in tetracene crystals by monitoring quantum beats relevant\nto the ME sublevels at room temperature. The resonances of ME sublevels\napproached by tuning an external magnetic field are observed to be avoided,\nwhich agrees well with the theoretical predictions considering a magnetic\ndipolar interaction of ~ 0.008 GHz. Our work paves a way to quantify the\nmagnetic dipolar interaction in organic materials and marks an important step\ntowards understanding the underlying physics of the ME state.", "category": "physics_chem-ph" }, { "text": "DMRG-SCF study of the singlet, triplet, and quintet states of\n oxo-Mn(Salen): We use CheMPS2, our free open-source spin-adapted implementation of the\ndensity matrix renormalization group (DMRG) [Wouters et al., Comput. Phys.\nCommun. 185, 1501 (2014)], to study the lowest singlet, triplet, and quintet\nstates of the oxo-Mn(Salen) complex. We describe how an initial approximate\nDMRG calculation in a large active space around the Fermi level can be used to\nobtain a good set of starting orbitals for subsequent complete-active-space or\nDMRG self-consistent field (CASSCF or DMRG-SCF) calculations. This procedure\nmitigates the need for a localization procedure, followed by a manual selection\nof the active space. Per multiplicity, the same active space of 28 electrons in\n22 orbitals (28e, 22o) is obtained with the 6-31G*, cc-pVDZ, and ANO-RCC-VDZP\nbasis sets (the latter with DKH2 scalar relativistic corrections). Our\ncalculations provide new insight into the electronic structure of the quintet.", "category": "physics_chem-ph" }, { "text": "First Order Static Excitation Potential: Scheme for Excitation Energies\n and Transition Moments: We present an approximation scheme for the calculation of the principal\nexcitation energies and transition moments of finite many-body systems. The\nscheme is derived from a first order approximation to the self energy of a\nrecently proposed extended particle-hole Green's function. A hermitian\neigenvalue problem is encountered of the same size as the well-known Random\nPhase Approximation (RPA). We find that it yields a size consistent description\nof the excitation properties and removes an inconsistent treatment of the\nground state correlation by the RPA. By presenting a hermitian eigenvalue\nproblem the new scheme avoids the instabilities of the RPA and should be well\nsuited for large scale numerical calculations. These and additional properties\nof the new approximation scheme are illuminated by a very simple exactly\nsolvable model.", "category": "physics_chem-ph" }, { "text": "Semiclassical propagation of Wigner functions: We present a comprehensive study of semiclassical phase-space propagation in\nthe Wigner representation, emphasizing numerical applications, in particular as\nan initial-value representation. Two semiclassical approximation schemes are\ndiscussed: The propagator of the Wigner function based on van Vleck's\napproximation replaces the Liouville propagator by a quantum spot with an\noscillatory pattern reflecting the interference between pairs of classical\ntrajectories. Employing phase-space path integration instead, caustics in the\nquantum spot are resolved in terms of Airy functions. We apply both to two\nbenchmark models of nonlinear molecular potentials, the Morse oscillator and\nthe quartic double well, to test them in standard tasks such as computing\nautocorrelation functions and propagating coherent states. The performance of\nsemiclassical Wigner propagation is very good even in the presence of marked\nquantum effects, e.g., in coherent tunneling and in propagating Schr\\\"odinger\ncat states, and of classical chaos in four-dimensional phase space. We suggest\noptions for an effective numerical implementation of our method and for\nintegrating it in Monte-Carlo--Metropolis algorithms suitable for\nhigh-dimensional systems.", "category": "physics_chem-ph" }, { "text": "Dual-Topology Hamiltonian-Replica-Exchange Overlap Histogramming Method\n to Calculate Relative Free Energy Difference in Rough Energy Landscape: A novel overlap histogramming method based on Dual-Topology\nHamiltonian-Replica-Exchange simulation technique is presented to efficiently\ncalculate relative free energy difference in rough energy landscape, in which\nmultiple conformers coexist and are separated by large energy barriers. The\nproposed method is based on the realization that both DT-HERM exchange\nefficiency and confidence of free energy determination in overlap histogramming\nmethod depend on the same criteria: neighboring states' energy derivative\ndistribution overlap. In this paper, we demonstrate this new methodology by\ncalculating free energy difference between amino acids: Leucine and Asparagine,\nwhich is an identified chanllenging system for free energy simulations.", "category": "physics_chem-ph" }, { "text": "Study of the Ne(^3P_2) + CH_3F Electron Transfer Reaction below 1 Kelvin: Relatively little is known about the dynamics of electron transfer reactions\nat low collision energy. We present a study of Penning ionization of ground\nstate methyl fluoride molecules by electronically excited neon atoms in the 13\n$\\mu$eV--4.8 meV (150 mK--56 K) collision energy range, using a neutral-neutral\nmerged beam setup. Relative cross sections have been measured for three\nNe($^3P_2$)+ CH$_3$F reaction channels by counting the number of CH$_3$F$^+$,\nCH$_2$F$^+$, and CH$_3^+$ product ions, as a function of relative velocity\nbetween the neon and methyl fluoride molecular beams. Experimental cross\nsections markedly deviate from the Langevin capture model at collision energies\nabove 20 K. The branching ratios are constant. In other words, the chemical\nshape of the CH$_3$F molecule, as seen by Ne($^3P_2$) atom, appears not to\nchange as the collision energy is varied, in contrast to related Ne($^3P_J$) +\nCH$_3$X (X=Cl and Br) reactions at higher collision energies.", "category": "physics_chem-ph" }, { "text": "Electron transfer in confined electromagnetic fields: The interaction between molecular (atomic) electron(s) and the vacuum field\nof a reflective cavity generates a significant interest thanks to the rapid\ndevelopments in nanophotonics. Such interaction which lies within the realm of\ncavity quantum electrodynamic can substantially affect transport properties of\nmolecular systems. In this work we consider non-adiabatic electron transfer\nprocess in the presence of a cavity mode. We present a generalized framework\nfor the interaction between a charged molecular system and a quantized\nelectromagnetic field of a cavity and apply it to the problem of electron\ntransfer between a donor and an acceptor placed in a confined vacuum\nelectromagnetic field. The effective system Hamiltonian corresponds to a\nunified Rabi and spin-boson model which includes a self-dipole energy term. Two\nlimiting cases are considered: one where the electron is assumed much faster\nthan the cavity mode and another in which the electron tunneling time is\nsignificantly larger than the mode period. In both cases a significant rate\nenhancement can be produced by coupling to the cavity mode in the Marcus\ninverted region. The results of this work offer new possibilities for\ncontrolling electron transfer processes using visible and infrared plasmonics", "category": "physics_chem-ph" }, { "text": "Simulation of electrochemical processes during oxygen evolution on\n $\\mathrm{Pb-MnO_2}$ composite electrodes: The geometric properties of $\\mathrm{Pb-MnO_2}$ composite electrodes are\nstudied, and a general formula is presented for the length of the triple phase\nboundary (TPB) on two dimensional (2D) composite electrodes using sphere\npacking and cutting simulations. The difference in the geometrical properties\nof 2D (or compact) and 3D (or porous) electrodes is discussed. It is found that\nthe length of the TPB is the only reasonable property of a 2D electrode that\nfollows a 1/r particle radius relationship. Subsequently, sphere packing cuts\nare used to derive a statistical electrode surface that is the basis for the\nearlier proposed simulations of different electrochemical mechanisms. It is\nshown that two of the proposed mechanisms (conductivity and a\ntwo-step-two-material kinetic mechanism) can explain the current increase at\n$\\mathrm{Pb-MnO_2}$ anodes compared to standard lead anodes. The results show\nthat although $\\mathrm{MnO_2}$ has low conductivity, when combined with Pb as\nthe metal matrix, the behaviour of the composite is not purely ohmic but is\nalso affected by activation overpotentials, increasing the current density\nclose to the TPB. Current density is inversely proportional to the radius of\nthe catalyst particles, matching with earlier experimental results. A\nhypothetical two-step-two-material mechanism with intermediate\n$\\mathrm{H_2O_2}$ that reacts on both the Pb matrix and $\\mathrm{MnO_2}$\ncatalyst is studied. It was found that assuming quasi-reversible generation of\n$\\mathrm{H_2O_2}$ followed by its chemical decomposition on $\\mathrm{MnO_2}$,\nresults are obtained that agree with the experiments. It is further emphasised\nthat both the Pb matrix and $\\mathrm{MnO_2}$ catalyst are necessary and their\noptimum ratio depends on the used current density. Yet, additional experimental\nevidence is needed to support the postulated mechanism.", "category": "physics_chem-ph" }, { "text": "Polarizable embedding complex polarization propagator in four- and\n two-component frameworks: Explicit embedding methods combined with the complex polarization propagator\n(CPP) enable modeling of spectroscopy for increasingly complex systems with a\nhigh density of states. We present the first derivation and implementation of\nthe CPP in four- and exact two-component (X2C) polarizable embedding (PE)\nframeworks. We denote the developed methods PE-4c-CPP and PE-X2C-CPP,\nrespectively. We illustrate the methods by estimating the solvent effect on\nUV-vis and X-ray atomic absorption (XAS) spectra of [Rh(H2O)6]3+ and\n[Ir(H2O)6]3+ immersed in aqueous solution. We moreover estimate solvent effects\non UV-vis spectra of a platinum complex that can be photo-chemically activated\n(in water) to kill cancer cells. Our results clearly show that inclusion of the\nenvironment is required: UV-vis and (to a lesser degree) XAS spectra can become\nqualitatively different from vacuum calculations. Comparison of PE-4c-CPP and\nPE-X2C-CPP methods shows that X2C essentially reproduces the solvent effect\nobtained with the 4c methods.", "category": "physics_chem-ph" }, { "text": "The influence of microwave pulse conditions on enantiomer-specific state\n transfer: We report a combined experimental and theoretical study on the influence of\nmicrowave pulse durations on enantiomer-specific state transfer. Two triads of\nrotational states within a chiral molecule (1-indanol) are selected to address\nthe possible scenarios. In the triad connected to the absolute ground state,\nthe simplest triad that exists for all chiral molecules, the\nenantiomer-specific state transfer process simplifies into a sequence of\ntwo-level transitions. The second triad, including higher rotational states,\nrepresents a more generic scenario that involves multiple Rabi frequencies for\neach transition. Our study reveals that the conventional\n$\\frac{\\pi}{2}-\\pi-\\frac{\\pi}{2}$ pulse sequence is not the optimal choice,\nexcept for the ideal case when in the simplest triad only the lowest level is\ninitially populated. We find that employing a shorter duration for the first\nand last pulse of the sequence leads to significantly higher state-specific\nenantiomeric enrichment, albeit at the expense of overall population in the\ntarget state. Our experimental results are in very good agreement with theory,\nsubstantiating the quantitative understanding of enantiomer-specific state\ntransfer.", "category": "physics_chem-ph" }, { "text": "Equilibrium molecular energies used to obtain molecular dissociation\n energies and heats of formation within the bond-order correlation approach: Ab initio calculations including electron correlation are still extremely\ncostly except for the smallest atoms and molecules. Therefore, our purpose in\nthe present study is to employ a bond-order correlation approach to obtain, via\nequilibrium molecular energies, molecular dissociation energies and heats of\nformation for some 20 molecules containing C, H, and O atoms, with a maximum\nnumber of electrons around 40. Finally, basis set choice is shown to be\nimportant in the proposed procedure to include electron correlation effects in\ndetermining thermodynamic properties. With the optimum choice of basis set, the\naverage percentage error for some 20 molecules is approximately 20% for heats\nof formation. For molecular dissociation energies the average error is much\nsmaller: ~0.4.", "category": "physics_chem-ph" }, { "text": "Annihilation rate in positronic systems by quantum Monte Carlo. e$^+$LiH\n as test case: An accurate method to compute the annihilation rate in positronic systems by\nmeans of quantum Monte Carlo simulations is tested and compared with previously\nproposed methods using simple model systems. This method can be applied within\nall the quantum Monte Carlo techniques, just requiring to accumulate the\npositron-electron distribution function. The annihilation rate of e$^+$LiH as a\nfunction of the internuclear distance is studied using a model potential\napproach to eliminate the core electrons of Li, and explicitly correlated wave\nfunctions to deal with all the remaining particles. These results allow us to\ncompute vibrationally averaged annihilation rates, and to understand the effect\nof the Li$^+$ electric field on positron and electron distributions.", "category": "physics_chem-ph" }, { "text": "UConnRCMPy: Python-based data analysis for rapid compression machines: The ignition delay of a fuel/air mixture is an important quantity in\ndesigning combustion devices, and these data are also used to validate chemical\nkinetic models for combustion. One of the typical experimental devices used to\nmeasure the ignition delay is called a Rapid Compression Machine (RCM). This\npaper presents UConnRCMPy, an open-source Python package to process\nexperimental data from the RCM at the University of Connecticut. Given an\nexperimental measurement, UConnRCMPy computes the thermodynamic conditions in\nthe reaction chamber of the RCM during an experiment along with the ignition\ndelay. UConnRCMPy implements an extensible framework, so that alternative\nexperimental data formats can be incorporated easily. In this way, UConnRCMPy\nimproves the consistency of RCM data processing and enables the community to\nreproduce data analysis procedures.", "category": "physics_chem-ph" }, { "text": "Tin-DNA Complexes Investigated by Nuclear Inelastic Scattering of\n Synchrotron Radiation: Nuclear inelastic scattering (NIS) of synchrotron radiation has been used to\ninvestigate the dynamics of tin ions chelated by DNA. Theoretical NIS spectra\nhave been simulated with the help of density functional theory (DFT)\ncalculations using 12 models for different binding sites of the tin ion in\n(CH3)Sn(DNAPhosphate)2. The simulated spectra are compared with the measured\nspectrum of the tin-DNA complex.", "category": "physics_chem-ph" }, { "text": "Accurate ionization potential of gold anionic clusters from density\n functional theory and many-body perturbation theory: We present a theoretical study of the ionization potential in small anionic\ngold clusters, using density functional theory, with and without\nexact-exchange, and many body perturbation theory, namely the G0W0 approach. We\nfind that G0W0 is the best approach and correctly describes the first\nionization potential with an accuracy of about 0.1 eV.", "category": "physics_chem-ph" }, { "text": "Empirical model of the Gibbs free energy for saline solutions of\n arbitrary concentration: Application for H2O-NaCl solutions at\n 423.15K-573.15K and pressures from saturation up to 5kbar: An empirical model of the concentration dependence of the excess Gibbs free\nenergy Gex for saline solutions is proposed. Our simple analytical form of Gex\nallows obtaining equations of state of saline solutions equally precise in the\nwhole range of the salt concentrations, from dilute solutions up to the limit\nof solubility. Our equation for Gex includes one term responsible for\nconcentration dependence of Gex at low salt concentrations and two terms of\nMargules type dependent on powers of mole fractions of the components. These\nterms contain four parameters dependent on temperature and pressure. As an\nexample of application of the proposed model we took the system H2O-NaCl. For\nfixed T and P, our four-parameter form of Gex allows precisely reproduce\nexperimental data for NaCl water solutions, including both regions of low and\nhigh concentrations. An introduction of temperature dependence of the\nparameters allowed us to build a precise analytic fit of experimental data on\nosmotic coefficients of NaCl solutions for saturation pressures of NaCl at\ntemperatures 423.15K-573.15K. On the basis of PVTx data by Driesner (2007) the\nmodel was extended towards pressures up to 5kbar. Our form of Gex allows\nobtaining the molar volumes, activities of components and other thermodynamic\nproperties of NaCl-H2O solutions in the range of temperatures 423.15K-573.15K\nand pressures from saturation up to 5kbar in the whole range of concentrations\npossible for H2O-NaCl solutions (from zero up to approximately 10 molal at\n573.15K).", "category": "physics_chem-ph" }, { "text": "Reaction extent or advancement of the reaction: A new general definition: The concept of reaction extent (the progress of a reaction, advancement of\nthe reaction, conversion, etc.) was introduced around 100 years ago. Most of\nthe literature provides a definition for the exceptional case of a single\nreaction step or gives an implicit definition that cannot be made explicit.\nThere are views that the reaction extent somehow has to tend to 1 when the\nreaction goes to completion as time tends to infinity. However, there is no\nagreement on which function should tend to 1. Starting from the standard\ndefinition by IUPAC and following the classical works by De Donder, Aris, and\nCroce we extend the classic definition of the reaction extent for an arbitrary\nnumber of species and reaction steps. The new general, explicit definition is\nalso valid for non-mass action kinetics. We also studied the mathematical\nproperties (evolution equation, continuity, monotony, differentiability, etc.)\nof the defined quantity, connecting them to the formalism of modern reaction\nkinetics. Our approach tries to adhere to the customs of chemists and be\nmathematically correct simultaneously. To make the exposition easy to\nunderstand, we use simple chemical examples and many figures, throughout. We\nalso show how to apply this concept to exotic reactions: reactions with more\nthan one stationary state, oscillatory reactions, and reactions showing chaotic\nbehavior. The main advantage of the new definition of reaction extent is that\nby knowing the kinetic model of a reacting system one can now calculate not\nonly the time evolution of the concentration of each reacting species but also\nthe number of occurrences of the individual reaction events.", "category": "physics_chem-ph" }, { "text": "Spin-selective electron transfer reactions of radical pairs: beyond the\n Haberkorn master equation: Radical pair recombination reactions are normally described using a quantum\nmechanical master equation for the electronic and nuclear spin density\noperator. The electron spin state selective (singlet and triplet) recombination\nprocesses are described with a Haberkorn reaction term in this master equation.\nHere we consider a general spin state selective electron transfer reaction of a\nradical pair and use Nakajima-Zwanzig theory to derive the master equation for\nthe spin density operator, thereby elucidating the relationship between\nnon-adiabatic reaction rate theory and the Haberkorn reaction term. A second\norder perturbation theory treatment of the diabatic coupling naturally results\nin the Haberkorn master equation with an additional reactive scalar electron\nspin coupling term. This term has been neglected in previous spin chemistry\ncalculations, but we show that it will often be quite significant. We also show\nthat beyond second order in perturbation theory, i.e., beyond the Fermi golden\nrule limit, an additional reactive singlet-triplet dephasing term appears in\nthe master equation. A closed form expression for the reactive scalar electron\nspin coupling in terms of the Marcus theory parameters that determine the\nsinglet and triplet recombination rates is presented. By performing simulations\nof radical pair reactions with the exact Hierarchical Equations of Motion\n(HEOM) method, we demonstrate that our master equations provide a very accurate\ndescription of radical pairs undergoing spin-selective non-adiabatic electron\ntransfer reactions. The existence of a reactive electron spin coupling may well\nhave implications for biologically relevant radical pair reactions such as\nthose which have been suggested to play a role in avian magnetoreception.", "category": "physics_chem-ph" }, { "text": "Nuclear Resonance Vibrational Spectroscopy of Iron Sulfur Proteins: Nuclear inelastic scattering in conjunction with density functional theory\n(DFT) calculations has been applied for the identification of vibrational modes\nof the high-spin ferric and the high-spin ferrous iron-sulfur center of a\nrubredoxin-type protein from the thermophylic bacterium Pyrococcus abysii.", "category": "physics_chem-ph" }, { "text": "Homogeneous Gold Catalysis through Relativistic Effects: Addition of\n Water to Propyne: In the catalytic addition of water to propyne the Au(III) catalyst is not\nstable under non-relativistic conditions and dissociates into a Au(I) compound\nand Cl2. This implies that one link in the chain of events in the catalytic\ncycle is broken and relativity may well be seen as the reason why Au(III)\ncompounds are effective catalysts.", "category": "physics_chem-ph" }, { "text": "IRFEL Selective Irradiation of Amorphous Solid Water: from Dangling to\n Bulk Modes: Amorphous solid water (ASW) is one of the most widely studied solid phase\nsystems. A better understanding of the nature of inter- and intramolecular\nforces in ASW is, however, still required to correctly interpret the catalytic\nrole of ASW in the formation and preservation of molecular species in\nenvironments such as the icy surfaces of Solar System objects, on interstellar\nicy dust grains and potentially even in the upper layers of the Earth's\natmosphere. In this work, we have systematically exposed porous ASW (pASW) to\nmid-infrared radiation generated by a free-electron laser at the HFML-FELIX\nfacility in the Netherlands to study the effect of vibrational energy injection\ninto the surface and bulk modes of pASW. During multiple sequential\nirradiations on the same ice spot, we observed selective effects both at the\nsurface and in the bulk of the ice. Although the density of states in pASW\nshould allow for a fast vibrational relaxation through the H-bonded network,\npart of the injected energy is converted into structural ice changes as\nillustrated by the observation of spectral modifications when performing\nFourier transform infrared spectroscopy in reflection-absorption mode. Future\nstudies will include the quantification of such effects by systematically\ninvestigating ice thickness, ice morphology, and ice composition.", "category": "physics_chem-ph" }, { "text": "Calculation of single-beam two-photon absorption transition rate of\n rare-earth ions using effective operator and diagrammatic representation: Effective operators needed in single-beam two-photon transition calculations\nhave been represented with modified Goldstone diagrams similar to the type\nsuggested by Duan and co-workers [J. Chem. Phys. 121, 5071 (2004) ]. The rules\nto evaluate these diagrams are different from those for effective Hamiltonian\nand one-photon transition operators. It is verified that the perturbation terms\nconsidered contain only connected diagrams and the evaluation rules are\nsimplified and given explicitly.", "category": "physics_chem-ph" }, { "text": "An efficient and flexible approach for computing rovibrational\n polaritons from first principles: A theoretical framework is presented for the computation of rovibrational\npolaritonic states of a molecule in a lossless infrared (IR) microcavity. In\nthe proposed approach the quantum treatment of the rotational and vibrational\nmotion of the molecule can be formulated using arbitrary approximations. The\ncavity-induced changes in electronic structure are treated perturbatively,\nwhich allows using the existing polished tools of standard quantum chemistry\nfor determining electronic molecular properties. As a case study, the\nrovibrational polaritons and related thermodynamic properties of H$_2$O in an\nIR microcavity are computed for varying cavity parameters and applying various\napproximations to describe the molecular degrees of freedom. The self-dipole\ninteraction is found to be significant for nearly all light-matter coupling\nstrengths investigated, and the molecular polarizability proved to be important\nfor the correct qualitative behavior of the energy level shifts induced by the\ncavity. On the other hand, the magnitude of polarization remains small,\njustifying the perturbative approach for the cavity-induced changes in\nelectronic structure. Comparing results obtained using a high-accuracy\nvariational molecular model with those obtained utilizing the rigid rotor and\nharmonic oscillator approximations revealed that as long as the rovibrational\nmodel is appropriate for describing the field-free molecule, the computed\nrovibropolaritonic properties can be expected to be accurate as well. Strong\nlight-matter coupling between the radiation mode of an IR cavity and the\nrovibrational states of H$_2$O lead to minor changes in the thermodynamic\nproperties of the system, and these changes seem to be dominated by\nnon-resonant interactions between the quantum light and matter.", "category": "physics_chem-ph" }, { "text": "First-Passage Time: A Conception Leading to Superstatistics. II.\n Continuous Distributions and their Applications: A continuous approximation for the results of [1] is obtained. In this\napproximation the energy distribution is represented in the form of the product\nof the Gibbs factor and superstatistics factor. The mutual weights of the\nfactors are defined by the control parameter of the problem. Various\napproximations for the superstatistics factor are written. The resulting\ndistribution is compared to a number of known results (multiplicative noise,\nVan der Pol generator etc). It is applied to the description of self-organized\ncriticality, statistics of cosmic rays etc as well.", "category": "physics_chem-ph" }, { "text": "Understanding the Spin Crossover Dynamical Effects of the Dioxygen\n Binding and Activation on HOD enzyme: For the cofactor-free 1-H-3-hydroxy-4-oxoquinaldine-2,4-dioxygenase (HOD),\nthe dioxygen (O2) dependent steps are rate-limiting along with a spin state\ncrossover to the singlet spin state. Here, the primary triplet O2 molecule\nactivation on the 2-methyl-3-hydroxy-4(1H)-quinolone (MHQ) is investigated, and\nthe catalytic role of the intersystem crossing effects is highlighted by\ndirectly comparing results from the Born-Oppenheimer dynamics and non-adiabatic\nsurface hopping dynamics. This work confirms non-adiabatic dynamical effects\nare essential to modulate the O2 activation on the substrate MHQ. The time\nscale of the equilibration and conversion from triplet to singlet state should\nbe in the range of a few hundreds of femtoseconds. We hope this work provides\nus a fresh look at the underlying physics of dioxygen activation reactions\ninvolving more than one spin state.", "category": "physics_chem-ph" }, { "text": "Revealing a full quantum ladder by nonlinear spectroscopy: Coherent two-dimensional spectroscopy in IR or visible region is very\neffective for studying correlations, energy relaxation/transfer pathways in\ncomplex multi-chromophore or multi-mode systems. However it is usually\nrestricted up to two-quanta excitations and their properties. In this paper an\narbitrary level of excitation is suggested as the utility to scan nonlinear\npotential surfaces of quantum systems up to a desired excitation degree. This\ncan be achieved by a simple three-pulse laser spectroscopy approach. Accurate\nevaluation of high-level anharmonicities as well as transition amplitudes can\nbe directly obtained. Additionally, questions regarding the quantum nature of\nthe probed system can be addressed by studying absolute peak positions.", "category": "physics_chem-ph" }, { "text": "Extracting Work From A Single Heat Bath: We present here a machine that is capable of extracting work from a single\nheat bath. Although no significant temperature gradient is involved in the\noperation of the machine, yet the Carnot efficiency as high as one is\nachievable. Working of the machine is explained on the basis of a demon\nsuggested by Maxwell. Utilizing the kinetic energy spectrum of the molecules in\nsolution, the demon can send \"hotter\" molecules to a higher gravitational\npotential at the expense of their own energies. Difference in chemical\npotentials due to concentration gradients and use of semi-permeable membranes\nensure the continuing cyclic process.", "category": "physics_chem-ph" }, { "text": "Molecular chirality quantification: tools and benchmarks: Molecular chirality has traditionally been viewed as a binary property where\na molecule is classified as either chiral or achiral, yet in the recent decades\nmathematical methods for quantifying chirality have been explored. Here we use\ntoy molecular systems to systematically compare the performance of two state of\nthe art chirality measures (1) the Continuous Chirality Measure (CCM) and (2)\nthe Chirality Characteristic ($\\chi$). We find that both methods exhibit\nqualitatively similar behavior when applied to simple molecular systems such as\na four-site molecule or the polymer double-helix, but we show that the CCM may\nbe more suitable for evaluating the chirality of arbitrary molecules or\nabstract structures such as normal vibrational modes. We discuss a range of\nconsiderations for applying these methods to molecular systems in general, and\nwe provide links to user-friendly codes for both methods. We aim this paper to\nserve as a concise resource for scientists attempting to familiarize themselves\nwith these chirality measures or attempting to implement chirality measures in\ntheir own work.", "category": "physics_chem-ph" }, { "text": "Performance and Analysis of the Alchemical Transfer Method for Binding\n Free Energy Predictions of Diverse Ligands: The Alchemical Transfer Method (ATM) is herein validated against the relative\nbinding free energies of a diverse set of protein-ligand complexes. We employed\na streamlined setup workflow, a bespoke force field, and the AToM-OpenMM\nsoftware to compute the relative binding free energies (RBFE) of the benchmark\nset prepared by Schindler and collaborators at Merck KGaA. This benchmark set\nincludes examples of standard small R-group ligand modifications as well as\nmore challenging scenarios, such as large R-group changes, scaffold hopping,\nformal charge changes, and charge-shifting transformations. The novel\ncoordinate perturbation scheme and a dual-topology approach of ATM address some\nof the challenges of single-topology alchemical relative binding free energy\nmethods. Specifically, ATM eliminates the need for splitting electrostatic and\nLennard-Jones interactions, atom mapping, defining ligand regions, and\npost-corrections for charge-changing perturbations. Thus, ATM is simpler and\nmore broadly applicable than conventional alchemical methods, especially for\nscaffold-hopping and charge-changing transformations. Here, we performed well\nover 500 relative binding free energy calculations for eight protein targets\nand found that ATM achieves accuracy comparable to existing state-of-the-art\nmethods, albeit with larger statistical fluctuations. We discuss insights into\nspecific strengths and weaknesses of the ATM method that will inform future\ndeployments. This study confirms that ATM is applicable as a production tool\nfor relative binding free energy (RBFE) predictions across a wide range of\nperturbation types within a unified, open-source framework.", "category": "physics_chem-ph" }, { "text": "Intramolecular Vibrations Complement the Robustness of Primary Charge\n Separation in a Dimer Model of the Photosystem II Reaction Center: The energy conversion of oxygenic photosynthesis is triggered by primary\ncharge separation in proteins at the photosystem II reaction center. Here, we\ninvestigate the impacts of the protein environment and intramolecular\nvibrations on primary charge separation at the photosystem II reaction center.\nThis is accomplished by combining the quantum dynamic theories of condensed\nphase electron transfer with quantum chemical calculations to evaluate the\nvibrational Huang-Rhys factors of chlorophyll and pheophytin molecules. We\nreport that individual vibrational modes play a minor role in promoting the\ncharge separation, contrary to the discussion in recent publications.\nNevertheless, these small contributions accumulate to considerably influence\nthe charge separation rate, resulting in sub-picosecond charge separation\nalmost independent of the driving force and temperature. We suggest that the\nintramolecular vibrations complement the robustness of the charge separation in\nthe photosystem II reaction center against the inherently large static disorder\nof the involved electronic energies.", "category": "physics_chem-ph" }, { "text": "Relativistic semistochastic heat-bath configuration interaction: In this work we present the extension of semistochastic heat-bath\nconfiguration interaction (SHCI) to work with any two-component and\nfour-component Hamiltonian. Vertical detachment energy (VDE) of AuH_2^- and\nzero-field splitting (ZFS) of NpO2 2+ are calculated by correlating more than\n100 spinors in both cases. This work demonstrates the capability of SHCI to\ntreat problems where both relativistic effect and electron correlation are\nimportant.", "category": "physics_chem-ph" }, { "text": "Gradual Optimization Learning for Conformational Energy Minimization: Molecular conformation optimization is crucial to computer-aided drug\ndiscovery and materials design. Traditional energy minimization techniques rely\non iterative optimization methods that use molecular forces calculated by a\nphysical simulator (oracle) as anti-gradients. However, this is a\ncomputationally expensive approach that requires many interactions with a\nphysical simulator. One way to accelerate this procedure is to replace the\nphysical simulator with a neural network. Despite recent progress in neural\nnetworks for molecular conformation energy prediction, such models are prone to\ndistribution shift, leading to inaccurate energy minimization. We find that the\nquality of energy minimization with neural networks can be improved by\nproviding optimization trajectories as additional training data. Still, it\ntakes around $5 \\times 10^5$ additional conformations to match the physical\nsimulator's optimization quality. In this work, we present the Gradual\nOptimization Learning Framework (GOLF) for energy minimization with neural\nnetworks that significantly reduces the required additional data. The framework\nconsists of an efficient data-collecting scheme and an external optimizer. The\nexternal optimizer utilizes gradients from the energy prediction model to\ngenerate optimization trajectories, and the data-collecting scheme selects\nadditional training data to be processed by the physical simulator. Our results\ndemonstrate that the neural network trained with GOLF performs on par with the\noracle on a benchmark of diverse drug-like molecules using $50$x less\nadditional data.", "category": "physics_chem-ph" }, { "text": "Temperature-dependent structure of methanol-water mixtures on cooling:\n X-ray and neutron diffraction and molecular dynamics simulations: Methanol-water liquid mixtures have been investigated by high-energy\nsynchrotron X-ray and neutron diffraction at low temperatures. We are thus able\nto report the first complete sets of both X-ray and neutron weighted total\nscattering structure factors over the entire composition range (at 12 different\nmethanol concentrations (x$_M$) from 10 to 100 mol%) and at temperatures from\nambient down to the freezing points of the mixtures. The new diffraction data\nmay later be used as reference in future theoretical and simulation studies.\nThe measured data are interpreted by molecular dynamics simulations, in which\nthe all atom OPLS/AA force field model for methanol is combined with both the\nSPC/E and TIP4P/2005 water potentials. Although the TIP4P/2005 water model was\nfound to be somewhat more successful, both combinations provide at least\nsemi-quantitative agreement with measured diffraction data. From the simulated\nparticle configurations, partial radial distribution functions, as well as\nvarious distributions of the number of hydrogen bonds have been determined. As\na general trend, the average number of hydrogen bonds increases upon cooling.\nHowever, the number of hydrogen bonds between methanol molecules slightly\ndecreases with lowering temperatures in the concentration range between ca. 30\nand 60 mol % alcohol content. The same is valid for water-water hydrogen bonds\nabove 70 mol % of methanol content, from room temperature down to 193 K.", "category": "physics_chem-ph" }, { "text": "Spectral Functions from Auxiliary-Field Quantum Monte Carlo without\n Analytic Continuation: The Extended Koopmans' Theorem Approach: We explore the extended Koopmans' theorem (EKT) within the phaseless\nauxiliary-field quantum Monte Carlo (AFQMC) method. The EKT allows for the\ndirect calculation of electron addition and removal spectral functions using\nreduced density matrices of the $N$-particle system, and avoids the need for\nanalytic continuation. The lowest level of EKT with AFQMC, called EKT1-AFQMC,\nis benchmarked using small molecules, 14-electron and 54-electron uniform\nelectron gas supercells, and diamond at the $\\Gamma$-point. Via comparison with\nnumerically exact results (when possible) and coupled-cluster methods, we find\nthat EKT1-AFQMC can reproduce the qualitative features of spectral functions\nfor Koopmans-like charge excitations with errors in peak locations of less than\n0.25 eV in a finite basis. We also note the numerical difficulties that arise\nin the EKT1-AFQMC eigenvalue problem, especially when back-propagated\nquantities are very noisy. We show how a systematic higher order EKT approach\ncan correct errors in EKT1-based theories with respect to the satellite region\nof the spectral function. Our work will be of use for the study of low-energy\ncharge excitations and spectral functions in correlated molecules and solids\nwhere AFQMC can be reliably performed.", "category": "physics_chem-ph" }, { "text": "A machine learning framework for quantifying chemical segregation and\n microstructural features in atom probe tomography data: Atom probe tomography (APT) is ideally suited to characterize and understand\nthe interplay of chemical segregation and microstructure in modern\nmulticomponent materials. Yet, the quantitative analysis typically relies on\nhuman expertise to define regions of interest. We introduce a computationally\nefficient, multistage machine learning strategy to identify chemically distinct\ndomains in a semi automated way, and subsequently quantify their geometric and\ncompositional characteristics. In our algorithmic pipeline, we first coarse\ngrain the APT data into voxels, collect the composition statistics, and\ndecompose it via clustering in composition space. The composition\nclassification then enables the real space segmentation via a density based\nclustering algorithm, thus revealing the microstructure at voxel resolution.\nOur approach is demonstrated for a Sm(Co,Fe)ZrCu alloy. The alloy exhibits two\nprecipitate phases with a plate-like, but intertwined morphology. The primary\nsegmentation is further refined to disentangle these geometrically complex\nprecipitates into individual plate like parts by an unsupervised approach based\non principle component analysis, or a U-Net based semantic segmentation trained\non the former. Following the chemical and geometric analysis, detailed chemical\ndistribution and segregation effects relative to the predominant plate-like\ngeometry can be readily mapped without resorting to the initial voxelization.", "category": "physics_chem-ph" }, { "text": "A study of the density functional methods on the photoabsorption of\n Bodipy dyes: Tunability of the photoabsorption and directional charge injection\ncharacteristics of Bodipy-based dye molecules with different carbonyl groups\nmake them promising candidates for photovoltaic applications. In order to study\nthe effect of screening in the Coulomb interaction on the electronic and\noptical properties of two Bodipy derivatives, we have used linear response\ntime-dependent and exact exchange hybrid density functional approaches. The\neffect of linear and non-linear solvation models on the electrochemical\nproperties of the dyes has also been discussed.", "category": "physics_chem-ph" }, { "text": "Measuring Time-Dependent Induced Quantum Coherences via Two-Dimensional\n Coherence Spectroscopy: We propose a two-dimensional spectroscopic protocol for measuring the\ntime-dependent coherences between the stationary states of a system induced by\na time-dependent system-bath interaction. We also investigate the role of\ntemporally-correlated noise on coherence dephasing. This protocol enables\ndynamical information about the system and its coupling to the environment to\nbe determined. Our results are based on the quantum-trajectory method, and are\nobtained from both approximate, analytical and exact, numerical solutions of\nthe time-dependent Schroedinger equation. As an example, we show how this\nprotocol can be used to investigate exciton dynameds in conjugated polymers\ninduced by the coupling of their torsional modes with the environment.", "category": "physics_chem-ph" }, { "text": "Lasercooled RaF as a promising candidate to measure molecular parity\n violation: The parameter $W_\\mathrm{a}$, which characterizes nuclear spin-dependent\nparity violation effects within the effective molecular spin-rotational\nHamiltonian, was computed for the electronic ground state of radium fluoride\n(RaF) and found to be one of the largest absolute values predicted so far.\nThese calculations were performed with the complex generalised Hartree-Fock\nmethod within a two-component (quasi-relativistic) zeroth-order regular\napproximation framework. Peculiarities of the molecular electronic structure of\nRaF lead to highly diagonal Franck-Condon matrices between vibrational states\nof the electronic ground and first excited states, which renders the molecule\nin principle suitable for direct laser cooling. As a trapped gas of cold\nmolecules offers a superior coherence time, RaF can be considered a promising\ncandidate for high-precision spectroscopic experiments aimed at the search of\nmolecular parity-violation effects.", "category": "physics_chem-ph" }, { "text": "Determination of Trace Moisture Content in Dimethylacetamide by Gas\n Chromatography: Dimethylacetamide is used as a solvent in polymer processing and moisture in\nDMA affects the morphology and mechanical properties of the polymer products.\nThis paper describes a method for determination of trace moisture content in\nDMA by acetylene production - gas chromatography. In the condition of 30\ncentigrade and ultrasonic dispersion, moisture in DMA sample was reacted with\ncalcium carbide and its product of acetylene was measured by gas\nchromatography. By this way, trace moisture in DMA was determined with RSD of\n2.272 percent and limit of measurement was 0.002 percent.", "category": "physics_chem-ph" }, { "text": "Mind the Retrosynthesis Gap: Bridging the divide between Single-step and\n Multi-step Retrosynthesis Prediction: Retrosynthesis is the task of breaking down a chemical compound recursively\nstep-by-step into molecular precursors until a set of commercially available\nmolecules is found. Consequently, the goal is to provide a valid synthesis\nroute for a molecule. As more single-step models develop, we see increasing\naccuracy in the prediction of molecular disconnections, potentially improving\nthe creation of synthetic paths. Multi-step approaches repeatedly apply the\nchemical information stored in single-step retrosynthesis models. However, this\nconnection is not reflected in contemporary research, fixing either the\nsingle-step model or the multi-step algorithm in the process. In this work, we\nestablish a bridge between both tasks by benchmarking the performance and\ntransfer of different single-step retrosynthesis models to the multi-step\ndomain by leveraging two common search algorithms, Monte Carlo Tree Search and\nRetro*. We show that models designed for single-step retrosynthesis, when\nextended to multi-step, can have a tremendous impact on the route finding\ncapabilities of current multi-step methods, improving performance by up to +30%\ncompared to the most widely used model. Furthermore, we observe no clear link\nbetween contemporary single-step and multi-step evaluation metrics, showing\nthat single-step models need to be developed and tested for the multi-step\ndomain and not as an isolated task to find synthesis routes for molecules of\ninterest.", "category": "physics_chem-ph" }, { "text": "Beyond Cavity Born-Oppenheimer: On Non-Adiabatic Coupling and Effective\n Ground State Hamiltonians in Vibro-Polaritonic Chemistry: The emerging field of vibro-polaritonic chemistry studies the impact of\nlight-matter hybrid states known as vibrational polaritons on chemical\nreactivity and molecular properties. Here, we discuss vibro-polaritonic\nchemistry from a quantum chemical perspective beyond the cavity\nBorn-Oppenheimer (CBO) approximation and examine the role of electron-photon\ncorrelation in effective ground state Hamiltonians. We first quantitatively\nreview ab initio vibro-polaritonic chemistry based on the molecular Pauli-Fierz\nHamiltonian in dipole approximation and a vibrational strong coupling (VSC)\nBorn-Huang expansion. We then derive non-adiabatic coupling elements arising\nfrom both ``slow'' nuclei and cavity modes compared to ``fast'' electrons via\nthe generalized Hellmann-Feynman theorem, discuss their properties and\nre-evaluate the CBO approximation. In the second part, we introduce a crude VSC\nBorn-Huang expansion based on adiabatic electronic states, which provides a\nfoundation for widely employed effective Pauli-Fierz Hamiltonians in ground\nstate vibro-polaritonic chemistry. The latter do not strictly respect the CBO\napproximation but an alternative scheme, which we name crude CBO approximation.\nWe argue that the crude CBO ground state misses electron-photon entanglement\nrelative to the CBO ground state due to neglected cavity-induced non-adiabatic\ntransition dipole couplings to excited states. A perturbative connection\nbetween both ground state approximations is proposed, which identifies the\ncrude CBO ground state as first-order approximation to its CBO counterpart. We\nprovide an illustrative numerical analysis of the cavity Shin-Metiu model with\na focus on non-adiabatic coupling under VSC and electron-photon correlation\neffects on classical activation barriers. We finally discuss potential\nshortcomings of the electron-polariton Hamiltonian when employed in the VSC\nregime.", "category": "physics_chem-ph" }, { "text": "Simulating rotationally inelastic collisions using a Direct Simulation\n Monte Carlo method: A new approach to simulating rotational cooling using a direct simulation\nMonte Carlo (DSMC) method is described and applied to the rotational cooling of\nammonia seeded into a helium supersonic jet. The method makes use of ab initio\nrotational state changing cross sections calculated as a function of collision\nenergy. Each particle in the DSMC simulations is labelled with a vector of\nrotational populations that evolves with time. Transfer of energy into\ntranslation is calculated from the mean energy transfer for this population at\nthe specified collision energy. The simulations are compared with a continuum\nmodel for the on-axis density, temperature and velocity; rotational temperature\nas a function of distance from the nozzle is in accord with expectations from\nexperimental measurements. The method could be applied to other types of gas\nmixture dynamics under non-uniform conditions, such as buffer gas cooling of\nNH$_3$ by He.", "category": "physics_chem-ph" }, { "text": "Universal Bound on the Fano Factor in Enzyme Kinetics: The Fano factor, an observable quantifying fluctuations of product generation\nby a single enzyme, can reveal information about the underlying reaction\nscheme. A lower bound on this Fano factor that depends on the thermodynamic\naffinity driving the transformation from substrate to product constrains the\nnumber of intermediate states of an enzymatic cycle. So far, this bound has\nbeen proven only for a unicyclic network of states. We show that the bound can\nbe extended to arbitrary multicyclic networks, with the Fano factor\nconstraining the largest value of the effective length, which is the ratio\nbetween the number of states and the number of products, among all cycles.", "category": "physics_chem-ph" }, { "text": "Comment on \"Orientational Distribution of Free O-H Groups of Interfacial\n Water is Exponential\": In a recent letter (PRL,121,246101,2018), Sun et al. reported that combined\nMD simulation and sum frequency generation vibrational spectroscopy (SFG-VS)\nmeasurements led to conclusions of a broad and exponentially decaying\norientational distribution, and the presence of the free O-H group pointing\ndown to the bulk at the air/water interface. In this comment, we show that\ntheir main conclusions are based on questionable interpretation of the SFG-VS\ndata presented in the letter [1], and are also contrary to the established data\nanalysis and interpretations in the literature [2-5].", "category": "physics_chem-ph" }, { "text": "Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics\n Study of the Aqueous Fe$^{2+}$/Fe$^{3+}$ Redox Reaction: Kohn-Sham density functional theory and plane wave basis set based ab initio\nmolecular dynamics (AIMD) simulation is a powerful tool for studying complex\nreactions in solutions, such as electron transfer (ET) reactions involving\nFe$^{2+}$/Fe$^{3+}$ ions in water. In most cases, such simulations are\nperformed using density functionals at the level of Generalized Gradient\nApproximation (GGA). The challenge in modelling ET reactions is the poor\nquality of GGA functionals in predicting properties of such open-shell systems\ndue to the inevitable self-interaction error (SIE). While hybrid functionals\ncan minimize SIE, AIMD at that level of theory is typically 150 times slower\nthan GGA for systems containing ~100 atoms. Among several approaches reported\nto speed-up AIMD simulations with hybrid functionals, the noise-stabilized MD\n(NSMD) procedure, together with the use of localized orbitals to compute the\nrequired exchange integrals, is an attractive option. In this work, we\ndemonstrate the application of the NSMD approach for studying the\nFe$^{2+}$/Fe$^{3+}$ redox reaction in water. It is shown here that long AIMD\ntrajectories at the level of hybrid density functionals can be obtained using\nthis approach. Redox properties of the aqueous Fe$^{2+}$/Fe$^{3+}$ system\ncomputed from these simulations are compared with the available experimental\ndata for validation.", "category": "physics_chem-ph" }, { "text": "Numerical Investigation of Critical Electrochemical Factors for\n Localized Corrosion using a Multi-species Reactive Transport Model: A multi-species reactive transport model based on the sequential\nnon-iterative approach is employed to investigate two major stages involved in\nartificial pit experiments of stainless steel: I. Stable pitting under a salt\nfilm and II. Film-free dissolution that transitions to repassivation. Data of\ncurrent density and electrical potential obtained from rapid polarization scans\nof pits with different depths are utilized to calibrate the elapsed time and\nthe electrode kinetics of each stage. The local chemistry near the base of pits\nat different temperature and bulk concentrations is simulated to determine\nseveral critical electrochemical factors at saturation and repassivation.", "category": "physics_chem-ph" }, { "text": "Collisional Quenching at Ultralow Energies: Controlling Efficiency with\n Internal State Selection: Calculations have been carried out for the vibrational quenching of excited\nH$_2$ molecules which collide with Li$^+$ ions at ultralow energies. The\ndynamics has been treated exactly using the well known quantum coupled-channel\nexpansions over different initial vibrational levels. The overall interaction\npotential has been obtained from the calculations carried out earlier in our\ngroup using highly correlated ab initio methods. The results indicate that\nspecific features of the scattering observables, e.g. the appearance of\nRamsauer-Townsend minima in elastic channel cross sections and the marked\nincrease of the cooling rates from specific initial states, can be linked to\npotential properties at vanishing energies (sign and size of scattering\nlengths) and to the presence of either virtual states or bound states. The\nsuggestion is made that by selecting the initial state preparation of the\nmolecular partners, the ionic interactions would be amenable to controlling\nquenching efficiency at ultralow energies.", "category": "physics_chem-ph" }, { "text": "Tailored Porous Electrode Resistance for Controlling Electrolyte\n Depletion and Improving Charging Response in Electrochemical Systems: The rapid charging and/or discharging of electrochemical cells can lead to\nlocalized depletion of electrolyte concentration. This depletion can\nsignificantly impact the system's time dependent resistance. For systems with\nporous electrodes, electrolyte depletion can limit the rate of charging and\nincrease energy dissipation. Here we propose a theory to control and avoid\nelectrolyte depletion by tailoring the value and spatial distribution of\nresistance in a porous electrode. We explore the somewhat counterintuitive idea\nthat increasing local spatial resistances of the solid electrode itself leads\nto improved charging rate and minimal change in energy loss. We analytically\nderive a simple expression for an electrode resistance profile that leads to\nhighly uniform electrolyte depletion. We use numerical simulations to explore\nthis theory and simulate spatiotemporal dynamics of electrolyte concentration\nin the case of a supercapacitor with various tailored electrode resistance\nprofiles which avoid localized depletion. This increases charging rate up to\naround 2-fold with minimal effect on overall dissipated energy in the system.", "category": "physics_chem-ph" }, { "text": "Core excitations and ionizations of uranyl in Cs$_{2}$UO$_{2}$Cl$_{4}$\n from relativistic embedded damped response time-dependent density functional\n theory and equation of motion coupled cluster calculations: X-ray spectroscopies, by their high selectivity and sensitivity to the\nchemical environment around the atoms probed, provide significant insight into\nthe electronic structure of molecules and materials. Interpreting experimental\nresults requires reliable theoretical models, accounting for environment,\nrelativistic, electron correlation, and orbital relaxation effects in a\nbalanced manner. = In this work, following up on prior work for valence\nprocesses [A. S. P. Gomes et al., Phys.\\ Chem.\\ Chem.\\ Phys. 15, 15153 (2013)],\nwe present a protocol for the simulation of core excited spectra (with damped\nresponse time-dependent density functional theory, 4c-DR-TD-DFT) and ionization\nenergies (with the core-valence separated equation of motion coupled cluster\ntheory, 4c-CVS-EOM-IP) based on the Dirac-Coulomb Hamiltonian, while\nenvironment effects are accounted for through the frozen density embedding\n(FDE) method. We showcase this approach for the uranium M$_4$-, L$_3$-edge and\noxygen K-edge of uranyl tetrachloride UO$_2$Cl$_4^{2-}$ in a host\nCs$_{2}$UO$_{2}$Cl$_{4}$ crystal. We have found that the 4c-DR-TD-DFT\nsimulations yield excitation spectra that very closely match the experiment for\nthe uranium M$_4$ and oxygen K-edges, with good agreement for the broad\nexperimental spectra for the L$_3$-edge. By investigating the sensitivity of\nspectral shapes to the lifetimes, and by decomposing each peak into its\ncomponents, we have been able to correlate our results with angle-resolved\nspectra. We have observed that for the uranium M$_4$ edge, a simplified model\nfor uranyl tetrachloride-in which an embedding potential replaces the chloride\nequatorial ligands-closely matches the spectral profile obtained for the uranyl\ntetrachloride system.", "category": "physics_chem-ph" }, { "text": "Energy Transfer from Individual Semiconductor Nanocrystals to Graphene: Energy transfer from photoexcited zero-dimensional systems to metallic\nsystems plays a prominent role in modern day materials science. A situation of\nparticular interest concerns the interaction between a photoexcited dipole and\nan atomically thin metal. The recent discovery of graphene layers permits\ninvestigation of this phenomenon. Here we report a study of fluorescence from\nindividual CdSe/ZnS nanocrystals in contact with single- and few-layer graphene\nsheets. The rate of energy transfer is determined from the strong quenching of\nthe nanocrystal fluorescence. For single-layer graphene, we find a rate of ~\n4ns-1, in agreement with a model based on the dipole approximation and a\ntight-binding description of graphene. This rate increases significantly with\nthe number of graphene layers, before approaching the bulk limit. Our study\nquantifies energy transfer to and fluorescence quenching by graphene, critical\nproperties for novel applications in photovoltaic devices and as a molecular\nruler.", "category": "physics_chem-ph" }, { "text": "Valence-bond Non-equilibrium Solvation Model for a Twisting Monomethine\n Cyanine: We propose and analyze a two-state valence-bond model of non-equilibrium\nsolvation effects on the excited-state twisting reaction of monomethine\ncyanines. Suppression of this reaction is thought responsible for\nenvironment-dependent fluorescence yield enhancement in these dyes.\nFluorescence is quenched because twisting is accompanied via the formation of\ndark twisted intramolecular charge-transfer (TICT) states. For monomethine\ncyanines, where the ground state is a superposition of structures with\ndifferent bond and charge localization, there are two possible twisting\npathways with different charge localization in the excited state. For\nparameters corresponding to symmetric monomethines, the model predicts two\nlow-energy twisting channels on the excited-state surface that lead to a\nmanifold of twisted intramolecular charge-transfer (TICT) states. For typical\nmonomethines, twisting on the excited state surface will occur with a small\nbarrier or no barrier. Changes in the solvation configuration can\ndifferentially stabilize TICT states in channels corresponding to different\nbonds, and that the position of a conical intersection between adiabatic states\nmoves in response to solvation to stabilize either one channel or the other.\nThere is a conical intersection seam that grows along the bottom of the\nexcited-state potential with increasing solvent polarity. For monomethine\ncyanines with modest-sized terminal groups in moderately polar solution, the\nbottom of the excited-state potential surface is completely spanned by a\nconical intersection seam.", "category": "physics_chem-ph" }, { "text": "DQC: a Python program package for Differentiable Quantum Chemistry: Automatic differentiation represents a paradigm shift in scientific\nprogramming, where evaluating both functions and their derivatives is required\nfor most applications. By removing the need to explicitly derive expressions\nfor gradients, development times can be be shortened, and calculations\nsimplified. For these reasons, automatic differentiation has fueled the rapid\ngrowth of a variety of sophisticated machine learning techniques over the past\ndecade, but is now also increasingly showing its value to support {\\it ab\ninitio} simulations of quantum systems, and enhance computational quantum\nchemistry. Here we present an open-source differentiable quantum chemistry\nsimulation code, DQC, and explore applications facilitated by automatic\ndifferentiation: (1) calculating molecular perturbation properties; (2)\nreoptimizing a basis set for hydrocarbons; (3) checking the stability of\nself-consistent field wave functions; and (4) predicting molecular properties\nvia alchemical perturbations.", "category": "physics_chem-ph" }, { "text": "Electrostatic fluctuations in cavities within polar liquids and\n thermodynamics of polar solvation: We present the results of numerical simulations of fluctuations of the\nelectrostatic potential and electric field inside cavities created in the fluid\nof dipolar hard spheres. We found that the thermodynamics of polar solvation\ndramatically changes its regime when the cavity size becomes about 4-5 times\nlarger than the size of the liquid particle. The range of small cavities can be\nreasonably understood within the framework of current solvation models. On the\ncontrary, the regime of large cavities is characterized by a significant\nsoftening of the cavity interface resulting in a decay of the fluctuation\nvariances with the cavity size much faster than anticipated by both the\ncontinuum electrostatics and microscopic theories. For instance, the variance\nof potential decays with the cavity size $R_0$ approximately as $1/R_0^{4-6}$\ninstead of the $1/R_0$ scaling expected from standard electrostatics. Our\nresults suggest that cores of non-polar molecular assemblies in polar liquids\nlose solvation strength much faster than is traditionally anticipated.", "category": "physics_chem-ph" }, { "text": "Elucidating the NuclearQuantum Dynamics of Intramolecular Double\n Hydrogen Transfer in Porphycene: We address the double hydrogen transfer (DHT) dynamics of the porphycene\nmolecule: A complex paradigmatic system where the making and breaking of\nH-bonds in a highly anharmonic potential energy surface requires a quantum\nmechanical treatment not only of the electrons, but also of the nuclei. We\ncombine density-functional theory calculations, employing hybrid functionals\nand van der Waals corrections, with recently proposed and optimized\npath-integral ring-polymer methods for the approximation of quantum vibrational\nspectra and reaction rates. Our full-dimensional ring-polymer instanton\nsimulations show that below 100 K the concerted DHT tunneling pathway\ndominates, but between 100 K and 300 K there is a competition between concerted\nand stepwise pathways when nuclear quantum effects are included. We obtain\nground-state reaction rates of $2.19 \\times 10^{11} \\mathrm{s}^{-1}$ at 150 K\nand $0.63 \\times 10^{11} \\mathrm{s}^{-1}$ at 100 K, in good agreement with\nexperiment. We also reproduce the puzzling N-H stretching band of porphycene\nwith very good accuracy from thermostatted ring-polymer molecular dynamics\nsimulations. The position and lineshape of this peak, centered at around 2600\ncm$^{-1}$ and spanning 750 cm$^{-1}$, stems from a combination of very strong\nH-bonds, the coupling to low-frequency modes, and the access to $cis$-like\nisomeric conformations, which cannot be appropriately captured with\nclassical-nuclei dynamics. These results verify the appropriateness of our\ngeneral theoretical approach and provide a framework for a deeper physical\nunderstanding of hydrogen transfer dynamics in complex systems.", "category": "physics_chem-ph" }, { "text": "Modulated conjugation as a means for attaining a record high intrinsic\n hyperpolarizability: We report on a series of chromophores that have been synthesized with a\nmodulated conjugation path between donor and acceptor. Hyper-Rayleigh\nscattering measurements of the best molecule show an enhanced intrinsic\nhyperpolarizability that breaches the apparent limit of all previously studied\nmolecules.", "category": "physics_chem-ph" }, { "text": "Molecular Dynamics Simulations of the O2- Ion Mobility in Dense Neon Gas: We report here the results of Molecular Dynamics simulations of the drift\nmobility of negative oxygen ions in very dense neon gas in the supercritical\nphase. The simulations relatively well reproduce the trend of the experimental\ndata. The rationalization of the mobility behavior as a function of the gas\ndensity is given in terms of the number of atoms correlated in the first\nsolvation shell around the ion.", "category": "physics_chem-ph" }, { "text": "Radiation damage of polyethylene exposed in the stratosphere at an\n altitude of 40 km: Low Density Polyethylene (LDPE) films were exposed at an altitude of 40 km\nover a 3 day NASA stratospheric balloon mission from Alice Springs, Australia.\nThe radiation damage, oxidation and nitration in the LDPE films exposed in\nstratosphere were measured using ESR, FTIR and XPS spectroscopy. The results\nwere compared with those from samples stored on the ground and exposed in a\nlaboratory plasma. The types of free radicals, unsaturated hydrocarbon groups,\noxygen-containing and nitrogen-containing groups in LDPE film exposed in the\nstratosphere and at the Earth's surface are different. The radiation damage in\nfilms exposed in the stratosphere are observed in the entire film due to the\npenetration of high energy cosmic rays through their thickness, while the\nradiation damage in films exposed on the ground is caused by sunlight\npenetrating into only a thin surface layer. A similarly thin layer of the film\nis damaged by exposure to plasma due to the low energy of the plasma particles.\nThe intensity of oxidation and nitration of LDPE films reflects the difference\nof atmospheric pressure on the ground and in the stratosphere. The high-density\nradiation damage of the LDPE films above the ozone layer in the stratosphere is\ncaused by primary cosmic rays as well as collision induced cosmic ray air\nshowers, and is consistent with the measured flux of cosmic radiation. The\nresults show, that stratospheric flights can be used to simulate the effects of\nspace environments during interplanet space flights for the purposes of\ninvestigating the degradation of polymer materials.", "category": "physics_chem-ph" }, { "text": "Interpretable Embeddings From Molecular Simulations Using Gaussian\n Mixture Variational Autoencoders: Extracting insight from the enormous quantity of data generated from\nmolecular simulations requires the identification of a small number of\ncollective variables whose corresponding low-dimensional free-energy landscape\nretains the essential features of the underlying system. Data-driven techniques\nprovide a systematic route to constructing this landscape, without the need for\nextensive a priori intuition into the relevant driving forces. In particular,\nautoencoders are powerful tools for dimensionality reduction, as they naturally\nforce an information bottleneck and, thereby, a low-dimensional embedding of\nthe essential features. While variational autoencoders ensure continuity of the\nembedding by assuming a unimodal Gaussian prior, this is at odds with the\nmulti-basin free-energy landscapes that typically arise from the identification\nof meaningful collective variables. In this work, we incorporate this physical\nintuition into the prior by employing a Gaussian mixture variational\nautoencoder (GMVAE), which encourages the separation of metastable states\nwithin the embedding. The GMVAE performs dimensionality reduction and\nclustering within a single unified framework, and is capable of identifying the\ninherent dimensionality of the input data, in terms of the number of Gaussians\nrequired to categorize the data. We illustrate our approach on two toy models,\nalanine dipeptide, and a challenging disordered peptide ensemble, demonstrating\nthe enhanced clustering effect of the GMVAE prior compared to standard VAEs.\nThe resulting embeddings appear to be promising representations for\nconstructing Markov state models, highlighting the transferability of the\ndimensionality reduction from static equilibrium properties to dynamics.", "category": "physics_chem-ph" }, { "text": "Extent of hydrogen coverage of Si(001) under chemical vapor deposition\n conditions from ab initio approaches: The extent of hydrogen coverage of the Si(001)c(4x2) surface in the presence\nof hydrogen gas has been studied with dispersion corrected density functional\ntheory. Electronic energy contributions are well described using a hybrid\nfunctional. The temperature dependence of the coverage in thermodynamic\nequilibrium was studied computing the phonon spectrum in a supercell approach.\nAs an approximation to these demanding computations, an interpolated phonon\napproach was found to give comparable accuracy. The simpler ab initio\nthermodynamic approach is not accurate enough for the system studied, even if\ncorrections by the Einstein model for surface vibrations are considered. The\non-set of H2 desorption from the fully hydrogenated surface is predicted to\noccur at temperatures around 750 K. Strong changes in hydrogen coverage are\nfound between 1000 and 1200 K in good agreement with previous reflectance\nanisotropy spectroscopy experiments. These findings allow a rational choice for\nthe surface state in the computational treatment of chemical reactions under\ntypical metal organic vapor phase epitaxy conditions on Si(001).", "category": "physics_chem-ph" }, { "text": "Hybrid gausslet/Gaussian basis sets: We introduce hybrid gausslet/Gaussian basis sets, where a standard Gaussian\nbasis is added to a gausslet basis in order to increase accuracy near the\nnuclei while keeping the spacing of the grid of gausslets relatively large. The\nGaussians are orthogonalized to the gausslets, which are already orthonormal,\nand approximations are introduced to maintain the diagonal property of the two\nelectron part of the Hamiltonian, so that it continues to scale as the second\npower of the number of basis functions, rather than the fourth. We introduce\nseveral corrections to the Hamiltonian designed to enforce certain exact\nproperties, such as the values of certain two-electron integrals. We also\nintroduce a simple universal energy correction which compensates for the\nincompleteness of the basis stemming from the electron-electron cusps, based on\nthe measured double occupancy of each basis function. We perform a number of\nHartree Fock and full configuration interaction (full-CI) test calculations on\ntwo electron systems, and Hartree Fock on a ten-atom hydrogen chain, to\nbenchmark these techniques. The inclusion of the cusp correction allows us to\nobtain complete basis set full-CI results, for the two electron cases, at the\nlevel of several microHartrees, and we see similar apparent accuracy for\nHartree Fock on the ten-atom hydrogen chain.", "category": "physics_chem-ph" }, { "text": "Continuous probe of cold complex molecules with infrared frequency comb\n spectroscopy: Cavity-enhanced frequency comb spectroscopy for molecule detection in the\nmid-infrared powerfully combines high resolution, high sensitivity, and broad\nspectral coverage. However, this technique, and essentially all spectroscopic\nmethods, is limited in application to relatively small, simple molecules. Here\nwe integrate comb spectroscopy with continuous, cold samples of molecules\nproduced via buffer gas cooling, thus enabling the study of significantly more\ncomplex molecules. We report simultaneous gains in resolution, sensitivity, and\nbandwidth and demonstrate this combined capability with the first rotationally\nresolved direct absorption spectra in the CH stretch region of several complex\nmolecules. These include nitromethane (CH$_3$NO$_2$), a model system that\npresents challenging questions to the understanding of large amplitude\nvibrational motion, as well as several large organic molecules with fundamental\nspectroscopic and astrochemical relevance, including naphthalene\n(C$_{10}$H$_8$), adamantane (C$_{10}$H$_{16}$), and hexamethylenetetramine\n(C$_{6}$N$_4$H$_{12}$). This general spectroscopic tool has the potential to\nsignificantly impact the field of molecular spectroscopy, simultaneously\nimproving efficiency, spectral resolution, and specificity by orders of\nmagnitude. This realization could open up new molecular species and new\nkinetics for precise investigations, including the study of complex molecules,\nweakly bound clusters, and cold chemistry.", "category": "physics_chem-ph" }, { "text": "Low-scaling $GW$ with benchmark accuracy and application to phosphorene\n nanosheets: $GW$ is an accurate method for computing electron addition and removal\nenergies of molecules and solids. In a conventional $GW$ implementation,\nhowever, its computational cost is $O(N^4)$ in the system size $N$, which\nprohibits its application to many systems of interest. We present a low-scaling\n$GW$ algorithm with notably improved accuracy compared to our previous\nalgorithm [J. Phys. Chem. Lett. 2018, 9, 306-312]. This is demonstrated for\nfrontier orbitals using the $GW100$ benchmark set, for which our algorithm\nyields a mean absolute deviation of only 6 meV with respect to canonical\nimplementations. We show that also excitations of deep valence, semi-core and\nunbound states match conventional schemes within 0.1 eV. The high accuracy is\nachieved by using minimax grids with 30 grid points and the resolution of the\nidentity with the truncated Coulomb metric. We apply the low-scaling $GW$\nalgorithm with improved accuracy to phosphorene nanosheets of increasing size.\nWe find that their fundamental gap is strongly size-dependent varying from 4.0\neV (1.8 nm $\\times$ 1.3 nm, 88 atoms) to 2.4 eV (6.9 nm $\\times$ 4.8 nm, 990\natoms) at the $\\text{ev}GW_0$@PBE level.", "category": "physics_chem-ph" }, { "text": "Jumping kinetic Monte Carlo: Fast and accurate simulations of partially\n delocalised charge transport in organic semiconductors: Developing devices using disordered organic semiconductors requires accurate\nand practical models of charge transport. In these materials, charge transport\noccurs through partially delocalised states in an intermediate regime between\nlocalised hopping and delocalised band conduction. Partial delocalisation can\nincrease mobilities by orders of magnitude over conventional hopping, making it\nimportant for materials and device design. Although delocalisation, disorder,\nand polaron formation can be described using delocalised kinetic Monte Carlo\n(dKMC), it is a computationally expensive method. Here, we develop jumping\nkinetic Monte Carlo (jKMC), a model that approaches the accuracy of dKMC with a\ncomputational cost comparable to conventional hopping. jKMC achieves its\ncomputational performance by modelling conduction using identical spherical\npolarons, yielding a simple delocalisation correction to the Marcus hopping\nrate that allows polarons to jump over their nearest neighbours. jKMC can be\nused in regimes of partial delocalisation inaccessible to dKMC to show that\nmodest delocalisation can increase mobilities by as much as two orders of\nmagnitude.", "category": "physics_chem-ph" }, { "text": "Determination of some solubilization parameters with surfactants of\n egg-yolk lecithin multilamellar vesicles by static light-scattering\n measurements: Effective surfactant:phospholipid ratios (i.e. molar ratios in the mixed\naggregates, vesicles or micelles) have been determined by static\nlight-scattering for the interaction of egg-yolk lecithin (EYL) multilamellar\nvesicles (MLV) with Triton X-100 (TX-100), sodium deoxycholate (DOCNa) and\ncetyltrimethylammonium bromide (CTMB). The suspension of MLV-EYL was mixed with\nappropriate volumes of surfactant solution and was left overnight to reaches\nthermodynamic equilibrium. Rectan-gular optic diffusion data were used to\ncompute the solubilization parameters: total surfactant concentrations, at\nsaturation and solubilization Dtsat and Dtsol respectively, and effective molar\nratios, Resat and Resol respectively. From the Resat value ob-tained\ngraphically for interaction of vesicles with TX-100 resulted that in vesicle\nbilayers a surfactant molecule is surrounded with seven phospholipid molecules\nand the Resol value suggests that in mixed micelles ten lipid molecules with\nabout fifteen surfactant molecules coexist. The values of Resat and Resol in\ncase of MLV solubilization with DOCNa are 0.07 and 1.1 re-spectively. In case\nof vesicles solubilization with CTMB, Resat =0.25 and Resol =3.6 These data\nshow that the solubilization power at thermodynamic equilibrium for the three\nsurfactants is in the sequence: CTMB HD(v'=0,j')+CO(v'=0,j') collisions through\nfull-dimensional quantum scattering calculations at collision energies near 1\nK. It is shown that the collision dynamics at energies between 0.01--1K are\ncontrolled by an interplay of L=1 and L=2 partial wave resonances depending on\nthe final rotational levels of the two molecules. Polarized cross-sections\nresolved into magnetic sub-levels of the initial and final rotational quantum\nnumbers of the two molecules also reveal a significant stereodynamic effect in\nthe cold energy regime. Overall, the stereodynamic effect is controlled by both\ngeometric and dynamical factors, with parity conservation playing an important\nrole in modulating these contributions depending on the particular final state.", "category": "physics_chem-ph" }, { "text": "Interfacial Thermal Conductance of Thiolate-Protected Gold Nanospheres: Molecular dynamics simulations of thiolate-protected and solvated gold\nnanoparticles were carried out in the presence of a non-equilibrium heat flux\nbetween the solvent and the core of the particle. The interfacial thermal\nconductance ($G$) was computed for these interfaces, and the behavior of the\nthermal conductance was studied as a function of particle size, ligand\nflexibility, and ligand chain length. In all cases, thermal conductance of the\nligand-protected particles was higher than the bare metal-solvent interface. A\nnumber of mechanisms for the enhanced conductance were investigated, including\nthiolate-driven corrugation of the metal surface, solvent ordering at the\ninterface, solvent-ligand interpenetration, and ligand ordering relative to the\nparticle surface. Only the smallest particles exhibited significant\ncorrugation. All ligands permitted substantial solvent-ligand interpenetration,\nand ligand chain length has a significant influence on the orientational\nordering of interfacial solvent. Solvent-ligand vibrational overlap,\nparticularly in the low frequency range ($< 80 \\mathrm{cm}^{-1}$) was\nsignificantly altered by ligand rigidity, and had direct influence on the\ninterfacial thermal conductance.", "category": "physics_chem-ph" }, { "text": "Molecular and solid-state topological polaritons induced by population\n imbalance: Strong coupling between electronic excitations in materials and photon modes\nresults in the formation of polaritons, which display larger nonlinearities\nthan their photonic counterparts due to their material component. We\ntheoretically investigate how to optically control the topological properties\nof molecular and solid-state exciton-polariton systems by exploiting one such\nnonlinearity: saturation of electronic transitions. We demonstrate modification\nof the Berry curvature of three different materials when placed within a\nFabry-Perot cavity and pumped with circularly polarized light, illustrating the\nbroad applicability of our scheme. Importantly, while optical pumping leads to\nnon-zero Chern invariants, unidirectional edge states do not emerge in our\nsystem as the bulk-boundary correspondence is not applicable. This work\ndemonstrates a versatile approach to control topological properties of novel\noptoelectronic materials.", "category": "physics_chem-ph" }, { "text": "Are multi-quasiparticle interactions important in molecular ionization?: Photo-emission spectroscopy directly probes individual electronic states,\nranging from single excitations to high-energy satellites, which simultaneously\nrepresent multiple quasiparticles (QPs) and encode information about electronic\ncorrelation. First-principles description of the spectra requires an efficient\nand accurate treatment of all many-body effects. This is especially challenging\nfor inner valence excitations where the single QP picture breaks down. Here, we\nprovide the full valence spectra of small closed-shell molecules, exploring the\nindependent and interacting quasiparticle regimes, computed with the\nfully-correlated adaptive sampling configuration interaction (ASCI) method. We\ncritically compare these results to calculations with the many-body\nperturbation theory, based on the $GW$ and vertex corrected $GW\\Gamma$\napproaches. The latter explicitly accounts for two-QP quantum interactions,\nwhich have been often neglected. We demonstrate that for molecular systems, the\nvertex correction universally improves the theoretical spectra, and it is\ncrucial for accurate prediction of QPs as well as capturing the rich satellite\nstructures of high-energy excitations. $GW\\Gamma$ offers a unified description\nacross all relevant energy scales. Our results suggest that the multi-QP regime\ncorresponds to dynamical correlations, which can be described via perturbation\ntheory.", "category": "physics_chem-ph" }, { "text": "Learning electron densities in the condensed phase: We introduce a local machine-learning method for predicting the electron\ndensities of periodic systems. The framework is based on a numerical,\natom-centred auxiliary basis, which enables an accurate expansion of the\nall-electron density in a form suitable for learning isolated and periodic\nsystems alike. We show that using this formulation the electron densities of\nmetals, semiconductors and molecular crystals can all be accurately predicted\nusing symmetry-adapted Gaussian process regression models, properly adjusted\nfor the non-orthogonal nature of the basis. These predicted densities enable\nthe efficient calculation of electronic properties which present errors on the\norder of tens of meV/atom when compared to ab initio density-functional\ncalculations. We demonstrate the key power of this approach by using a model\ntrained on ice unit cells containing only 4 water molecules to predict the\nelectron densities of cells containing up to 512 molecules, and see no increase\nin the magnitude of the errors of derived electronic properties when increasing\nthe system size. Indeed, we find that these extrapolated derived energies are\nmore accurate than those predicted using a direct machine-learning model.\nFinally, on heterogeneous datasets SALTED can predict electron densities with\nerrors below 4%.", "category": "physics_chem-ph" }, { "text": "Accurate non-empirical range-separated hybrid van der Waals density\n functional for complex molecular problems, solids, and surfaces: We introduce a new, general-purpose, range-separated hybrid van der Waals\ndensity \\ph{functional, termed vdW-DF-ahbr,} within the non-empirical vdW-DF\nmethod [JPCM 32, 393001 (2020)]. It combines correlation from vdW-DF2 with a\nscreened Fock exchange that is fixed by \\ph{a new model of exchange effects} in\nthe density-explicit vdW-DF2-b86r functional [PRB 89, 121103(R) (2014)]. The\nnew vdW-DF2-ahbr prevents spurious exchange binding and has a\nsmall-density-gradient form set from many-body perturbation analysis. It is\naccurate for \\ph{bulk as well as layered materials} and it systematically and\nsignificantly improves the performance of present vdW-DFs for molecular\nproblems. Importantly, vdW-DF2-ahbr also outperforms present-standard\n(dispersion-corrected) range-separated hybrids on a broad collection of\nnoncovalent-interaction benchmark sets, while at the same time successfully\nmitigating the density-driven errors that often affect the description of\nmolecular transition states and isomerization calculations. vdW-DF2-ahbr\nfurthermore improves on state of the art density functional theory approaches\nby 1) correctly predicting both the substrate structure and the site preference\nfor CO adsorption on Pt(111), 2) outperforming existing non-empirical vdW-DFs\nfor the description of CO$_2$ adsorption in both a functionalized and in a\nsimple metal-organic framework, and 3) being highly accurate \\ph{for the} set\nof base-pair interactions in a model of DNA assembly.", "category": "physics_chem-ph" }, { "text": "Two-dimensional electrochemical model for mixed conductors: a study of\n ceria: A two-dimensional small bias model has been developed for a patterned metal\ncurrent collector $|$ mixed oxygen ion and electronic conductor (MIEC) $|$\npatterned metal current collector electrochemical cell in a symmetric gas\nenvironment. Specifically, we compute the electrochemical potential\ndistributions of oxygen vacancies and electrons in the bulk and near the\nsurface for $\\text{Pt} | \\text{Sm}_{0.15}\\text{Ce}_{0.85}\\text{O}_{1.925} |\n\\text{Pt}$ symmetric cell in a $\\text{H}_2-\\text{H}_2\\text{O}-\\text{Ar}$\n(reducing) atmosphere from 500 to $650^o C$. Using a two-dimensional\nfinite-element model, we show that two types of electronic current exist within\nthe cell: an in-plane drift-diffusion current that flows between the gas $|$\nceria chemical reaction site and the metal current collector, and a cross-plane\ncurrent that flows between the two metal electrodes on the opposite side of the\ncell. By fitting the surface reaction constant $\\tilde k_f^0$ to experimental\nelectrode resistance values while fixing material properties such as bulk ionic\nand electronic equilibrium defect concentrations and mobilities, we are able to\nseparate the electrode polarization into the surface reaction component and the\nin-plane electron drift-diffusion component. We show that for mixed conductors\nwith a low electronic conductivity (a function of oxygen partial pressure) or a\nhigh surface reaction rate constant, the in-plane electron drift-diffusion\nresistance can become rate-limiting in the electrode reaction.", "category": "physics_chem-ph" }, { "text": "Nonequilibrium dynamics of localized and delocalized excitons in\n colloidal quantum dot solids: Self-assembled quantum dot (QD) solids are a highly tunable class of\nmaterials with a wide range of applications in solid-state electronics and\noptoelectronic devices. In this perspective, we highlight how the presence of\nmicroscopic disorder in these materials can influence their macroscopic\noptoelectronic properties. Specifically, we consider the dynamics of excitons\nin energetically disordered QD solids using a theoretical model framework for\nboth localized and delocalized excitonic regimes. In both cases, we emphasize\nthe tendency of energetic disorder to promote nonequilibrium relaxation\ndynamics and discuss how the signatures of these nonequilibrium effects\nmanifest in time-dependent spectral measurements. Moreover, we describe the\nconnection between the microscopic dynamics of excitons within the material and\nthe measurement of material specific parameters, such as emission linewidth\nbroadening and energetic dissipation rate.", "category": "physics_chem-ph" }, { "text": "Nature of the anomalies in the supercooled liquid state of the mW model\n of water: The thermodynamic properties of the supercooled liquid state of the mW model\nof water show anomalous behavior. Like in real water, the heat capacity and\ncompressibility sharply increase upon supercooling. One of the possible\nexplanations of these anomalies, the existence of a second (liquid-liquid)\ncritical point, is not supported by simulations for this model. In this work,\nwe reproduce the anomalies of the mW model with two thermodynamic scenarios:\none based on a non-ideal \"mixture\" with two different types of local order of\nthe water molecules, and one based on weak crystallization theory. We show that\nboth descriptions accurately reproduce the model's basic thermodynamic\nproperties. However, the coupling constant required for the power laws implied\nby weak crystallization theory is too large relative to the regular\nbackgrounds, contradicting assumptions of weak crystallization theory.\nFluctuation corrections outside the scope of this work would be necessary to\nfit the forms predicted by weak crystallization theory. For the two-state\napproach, the direct computation of the low-density fraction of molecules in\nthe mW model is in agreement with the prediction of the phenomenological\nequation of state. The non-ideality of the \"mixture\" of the two states never\nbecomes strong enough to cause liquid-liquid phase separation, also in\nagreement with simulation results.", "category": "physics_chem-ph" }, { "text": "The Impact of Organic Friction Modifiers on Engine Oil Tribofilms: Organic friction modifiers (OFMs) are important additives in the lubrication\nof machines and especially of car engines where performance improvements are\nconstantly sought-after. Together with zinc dialkyldithiophosphates (ZDDPs)\nantiwear additives, OFMs have a predominant impact on the tribological\nbehaviour of the lubricant. In the current study, the influence of OFMs on the\ngeneration, tribological properties and chemistry of ZDDP tribofilms has been\ninvestigated by combining tribological experiments (MTM) with in-situ film\nthickness measurements through optical interference imaging (SLIM), Alicona\nprofilometry and X-ray photoelectron spectroscopy. OFMs and antiwear additives\nhave been found to competitively react/adsorb on the rubbing ferrous substrates\nin a tribological contact. The formation and removal (through wear) of\ntribofilms are dynamic processes which result from the simultaneous interaction\nof these two additives with the surface of the wear track. By carefully\nselecting the chemistry of OFMs, the formulator can achieve lubricants that\ngenerate ZDDP antiwear films of optimum thickness, morphology and friction\naccording to the application-specific requirements.", "category": "physics_chem-ph" }, { "text": "The electrostatic potential profile along a biased molecular wire: A\n model quantum mechanical calculation: We study the electrostatic potential of a molecular wire bridging two\nmetallic electrodes in the limit of weak contacts. With the use of a\ntight-binding model including a fully three-dimensional treatment of the\nelectrostatics of the molecular junction, the potential is shown to be poorly\nscreened, dropping mostly along the entire molecule. In addition, we observe\npronounced Friedel oscillations that can be related to the breaking of\nelectron-hole symmetry. Our results are in semi-quantitative agreement with\nrecent state-of-the-art ab initio calculations and point to the need of a\nthree-dimensional treatment to properly capture the behavior of the\nelectrostatic potential. Based on these results, current-voltage curves are\ncalculated within the Landauer formalism. It is shown that Coulomb interaction\npartially compensates the localization of the charges induced by the electric\nfield and consequently tends to suppress zones of negative differential\nresistance.", "category": "physics_chem-ph" }, { "text": "Synthesis technique and electron beam damage study of nanometer-thin\n single-crystalline Thymine: Samples suitable for electron diffraction studies must satisfy certain\ncharacteristics such as having a thickness in the range of 10 - 100 nm. We\nreport, to our knowledge, the first successful synthesis technique of\nnanometer-thin sheets of single-crystalline thymine suitable for electron\ndiffraction and spectroscopy studies. This development provides a well defined\nsystem to explore issues related to UV photochemistry of DNA and high intrinsic\nstability essential to maintaining integrity of genetic information. The\ncrystals are grown using the evaporation technique and the nanometer-thin\nsheets are obtained via microtoming. The sample is characterized via x-ray\ndiffraction (XRD) and is subsequently studied using electron diffraction via a\ntransmission electron microscope (TEM). Thymine is found to be more radiation\nresistant than similar molecular moieties (e.g., carbamazepine) by a factor of\n5. This raises interesting questions about the role of the fast relaxation\nprocesses of electron scattering-induced excited states, extending the concept\nof radiation hardening beyond photoexcited states. The high stability of\nthymine in particular opens the door for further studies of these ultrafast\nrelaxation processes giving rise to the high stability of DNA to UV radiation.", "category": "physics_chem-ph" }, { "text": "The Sabatier principle for Battery Anodes: Chemical Kinetics and\n Reversible Electrodeposition at Heterointerfaces: How surface chemistry influences reactions occurring thereupon has been a\nlong-standing question of broad scientific and technological interest for\ncenturies. Recently, it has re-emerged as a critical question in a\nsubdiscipline of chemistry - electrochemistry at heterointerphases, where the\nanswers have implications for both how, and in what forms, humanity stores the\nrising quantities of renewable electric power generated from solar and wind\ninstallations world-wide. Here we consider the relation between the surface\nchemistry at such interphases and the reversibility of electrochemical\ntransformations at a rechargeable battery electrode. Conventional wisdom holds\nthat stronger chemical interaction between the metal deposits and electrode\npromotes reversibility. We report instead that a moderate strength of chemical\ninteraction between the deposit and the substrate, neither too weak nor too\nstrong, enables highest reversibility and stability of the plating/stripping\nredox processes at a battery anode. Analogous to the empirical Sabatier\nprinciple for chemical heterogeneous catalysis, our finding arises from the\nconfluence of competing processes - one driven by electrochemistry and the\nother by chemical alloying. Based on experimental evaluation of metal\nplating/stripping systems in battery anodes of contemporary interest, we show\nthat such knowledge provides a powerful tool for designing key materials in\nhighly reversible electrochemical energy storage technologies based on\nearth-abundant, low-cost metals.", "category": "physics_chem-ph" }, { "text": "Observation of different reactivities of para- and ortho-water towards\n cold diazenylium ions: Water, H$_2$O, is one of the fundamental molecules in chemistry, biology and\nastrophysics. It exists as two distinct nuclear-spin isomers, para- and\northo-water, which do not interconvert in isolated molecules. The experimental\nchallenges in preparing pure samples of the two isomers have thus far precluded\na characterization of their individual chemical behaviour. Capitalizing on\nrecent advances in the electrostatic deflection of polar molecules, we\nseparated the ground states of para- and ortho-water in a molecular beam to\nshow that the two isomers exhibit different reactivities in a prototypical\nreaction with cold diazenylium ions (N$_2$H$^+$). Based on ab initio\ncalculations and a modelling of the reaction kinetics using rotationally\nadiabatic capture theory, we rationalize this finding in terms of different\nrotational averaging of ion-dipole interactions during the reaction. The\npresent results highlight the subtle interplay between nuclear-spin and\nrotational symmetry and its ramifications on chemical reactivity.", "category": "physics_chem-ph" }, { "text": "Heat and Moisture Transport in Unsaturated Porous Media -- A Coupled\n Model in Terms of Chemical Potential: Transport phenomena in porous media are commonplace in our daily lives.\nExamples and applications include heat and moisture transport in soils, baking\nand drying of food stuffs, curing of cement, and evaporation of fuels in wild\nfires. Of particular interest to this study are heat and moisture transport in\nunsaturated soils. Historically, mathematical models for these processes are\nderived by coupling classical Darcy's, Fourier's, and Fick's laws with volume\naveraged conservation of mass and energy and empirically based source and sink\nterms. Recent experimental and mathematical research has proposed modifications\nand suggested limitations in these classical equations. The primary goal of\nthis thesis is to derive a thermodynamically consistent system of equations for\nheat and moisture transport in terms of the chemical potential that addresses\nsome of these limitations. The physical processes of interest are primarily\ndiffusive in nature and, for that reason, we focus on using the macroscale\nchemical potential to build and simplify the models. The resulting coupled\nsystem of nonlinear partial differential equations is solved numerically and\nvalidated against the classical equations and against experimental data. It\nwill be shown that under a mixture theoretic framework, the classical Richards'\nequation for saturation is supplemented with gradients in temperature, relative\nhumidity, and the time rate of change of saturation. Furthermore, it will be\nshown that restating the water vapor diffusion equation in terms of chemical\npotential eliminates the necessity for an empirically based fitting parameter.", "category": "physics_chem-ph" }, { "text": "The S$^+$($^4$S) + SiH$_{2}$($^1$A$_1$) Reaction: Toward the Synthesis\n of Interstellar SiS: We have performed a theoretical investigation of the S$^+$($^4$S) +\nSiH$_{2}$($^1$A$_1$) reaction, a possible formation route of the HSiS$^+$ and\nSiSH$^+$ cations that are alleged to be precursors of interstellar silicon\nsulfide, SiS. Electronic structure calculations allowed us to identify the main\nreaction pathways for the systems. The reaction has two exothermic channels\nleading to the isomeric species $^3$HSiS$^{+}$ and $^3$SiSH$^{+}$ formed in\nconjunction with H atoms. The reaction is not characterized by an entrance\nbarrier and, therefore, it is believed to be fast also under the very low\ntemperature conditions of interstellar clouds. The two ions are formed in their\nfirst electronically excited state because of the spin multiplicity of the\noverall potential energy surface. In addition, following the suggestion that\nneutral species are formed by proton transfer of protonated cations to ammonia,\nwe have derived the potential energy surface for the reactions\n$^3$HSiS$^{+}$/$^3$SiSH$^{+}$ + NH$_{3}$($^{1}$A$_1$).", "category": "physics_chem-ph" }, { "text": "Sn-modification of Pt7/alumina model catalysts: Suppression of carbon\n deposition and enhanced thermal stability: An atomic layer deposition process is used to modify size-selected\nPt7/alumina model catalysts by Sn addition, both before and after Pt7 cluster\ndeposition. Surface science methods are used to probe the effects of\nSn-modification on the electronic properties, reactivity, and morphology of the\nclusters. Sn addition, either before or after cluster deposition, is found to\nstrongly affect the binding properties of a model alkene, ethylene, changing\nthe number and type of binding sites, and suppressing decomposition leading to\ncarbon deposition and poisoning of the catalyst. Density functional theory on a\nmodel system, Pt4Sn3/alumina, shows that the Sn and Pt atoms are mixed, forming\nalloy clusters with substantial electron transfer from Sn to Pt. The presence\nof Sn also makes all the thermally accessible structures closed shell, such\nthat ethylene binds only by {\\pi}-bonding to a single Pt atom. The Sn-modified\ncatalysts are quite stable in repeated ethylene temperature programmed reaction\nexperiments, suggesting that the presence of Sn also reduces the tendency of\nthe sub-nano-clusters to undergo thermal sintering.", "category": "physics_chem-ph" }, { "text": "Current density functional framework for spin-orbit coupling: Extension\n to periodic systems: Spin-orbit coupling induces a current density in the ground state, which\nconsequently requires a generalization for meta-generalized gradient\napproximations. That is, the exchange-correlation energy has to be constructed\nas an explicit functional of the current density and a generalized kinetic\nenergy density has to be formed to satisfy theoretical constraints. Herein, we\ngeneralize our previously presented formalism of spin-orbit current density\nfunctional theory [Holzer et al., J. Chem. Phys. 157, 204102 (2022)] to\nnon-magnetic and magnetic periodic systems of arbitrary dimension. Besides the\nground-state exchange-correlation potential, analytical derivatives such as\ngeometry gradients and stress tensors are implemented. The importance of the\ncurrent density is assessed for band gaps, lattice constants, magnetic\ntransitions, and Rashba splittings. For the latter, the impact of the current\ndensity may be larger than the deviation between different density functional\napproximations.", "category": "physics_chem-ph" }, { "text": "Electron transfer pathway analysis in bacterial photosynthetic reaction\n center: A new computational scheme to analyze electron transfer (ET) pathways in\nlarge biomolecules is presented with applications to ETs in bacterial\nphotosynthetic reaction center. It consists of a linear combination of fragment\nmolecular orbitals and an electron tunneling current analysis, which enables an\nefficient first-principles analysis of ET pathways in large biomolecules. The\nscheme has been applied to the ET from menaquinone to ubiquinone via nonheme\niron complex in bacterial photosynthetic reaction center. It has revealed that\nnot only the central Fe$^{2+}$ ion but also particular histidine ligands are\ninvolved in the ET pathways in such a way to mitigate perturbations that can be\ncaused by metal ion substitution and depletion, which elucidates the\nexperimentally observed insensitivity of the ET rate to these perturbations.", "category": "physics_chem-ph" }, { "text": "Relation between static short-range order and dynamic heterogeneities in\n a nanoconfined liquid crystal: We analyze the molecular dynamics heterogeneity of the liquid crystal\n4-n-octyl-4'-cyanobiphenyl nanoconfined in porous silicon. We show that the\ntemperature dependence of the dynamic correlation length ?wall, which measures\nthe distance over which a memory of the interfacial slowing down of the\nmolecular dynamics persists, is closely related to the growth of the\nshort-range static order arising from quenched random fields. More generally,\nthis result may also shed some light on the connection between static and\ndynamic heterogeneities in a wide class of condensed and soft matter systems.", "category": "physics_chem-ph" }, { "text": "Quantum tunnelling driven H$_2$ formation on graphene: It is commonly believed that it is unfavourable for adsorbed H atoms on\ncarbonaceous surfaces to form H$_2$ without the help of incident H atoms. Using\nring-polymer instanton theory to describe multidimensional tunnelling effects,\ncombined with ab initio electronic structure calculations, we find that these\nquantum-mechanical simulations reveal a qualitatively different picture.\nRecombination of adsorbed H atoms, which was believed to be irrelevant at low\ntemperature due to high barriers, is enabled by deep tunnelling, with reaction\nrates enhanced by tens of orders of magnitude. Furthermore, we identify a new\npath for H recombination that proceeds via multidimensional tunnelling, but\nwould have been predicted to be unfeasible by a simple one-dimensional\ndescription of the reaction. The results suggest that hydrogen molecule\nformation at low temperatures are rather fast processes that should not be\nignored in experimental settings and natural environments with graphene,\ngraphite and other planar carbon segments.", "category": "physics_chem-ph" }, { "text": "At what chain length do unbranched alkanes prefer folded conformations?: Short unbranched alkanes are known to prefer linear conformations, while long\nunbranched alkanes are folded. It is not known with certainty at what chain\nlength the linear conformation is no longer the global minimum. To clarify this\npoint, we use {\\it ab initio} and density functional methods to compute the\nrelative energies of the linear and hairpin alkane conformers for increasing\nchain lengths. Extensive electronic structure calculations are performed to\nobtain optimized geometries, harmonic frequencies and accurate single point\nenergies for the selected alkane conformers from octane through octadecane.\nBenchmark CCSD(T)/cc-pVTZ single point calculations are performed for chains\nthrough tetradecane, while approximate methods are required for the longer\nchains up to octadecane. Using frozen natural orbitals to unambiguously\ntruncate the virtual orbital space, we are able to compute composite CCSD\nFNO(T) single point energies for all the chain lengths. This approximate\ncomposite method has significant computational savings compared to full CCSD(T)\nwhile retaining $\\sim0.15$ kcal/mol accuracy compared to the benchmark results.\nMore approximate dual-basis resolution-of-the-identity double-hybrid DFT\ncalculations are also performed and shown to have reasonable $0.2-0.4$ kcal/mol\nerrors compared with our benchmark values. After including contributions from\ntemperature dependent internal energy shifts, we find the preference for folded\nconformations to lie between hexadecane and octadecane, in excellent agreement\nwith recent experiments [L\\\"{u}ttschwager, N. O.; Wassermann, T. N.; Mata, R.\nA.; Suhm, M. A. {\\it Angew. Chem. Int. Ed.} 2013, 52, 463].", "category": "physics_chem-ph" }, { "text": "Exact-factorization-based surface-hopping without velocity adjustment: While surface-hopping has emerged as a powerful method to simulate\nnon-adiabatic dynamics in large molecules, the ad hoc nature of the necessary\nvelocity adjustments and decoherence corrections in the algorithm somewhat\nreduces its reliability. Here we propose a new scheme that eliminates these\naspects, by combining the nuclear equation from the quantum trajectory\nsurface-hopping approach with the electronic equation derived from the exact\nfactorization approach. The resulting method, denoted QTSH-XF, places\nsurface-hopping on a firmer ground and is shown to successfully capture\ndynamics in Tully models and in a linear vibronic coupling model of the\nphoto-excited uracil cation.", "category": "physics_chem-ph" }, { "text": "Geometrical optimization approach to isomerization: Models and\n limitations: We study laser-driven isomerization reactions through an excited electronic\nstate using the recently developed Geometrical Optimization procedure [J. Phys.\nChem. Lett. 6, 1724 (2015)]. The goal is to analyze whether an initial wave\npacket in the ground state, with optimized amplitudes and phases, can be used\nto enhance the yield of the reaction at faster rates, exploring how the\ngeometrical restrictions induced by the symmetry of the system impose\nlimitations in the optimization procedure. As an example we model the\nisomerization in an oriented 2,2'-dimethyl biphenyl molecule with a simple\nquartic potential. Using long (picosecond) pulses we find that the\nisomerization can be achieved driven by a single pulse. The phase of the\ninitial superposition state does not affect the yield. However, using short\n(femtosecond) pulses, one always needs a pair of pulses to force the reaction.\nHigh yields can only be obtained by optimizing both the initial state, and the\nwave packet prepared in the excited state, implying the well known pump-dump\nmechanism.", "category": "physics_chem-ph" }, { "text": "Development and validation of a parameter-free model chemistry for the\n computation of reliable reaction rates: A recently developed model chemistry (jun-Cheap) has been slightly modified\nand proposed as an effective, reliable and parameter-free scheme for the\ncomputation of accurate reaction rates with special reference to astrochemical\nand atmospheric processes. Benchmarks with different sets of state-of-the-art\nenergy barriers spanning a wide range of values show that, in the absence of\nstrong multi-reference contributions, the proposed model outperforms the most\nwell-known model chemistries, reaching a sub-chemical accuracy without any\nempirical parameter and with affordable computer times. Some test cases show\nthat geometries, energy barriers, zero point energies and thermal contributions\ncomputed at this level can be used in the framework of the master equation\napproach based on ab-initio transition state theory (AITSTME) for obtaining\naccurate reaction rates.", "category": "physics_chem-ph" }, { "text": "Analytic energy gradients for variational two-electron reduced-density\n matrix methods within the density-fitting approximation: Analytic energy gradients are presented for a variational two-electron\nreduced-density-matrix-driven complete active space self-consistent field\n(v2RDM-CASSCF) procedure that employs the density-fitting (DF) approximation to\nthe two-electron repulsion integrals. The DF approximation significantly\nreduces the computational cost of v2RDM-CASSCF gradient evaluation, in terms of\nboth the number of floating-point operations and memory requirements, enabling\ngeometry optimizations on much larger chemical systems than could previously be\nconsidered at the this level of theory [E. Maradzike et al., J. Chem. Theory\nComput., 2017, 13, 4113-4122]. The efficacy of v2RDM-CASSCF for computing\nequilibrium geometries and harmonic vibrational frequencies is assessed using a\nset of 25 small closed- and open-shell molecules. Equilibrium bond lengths from\nv2RDM-CASSCF differ from those obtained from configuration-interaction-driven\nCASSCF (CI-CASSCF) by 0.62 pm and 0.05 pm, depending on whether the optimal\nreduced-density matrices from v2RDM-CASSCF satisfy two-particle\nN-representability conditions (PQG) or PQG plus partial three-particle\nconditions (PQG+T2), respectively. Harmonic vibrational frequencies, which are\nobtained by finite differences of v2RDM-CASSCF analytic energy gradients,\nsimilarly demonstrate that quantitative agreement between v2RDM- and CI-CASSCF\nrequires the consideration of partial three-particle N-representability\nconditions. Lastly, optimized geometries are obtained for the lowest-energy\nsinglet and triplet states of the linear polyacene series up to dodecacene\n(C50H28), in which case the active space is comprised of 50 electrons in 50\norbitals. The v2RDM-CASSCF singlet-triplet energy gap extrapolated to an\ninfinitely-long linear acene molecule is found to be 7.8 kcal/mol", "category": "physics_chem-ph" }, { "text": "Rydberg-State-Resolved Resonant Energy Transfer in Cold\n Electric-Field-Controlled Intrabeam Collisions of NH$_3$ with Rydberg He\n Atoms: The resonant transfer of energy from the inversion sublevels in NH$_3$ to He\natoms in triplet Rydberg states with principal quantum number $n=38$ has been\ncontrolled using electric fields below 15 V/cm in intrabeam collisions at\ntranslational temperatures of $\\sim1$ K. The experiments were performed in\npulsed supersonic beams of NH$_3$ seeded in He at a ratio of 1:19. The He atoms\nwere prepared in the metastable 1s2s $^3$S$_1$ level in a pulsed electric\ndischarge in the trailing part of the beams. The velocity slip between the\nheavy NH$_3$ and the lighter metastable He was exploited to perform collision\nstudies at center-of-mass collision speeds of $\\sim70$ m/s. Resonant energy\ntransfer in the atom-molecule collisions was identified by\nRydberg-state-selective electric-field ionization. The experimental data have\nbeen compared to a theoretical model of the resonant dipole-dipole interactions\nbetween the collision partners based on the impact parameter method.", "category": "physics_chem-ph" }, { "text": "Unexpectedly high pressure for molecular dissociation in liquid hydrogen\n by a reliable electronic simulation: The study of the high pressure phase diagram of hydrogen has continued with\nrenewed effort for about one century as it remains a fundamental challenge for\nexperimental and theoretical techniques. Here we employ an efficient molecular\ndynamics based on the quantum Monte Carlo method, which can describe accurately\nthe electronic correlation and treat a large number of hydrogen atoms, allowing\na realistic and reliable prediction of thermodynamic roperties. We find that\nthe molecular liquid phase is unexpectedly stable and the transition towards a\nfully atomic liquid phase occurs at much higher pressure than previously\nbelieved. The old standing problem of low temperature atomization is,\ntherefore, still far from experimental reach.", "category": "physics_chem-ph" }, { "text": "Structural Analysis of Combustion Mechanisms: 39 detailed mechanisms for combustion of hydrogen, carbon monoxide and\nmethanol are investigated using ReactionKinetics, a Mathematica based package.\nThe obtained results in most cases do not depend on the choice of reaction rate\ncoefficients, the methods only use the underlying sets of reaction steps, thus\nthe results are robust and general in a certain sense. These investigations can\nbe used before or in parallel with usual numerical investigations, such as\npathway analysis, sensitivity analysis, parameter estimation or simulation.\n The considered hydrogen mechanisms shared 90% of common reaction steps. The\nCO combustion mechanisms show a larger variety both in species and in reaction\nsteps. There exist only a few methanol combustion mechanisms; the big\ndifferences between them shows that the modelling community is only at the very\nbeginning of exploring this process.\n The package and the methods may be useful for automatic mechanism\ngenerations, testing, comparing and reduction of mechanisms as well, especially\nin the case of large systems.", "category": "physics_chem-ph" }, { "text": "Improving the electronic and optical properties of Carbz-PAHTDDT-based\n dyes through chemical modifications: To investigate geometric and electronic structure, a theoretical study is\nperformed on the Carbz-PAHTDDT (S9) organic dye sensitizer. This dye has a\nreported promising efficiency when coupled with ferrocene-based electrolyte\ncomposition. The present study indicated that the long-range correction to the\ntheoretical model in the time-dependent density functional theory is important\nto produce accurate absorption wavelengths. In the present study, the chemical\nstructure of the original Carbz-PAHTDDT dye on the {\\pi}-conjugated bridge is\nalso rationally changed to produce new dyes aiming at enhancing the spectral\nresponse as a desirable property of organic dyes in DSSC application. The\ntheoretical studies on the new dyes have shown a significant red-shifting and\nbroadening of their absorption spectra.", "category": "physics_chem-ph" }, { "text": "Electron transfer under the Floquet modulation in donor-bridge-acceptor\n systems: Electron transfer (ET) processes are of broad interest in modern chemistry.\nWith the advancements of experimental techniques, one may modulate the ET via\nsuch as the light-matter interactions. In this work, we study the ET under a\nFloquet modulation occurring in the donor-bridge-acceptor systems, with the\nrate kernels projected out from the exact disspaton equation of motion\nformalism. This together with the Floquet theorem enables us to investigate the\ninterplay between the intrinsic non-Markovianity and the driving periodicity.\nThe observed rate kernel exhibits a Herzberg-Teller-like mechanism induced by\nthe bridge fluctuation subject to effective modulation.", "category": "physics_chem-ph" }, { "text": "Nonadiabatic dynamics and multiphoton resonances in strong field\n molecular ionization with few cycle laser pulses: We study strong field molecular ionization using few- (four to ten) cycle\nlaser pulses. Employing a supercontinuum light source, we are able to tune the\noptical laser wavelength (photon energy) over a range of about $\\sim$200 nm\n(500 meV). We measure the photoelectron spectrum for a series of different\nmolecules as a function of laser intensity, frequency, and bandwidth and\nillustrate how the ionization dynamics vary with these parameters. We find that\nmultiphoton resonances and nonadiabatic dynamics (internal conversion) play an\nimportant role and result in ionization to different ionic continua.\nInterestingly, while nuclear dynamics can be \"frozen\" for sufficiently short\nlaser pulses, we find that resonances strongly influence the photoelectron\nspectrum and final cationic state of the molecule regardless of pulse duration\n-- even for pulses that are less than four cycles in duration.", "category": "physics_chem-ph" }, { "text": "Transition Events in Butane Simulations: Similarities Across Models: From a variety of long simulations of all-atom butane using both stochastic\nand fully-solved molecular dynamics, we have uncovered striking generic\nbehavior which also occurs in one-dimensional systems. We find an apparently\nuniversal distribution of transition event durations, as well as a\ncharacteristic speed profile along the reaction coordinate. An approximate\nanalytic distribution of event durations, derived from a one-dimensional model,\ncorrectly predicts the asymptotic behavior of the universal distribution for\nboth short and long durations.", "category": "physics_chem-ph" }, { "text": "Comments on the Discrete Variable Representation: We discuss the application of the Discrete Variable Representation to\nSchr\\\"odinger problems which involve singular Hamiltonians. Unlike recent\nauthors who invoke transformations to rid the eigenvalue equation of\nsingularities at the cost of added complexity, we show that an approach based\nsolely on an orthogonal polynomial basis is adequate, provided the\nGauss-Lobatto or Gauss-Radau quadrature rule is used. This ensures that the\nmesh contains the singular points and by simply discarding the DVR functions\ncorresponding to those points, all matrix elements become well-behaved, the\nboundary conditions are satisfied and the calculation is rapidly convergent.\nThe accuracy of the method is demonstrated by applying it to the hydrogen atom.\nWe emphasize that the method is equally capable of describing bound states and\ncontinuum solutions.", "category": "physics_chem-ph" }, { "text": "Interatomic-Potential-Free, Data-Driven Molecular Dynamics: We present a Data-Driven (DD) paradigm that enables molecular dynamics\ncalculations to be performed directly from sampled force-field data such as\nobtained, e.g., from ab initio calculations, thereby eschewing the conventional\nstep of modeling the data by empirical interatomic potentials entirely. The\ndata required by the DD solvers consists of local atomic configurations and\ncorresponding atomic forces and is, therefore, fundamental, i.e., it is not\nbeholden to any particular model. The resulting DD solvers, including a fully\nexplicit DD-Verlet algorithm, are provably convergent and exhibit robust\nconvergence with respect to the data in selected test cases. We present an\nexample of application to C60 buckminsterfullerenes that showcases the\nfeasibility, range and scope of the DD molecular dynamics paradigm.", "category": "physics_chem-ph" }, { "text": "Initial Sampling in Symmetrical Quasiclassical Dynamics Based on\n Li-Miller Mapping Hamiltonian: A symmetrical quasiclassical (SQC) dynamics approach based on the Li-Miller\n(LM) mapping Hamiltonian (SQC-LM) was employed to describe nonadiabatic\ndynamics. In principle, the different initial sampling procedures may be\napplied in the SQC-LM dynamics, and the results may be dependent on the initial\nsampling. We provided various initial sampling approaches and checked their\ninfluence. We selected two groups of models including site-exciton models for\nexciton dynamics and linear vibronic coupling models for conical intersections\nto test the performance of SQC-LM dynamics with the different initial sampling\nmethods. The results were examined with respect to those of the accurate\nmultilayer multiconfigurational time-dependent Hartree (ML-MCTDH) quantum\ndynamics. For both two models, the SQC-LM method more-or-less gives a\nreasonable description of the population dynamics, while the influence of the\ninitial sampling approaches on the final results is noticeable. It seems that\nthe proper initial sampling methods should be determined by the system under\nstudy. This indicates that the combination of the SQC-LM method with a suitable\nsampling approach may be a potential method in the description of nonadiabatic\ndynamics.", "category": "physics_chem-ph" }, { "text": "Finding Multiple Reaction Pathways of Ligand Unbinding: Searching for reaction pathways describing rare events in large systems\npresents a long-standing challenge in chemistry and physics. Incorrectly\ncomputed reaction pathways result in the degeneracy of microscopic\nconfigurations and inability to sample hidden energy barriers. To this aim, we\npresent a general enhanced sampling method to find multiple diverse reaction\npathways of ligand unbinding through non-convex optimization of a loss function\ndescribing ligand-protein interactions. The method successfully overcomes large\nenergy barriers using an adaptive bias potential, and constructs possible\nreaction pathways along transient tunnels without the initial guesses of\nintermediate or final states, requiring crystallographic information only. We\nexamine the method on the T4 lysozyme L99A mutant which is often used as a\nmodel system to study ligand binding to proteins, provide a previously unknown\nreaction pathway, and show that using the bias potential and the tunnel widths\nit is possible to capture heterogeneity of the unbinding mechanisms between the\nfound transient protein tunnels.", "category": "physics_chem-ph" }, { "text": "Potential energy surfaces of the low-lying electronic states of the Li +\n LiCs system: Ab initio quantum chemistry calculations are performed for the mixed alkali\ntriatomic system. Global minima of the ground and first excited doublet states\nof the trimer are found and Born-Oppenheimer potential energy surfaces of the\nLi atom interacting with the LiCs molecule were calculated for these states.\nThe lithium atom is placed at various distances and bond angles from the\nlithium-caesium dimer. Three-body nonadditive forces of the Li$_2$Cs molecule\nin the global minimum are investigated. Dimer-atom interactions are found to be\nstrongly attractive and may be important in the experiments, particularly\ninvolving cold alkali polar dimers.", "category": "physics_chem-ph" }, { "text": "Optimal choice of dividing surface for the computation of quantum\n reaction rates: See http://pubs.acs.org/journals/jpcafh/ for the latest revision", "category": "physics_chem-ph" }, { "text": "Identifying sequential residue patterns in bitter and umami peptides: The primary structures of peptides, originating from food proteins, affect\ntheir taste. Connecting primary structure to taste, however, is difficult\nbecause the size of the peptide sequence space increases exponentially with\nincreasing peptide length, while experimentally-labeled data on peptides'\ntastes remain scarce. We propose a method that coarse-grains the sequence space\nto reduce its size and systematically identifies the most common coarse-grained\nresidue patterns found in known bitter and umami peptides. We select the\noptimal patterns by performing extensive out-of-sample tests. The optimal\npatterns better represent the bitter and umami peptides when compared against\nbaseline peptides, bitter peptides with all hydrophobic residues and umami\npeptides with all negatively charged residues, and peptides with\nrandomly-chosen residues. Our method complements quantitative\nstructure--activity relationship methods by offering generic, coarse-grained\nbitter and umami residue patterns that can aid in locating short bitter or\numami segments in a protein and in designing new umami peptides.", "category": "physics_chem-ph" }, { "text": "Simultaneous Detection of H and D NMR Signals in a micro-Tesla Field: We present NMR spectra of remote-magnetized deuterated water, detected in an\nunshielded environment by means of a differential atomic magnetometer. The\nmeasurements are performed in a $\\mu$T field, while pulsed techniques are\napplied -following the sample displacement- in a 100~$\\mu$T field, to tip both\nD and H nuclei by controllable amounts. The broadband nature of the detection\nsystem enables simultaneous detection of the two signals and accurate\nevaluation of their decay times. The outcomes of the experiment demonstrate the\npotential of ultra-low-field NMR spectroscopy in important applications where\nthe correlation between proton and deuteron spin-spin relaxation rates as a\nfunction of external parameters contains significant information.", "category": "physics_chem-ph" }, { "text": "Landau-Zener type surface hopping algorithms: A class of surface hopping algorithms is studied comparing two recent\nLandau-Zener (LZ) formulas for the probability of nonadiabatic transitions. One\nof the formulas requires a diabatic representation of the potential matrix\nwhile the other one depends only on the adiabatic potential energy surfaces.\nFor each classical trajectory, the nonadiabatic transitions take place only\nwhen the surface gap attains a local minimum. Numerical experiments are\nperformed with deterministically branching trajectories and with probabilistic\nsurface hopping. The deterministic and the probabilistic approach confirm the\ngood agreement of both the LZ probabilities as well the good approximation of\nthe reference solution computed solving the Schroedinger equation via a grid\nbased pseudo-spectral method. Visualizations of position expectations and\nsuperimposed surface hopping trajectories with reference position densities\nillustrate the effective dynamics of the investigated algorithms.", "category": "physics_chem-ph" }, { "text": "Diversity of coherences and origin of electronic transitions of\n supermolecular nanoring: Quantum coherence is highly involved in photochemical functioning of complex\nmolecular systems. Co-existence and intermixing of electronic and/or\nvibrational coherences, while never unambiguously identified experimentally,\nhas been proposed to be responsible for this phenomenon. Analysis of\nmultidimensional spectra of a synthetic belt-shaped molecular six-porphyrin\nnanoring with an inner template clearly shows a great diversity of separable\nelectronic, vibrational and mixed coherences and their cooperation shaping the\noptical response. The results yield clear assignment of electronic and vibronic\nstates, estimation of excitation transfer rates, and decoherence times.\nTheoretical considerations prove that the complexity of excitation dynamics and\nspectral features of the nanoring excitation spectrum is due to combined effect\nof cyclic symmetry, small geometrical deformations, and vibronic coupling.", "category": "physics_chem-ph" }, { "text": "Comment on Cartesian expressions for surface and regular solid spherical\n harmonics using binomial coefficients and its use in the evaluation of\n multicenter integrals: Recently published formulas for the surface and regular solid spherical\nharmonics and for the expansion of the product of two normalized associated\nLegendre functions with different centers in ellipsoidal coordinates (Telhat\nOzdogan, Metin Orbay, Czech.J.Phys., 52(2002)1297) are critically analyzed. It\nis demonstrated that the presented in this work formulas are not original and\nthey are available in the literature or can easily be obtained from the\npublished in the literature formulas by changing the summation indices.", "category": "physics_chem-ph" }, { "text": "Path Integral Molecular Dynamics within the Grand Canonical-like\n Adaptive Resolution Technique: Simulation of Liquid Water: Quantum effects due to the spatial delocalization of light atoms are treated\nin molecular simulation via the path integral technique. Among several methods,\nPath Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to\ninvestigate properties induced by spatial delocalization of atoms; however\ncomputationally this technique is very demanding. The abovementioned limitation\nimplies the restriction of PIMD applications to relatively small systems and\nshort time scales. One possible solution to overcome size and time limitation\nis to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme\n(AdResS). AdResS requires a relatively small region treated at path integral\nlevel and embeds it into a large molecular reservoir consisting of generic\nspherical coarse grained molecules. It was previously shown that the\nrealization of the idea above, at a simple level, produced reasonable results\nfor toy systems or simple/test systems like liquid parahydrogen. Encouraged by\nprevious results, in this paper we show the simulation of liquid water at room\nconditions where AdResS, in its latest and more accurate Grand-Canonical-like\nversion (GC-AdResS), is merged with two of the most relevant PIMD techniques\navailable in literature. The comparison of our results with those reported in\nliterature and/or with those obtained from full PIMD simulations shows a highly\nsatisfactory agreement.", "category": "physics_chem-ph" }, { "text": "A comparative study of aqueous DMSO mixtures by computer simulations and\n integral equation theories: Several computer simulation studies of aqueous dimethylsulfoxyde with\ndifferent force field models, and conducted by different authors, point out to\nan anomalous depressing of second and third neighbour correlations of the\nwater-water radial distribution functions. This seemingly universal feature can\nbe interpreted as the formation of linear water clusters. We test here the\nability of liquid state integral equation theories to reproduce this feature.\nIt is found that the incorporation of the water bridge diagram function is\nrequired to reproduce this feature. These theories are generally unable to\nproperly reproduce atom-atom distribution functions. However, the near-ideal\nKirkwood-Buff integrals are relatively well reproduced. We compute the Xray\nscattering function and compare with available experimental results, with the\nparticular focus to explain why this data does not reproduce the cluster\npre-peak observed in the water-water structure factor.", "category": "physics_chem-ph" }, { "text": "Grand Equilibrium: vapour-liquid equilibria by a new molecular\n simulation method: A new molecular simulation method for the calculation of vapour-liquid\nequilibria of mixtures is presented. In this method, the independent\nthermodynamic variables are temperature and liquid composition. In the first\nstep, one isobaric isothermal simulation for the liquid phase is performed, in\nwhich the chemical potentials of all components and their derivatives with\nrespect to the pressure, i.e., the partial molar volumes, are calculated. From\nthese results, first order Taylor series expansions for the chemical potentials\nas functions of the pressure $\\mu_i(p)$ at constant liquid composition are\ndetermined. That information is needed, as the specified pressure in the liquid\nwill generally not be equal to the equilibrium pressure, which has to be found\nin the course of a vapour simulation. In the second step, one pseudo grand\ncanonical simulation for the vapour phase is performed, where the chemical\npotentials are set according to the instantaneous pressure $p^v$ using the\npreviously determined function $\\mu_i(p^v)$. In this way, results for the\nvapour pressure and vapour composition are achieved which are consistent to the\ngiven temperature and liquid composition.The new method is applied to the pure\nLennard-Jones fluid, a binary, and a ternary mixture of Lennard-Jones spheres\nand shows very good agreement with corresponding data from the literature.", "category": "physics_chem-ph" }, { "text": "Improved prediction of molecular response to pulling by combining force\n tempering with replica exchange methods: Small mechanical forces play important functional roles in many crucial\ncellular processes, including in the dynamical behavior of the cytoskeleton and\nin the regulation of osmotic pressure through membrane-bound proteins.\nMolecular simulations offer the promise of being able to design the behavior of\nproteins that sense and respond to these forces. However, it is difficult to\npredict and identify the effect of the relevant piconewton (pN) scale forces\ndue to their small magnitude. Previously, we introduced the Infinite Switch\nSimulated Tempering in Force (FISST) method which allows one to estimate the\neffect of a range of applied forces from a single molecular dynamics\nsimulation, and also demonstrated that FISST additionally accelerates sampling\nof a molecule's conformational landscape. For some problems, we find that this\nacceleration is not sufficient to capture all relevant conformational\nfluctuations, and hence here we demonstrate that FISST can be combined with\neither temperature replica exchange or solute tempering approaches to produce a\nhybrid method that enables more robust prediction of the effect of small forces\non molecular systems.", "category": "physics_chem-ph" }, { "text": "Stochastic Multi Configuration Time-Dependent Hartree for Dissipative\n Quantum Dynamics with Strong Intramolecular Coupling: In this article, we explore the dissipation dynamics of a strongly coupled\nmultidimensional system in contact with a Markovian bath following a\nsystem-bath approach. We use in this endeavour the recently developed\nstochastic Multi-Configuration Time-Dependent Hartree approach within the Monte\nCarlo wave packet formalism [J.Chem.Phys.156, 094109 (2022)]. The method proved\nto yield thermalized ensembles of wave packets when intramolecular coupling is\nweak. To treat strongly coupled systems, new Lindblad dissipative operators are\nconstructed as linear combinations of the system coordinates and associated\nmomenta. These are obtained by an unitary transformation to a normal mode\nrepresentation, which reduces intermode coupling up to second order.\nAdditionally, we use combinations of generalized raising/lowering operators to\nenforce the Boltzmann distribution in the dissipation operators, which yield\nperfect thermalization in the harmonic limit. The two ansatz are tested using a\nmodel two-dimensional hamiltonian parameterized to disentangle the effects of\nintramolecular potential coupling, of strong mode mixing observed in Fermi\nresonances, and of anharmonicity.", "category": "physics_chem-ph" }, { "text": "Extended Lagrangian Born-Oppenheimer Molecular Dynamics with DFT+U: Extended Lagrangian Born-Oppenheimer molecular dynamics (XL-BOMD) [Phys. Rev.\nLett. vol. 100, 123004 (2008)] is combined with Kohn-Sham density functional\ntheory (DFT) using a DFT+U correction based on the Hubbard model. This combined\nXL-BOMD and DFT+U approach allows efficient Born-Oppenheimer molecular dynamics\nsimulations with orbital-dependent corrections beyond regular Kohn-Sham density\nfunctional theory. The extended Lagrangian formulation eliminates the need for\nthe iterative self-consistent-field optimization of the electronic ground state\nprior to the force evaluations, which is required in regular direct\nBorn-Oppenheimer molecular dynamics simulations. This method provides accurate\nand stable molecular trajectories, while reducing the computational cost per\ntime step. The combined XL-BOMD and DFT+U approach is demonstrated with\nmolecular dynamics simulations of a nitromethane molecular liquid and a system\nof solid nuclear fuel, UO$_2$, using self-consistent-charge density functional\nbased tight-binding theory.", "category": "physics_chem-ph" }, { "text": "Effect of off-diagonal exciton-phonon coupling on intramolecular singlet\n fission: Intramolecular singlet fission (iSF) materials provide remarkable advantages\nin terms of tunable electronic structures, and quantum chemistry studies have\nindicated strong electronic coupling modulation by high frequency phonon modes.\nIn this work, we formulate a microscopic model of iSF with simultaneous\ndiagonal and off-diagonal coupling to high-frequency modes. A non-perturbative\ntreatment, the Dirac-Frenkel time-dependent variational approach is adopted\nusing the multiple Davydov trial states. It is shown that both diagonal and\noff-diagonal coupling can aid efficient singlet fission if excitonic coupling\nis weak, and fission is only facilitated by diagonal coupling if excitonic\ncoupling is strong. In the presence of off-diagonal coupling, it is found that\nhigh frequency modes create additional fission channels for rapid iSF. Results\npresented here may help provide guiding principles for design of efficient\nsinglet fission materials by directly tuning singlet-triplet interstate\ncoupling.", "category": "physics_chem-ph" }, { "text": "First-principles calculation of the frequency-dependent dipole\n polarizability of argon: In this work we report state-of-the-art theoretical calculations of the\ndipole polarizability of the argon atom. Frequency dependence of the\npolarizability is taken into account by means of the dispersion coefficients\n(Cauchy coefficients) which is sufficient for experimentally relevant\nwavelengths below the first resonant frequency. In the proposed theoretical\nframework, all known physical effects including the relativistic, quantum\nelectrodynamics, finite nuclear mass, and finite nuclear size corrections are\naccounted for. We obtained $\\alpha_0=11.0763(19)$ for the static polarizability\nand $\\alpha_2=27.976(15)$ and $\\alpha_4=95.02(11)$ for the second and fourth\ndispersion coefficients, respectively. The result obtained for the static\npolarizability agrees (within the estimated uncertainty) with the most recent\nexperimental data [C. Gaiser and B. Fellmuth, Phys. Rev. Lett. 120, 123203\n(2018)], but is less accurate. The dispersion coefficients determined in this\nwork appear to be most accurate in the literature, improving by more than an\norder of magnitude upon previous estimates. By combining the experimentally\ndetermined value of the static polarizability with the dispersion coefficients\nfrom our calculations, the polarizability of argon can be calculated with\naccuracy of around $10\\,$ppm for wavelengths above roughly $450\\,$nm. This\nresult is important from the point of view of quantum metrology, especially for\na new pressure standard based on thermophysical properties of gaseous argon.\nAdditionally, in this work we calculate the static magnetic susceptibility of\nargon which relates the refractive index of dilute argon gas with its pressure.\nWhile our results for this quantity are less accurate than in the case of the\npolarizability, they can provide, via Lorenz-Lorentz formula, the best\navailable theoretical estimate of the refractive index of argon.", "category": "physics_chem-ph" }, { "text": "Examining the order-of-limits problem and lattice constant performance\n of the Tao--Mo Functional: In their recent communication [Phys. Rev. Lett., 117, 073001 (2016)] Tao and\nMo presented a semi-local density functional derived from the density matrix\nexpansion of the exchange hole localised by a general coordinate\ntransformation. We show that the order-of-limits problem present in the\nfunctional, dismissed as harmless in the original publication, causes severe\nerrors in predicted phase transition pressures. We also show that the claim\nthat lattice volume prediction accuracy exceeds that of existing similar\nfunctionals was based on comparison to reference data that misses anharmonic\nzero-point expansion and consequently overestimates accuracy. By highlighting\nthese omissions, we give a more accurate assessment of the Tao-Mo functional\nand show a simple route to resolving the problems.", "category": "physics_chem-ph" }, { "text": "Embedded equation-of-motion coupled-cluster theory for electronic\n excitation, ionization, electron attachment, and electronic resonances: The projection-based quantum embedding method is applied to electronically\nexcited states of valence, Rydberg, and charge-transfer character, valence- and\ncore-ionized states, as well as bound and temporary radical anions. We embed\ndifferent variants of equation-of-motion coupled-cluster singles and doubles\n(EOM-CCSD) theory in density functional theory and investigate the performance\nof the resulting methods using small organic molecules microsolvated by a\nvarying number of water molecules as test cases. States that are unstable\ntowards electron loss are treated by means of a complex-absorbing potential.\nBesides transition energies, we also present Dyson orbitals and natural\ntransition orbitals for embedded EOM-CCSD. Our results illustrate that embedded\nEOM-CCSD describes ionization and valence excitation very well and that these\ntransitions are quite insensitive towards technical details of the embedding\nprocedure. On the contrary, more care is required when dealing with Rydberg\nexcitations or electron attachment. For the latter type of transition in\nparticular, the use of long-range corrected density functionals is mandatory\nand truncation of the virtual orbital space -- which is indispensable for the\napplication of projection-based embedding to large systems -- proves to be\ndifficult.", "category": "physics_chem-ph" }, { "text": "QUESTDB: a database of highly-accurate excitation energies for the\n electronic structure community: We describe our efforts of the past few years to create a large set of more\nthan 500 highly-accurate vertical excitation energies of various natures ($\\pi\n\\to \\pi^*$, $n \\to \\pi^*$, double excitation, Rydberg, singlet, doublet,\ntriplet, etc) in small- and medium-sized molecules. These values have been\nobtained using an incremental strategy which consists in combining high-order\ncoupled cluster and selected configuration interaction calculations using\nincreasingly large diffuse basis sets in order to reach high accuracy. One of\nthe key aspect of the so-called QUEST database of vertical excitations is that\nit does not rely on any experimental values, avoiding potential biases\ninherently linked to experiments and facilitating theoretical cross\ncomparisons. Following this composite protocol, we have been able to produce\ntheoretical best estimate (TBEs) with the aug-cc-pVTZ basis set for each of\nthese transitions, as well as basis set corrected TBEs (i.e., near the complete\nbasis set limit) for some of them. The TBEs/aug-cc-pVTZ have been employed to\nbenchmark a large number of (lower-order) wave function methods such as CIS(D),\nADC(2), CC2, STEOM-CCSD, CCSD, CCSDR(3), CCSDT-3, ADC(3), CC3, NEVPT2, and\nothers (including spin-scaled variants). In order to gather the huge amount of\ndata produced during the QUEST project, we have created a website\n[https://lcpq.github.io/QUESTDB_website] where one can easily test and compare\nthe accuracy of a given method with respect to various variables such as the\nmolecule size or its family, the nature of the excited states, the type of\nbasis set, etc. We hope that the present review will provide a useful summary\nof our effort so far and foster new developments around excited-state methods.", "category": "physics_chem-ph" }, { "text": "Molecular scale ion separation driven by surface roughness and ion size\n asymmetry: new analytical solutions for differential capacitance of EDL: Electrode surface roughness significantly impacts the structure of electric\ndouble layer on a molecular scale. We derive analytical solutions for\ndifferential capacitance (DC) of electric double layer near rough electrode\nsurface, comparing them with a range of experimental and numerical studies. Two\ncauses of ions separation are considered: ion size asymmetry and electrode\nsurface roughness. The model has three scale parameters determining DC\nproperties: the Debye length, difference of ion penetration depths, and surface\nroughness parameter. For the first time, DC profile with more than two peaks\nwas obtained analytically due to account for ions reorientation effect. The\nmodel predicts DC curve transform from bell to camel and inverse induced by\nelectrode surface roughness. The behavior of DC-potential relation with\ntemperature and ion size ratio diverges depending on the type of ions\nseparation. Additionally, we provide analytical solutions for zero charge\npotential and demonstrate roughness effect on its value. Based on the results,\nwe give recommendations for properties required to design effective electric\ndouble layer capacitors.", "category": "physics_chem-ph" }, { "text": "Is CCSD(T) a proper standard for dipole moment calculations? An analysis\n considering diverse diatomic species: Coupled cluster with single, double, and perturbative triple excitations\n[CCSD(T)] has been extensively employed as the reference method in benchmarking\ndifferent quantum chemistry methods. In this work, we test the accuracy of\nCCSD(T) calculating ground state electric dipole moments at the extrapolated\ncomplete basis set (CBS) limit. The calculated dipole moments have been\ncompared to an experimental dataset consisted of diatomic molecules with\nvarious kinds of bond natures and spin configurations. As a result, to reach a\nsatisfactory agreement with experimental dipole moments, core-correlations\nshould be included for some molecules. However, even when core-correlations are\nincluded, the predicted dipole moment deviates considerably from the\nexperimental values for molecules involving transition metal atoms.", "category": "physics_chem-ph" }, { "text": "Potential energy surface of the 2A' Li2+Li doublet ground state: The lowest doublet electronic state for the lithium trimer (2A') is\ncalculated for use in three-body scattering calculations using the valence\nelectron FCI method with atomic cores represented using an effective core\npotential. It is shown that an accurate description of core-valence correlation\nis necessary for accurate calculations of molecular bond lengths, frequencies\nand dissociation energies. Interpolation between 2A' ab initio surface data\npoints in a sparse grid is done using the global interpolant moving least\nsquares method with a smooth radial data cutoff function included in the\nfitting weights and bivariate polynomials as a basis set. The Jahn-Teller\nsplitting of the 2E' surface into the 2A1 and 2B2 states is investigated using\na combination of both CASSCF and FCI levels of theory. Additionally,\npreliminary calculations of the 2A'' surface are also presented using second\norder spin restricted open-shell Moller-Plesset perturbation theory.", "category": "physics_chem-ph" }, { "text": "Molecular Auger Decay Rates from Complex-Variable Coupled-Cluster Theory: The emission of an Auger electron is the predominant relaxation mechanism of\ncore-vacant states in molecules composed of light nuclei. In this non-radiative\ndecay process, one valence electron fills the core vacancy while a second\nvalence electron is emitted into the ionization continuum. Because of this\ncoupling to the continuum, core-vacant states represent electronic resonances\nthat can be tackled with standard quantum-chemical methods only if they are\napproximated as bound states, meaning that Auger decay is neglected. Here, we\npresent an approach to compute Auger decay rates of core-vacant states from\ncoupled-cluster and equation-of-motion coupled-cluster wave functions combined\nwith complex scaling of the Hamiltonian or, alternatively, complex-scaled basis\nfunctions. Through energy decomposition analysis, we illustrate how\ncomplex-scaled methods are capable of describing the coupling to the ionization\ncontinuum without the need to model the wave function of the Auger electron\nexplicitly. In addition, we introduce in this work several approaches for the\ndetermination of partial decay widths and Auger branching ratios from\ncomplex-scaled coupled-cluster wave functions. We demonstrate the capabilities\nof our new approach by computations on core-ionized states of neon, water,\ndinitrogen, and benzene. Coupled-cluster and equation-of-motion coupled-cluster\ntheory in the singles and doubles approximation both deliver excellent results\nfor total decay widths, whereas we find partial widths more straightforward to\nevaluate with the former method. We also observe that the requirements towards\nthe basis set are less arduous for Auger decay than for other types of\nresonances so that extensions to larger molecules are readily possible.", "category": "physics_chem-ph" }, { "text": "Origin of power laws for reactions at metal surfaces mediated by hot\n electrons: A wide range of experiments have established that certain chemical reactions\nat metal surfaces can be driven by multiple hot electron mediated excitations\nof adsorbates. A high transient density of hot electrons is obtained by means\nof femtosecond laser pulses and a characteristic feature of such experiments is\nthe emergence of a power law dependence of the reaction yield on the laser\nfluence $Y\\sim F^n$. We propose a model of multiple inelastic scattering by hot\nelectrons, which reproduces this power law and the experimentally found\nexponents of several experiments. All parameters are calculated within Density\nFunctional Theory and the Delta Self-Consistent Field method. With a simplified\nassumption, the power law becomes exact and we obtain a simple and very useful\nphysical interpretation of the exponent $n$, which represents the number of\nadsorbate vibrational states participating in the reaction.", "category": "physics_chem-ph" }, { "text": "Accelerating convergence to the thermodynamic limit with twist angle\n selection applied to methods beyond many-body perturbation theory: We recently developed a scheme to use low-cost calculations to find a single\ntwist angle where the couple cluster doubles energy of a single calculation\nmatches the twist-averaged coupled cluster doubles energy in a finite unit\ncell. We used initiator full configuration interaction quantum Monte Carlo\n($i$-FCIQMC) as an example of an exact method beyond coupled cluster doubles\ntheory to show that this selected twist angle approach had comparable accuracy\nin methods beyond coupled cluster. Further, at least for small system sizes, we\nshow that the same twist angle can also be found by comparing the energy\ndirectly (at the level of second-order Moller-Plesset theory) suggesting a\nroute toward twist angle selection which requires minimal modification to\nexisting codes which can perform twist averaging.", "category": "physics_chem-ph" }, { "text": "Greater Transferability and Accuracy of Norm-conserving Pseudopotentials\n using Nonlinear Core Corrections: We present an investigation into the transferability of pseudopotentials\n(PPs) with a nonlinear core correction (NLCC) using the Goedecker, Teter, and\nHutter (GTH) protocol across a range of pure GGA, meta-GGA and hybrid\nfunctionals, and their impact on thermochemical and non-thermochemical\nproperties. The GTH-NLCC PP for the PBE density functional demonstrates\nremarkable transferability to the PBE0 and $\\omega$B97X-V exchange-correlation\nfunctionals, and relative to no NLCC, improves agreement significantly for\nthermochemical benchmarks compared to all-electron calculations. On the other\nhand, the B97M-rV meta-GGA functional performs poorly with the PBE-derived\nGTH-NLCC PP, which is mitigated by reoptimizing the NLCC parameters for this\nspecific functional. The findings reveal that atomization energies exhibit the\ngreatest improvements from use of the NLCC, which thus provides an important\ncorrection needed for covalent interactions relevant to applications involving\nchemical reactivity. Finally we test the NLCC-GTH PPs when combined with\nmedium-size TZV2P molecularly optimized (MOLOPT) basis sets which are typically\nutilized in condensed phase simulations, and show that they lead to\nconsistently good results when compared to all-electron calculations for\natomization energies, ionization potentials, barrier heights, and non-covalent\ninteractions, but lead to somewhat larger errors for electron affinities.", "category": "physics_chem-ph" }, { "text": "Quintic-scaling rank-reduced coupled cluster theory with single and\n double excitations: We consider the rank-reduced coupled-cluster theory with single and double\nexcitations (RR-CCSD) introduced recently [Parrish \\emph{et al.}, J. Chem.\nPhys. {\\bf 150}, 164118 (2019)]. The main feature of this method is the\ndecomposed form of the doubly-excited amplitudes which are expanded in the\nbasis of largest magnitude eigenvectors of the MP2 or MP3 amplitudes. This\napproach enables a substantial compression of the amplitudes with only minor\nloss of accuracy. However, the formal scaling of the computational costs with\nthe system size ($N$) is unaffected in comparison with the conventional CCSD\ntheory ($\\propto N^6$) due to presence of some terms quadratic in the\namplitudes. We show how to solve this problem, exploiting the fact that their\neffective rank increases only linearly with the system size and reduce the\nscaling of the RR-CCSD iterations down to the level of $N^5$. This is combined\nwith an iterative method of finding dominant eigenpairs of the MP2 or MP3\namplitudes which eliminates the necessity to perform the complete\ndiagonalization. Next, we consider the evaluation of the perturbative\ncorrections to the CCSD energies resulting from triply excited configurations.\nThe triply-excited amplitudes present in the CCSD(T) method are decomposed to\nthe Tucker-3 format using the higher-order orthogonal iteration (HOOI)\nprocedure. This enables to compute the energy correction due to triple\nexcitations non-iteratively with $N^6$ cost. The accuracy of the resulting\nrank-reduced CCSD(T) method is studied both for total and relative correlation\nenergies of a diverse set of molecules. Accuracy levels better than 99.9\\% can\nbe achieved with a substantial reduction of the computational costs. Concerning\nthe computational timings, break-even point between the rank-reduced and\nconventional CCSD implementations occurs for systems with about $30-40$ active\nelectrons.", "category": "physics_chem-ph" }, { "text": "Analytic Calculation of Transition dipole moment using four-component\n relativistic equation-of-motion coupled-cluster expectation value approach: We have developed an efficient scheme for the calculation of transition\nproperties within the four-component relativistic coupled cluster method using\nthe EOM-CCSD expectation value approach. The calculation of transition\nproperties within the relativistic EOM-CCSD framework requires the solution of\nboth right and left eigenvectors using Davidson's iterative diagonalization\nscheme. The accuracy of the approach has been investigated by calculating\nlow-lying transitions of Xe atom and spin forbidden\n$^{1}$S$_{0}$$\\rightarrow$$^{3}$P$_{1}$ transition in Na$^{+}$ atom. The\ncalculated results show good agreement with the earlier finite-field Fock space\nmulti-reference coupled cluster results and experimental values", "category": "physics_chem-ph" }, { "text": "Path-integral Monte Carlo Simulations without the Sign Problem:\n Multilevel Blocking Approach for Effective Actions: The multilevel blocking algorithm recently proposed as a possible solution to\nthe sign problem in path-integral Monte Carlo simulations has been extended to\nsystems with long-ranged interactions along the Trotter direction. As an\napplication, new results for the real-time quantum dynamics of the spin-boson\nmodel are presented.", "category": "physics_chem-ph" }, { "text": "Computational investigations of dispersion interactions between small\n molecules and graphene-like flakes: In this work, we investigate dispersion interactions in a selection of\natomic, molecular, and molecule-surface systems, comparing high-level\ncorrelated methods with empirically-corrected density functional theory (DFT).\nWe assess the efficacy of functionals commonly used for surface-based\ncalculations, with and without the D3 correction of Grimme. We find that the\ninclusion of the correction is essential to get meaningful results, but there\nis otherwise little to distinguish between the functionals. We also present\ncoupled-cluster quality interaction curves for \\ce{H2} and \\ce{NO2} interacting\nwith large carbon flakes, acting as models for graphene surfaces, using novel\nabsolutely localised molecular orbital based methods. These calculations\ndemonstrate that the problems with empirically-corrected DFT when investigating\ndispersion appear to compound as the system size increases, with important\nimplications for future computational studies of molecule-surface interactions.", "category": "physics_chem-ph" }, { "text": "Correlation energy of anisotropic quantum dots: We study the $D$-dimensional high-density correlation energy $\\Ec$ of the\nsinglet ground state of two electrons confined by a harmonic potential with\nCoulombic repulsion. We allow the harmonic potential to be anisotropic, and\nexamine the behavior of $\\Ec$ as a function of the anisotropy $\\alpha^{-1}$. In\nparticular, we are interested in the limit where the anisotropy goes to\ninfinity ($\\alpha\\to0$) and the electrons are restricted to a lower-dimensional\nspace. We show that tuning the value of $\\alpha$ from 0 to 1 allows a smooth\ndimensional interpolation and we demonstrate that the usual model, in which a\nquantum dot is treated as a two-dimensional system, is inappropriate. Finally,\nwe provide a simple function which reproduces the behavior of $\\Ec$ over the\nentire range of $\\alpha$.", "category": "physics_chem-ph" }, { "text": "NO2 and Humidity Sensing Characteristics of Few-layer Graphene: Sensing characteristics of few-layer graphenes for NO2 and humidity have been\ninvestigated with graphene samples prepared by the thermal exfoliation of\ngraphitic oxide (EG), conversion of nanodiamond (DG) and arc-discharge of\ngraphite in hydrogen (HG). The sensitivity for NO2 is found to be highest with\nDG. Nitrogen-doped HG (n-type) shows increased sensitivity for NO2 compared to\npure HG. The highest sensitivity for humidity is observed with HG. The sensing\ncharacteristics of graphene have been examined for different aliphatic alcohols\nand the sensitivity is found to vary with the chain length and branching.", "category": "physics_chem-ph" }, { "text": "Observation of correlated excitations in bimolecular collisions: Whereas collisions between atoms and molecules are largely understood,\ncollisions between two molecules have proven much harder to study. In both\nexperiment and theory, our ability to determine quantum state-resolved\nbimolecular cross sections lags behind their atom-molecule counterparts by\ndecades. For many bimolecular systems, even rules of thumb -- much less\nintuitive understanding -- of scattering cross sections are lacking. Here, we\nreport the measurement of state-to-state differential cross sections on the\ncollision of state-selected and velocity-controlled nitric oxide (NO) radicals\nand oxygen (O2) molecules. Using velocity map imaging of the scattered NO\nradicals, the full product-pair correlations of rotational excitation that\noccurs in both collision partners from individual encounters are revealed. The\ncorrelated cross sections show surprisingly good agreement with quantum\nscattering calculations using ab initio NO-O2 potential energy surfaces. The\nobservations show that the well-known energy-gap law that governs atom-molecule\ncollisions does not generally apply to bimolecular excitation processes, and\nreveal a propensity rule for the vector correlation of product angular momenta.", "category": "physics_chem-ph" }, { "text": "Steric effects in the dynamics of electrolytes at large applied\n voltages: II. Modified Poisson-Nernst-Planck equations: In situations involving large potentials or surface charges, the Poisson\nBoltzman(PB) equation has shortcomings because it neglects ion-ion interactions\nand steric effects. This has been widely recognized by the electrochemistry\ncommunity, leading to the development of various alternative models resulting\nin different sets \"modified PB equations\", which have had at least qualitative\nsuccess in predicting equilibrium ion distributions. On the other hand, the\nliterature is scarce in terms of descriptions of concentration dynamics in\nthese regimes. Here, adapting strategies developed to modify the PB equation,\nwe propose a simple modification of the widely used Poisson-Nernst-Planck (PNP)\nequations for ionic transport, which at least qualitatively accounts for steric\neffects. We analyze numerical solutions of these MPNP equations on the model\nproblem of the charging of a simple electrolyte cell, and compare the outcome\nto that of the standard PNP equations. Finally, we repeat the asymptotic\nanalysis of Bazant, Thornton, and Ajdari(2004} for this new system of equations\nto further document the interest and limits of validity of the simpler\nequivalent electrical circuit models introduced in Part I for such problems.", "category": "physics_chem-ph" }, { "text": "Physics-inspired Equivariant Descriptors of Non-bonded Interactions: One essential ingredient in many machine learning (ML) based methods for\natomistic modeling of materials and molecules is the use of locality. While\nallowing better system-size scaling, this systematically neglects long-range\n(LR) effects, such as electrostatics or dispersion interaction. We present an\nextension of the long distance equivariant (LODE) framework that can handle\ndiverse LR interactions in a consistent way, and seamlessly integrates with\npreexisting methods by building new sets of atom centered features. We provide\na direct physical interpretation of these using the multipole expansion, which\nallows for simpler and more efficient implementations. The framework is applied\nto simple toy systems as proof of concept, and a heterogeneous set of molecular\ndimers to push the method to its limits. By generalizing LODE to arbitrary\nasymptotic behaviors, we provide a coherent approach to treat arbitrary two-\nand many-body non-bonded interactions in the data-driven modeling of matter.", "category": "physics_chem-ph" }, { "text": "WACSF - Weighted Atom-Centered Symmetry Functions as Descriptors in\n Machine Learning Potentials: We introduce weighted atom-centered symmetry functions (wACSFs) as\ndescriptors of a chemical system's geometry for use in the prediction of\nchemical properties such as enthalpies or potential energies via machine\nlearning. The wACSFs are based on conventional atom-centered symmetry functions\n(ACSFs) but overcome the undesirable scaling of the latter with increasing\nnumber of different elements in a chemical system. The performance of these two\ndescriptors is compared using them as inputs in high-dimensional neural network\npotentials (HDNNPs), employing the molecular structures and associated\nenthalpies of the 133855 molecules containing up to five different elements\nreported in the QM9 database as reference data. A substantially smaller number\nof wACSFs than ACSFs is needed to obtain a comparable spatial resolution of the\nmolecular structures. At the same time, this smaller set of wACSFs leads to\nsignificantly better generalization performance in the machine learning\npotential than the large set of conventional ACSFs. Furthermore, we show that\nthe intrinsic parameters of the descriptors can in principle be optimized with\na genetic algorithm in a highly automated manner. For the wACSFs employed here,\nwe find however that using a simple empirical parametrization scheme is\nsufficient in order to obtain HDNNPs with high accuracy.", "category": "physics_chem-ph" }, { "text": "Novel two-dimensional Ca-Cl crystals with metallicity, piezoelectric\n effect and room-temperature ferromagnetism: Recently we have reported the direct observation of two-dimensional (2D)\nCa-Cl crystals on reduced graphene oxide (rGO) membranes, in which the calcium\nions are only about monovalent (i.e. ~+1) and metallic rather than insulating\nproperties are displayed by those CaCl crystals. Here, we report the\nexperimental observation and demonstration of the formation of graphene-Ca-Cl\nheterojunction owing to the metallicity of 2D Ca-Cl crystals, unexpected\npiezoelectric effect, room-temperature ferromagnetism, as well as the distinct\nhydrogen storage and release capability of the Ca-Cl crystals in rGO membranes.\nTheoretical studies show that the formation of those abnormal crystals is\nattributed to the strong cation-pi interactions of the Ca2+ with the aromatic\nrings in the graphitic surfaces. Since strong cation-pi interactions also exist\nbetween other metal ions (such as Mg2+, Fe2+, Co2+, Cu2+, Cd2+, Cr2+ and Pb2+)\nand graphitic surfaces, similar 2D crystals with abnormal valence state of the\nmetal cations and corresponding abnormal properties as well as novel\napplications are highly expected. Those findings further show the realistically\npotential applications of such abnormal CaCl material with unusual electronic\nproperties in designing novel transistors and magnetic devices, hydrogen\nstorage, catalyzer, high-performance conducting electrodes and sensors, with a\nsize down to atomic scale.", "category": "physics_chem-ph" }, { "text": "Interfacial-Water-Modulated Photoluminescence of Single-Layer WS$_2$ on\n Mica: Because of their bandgap tunability and strong light-matter interactions,\ntwo-dimensional (2D) semiconductors are considered promising candidates for\nnext-generation optoelectronic devices. However, their photophysical properties\nare greatly affected by environments because of their 2D nature. In this work,\nwe report that the photoluminescence (PL) of single-layer WS$_2$ is\nsubstantially affected by interfacial water that is inevitably present between\nitself and supporting mica substrates. Using PL spectroscopy and wide-field\nimaging, we show that the emission signals from A excitons and their negative\ntrions decreased at distinctively different rates with increasing excitation\npower, which can be attributed to the more efficient annihilation between\nexcitons than trions. By gas-controlled PL imaging, we also prove that\ninterfacial water converts trions into excitons by depleting native negative\ncharges through an oxygen reduction reaction, which renders excited WS$_2$ more\nsusceptible to nonradiative decay via exciton-exciton annihilation.\nUnderstanding the roles of nanoscopic water in complex low-dimensional\nmaterials will eventually contribute to devising their novel functions and\ndevices.", "category": "physics_chem-ph" }, { "text": "Triplet-Pair Spin Signatures from Macroscopically Aligned Heteroacenes\n in an Oriented Single Crystal: The photo-driven process of singlet fission generates coupled triplet pairs\n(TT) with fundamentally intriguing and potentially useful properties. The\nquintet 5TT0 sublevel is particularly interesting for quantum information\nbecause it is highly entangled, addressable with microwave pulses, and could be\ndetected using optical techniques. Previous theoretical work on a model\nHamiltonian and nonadiabatic transition theory, called the JDE model, has\ndetermined that this sublevel can be selectively populated if certain\nconditions are met. Among the most challenging, the molecules within the dimer\nundergoing singlet fission must have their principal magnetic axes parallel to\none another and to an applied Zeeman field B0. Here, we present time-resolved\nparamagnetic resonance (TR-EPR) spectroscopy of a single crystal sample of a\nnovel tetracenethiophene compound featuring arrays of dimers aligned in this\nmanner, mounted so that the orientation of the field relative to the molecular\naxes could be controlled. The observed spin sublevel populations in the paired\nTT and unpaired (T+T) triplets are consistent with predictions from the JDE\nmodel, including preferential 5TT0 formation at z||B0, with one caveat - two\n5TT spin sublevels have little to no population. This may be due to crossings\nbetween the 5TT and 3TT manifolds in the field range investigated by TR-EPR,\nconsistent with the inter-triplet exchange energy determined by monitoring\nphotoluminescence at varying magnetic fields.", "category": "physics_chem-ph" }, { "text": "Effect of phase and time coupling on NMR relaxation rate by random walk\n in phase space: The phase time coupling effect on NMR relaxation is investigated based on\ncoupled and uncoupled phase diffusion. The results indicate that phase and time\ncoupling could significantly impact the NMR relaxation time. The spectral\ndensity term in the relaxation time expression is modified with an apparent\nangular frequency, which could be twice the conventional angular frequency when\nthe phase-time coupling is strong. A phase-time coupling constant is proposed\nto modify the conventional angular frequency to the apparent angular frequency.\nThe modified NMR relaxation time can successfully fit the experimental data\ntaken from Ref. [6]. The results could improve our understanding and analysis\nof NMR relaxation.", "category": "physics_chem-ph" }, { "text": "Variational principle to regularize machine-learned density functionals:\n the non-interacting kinetic-energy functional: Practical density functional theory (DFT) owes its success to the\ngroundbreaking work of Kohn and Sham that introduced the exact calculation of\nthe non-interacting kinetic energy of the electrons using an auxiliary\nmean-field system. However, the full power of DFT will not be unleashed until\nthe exact relationship between the electron density and the non-interacting\nkinetic energy is found. Various attempts have been made to approximate this\nfunctional, similar to the exchange--correlation functional, with much less\nsuccess due to the larger contribution of kinetic energy and its more non-local\nnature. In this work we propose a new and efficient regularization method to\ntrain density functionals based on deep neural networks, with particular\ninterest in the kinetic-energy functional. The method is tested on\n(effectively) one-dimensional systems, including the hydrogen chain,\nnon-interacting electrons, and atoms of the first two periods, with excellent\nresults. For the atomic systems, the generalizability of the regularization\nmethod is demonstrated by training also an exchange--correlation functional,\nand the contrasting nature of the two functionals is discussed from a\nmachine-learning perspective.", "category": "physics_chem-ph" }, { "text": "Proton Dynamics in Protein Mass Spectrometry: Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS)\nallows an accurate determination of low-resolution structural features of\nproteins. Yet, the presence of proton dynamics, observed already by us for DNA\nin the gas phase, and its impact on protein structural determinants, have not\nbeen investigated so far. Here, we address this issue by a multi-step\nsimulation strategy on a pharmacologically relevant peptide, the N-terminal\nresidues of amyloid-beta peptide (Abeta(1-16)). Our calculations reproduce the\nexperimental maximum charge state from ESI-MS and are also in fair agreement\nwith collision cross section (CCS) data measured here by ESI/IM-MS. Although\nthe main structural features are preserved, subtle conformational changes do\ntake place in the first ~0.1 ms of dynamics. In addition, intramolecular proton\ndynamics processes occur on the ps-timescale in the gas phase as emerging from\nquantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of\ntheory. We conclude that proton transfer phenomena do occur frequently during\nfly time in ESI-MS experiments (typically on the ms timescale). However, the\nstructural changes associated with the process do not significantly affect the\nstructural determinants.", "category": "physics_chem-ph" }, { "text": "Extending the applicability of Redfield theories into highly\n non-Markovian regimes: We present a new, computationally inexpensive method for the calculation of\nreduced density matrix dynamics for systems with a potentially large number of\nsubsystem degrees of freedom coupled to a generic bath. The approach consists\nof propagation of weak-coupling Redfield-like equations for the high frequency\nbath degrees of freedom only, while the low frequency bath modes are\ndynamically arrested but statistically sampled. We examine the improvements\nafforded by this approximation by comparing with exact results for the\nspin-boson model over a wide range of parameter space. The results from the\nmethod are found to dramatically improve Redfield dynamics in highly\nnon--Markovian regimes, at a similar computational cost. Relaxation of the\nmode-freezing approximation via classical (Ehrenfest) evolution of the low\nfrequency modes results in a dynamical hybrid method. We find that this\nRedfield-based dynamical hybrid approach, which is computationally more\nexpensive than bare Redfield dynamics, yields only a marginal improvement over\nthe simpler approximation of complete mode arrest.", "category": "physics_chem-ph" }, { "text": "Spin-unrestricted random-phase approximation with range separation:\n Benchmark on atomization energies and reaction barrier heights: We consider several spin-unrestricted random-phase approximation (RPA)\nvariants for calculating correlation energies, with and without range\nseparation, and test them on datasets of atomization energies and reaction\nbarrier heights. We show that range separation greatly improves the accuracy of\nall RPA variants for these properties. Moreover, we show that a RPA variant\nwith exchange, hereafter referred to as RPAx-SO2, first proposed by Sz-abo and\nOstlund [A. Szabo and N. S. Ostlund, J. Chem. Phys. 67, 4351 (1977)] in a\nspin-restricted closed-shell formalism, and extended here to a\nspin-unrestricted formalism , provides on average the most accurate\nrange-separated RPA variant for atomization energies and reaction barrier\nheights. Since this range-separated RPAx-SO2 method had already been shown to\nbe among the most accurate range-separated RPA variants for weak intermolecular\ninteractions [J. Toulouse, W. Zhu, A. Savin, G. Jansen, and J. G.\n{\\'A}ngy{\\'a}n, J. Chem. Phys. 135, 084119 (2011)], this works confirms\nrange-separated RPAx-SO2 as a promising method for general chemical\napplications.", "category": "physics_chem-ph" }, { "text": "The Coupled-Trajectory Mixed Quantum-Classical Algorithm: A\n Deconstruction: We analyze a mixed quantum-classical algorithm recently derived from the\nexact factorization equations [Min, Agostini, Gross, PRL {\\bf 115}, 073001\n(2015)] to show the role of the different terms in the algorithm in bringing\nabout decoherence and wavepacket branching. The algorithm has the structure of\nEhrenfest equations plus a \"coupled-trajectory\" term for both the electronic\nand nuclear equations, and we analyze the relative roles played by the\ndifferent non-adiabatic terms in these equations, including how they are\ncomputed in practise. In particular, we show that while the coupled-trajectory\nterm in the electronic equation is essential in yielding accurate dynamics,\nthat in the nuclear equation has a much smaller effect. A decoherence time is\nextracted from the electronic equations and compared with that of augmented\nfewest-switches surface-hopping. We revisit a series of non-adiabatic Tully\nmodel systems to illustrate our analysis.", "category": "physics_chem-ph" }, { "text": "Localized Orbital Scaling Correction for Systematic Elimination of\n Delocalization Error in Density Functional Approximations: The delocalization error of popular density functional approximations (DFAs)\nleads to diversified problems in present-day density functional theory\ncalculations. For achieving a universal elimination of delocalization error, we\ndevelop a localized orbital scaling correction (LOSC) framework, which unifies\nour previously proposed global and local scaling approaches. The LOSC framework\naccurately characterizes the distributions of global and local fractional\nelectrons, and is thus capable of correcting system energy, energy derivative\nand electron density in a self-consistent and size-consistent manner. The\nLOSC-DFAs lead to systematically improved results, including the dissociation\nof cationic species, the band gaps of molecules and polymer chains, the energy\nand density changes upon electron addition and removal, and photoemission\nspectra.", "category": "physics_chem-ph" }, { "text": "Observation of inconsistent carbon isotope compositions of\n chlorine-isotopologue pairs of individual organochlorines by gas\n chromatography-high resolution mass spectrometry: This study investigated the consistency/inconsistency of carbon isotope\ncompositions of chlorine-isotopologue pairs, e.g., 12C235Cl4 vs. 12C13C35Cl4,\nof individual organochlorines including two chloroethylenes, three\npolychlorinated biphenyls, methyl-triclosan and hexachlorobenzene. The raw\ncarbon isotope ratios were measured by gas chromatography-high resolution mass\nspectrometry. Data simulations in terms of background subtraction, background\naddition, dual 13C-atoms substitution, deuterium substitution and\nhydrogen-transfer were conducted to confirm the validity of measured carbon\nisotope ratios and their differences. Inconsistent carbon isotope ratios\nderived from chlorine-isotopologue pairs of individual organochlorines were\nobserved, and the isotopologues of each organochlorine were thus inferred to be\nnon-randomly distributed. Mechanistic interpretation for these findings was\ntentatively proposed according to a basic principle in clumped-isotope\ngeochemistry, reaction thermodynamics and kinetics, along with isotope effects\noccurring on electron ionization mass spectrometry. This study sheds light on\nthe actual carbon isotope compositions of chlorine-isotopologue pairs of\norganochlorines, and yields new insights into the real distributions of carbon\nand chlorine isotopologues. The inconsistent carbon isotope compositions of\nchlorine-isotopologue pairs are anticipated to benefit the exploration of\nformation conditions and source identification of organochlorine pollutants.", "category": "physics_chem-ph" }, { "text": "A CCSD(T)-based permutationally invariant polynomial 4-body potential\n for water: We report a permutationally invariant polynomial (PIP) potential energy\nsurface for the water 4-body interaction. This 12-atom PES is a fit to 2119,\nsymmetry-unique, CCSD(T)-F12a/haTZ (aug-cc-pVTZ basis for 'O' atom and cc-pVTZ\nbasis for 'H' atom) 4-b interaction energies. These come from low-level,\ndirect-dynamics calculations, tetramer fragments from an MD water simulation at\n300 K, and from the water hexamer, heptamer, decamer, and 13-mer clusters. The\nPIP basis is purified to ensure that the 4-b potential goes rigorously to zero\nin monomer+trimer and dimer+dimer dissociations for all possible such\nfragments. The 4-b energies of isomers of the hexamer calculated with the new\nsurface are shown to be in better agreement with benchmark CCSD(T) results than\nthose from the MB-pol potential. Other tests validate the high-fidelity of the\nPES.", "category": "physics_chem-ph" }, { "text": "Properties of Reactive Oxygen Species by Quantum Monte Carlo: The electronic properties of the oxygen molecule, in its singlet and triplet\nstates, and of many small oxygen-containing radicals and anions have important\nroles in different fields of Chemistry, Biology and Atmospheric Science.\nNevertheless, the electronic structure of such species is a challenge for\nab-initio computational approaches because of the difficulties to correctly\ndescribe the statical and dynamical correlation effects in presence of one or\nmore unpaired electrons. Only the highest-level quantum chemical approaches can\nyield reliable characterizations of their molecular properties, such as binding\nenergies, equilibrium structures, molecular vibrations, charge distribution and\npolarizabilities. In this work we use the variational Monte Carlo (VMC) and the\nlattice regularized Monte Carlo (LRDMC) methods to investigate the equilibrium\ngeometries and molecular properties of oxygen and oxygen reactive species.\nQuantum Monte Carlo methods are used in combination with the Jastrow\nAntisymmetrized Geminal Power (JAGP) wave function ansatz, which has been\nrecently shown to effectively describe the statical and dynamical correlation\nof different molecular systems. In particular we have studied the oxygen\nmolecule, the superoxide anion, the nitric oxide radical and anion, the\nhydroxyl and hydroperoxyl radicals and their corresponding anions, and the\nhydrotrioxyl radical. Overall, the methodology was able to correctly describe\nthe geometrical and electronic properties of these systems, through compact but\nfully-optimised basis sets and with a computational cost which scales as\n$N^3-N^4$, where $N$ is the number of electrons. This work is therefore opening\nthe way to the accurate study of the energetics and of the reactivity of large\nand complex oxygen species by first principles.", "category": "physics_chem-ph" }, { "text": "Optical Signatures of the Coupling between Excitons and Charge Transfer\n States in Linear Molecular Aggregates: Charge Transfer (CT) has enjoyed continuous interest due to increasing\nexperimental control over molecular structure leading to applications in, for\nexample, photovoltaics and hydrogen production. In this paper, we investigate\nthe effect of CT states on the absorption spectrum of linear molecular\naggregates using a scattering matrix technique that allows us to deal with\narbitrarily large systems. The presented theory performs well for both strong\nand weak mixing of exciton and CT states, bridging the gap between previously\nemployed methods which are applicable in only one of these limits. In\nexperimental spectra the homogeneous linewidth is often too large to resolve\nall optically allowed transitions individually, resulting in a characteristic\ntwo-peak absorption spectrum in both the weak- and strong-coupling regime.\nUsing the scattering matrix technique we examine the contributions of free and\nbound states in detail. We conclude that the skewness of the high-frequency\npeak may be used as a new way to identify the exciton-CT-state coupling\nstrength.", "category": "physics_chem-ph" }, { "text": "Molecular hyperdynamics coupled with the nonorthogonal tight-binding\n approach: Implementation and validation: We present the molecular hyperdynamics algorithm and its implementation to\nthe nonorthogonal tight-binding model NTBM and the corresponding software. Due\nto its multiscale structure, the proposed approach provides the long time scale\nsimulations (more than 1 s), unavailable for conventional molecular dynamics.\nNo preliminary information about the system potential landscape is needed for\nthe use of this technique. The optimal interatomic potential modification is\nautomatically derived from the previous simulation steps. The average time\nbetween adjusted potential energy fluctuations provides an accurate evaluation\nof physical time during the hyperdynamics simulation. The main application of\nthe presented hyperdynamics method is the study of thermal-induced defects\narising in the middle-sized or relatively large atomic systems at low\ntemperatures. To validate the presented method, we apply it to the C$_{60}$\ncage and its derivative C$_{60}$NH$_{2}$. Hyperdynamics leads to the same\nresults as a conventional molecular dynamics, but the former possesses much\nhigher performance and accuracy due to the wider temperature region. The\ncoefficient of acceleration achieves 10$^{7}$ and more.", "category": "physics_chem-ph" }, { "text": "Coherent Atomic Orbital Polarization Probes the Geometric Phase in\n Photodissociation of Polyatomic Molecules: Quantum interference between multiple pathways in molecular photodissociation\noften results in angular momentum polarization of atomic products and this can\ngive deep insight into fundamental physical processes. For dissociation of\ndiatomic molecules the resulting orbital polarization is fully understood and\nconsistent with quantum mechanical theory. For polyatomic molecules, however,\ncoherent photofragment orbital polarization is frequently observed but so far\nhas eluded theoretical explanation, and physical insight is lacking. Here we\npresent a model of these effects for ozone photodissociation that reveals the\nimportance of a novel manifestation of the geometric phase. We show this\ngeometric phase effect permits the existence of coherent polarization in cases\nwhere it would otherwise vanish, and cancels it in some cases where it might\notherwise exist. The model accounts for measurements in ozone that have\nhitherto defied explanation, and represents a step toward a deeper\nunderstanding of coherent electronic excitation in polyatomic molecules and a\nnew role of the geometric phase.", "category": "physics_chem-ph" }, { "text": "Mechanisms of localization in isotope-substituted dynamical Jahn-Teller\n systems: The mechanisms of localization of Jahn-Teller deformations and vibronic\nwavefunctions in isotope substituted dynamical Jahn-Teller systems are\nelucidated. It is found that the localization in the trough is of potential\ntype in the case of strong vibronic coupling, while it becomes of kinetic type\nin the case of intermediate and weak coupling. It is shown that the vibronic\nlevels in the linear $E\\otimes e$-problem remain double degenerate upon\narbitrary isotope substitution on the reasons similar to time reversal symmetry\nin which the role of spin is played by orbital pseudospin.", "category": "physics_chem-ph" }, { "text": "Laser-Induced Electronic and Vibronic Dynamics in the Pyrene Molecule\n and its Cation: Among polycyclic aromatic hydrocarbons, pyrene is widely used as an optical\nprobe thanks to peculiar ultraviolet absorption and infrared emission features.\nInterestingly, this molecule is also an abundant component of the interstellar\nmedium, where it is detected via its unique spectral fingerprints. In this\nwork, we present a comprehensive first-principles study on the electronic and\nvibrational response of pyrene and its cation to ultrafast, coherent pulses in\nresonance with their optically active excitations in the ultraviolet region.\nThe analysis of molecular symmetries, electronic structure, and linear optical\nspectra is used to interpret transient absorption spectra and kinetic energy\nspectral densities computed for the systems excited by ultrashort laser fields.\nBy disentangling the effects of the electronic and vibrational dynamics via\n\\textit{ad hoc} simulations with stationary and moving ions, and, in specific\ncases, with the aid of auxiliary model systems, we rationalize that the nuclear\nmotion is mainly harmonic in the neutral species, while strong anharmonic\noscillations emerge in the cation, driven by electronic coherence. Our results\nprovide additional insight into the ultrafast vibronic dynamics of pyrene and\nrelated compounds and set the stage for future investigations on more complex\ncarbon-conjugated molecules.", "category": "physics_chem-ph" }, { "text": "Efficient Approximations of Complete Interatomic Potentials for Crystal\n Property Prediction: We study property prediction for crystal materials. A crystal structure\nconsists of a minimal unit cell that is repeated infinitely in 3D space. How to\naccurately represent such repetitive structures in machine learning models\nremains unresolved. Current methods construct graphs by establishing edges only\nbetween nearby nodes, thereby failing to faithfully capture infinite repeating\npatterns and distant interatomic interactions. In this work, we propose several\ninnovations to overcome these limitations. First, we propose to model\nphysics-principled interatomic potentials directly instead of only using\ndistances as in many existing methods. These potentials include the Coulomb\npotential, London dispersion potential, and Pauli repulsion potential. Second,\nwe model the complete set of potentials among all atoms, instead of only\nbetween nearby atoms as in existing methods. This is enabled by our\napproximations of infinite potential summations, where we extend the Ewald\nsummation for several potential series approximations with provable error\nbounds. Finally, we propose to incorporate our computations of complete\ninteratomic potentials into message passing neural networks for representation\nlearning. We perform experiments on the JARVIS and Materials Project benchmarks\nfor evaluation. Results show that the use of interatomic potentials and\ncomplete interatomic potentials leads to consistent performance improvements\nwith reasonable computational costs. Our code is publicly available as part of\nthe AIRS library (https://github.com/divelab/AIRS/tree/main/OpenMat/PotNet).", "category": "physics_chem-ph" }, { "text": "Ultrafast Proton Transport between a Hydroxy Acid and a Nitrogen Base\n along Solvent Bridges Governed by Hydroxide/Methoxide Transfer Mechanism: Aqueous proton transport plays a key role in acid-base neutralization, and\nenergy transport through biological membranes and hydrogen fuel cells.\nExtensive experimental and theoretical studies have resulted in a highly\ndetailed elucidation of one of the underlying microscopic mechanisms for\naqueous excess proton transport, known as the von Grotthuss mechanism,\ninvolving different hydrated proton configurations with associated high\nfluxional structural dynamics. Hydroxide transport, with approximately two-fold\nlower bulk diffusion rates than those of excess protons, has received much less\nattention. We present femtosecond UV/IR pump-probe experiments and ab initio\nmolecular dynamics simulations of different proton transport pathways of the\nbifunctional photoacid 7-hydroxyquinoline (7HQ) in water-methanol mixtures. For\n7HQ solvent-dependent photoacidity, free energy-reactivity correlation\nbehaviour and QM/MM trajectories point to a dominant OH-/CH3O- transport\npathway, for all water-methanol mixing ratios investigated. This provides\nconclusive evidence for the hydrolysis/methanolysis acid-base neutralization\npathway formulated by Manfred Eigen half a century ago.", "category": "physics_chem-ph" }, { "text": "Anisotropic thermal characterisation of large-format lithium-ion pouch\n cells: Temperature strongly impacts battery performance, safety and durability, but\nmodelling heat transfer requires accurately measured thermal properties. Herein\nwe propose new approaches to characterise the heat capacity and anisotropic\nthermal-conductivity components for lithium-ion pouch cells. Heat capacity was\nestimated by applying Newton's law of cooling to an insulated container within\nwhich the cell was submerged in warmed dielectric fluid. Thermal conductivity\nwas quantified by heating one side of the cell and measuring the opposing\ntemperature distribution with infra-red thermography, then inverse modelling\nwith the anisotropic heat equation. Experiments were performed on commercial 20\nAh lithium iron phosphate (LFP) pouch cells. At 100% state-of-charge (SOC), the\nheat capacity of a 489 g, 224 mL pouch cell was 541 J/K. The through-plane and\nin-plane thermal conductivities were respectively 0.52 and 26.6 W/(mK).\nCapturing anisotropies in conductivity is important for accurate thermal\nsimulations. State-of-charge dependence was also probed by testing at 50% SOC:\nthe heat capacity dropped by 6% and thermal conductivity did not significantly\nchange.", "category": "physics_chem-ph" }, { "text": "Exact-Factorization-Based Surface-Hopping for Multi-State Dynamics: A surface-hopping algorithm recently derived from the exact factorization\napproach, SHXF, [Ha, Lee, Min, J. Phys. Chem. Lett. 9, 1097 (2018)] introduces\nan additional term in the electronic equation of surface-hopping, which couples\nelectronic states through the quantum momentum. This term not only provides a\nfirst-principles description of decoherence but here we show it is crucial to\naccurately capture non-adiabatic dynamics when more than two states are\noccupied at any given time. Using a vibronic coupling model of the uracil\ncation, we show that the lack of this term in traditional surface-hopping\nmethods, including those with decoherence-corrections, leads to failure to\npredict the dynamics through a three-state intersection, while SHXF performs\nsimilarly to the multi-configuration time-dependent Hartree quantum dynamics\nbenchmark.", "category": "physics_chem-ph" }, { "text": "Effect of Temperature Gradient on Quantum Transport: The recently introduced multisite tensor network path integral (MS-TNPI)\nmethod [Bose and Walters, J. Chem. Phys., 2022, 156, 24101.] for simulation of\nquantum dynamics of extended systems has been shown to be effective in studying\none-dimensional systems. Quantum transport in these systems are typically\nstudied at a constant temperature. However, temperature seems to be a very\nobvious parameter that can be spatially changed to control the quantum\ntransport. Here, MS-TNPI is used to study ``non-equilibrium'' effects of an\nexternally imposed temperature gradient on the quantum transport in\none-dimensional extended quantum systems.", "category": "physics_chem-ph" }, { "text": "Self-Adaptive Real-Time Time-Dependent Density Functional Theory for\n X-ray Absorptions: Real-time time-dependent density functional theory (RT-TDDFT) can in\nprinciple access the whole absorption spectrum of a many-electron system\nexposed to a narrow pulse. However, this requires an accurate and efficient\npropagator for the numerical integration of the time-dependent Kohn-Sham\nequation. While a low-order time propagator is already sufficient for the\nlow-lying valence absorption spectra, it is no longer the case for the X-ray\nabsorption spectra (XAS) of systems composed even only of light elements, for\nwhich the use of a high-order propagator is indispensable. It is then crucial\nto choose a largest possible time step and a shortest possible simulation time,\nso as to minimize the computational cost. To this end, we propose here a robust\nAutoPST approach to determine automatically (Auto) the propagator (P), step\n(S), and time (T) for relativistic RT-TDDFT simulations of XAS.", "category": "physics_chem-ph" }, { "text": "Extrapolative Analysis of Fast-Switching Free Energy Estimates in a\n Molecular System: We perform an extrapolative analysis of \"fast-growth\" free-energy-difference\n(DF) estimates of a computer-modeled, fully-solvated ethane<->methanol\ntransformation. The results suggest that extrapolation can greatly reduce the\nsystematic error in DF estimated from a small number of very fast switches. Our\nextrapolation procedure uses block-averages of finite-data estimates, and\nappears to be particularly useful for broad, non-Gaussian distributions of data\nwhich produce substantial systematic errors with insufficient data. In every\ntested case, the extrapolative results were better than direct estimates.", "category": "physics_chem-ph" }, { "text": "Optically induced anisotropy in time-resolved scattering: Imaging\n molecular scale structure and dynamics in disordered media with experiment\n and theory: Time-resolved scattering experiments enable imaging of materials at the\nmolecular scale with femtosecond time resolution. However, in disordered media\nthey provide access to just one radial dimension thus limiting the study of\norientational structure and dynamics. Here we introduce a rigorous and\npractical theoretical framework for predicting and interpreting experiments\ncombining optically induced anisotropy and time-resolved scattering. Using\nimpulsive nuclear Raman and ultrafast X-ray scattering experiments of\nchloroform and simulations, we demonstrate that this framework can accurately\npredict and elucidate both the spatial and temporal features of these\nexperiments.", "category": "physics_chem-ph" }, { "text": "Molecular modeling of interfacial properties of the\n hydrogen+water+decane mixture in three-phase equilibrium: The understanding of geochemical interactions between H2 and geofluids is of\ngreat importance for underground H2 storage but requires further study. We\nreport the first investigation on the three-phase fluid mixture containing H2,\nH2O, and n-C10H22. Molecular dynamics simulation and PC-SAFT density gradient\ntheory are employed to estimate the interfacial properties under various\nconditions (temperature ranges from 298 to 373 K and pressure is up to around\n100 MPa). Our results demonstrate that interfacial tensions (IFTs) of the\nH2-H2O interface in the H2+H2O+C10H22 three-phase mixture are smaller than IFTs\nin the H2+H2O two-phase mixture. This decrement of IFT can be attributed to\nC10H22 adsorption in the interface. Importantly, H2 accumulates in the\nH2O-C10H22 interface in the three-phase systems, which leads to weaker\nincrements of IFT with increasing pressure compared to IFTs in the water+C10H22\ntwo-phase mixture. In addition, the IFTs of the H2-C10H22 interface are hardly\ninfluenced by H2O due to the limited amount of H2O dissolved in bulk phases.\nNevertheless, relatively strong enrichments and positive surface excesses of\nH2O are seen in the H2-C10H22 interfacial region. Furthermore, the values of\nthe spreading coefficient are mostly negative revealing the presence of the\nthree-phase contact for the H2+H2O+C10H22 mixture under studied conditions.", "category": "physics_chem-ph" }, { "text": "Dimension-free path-integral molecular dynamics without preconditioning: Convergence with respect to imaginary-time discretization is an essential\npart of any path-integral-based calculation. However, an unfortunate property\nof existing non-preconditioned numerical integration schemes for path-integral\nmolecular dynamics (PIMD) - including ring-polymer molecular dynamics (RPMD)\nand thermostatted RPMD (T-RPMD) - is that for a given MD timestep, the overlap\nbetween the exact ring-polymer Boltzmann-Gibbs distribution and that sampled\nusing MD becomes zero in the infinite-bead limit. This has clear implications\nfor hybrid Metropolis Monte-Carlo/MD sampling schemes. We show that these\nproblems can be avoided through the introduction of \"dimension-free\" numerical\nintegration schemes for which the sampled ring-polymer position distribution\nhas non-zero overlap with the exact distribution in the infinite-bead limit for\nthe case of a harmonic potential. We show that dimension freedom can be\nachieved via mollification of the forces from the physical potential and with\nthe BCOCB integration scheme. The dimension-free numerical integration schemes\nyield finite error bounds for a given MD timestep as the number of beads is\ntaken to infinity; these conclusions are proven for harmonic potential and\nborne out numerically for anharmonic systems, including water. The numerical\nresults for BCOCB are particularly striking, allowing for three-fold increases\nin the stable timestep for liquid water with respect to the Bussi-Parrinello\n(OBABO) and Leimkuhler (BAOAB) integrators while introducing negligible errors\nin the statistical properties and absorption spectrum. Importantly, the\ndimension-free, non-preconditioned integration schemes introduced here preserve\nergodicity and global second-order accuracy, and they remain simple, black-box\nmethods that avoid additional computational costs, tunable parameters, or\nsystem-specific implementations.", "category": "physics_chem-ph" }, { "text": "Comprehensive study of the vapour-liquid equilibria of the pure\n two-centre Lennard-Jones plus pointquadrupole fluid: Results of a systematic investigation of the vapour-liquid equilibria (VLE)\nof 30 individual two-centre Lennard-Jones plus pointquadrupole model fluids\n(2CLJQ) are reported over a range of reduced quadrupolar momentum $0 \\le Q^{*2}\n\\le 4$ and of reduced elongation $0 \\le L^* \\le 0.8$. Temperatures investigated\nare from about 55 % to about 95 % of the critical temperature of each fluid.\nUniformly the $NpT$+Test Particle Method based on molecular dynamics\nsimulations is used for the generation of vapour pressures, saturated\ndensities, and saturated enthalpies. Critical temperatures $T^*_{\\rm c}$ and\ndensities $\\rho^*_{\\rm c}$ are obtained from Guggenheim's equations. Empirical\ncorrelations for critical data $T^*_{\\rm c}$ and $\\rho^*_{\\rm c}$ as well as\nfor saturated densities $\\rho'^*$, $\\rho''^*$, and vapour pressures\n$p^*_{\\sigma}$ are developed as global functions of the model parameters. In\nmost cases they describe the simulation data within their statistical\nuncertainties. Critical pressures and acentric factors of the 2CLJQ fluid can\nbe calculated from present correlations. The present simulations are a sound\nbasis for adjustments of the model parameters $Q^{*2}$, $L^*$, $\\sigma$, and\n$\\epsilon$ to experimental VLE data of real fluids.", "category": "physics_chem-ph" }, { "text": "Convergence of coupled cluster perturbation theory: The convergence of a recently proposed coupled cluster (CC) family of\nperturbation series [Eriksen, J. J. et al., J. Chem. Phys. 140, 064108 (2014)],\nin which the energetic difference between two CC models - a low-level parent\nand a high-level target model - is expanded in orders of the M{\\o}ller-Plesset\n(MP) fluctuation potential, is investigated for four prototypical closed-shell\nsystems (Ne, singlet methylene, distorted HF, and the fluoride anion) in\nstandard and augmented basis sets. In these investigations, energy corrections\nof the various series have been calculated to high orders and their convergence\nradii determined by probing for possible front- and back-door intruder states,\nthe existence of which would make the series divergent. In summary, we conclude\nhow it is primarily the choice of target state, and not the choice of parent\nstate, which ultimately governs the convergence behavior of a given series. For\nexample, restricting the target state to, say, triple or quadruple excitations\nmight remove intruders present in series that target the full configuration\ninteraction (FCI) limit, such as the standard MP series. Furthermore, we find\nthat whereas a CC perturbation series might converge within standard\ncorrelation consistent basis sets, it may start to diverge whenever these\nbecome augmented by diffuse functions, similar to the MP case. However, unlike\nfor the MP case, such potential divergences are not found to invalidate the\npractical use of the low-order corrections of the CC perturbation series.", "category": "physics_chem-ph" }, { "text": "Accounting for the kinetics in order parameter analysis: lessons from\n theoretical models and a disordered peptide: Molecular simulations as well as single molecule experiments have been widely\nanalyzed in terms order parameters, the latter representing candidate probes\nfor the relevant degrees of freedom. Notwithstanding this approach is very\nintuitive, mounting evidence showed that such description is not accurate,\nleading to ambiguous definitions of states and wrong kinetics. To overcome\nthese limitations a framework making use of order parameter fluctuations in\nconjunction with complex network analysis is investigated. Derived from recent\nadvances in the analysis of single molecule time traces, this approach takes\ninto account of the fluctuations around each time point to distinguish between\nstates that have similar values of the order parameter but different dynamics.\nSnapshots with similar fluctuations are used as nodes of a transition network,\nthe clusterization of which into states provides accurate Markov-State-Models\nof the system under study. Application of the methodology to theoretical models\nwith a noisy order parameter as well as the dynamics of a disordered peptide\nillustrates the possibility to build accurate descriptions of molecular\nprocesses on the sole basis of order parameter time series without using any\nsupplementary information.", "category": "physics_chem-ph" }, { "text": "Morse bifurcations of transition states in bimolecular reactions: The transition states and dividing surfaces used to find rate constants for\nbimolecular reactions are shown to undergo qualitative changes, known as Morse\nbifurcations, and to exist for a large range of energies, not just immediately\nabove the critical energy for first connection between reactants and products.\nSpecifically, we consider capture between two molecules and the associated\ntransition states for the case of non-zero angular momentum and general\nattitudes. The capture between an atom and a diatom, and then a general\nmolecule are presented, providing concrete examples of Morse bifurcations of\ntransition states and dividing surfaces. The reduction of the $n$-body systems\nrepresenting the reactions is discussed and reviewed with comments on the\ndifficulties associated with choosing appropriate charts and the global\ngeometry of the reduced spaces.", "category": "physics_chem-ph" }, { "text": "Coding Cross Sections of an Electron Charge Transfer Process: The paper presents the algorithm of a code written for computing the cross\nsection for a charge transfer process involving a neutral molecule and a\nmonatomic ion. The entrance and exit potential energy surfaces, driving the\ncollision dynamics, are computed employing the Improved Lennard-Jones function\nthat accounts for the role of non-electrostatic forces, due to size repulsion\nplus dispersion and induction attraction. In addition, electrostatic\ncomponents, affecting the entrance channels, are evaluated as sum of Coulomb\ncontributions, determined by the He$^+$ ion interacting with the charge\ndistribution on the molecular frame. The cross section is estimated by\nemploying the Landau-Zener-St\\\"uckelberg approach. The code implemented has\nbeen employed in systems involving helium cation and a small organic molecule,\nsuch as methanol, dimethyl ether and methyl formate.", "category": "physics_chem-ph" }, { "text": "The power-law reaction rate coefficient for barrierless reactions: The power-law reaction rate coefficient for the barrierless reactions is\nstudied if the reactions take place in systems with power-law distributions,\nand a generalized rate formula for the barrierless reactions in Gorin model is\nderived. We show that due to barrierless, different from those for bimolecular\nand unimolcular reactions, the power-law rate coefficient for the barrierless\nreactions does not have the factor of power-law distribution function and thus\nit is not very strongly dependent on the nu-parameter. Four barrierless\nreactions are taken as the application examples to calculate the new rate\ncoefficients, which with larger fitting nu-parameters can be exactly in\nagreement with the measurement values in experimental studies.", "category": "physics_chem-ph" }, { "text": "Determination of Wave Function Functionals: The\n Constrained-Search--Variational Method: In a recent paper [Phys. Rev. Lett. \\textbf{93}, 130401 (2004)], we proposed\nthe idea of expanding the space of variations in variational calculations of\nthe energy by considering the approximate wave function $\\psi$ to be a\nfunctional of functions $ \\chi: \\psi = \\psi[\\chi]$ rather than a function. The\nspace of variations is expanded because a search over the functions $\\chi$ can\nin principle lead to the true wave function. As the space of such variations is\nlarge, we proposed the constrained-search-- variational method whereby a\nconstrained search is first performed over all functions $\\chi$ such that the\nwave function functional $\\psi[\\chi]$ satisfies a physical constraint such as\nnormalization or the Fermi-Coulomb hole sum rule, or leads to the known value\nof an observable such as the diamagnetic susceptibility, nuclear magnetic\nconstant or Fermi contact term. A rigorous upper bound to the energy is then\nobtained by application of the variational principle. A key attribute of the\nmethod is that the wave function functional is accurate throughout space, in\ncontrast to the standard variational method for which the wave function is\naccurate only in those regions of space contributing principally to the energy.\nIn this paper we generalize the equations of the method to the determination of\narbitrary Hermitian single-particle operators as applied to two-electron atomic\nand ionic systems. The description is general and applicable to both ground and\nexcited states. A discussion on excited states in conjunction with the theorem\nof Theophilou is provided.", "category": "physics_chem-ph" }, { "text": "Zero- to Ultralow-Field Nuclear Magnetic Resonance $J$-Spectroscopy with\n Commercial Atomic Magnetometers: Zero- to ultralow-field nuclear magnetic resonance (ZULF NMR) is an\nalternative spectroscopic method to high-field NMR, in which samples are\nstudied in the absence of a large magnetic field. Unfortunately, there is a\nlarge barrier to entry for many groups, because operating the optical\nmagnetometers needed for signal detection requires some expertise in atomic\nphysics and optics. Commercially available magnetometers offer a solution to\nthis problem. Here we describe a simple ZULF NMR configuration employing\ncommercial magnetometers, and demonstrate sufficient functionality to measure\nsamples with nuclear spins prepolarized in a permanent magnet or initialized\nusing parahydrogen. This opens the possibility for other groups to use ZULF\nNMR, which provides a means to study complex materials without magnetic\nsusceptibility-induced line broadening, and to observe samples through\nconductive materials.", "category": "physics_chem-ph" }, { "text": "How to make electrons avoid each other: a nonlocal radius for strong\n correlation: We present here a model of the exchange-correlation hole for strongly\ncorrelated systems using a simple nonlocal generalization of the Wigner--Seitz\nradius. The model behaves similarly to the strictly correlated electron\napproach, which gives the infinitely correlated limit of density functional\ntheory. Unlike the strictly correlated method, however, the energies and\npotentials of this model can be presently calculated for arbitrary geometries\nin three dimensions. We discuss how to evaluate the energies and potentials of\nthe nonlocal model, and provide results for many systems where it is also\npossible to compare to the strictly correlated electron treatment.", "category": "physics_chem-ph" }, { "text": "Large Vibrationally Induced Parity Violation Effects in CHDBrI$^+$ $-$ A\n Promising Candidate for Future Experiments: The isotopically chiral molecular ion CHDBrI$^+$ is identified as an\nexceptionally promising candidate for the detection of parity violation in\nvibrational transitions. The largest predicted parity-violating frequency shift\nreaches 1.8 Hz for the hydrogen wagging mode which has a sub-Hz natural line\nwidth and its vibrational frequency auspiciously lies in the available laser\nrange. In stark contrast to this result, the parent neutral molecule is two\norders of magnitude less sensitive to parity violation. The origin of this\neffect is analyzed and explained. Precision vibrational spectroscopy of\nCHDBrI$^+$ is feasible as it is amenable to preparation at internally low\ntemperatures and resistant to predissociation, promoting long interrogation\ntimes (Landau et al.). The intersection of these properties in this molecular\nion places the first observation of parity violation in chiral molecules within\nreach.", "category": "physics_chem-ph" }, { "text": "On the Absence of Triplet Exciton Loss Pathways in Non-Fullerene\n Acceptor based Organic Solar Cells: We investigate the viability of highly efficient organic solar cells (OSCs)\nbased on non-fullerene acceptors (NFA) by taking into consideration efficiency\nloss channels and stability issues caused by triplet excitons (TE) formation.\nOSCs based on a blend of the conjugated donor polymer PBDB-T and ITIC as\nacceptor were fabricated and investigated with electrical, optical and\nspin-sensitive methods. The spin-Hamiltonian parameters of molecular TEs and\ncharge transfer TEs in ITIC e.g., zero-field splitting and charge distribution,\nwere calculated by Density Functional Theory (DFT) modelling. In addition, the\nenergetic model describing the photophysical processes in the donor-acceptor\nblend was derived. Spin-sensitive photoluminescence measurements prove the\nformation of charge transfer (CT) states in the blend and the formation of TEs\nin the pure materials and the blend. However, no molecular TE signal is\nobserved in the completed devices under working conditions by spin-sensitive\nelectrical measurements. The absence of a molecular triplet state population\nallows to eliminate a charge carrier loss channel and irreversible\nphotooxidation facilitated by long-lived triplet states. These results\ncorrelate well with the high power conversion efficiency of the\nPBDB-T:ITIC-based OSCs and their high stability.", "category": "physics_chem-ph" }, { "text": "A Protocol for Spectroscopists to Isolate The Effect of Berry Geometric\n Magnetic Forces on Molecular Dynamics: We propose a novel means to isolate and quantify the effects of Berry force\non molecular dynamics using two reasonably strong continuous wave (CW) laser\nfields with frequencies $\\omega$ and $2\\omega$. For molecules or materials with\nthree frequency-matching bright transitions\n($|{0}\\rangle\\rightarrow|{1}\\rangle$, $|{1}\\rangle\\rightarrow|{2}\\rangle$,\n$|{0}\\rangle\\rightarrow|{2}\\rangle$) at frequencies ($\\omega$, $\\omega$,\n$2\\omega$) respectively, the effects of Berry curvature can be isolated by\nvarying the phase between the two laser fields ($\\Delta \\phi$) and monitoring\nthe dynamics. Moreover, we find that the resulting chemical dynamics can depend\ncritically on the sign of $\\Delta \\phi$; in other words, the effects of Berry\ncurvature can be enormous. Thus, this manuscript represents an unusual step\nforward towards using light-matter interactions to affect chemical dynamics,\nsuggesting that topological concepts usually invoked in adiabatic quantum\noptics and condensed matter can be directly applied to non-adiabatic chemical\nexcited state dynamics.", "category": "physics_chem-ph" }, { "text": "High-Temperature Decomposition of Diisopropyl Methylphosphonate (DIMP)\n on Alumina: Mechanistic Predictions from Ab Initio Molecular Dynamics: The enhanced degradation of organophosphorous-based chemical warfare agents\n(CWAs) on metal-oxide surfaces holds immense promise for neutralization\nefforts; however, the underlying mechanisms in this process remain poorly\nunderstood. We utilize large-scale quantum calculations for the first time to\nprobe the high-temperature degradation of diisopropyl methylphosphonate (DIMP),\na nerve agent simulant. Our Born-Oppenheimer molecular dynamics (BOMD)\ncalculations show that the $\\gamma$-Al$_2$O$_3$ surface shows immense promise\nfor quickly adsorbing and destroying CWAs. We find that the alumina surface\nquickly adsorbs DIMP at all temperatures, and subsequent decomposition of DIMP\nproceeds via a propene elimination. Our BOMD calculations are complemented with\nmetadynamics simulations to produce free energy paths, which show that the\nactivation barrier decreases with temperature and DIMP readily decomposes on\n$\\gamma$-Al$_2$O$_3$. Our first-principle BOMD and metadynamics simulations\nprovide crucial diagnostics for sarin decomposition models and mechanistic\ninformation for examining CWA decomposition reactions on other candidate metal\noxide surfaces.", "category": "physics_chem-ph" }, { "text": "The Numerical Equivalence of Diabatic and Adiabatic Representations in\n Diatomic Molecules: The (stationary) Schr\\\"{o}dinger equation for atomistic systems is solved\nusing the adiabatic potential energy curves (PECs) and the associated adiabatic\napproximation. Despite being very simplistic, this approach is very powerful\nand used in nearly all practical applications. In cases when interactions\nbetween electronic states become important, the associated non-adiabatic\neffects are taken into account via the derivative couplings (DDRs), also known\nas non-adiabatic couplings (NACs). For diatomic molecules, the corresponding\nPECs in the adiabatic representation are characterized by avoided crossings.\nThe alternative to the adiabatic approach is the diabatic representation,\nobtained via a unitary transformation of the adiabatic states by minimizing the\nDDRs. For diatomics, the diabatic representation has zero DDR and non-diagonal\ndiabatic couplings (DCs) ensue. The two representations are fully equivalent\nand so should be the rovibronic energies and wavefunctions which result from\nthe solution of the corresponding Schr\\\"{o}dinger equations.\n We demonstrate (for the first time), the numerical equivalence between the\nadiabatic and diabatic rovibronic calculations of diatomic molecules, using the\nab initio curves of yttrium oxide (YO) and carbon monohydride (CH) as examples\nof two-state systems, where YO is characterized by a strong NAC, while CH has a\nstrong diabatic coupling. Rovibronic energies and wavefunctions are computed\nusing a new diabatic module implemented in variational rovibronic code DUO. We\nshow that it is important to include both the Diagonal Born-Oppenheimer\nCorrection (DBOC) and non-diagonal DDRs. We also show that convergence of the\nvibronic energy calculations can strongly depend on the representation of\nnuclear motion used and that no one representation is best in all cases.", "category": "physics_chem-ph" }, { "text": "Highly Efficient Fuel Cell Electrodes from Few-Layer Graphene Sheets and\n Electrochemically Deposited Palladium Nanoparticles: An extremely efficient ethanol fuel cell electrode is produced by combining\nthe large surface area of vertically oriented and highly conductive few-layer\ngraphene sheets with electrochemically deposited palladium nanoparticles. The\nelectrodes show an extraordinary high catalyst activity of up to 7977 mA/(mg\nPd) at low catalyst loadings of 0.64 $\\mu$g/cm$^2$ and a very high current\ndensity of up to 106 mA/cm$^2$ at high catalyst loadings of 83 $\\mu$g/cm$^2$.\nMoreover, the low onset potentials combined with a good poisoning resistance\nand long-term stability make these electrodes highly suitable for real\napplications. These features are achieved by using a newly developed\nelectrochemical catalyst deposition process exploiting high voltages of up to\n3.5 kV. This technique allows controlling the catalyst amount ranging from a\nhomogeneous widespread distribution of small ($\\leq$ 10 nm) palladium\nnanoparticles to rather dense layers of particles, while every catalyst\nparticle has electrical contact to the graphene electrode.", "category": "physics_chem-ph" }, { "text": "Unravelling the deterministic effect of the solid-state diffusion energy\n barrier for charge carrier on the self-discharge of supercapacitors: The further development of fast electrochemical devices is hindered by\nself-discharge. Current strategies for suppressing self-discharge are mainly\nfocused on the extrinsic and general mechanisms including faradaic reactions,\ncharge redistribution, and ohmic leakage. However, the self-discharge process\nis still severe for conventional supercapacitors. Herein, we unravel the\ndeterministic effect of solid-state diffusion energy barrier by constructing\nconjugately configured supercapacitors based on pairs of pre-lithiated niobium\noxides with similar intercalation pseudocapacitive process but different\nphases. This device works with a single type of charge carrier while materials\nwith various diffusion barriers can be implanted, thus serving as an ideal\nplatform to illustrate the influence of the diffusion barrier. The results show\nthat the comprehensive effect of solid-state diffusion energy barrier and\nextrinsic effects drives the self-discharge process. Noteworthy, the diffusion\nbarrier presents with an exponential form, which governs the self-discharge of\nsupercapacitors. This work is expected to unravel the deterministic effect of\nthe solid-state diffusion energy barrier and provide a general guidance for\nsuppressing self-discharge for supercapacitors.", "category": "physics_chem-ph" }, { "text": "Dissociative electron attachment to carbon dioxide via the ^2\u03a0_u shape\n resonance: Momentum imaging measurements from two experiments are presented and\ninterpreted with the aid of new ab initio theoretical calculations to describe\nthe dissociative electron attachment (DEA) dynamics. We address the problem of\nhow the 4 eV ^2\\Pi_u shape resonance in CO_2 proceeds to dissociate to\nCO(^1\\Sigma^+) + O^-(^2P) by DEA.", "category": "physics_chem-ph" }, { "text": "Scattering and Recombination of Two Triplet Excitons in polymer\n light-emitting diodes: The scattering and recombination processes between two triplet excitons in\nconjugated polymers are investigated by using a nonadiabatic evolution method,\nbased on an extended Su-Schrieffer-Heeger model including interchain\ninteractions. Due to the interchain coupling, the electron and/or hole in the\ntwo triplet excitons can exchange. The results show that the recombination\ninduces the formation of singlet excitons, excited polarons and biexcitons.\nMoreover, we also find the yields of these products, which can contribute to\nthe emission, increase with the interchain coupling strength, in good agreement\nwith results from experiments.", "category": "physics_chem-ph" }, { "text": "Symmetrical Graph Neural Network for Quantum Chemistry, with Dual R/K\n Space: Most of current neural network models in quantum chemistry (QC) exclude the\nmolecular symmetry, separate the well-correlated real space (R space), and\nmomenta space (K space) into two individuals, which lack the essential physics\nin molecular chemistry. In this work, by endorsing the molecular symmetry and\nelementals of group theory, we propose a comprehensive method to apply symmetry\nin the graph neural network (SY-GNN), which extends the property-predicting\ncoverage to all the orbital symmetry for both ground and excited states. SY-GNN\nshows excellent performance in predicting both the absolute and relative of R\nand K spaces quantities. Besides the numerical properties, SY-GNN also can\npredict the orbitals distributions in real space, providing the active regions\nof chemical reactions. We believe the symmetry endorsed deep learning scheme\ncovers the significant physics inside and is essential for the application of\nneural networks in QC and many other research fields in the future.", "category": "physics_chem-ph" }, { "text": "Improving Molecular Force Fields Across Configurational Space by\n Combining Supervised and Unsupervised Machine Learning: The training set of atomic configurations is key to the performance of any\nMachine Learning Force Field (MLFF) and, as such, the training set selection\ndetermines the applicability of the MLFF model for predictive molecular\nsimulations. However, most atomistic reference datasets are inhomogeneously\ndistributed across configurational space (CS), thus choosing the training set\nrandomly or according to the probability distribution of the data leads to\nmodels whose accuracy is mainly defined by the most common close-to-equilibrium\nconfigurations in the reference data. In this work, we combine unsupervised and\nsupervised ML methods to bypass the inherent bias of the data for common\nconfigurations, effectively widening the applicability range of MLFF to the\nfullest capabilities of the dataset. To achieve this goal, we first cluster the\nCS into subregions similar in terms of geometry and energetics. We iteratively\ntest a given MLFF performance on each subregion and fill the training set of\nthe model with the representatives of the most inaccurate parts of the CS. The\nproposed approach has been applied to a set of small organic molecules and\nalanine tetrapeptide, demonstrating an up to two-fold decrease in the root mean\nsquared errors for force predictions of these molecules. This result holds for\nboth kernel-based methods (sGDML and GAP/SOAP models) and deep neural networks\n(SchNet model). For the latter, the developed approach simultaneously improves\nboth energy and forces, bypassing the compromise to be made when employing\nmixed energy/force loss functions.", "category": "physics_chem-ph" }, { "text": "The role of geometric phase in the formation of electronic coherences at\n conical intersections: The direct observation of non-adiabatic dynamics at conical intersections is\na long-standing goal of molecular physics. Novel time-resolved spectroscopies\nhave been proposed which are sensitive to electronic coherences induced by the\npassage of an excited state wavepacket through a region of conical\nintersection. Here we demonstrate that inclusion of the geometric phase effect,\nand its manifestations, is essential for the correct description of the\ntransient electronic coherences that may or may not develop. For electronic\nstates of different symmetry, electronic coherences are suppressed by the\ngeometric phase. Conversely, for states of the same symmetry, appreciable\nelectronic coherences are possible, but their magnitude depends on both the\ntopography of and direction of approach to the conical intersection. These\ngeneral results have consequences for all studies of electronic coherences at\nconical intersections.", "category": "physics_chem-ph" }, { "text": "Facilitating method development for reverse fill/flush flow modulation\n by using a tunable auxiliary pressure source instead of a fixed bleed\n capillary: The conventional reverse fill/flush flow modulation for comprehensive\ntwo-dimensional gas chromatography requires a bleed capillary column to be\nconnected to the outlet of the modulator channel. The purpose of this\ncapillary, that does not contain the stationary phase, is to provide a pressure\nresistance to the modulator channel flow. In this way, the desired modulator\nflow can be achieved, and channel over-filling can be avoided. Normally, the\nlength and the internal diameter of the bleed capillary are chosen so as to\nobtain the modulator flow that is close to the flow of the first separation\ncolumn. Thus, for any chosen set of chromatographic conditions, the required\ndimensions of the bleed capillary can be completely different, making the GCxGC\nmethod development tedious and generating additional costs in consumables and\nanalyst time. In this work a tunable pressure source generating a suitable\nbackpressure was used instead of the fixed bleed capillary which has the\nadvantage of the possibility to freely adapt the pressure resistance and\ngenerate the required modulator channel flow for any conditions. This set-up\nhas been evaluated and compared in terms of the impact on the modulation\nperformance to the set-up involving a fixed bleed capillary demonstrating\ncomparable performance.", "category": "physics_chem-ph" }, { "text": "Unravelling of the chemistry and the performance in the oxygen reduction\n reaction of carbon nitride-supported bimetallic electrocatalysts through\n X-ray photoelectron spectroscopy: Five bimetallic electrocatalysts (ECs) including a carbon nitride (CN)\nsupport are synthesised through the pyrolysis of a solid precursor obtained\nthrough sol-gel and gel-plastic processes. The resulting ECs are characterised\nthrough ICP-AES (Inductively Coupled Plasma-Atomic Emission Spectroscopy) and\nXPS (X-ray Photoelectron spectroscopy); their performance and reaction\nmechanism in the oxygen reduction reaction (ORR) are evaluated with the\nCV-TF-RRDE method (Cyclic Voltammetry Thin-Film Rotating Ring-Disk Electrode).\nSpecial attention is given to XPS results with the aim to carry out a thorough\ninvestigation of the surface concentration and the chemical environments of the\ndifferent elements, as well as providing information on the structure of the\nmetal components of the ECs and their interactions with the carbon nitride\nsupport. The correlation of the results obtained from the chemical analyses,\nXPS and the electrochemical studies allows to improve the fundamental\nunderstanding of the factors controlling the ORR kinetics and reaction pathway\nin bimetallic CN-supported ECs.", "category": "physics_chem-ph" }, { "text": "Geminate recombination of hydroxyl radicals generated in 200 nm\n photodissociation of aqueous hydrogen peroxide: The picosecond dynamics of hydroxyl radicals generated in 200 nm photoinduced\ndissociation of aqueous hydrogen peroxide have been observed through their\ntransient absorbance at 266 nm. It is shown that these kinetics are nearly\nexponential, with a decay time of ca. 30 ps. The prompt quantum yield for the\ndecomposition of H2O2 is 0.56, and the fraction of hydroxyl radicals escaping\nfrom the solvent cage to the water bulk is 64-68%. These recombination kinetics\nsuggest strong caging of the geminate hydroxyl radicals by water.\nPhenomenologically, these kinetics may be rationalized in terms of the\ndiffusion of hydroxide radicals out of a shallow potential well (a solvent\ncage) with an Onsager radius of 0.24 nm.", "category": "physics_chem-ph" }, { "text": "Computing decay widths of autoionizing Rydberg states with\n complex-variable coupled cluster theory: We compute autoionization widths of various Rydberg states of neon and\ndinitrogen by equation-of-motion coupled-cluster theory combined with complex\nscaling and complex basis functions. This represents the first time that\ncomplex-variable methods are applied to Rydberg states represented in Gaussian\nbasis sets. A new computational protocol based on Kaufmann basis functions is\ndesigned to make these methods applicable to atomic and molecular Rydberg\nstates. As a first step, we apply our protocol to the neon atom and computed\nwidths of the $3s$, $3p$, $4p$ and $3d$ Rydberg states. We then proceed to\ncompute the widths of the $3s\\sigma_g$, $3d\\sigma_g$, and $3d\\pi_g$ Rydberg\nstates of dinitrogen, which belong to the Hopfield series. Our results\ndemonstrate a decrease in the decay width for increasing angular momentum and\nprincipal quantum number within both Rydberg series.", "category": "physics_chem-ph" }, { "text": "Ultrahigh molecular recognition specificity of competing DNA\n oligonucleotide strands in thermal equilibrium: a cooperative transition to\n order: The specificity of molecular recognition is important to molecular\nself-organization. A prominent example is the biological cell where, within a\nhighly crowded molecular environment, a myriad of different molecular receptor\npairs recognize their binding partner with astonishing accuracy. In thermal\nequilibrium it is usually admitted that the affinity of recognizer pairs only\ndepends on the nature of the two binding molecules. Accordingly, Boltzmann\nfactors of binding energy differences relate the molecular affinities among\ndifferent target molecules that compete for the same probe. Here, we consider\nthe molecular recognition of short DNA oligonucleotide single strands. We show\nthat a better matching oligonucleotide strand can prevail against a\ndisproportionally more concentrated competitor that exhibits reduced affinity\ndue to a mismatch. The magnitude of deviation from the simple picture above may\nreach several orders of magnitude. In our experiments the effective molecular\naffinity of a given strand remains elevated only as long as the better matching\ncompetitor is not present. We interpret our observations based on an\nenergy-barrier of entropic origin that occurs if two competing oligonucleotide\nstrands occupy the same probe simultaneously. In this situation the relative\nbinding affinities are reduced asymmetrically, which leads to an expression of\nthe free energy landscape that represents a formal analogue of a Landau\ndescription of phase transitions. Our mean field description reproduces the\nobservations in quantitative agreement. The advantage of improved molecular\nrecognition comes at no energetic cost other than the design of the molecular\nensemble, and the introduction of the competitor. It will be interesting to see\nif mechanisms along similar lines as exposed here, contribute to the molecular\nsynergy that occurs in biological systems.", "category": "physics_chem-ph" }, { "text": "High-dimensional neural network potentials for solvation: The case of\n protonated water clusters in helium: The design of accurate helium-solute interaction potentials for the\nsimulation of chemically complex molecules solvated in superfluid helium has\nlong been a cumbersome task due to the rather weak but strongly anisotropic\nnature of the interactions. We show that this challenge can be met by using a\ncombination of an effective pair potential for the He-He interactions and a\nflexible high-dimensional neural network potential (NNP) for describing the\ncomplex interaction between helium and the solute in a pairwise additive\nmanner. This approach yields an excellent agreement with a mean absolute\ndeviation as small as 0.04 kJ/mol for the interaction energy between helium and\nboth, hydronium and Zundel cations compared to CCSD(T) reference calculations\nwith an energetically converged basis set. The construction and improvement of\nthe potential can be performed in a highly automated way, which opens the door\nfor applications to a variety of reactive molecules to study the effect of\nsolvation on the solute as well as the solute-induced structuring of the\nsolvent. Furthermore, we show that this NNP approach yields very convincing\nagreement with the CCSD(T) reference for properties like many-body spatial and\nradial distribution functions. This holds for the microsolvation of the\nprotonated water monomer and dimer by a few helium atoms up to their solvation\nin bulk helium as obtained from path integral simulations at about 1 K.", "category": "physics_chem-ph" }, { "text": "Energy-level diagrams and their contribution to fifth-order Raman and\n second-order infrared responses: Distinction between relaxation mechanisms by\n two-dimensional spectroscopy: We develop a Feynman rule for energy-level diagrams emphasizing their\nconnections to the double-sided Feynman diagrams and physical processes in the\nLiouville space. Thereby we completely identify such diagrams and processes\ncontributing to the two-dimensional response function in the Brownian\noscillator model. We classify such diagrams or processes in quartet and\nnumerically present signals separately from each quartet of diagrams or\nLiouville-space processes. We find that the signal from each quartet is\ndistinctly different from the others; we can identify each peaks in frequency\ndomain with a certain quartet. This offers the basis for analyzing and\nassigning actual two-dimensional peaks and suggests the possibility of\nLiouville-space-path selective spectroscopy. As an application we demonstrate\nan example in which two familiar homogeneous mechanisms of relaxation are\ndistinguished by existence or non-existence of certain peaks on the\ntwo-dimensional map; appearance or disappearance of certain peak is sensitive\nto the coupling mechanism. We also point out some confusion in the literature\nwith regard to inclusion of relaxation effects.", "category": "physics_chem-ph" }, { "text": "REMPI Spectroscopy of HfF: The spectrum of electronic states at 30000--33000 cm$^{-1}$ in hafnium\nfluoride has been studied using (1+1) resonance-enhanced multi-photon\nionization (REMPI) and (1+1$'$) REMPI. Six $\\Omega' = 3/2$ and ten $\\Pi_{1/2}$\nvibronic bands have been characterized. We report the molecular constants for\nthese bands and estimate the electronic energies of the excited states using a\ncorrection derived from the observed isotope shifts. When either of two closely\nspaced $\\Pi_{1/2}$ electronic states is used as an intermediate state to access\nautoionizing Rydberg levels, qualitatively distinct autoionization spectra are\nobserved. The intermediate state-specificity of the autoionization spectra\nbodes well for the possibility of using a selected $\\Pi_{1/2}$ state as an\nintermediate state to create ionic HfF$^+$ in various selected quantum states,\nan important requirement for our electron electric dipole moment (eEDM) search\nin HfF$^+$.", "category": "physics_chem-ph" }, { "text": "Specification, Construction, and Exact Reduction of State Transition\n System Models of Biochemical Processes: Biochemical reaction systems may be viewed as discrete event processes\ncharacterized by a number of states and state transitions. These systems may be\nmodeled as state transition systems with transitions representing individual\nreaction events. Since they often involve a large number of interactions, it\ncan be difficult to construct such a model for a system, and since the\nresulting state-level model can involve a huge number of states, model analysis\ncan be difficult or impossible. Here, we describe methods for the high-level\nspecification of a system using hypergraphs, for the automated generation of a\nstate-level model from a high-level model, and for the exact reduction of a\nstate-level model using information from the high-level model. Exact reduction\nis achieved through the automated application of symmetry reduction and\ninvariant manifold reduction techniques to the high-level model, allowing\npotentially significant reductions without the need to generate a full model.\nThe application of the method to biochemical reaction systems is illustrated by\nmodels describing a hypothetical ion-channel at several levels of complexity.\nThe method allows for the reduction of the otherwise intractable example models\nto a manageable size.", "category": "physics_chem-ph" }, { "text": "PubChemQC PM6: A dataset of 221 million molecules with optimized\n molecular geometries and electronic properties: We report on the largest dataset of optimized molecular geometries and\nelectronic properties calculated by the PM6 method for 92.9% of the 91.2\nmillion molecules cataloged in PubChem Compounds retrieved on Aug. 29, 2016. In\naddition to neutral states, we also calculated those for cationic, anionic, and\nspin flipped electronic states of 56.2%, 49.7%, and 41.3% of the molecules,\nrespectively. Thus, the grand total calculated is 221 million molecules. The\ndataset is available at http://pubchemqc.riken.jp/pm6_dataset.html under the\nCreative Commons Attribution 4.0 International license.", "category": "physics_chem-ph" }, { "text": "Improving Accuracy of Electrochemical Capacitance and Solvation\n Energetics in First-Principles Calculations: Reliable first-principles calculations of electrochemical processes require\naccurate prediction of the interfacial capacitance, a challenge for current\ncomputationally-efficient continuum solvation methodologies. We develop a model\nfor the double layer of a metallic electrode that reproduces the features of\nthe experimental capacitance of Ag(100) in a non-adsorbing, aqueous\nelectrolyte, including a broad hump in the capacitance near the Potential of\nZero Charge (PZC), and a dip in the capacitance under conditions of low ionic\nstrength. Using this model, we identify the necessary characteristics of a\nsolvation model suitable for first-principles electrochemistry of metal\nsurfaces in non-adsorbing, aqueous electrolytes: dielectric and ionic\nnonlinearity, and a dielectric-only region at the interface. The dielectric\nnonlinearity, caused by the saturation of dipole rotational response in water,\ncreates the capacitance hump, while ionic nonlinearity, caused by the\ncompactness of the diffuse layer, generates the capacitance dip seen at low\nionic strength. We show that none of the previously developed solvation models\nsimultaneously meet all these criteria. We design the Nonlinear Electrochemical\nSoft-Sphere solvation model (NESS) which both captures the capacitance features\nobserved experimentally, and serves as a general-purpose continuum solvation\nmodel.", "category": "physics_chem-ph" }, { "text": "Dynamical Insights into the Decomposition of 1,2-Dioxetane: Chemiluminescence in 1,2-dioxetane occurs through a thermally activated\ndecomposition reaction into two formaldehyde molecules. Both ground-state and\nnonadiabatic dynamics (including singlet excited states) of the decomposition\nreaction have been simulated, starting from the first O-O bond-breaking\ntransition structure. The ground-state dissociation occurs between t = 30 fs\nand t = 140 fs. The so-called entropic trap leads to frustrated dissociations,\npostponing the decomposition reaction. Specific geometrical conditions are\nnecessary for the trajectories to escape from the entropic trap and for\ndissociation to be possible. The singlet excited states participate as well in\nthe trapping of the molecule: dissociation including the nonadiabatic\ntransitions to singlet excited states now occurs from t = 30 fs to t = 250 fs\nand later. Specific regions of the seam of the S0/S1 conical intersections that\nwould \"retain\" the molecule for longer on the excited state have been\nidentified.", "category": "physics_chem-ph" }, { "text": "QED corrections to the correlated relativistic energy: one-photon\n processes: This work is a collection of initial calculations and formal considerations\nwithin the Salpeter-Sucher exact equal-time relativistic quantum\nelectrodynamics framework. The calculations are carried out as preparation for\nthe computation of pair, retardation, and radiative corrections to the\nrelativistic energy of correlated two-spin-1/2-fermion systems. In this work,\nparticular attention is paid to the retardation and the `one-loop' self-energy\ncorrections, which are known to be among the largest corrections to the\ncorrelated relativistic energy. The theoretical development is supplemented\nwith identifying formal connections to the non-relativistic quantum\nelectrodynamics framework, which is based on a correlated but non-relativistic\nreference, as well as to the `$1/Z$ approach', which is built on a relativistic\nbut one-particle zeroth order. The two complementary directions currently\nprovide the theoretical framework for light atomic-molecular precision\nspectroscopy and heavy-atom phenomena. The present theoretical efforts pave the\nway for relativistic QED corrections to (explicitly) correlated relativistic\ncomputations.", "category": "physics_chem-ph" }, { "text": "Functional Derivative of the Zero Point Energy Functional from the\n Strong Interaction Limit of Density Functional Theory: We derive an explicit expression for the functional derivative of the\nsubleading term in the strong interaction limit expansion of the generalized\nLevy--Lieb functional for the special case of two electrons in one dimension.\nThe expression is derived from the zero point energy (ZPE) functional, which is\nvalid if the quantum state reduces to strongly correlated electrons in the\nstrong coupling limit. The explicit expression is confirmed numerically and\nrespects the relevant sum-rule. We also show that the ZPE potential is able to\ngenerate a bond mid-point peak for homo-nuclear dissociation and is properly of\npurely kinetic origin. Unfortunately, the ZPE diverges for Coulomb systems,\nwhereas the exact peaks should be finite.", "category": "physics_chem-ph" }, { "text": "Irradiation driven molecular dynamics simulation of the FEBID process\n for Pt(PF$_3$)$_4$: This paper presents a detailed computational protocol for atomistic\nsimulation of the formation and growth of metal-containing nanostructures\nduring the Focused Electron Beam Induced Deposition (FEBID) process. The\nprotocol is based upon the Irradiation-Driven Molecular Dynamics (IDMD) - a\nnovel and general methodology for computer simulations of irradiation-driven\ntransformations of complex molecular systems by means of the advanced software\npackages MBN Explorer and MBN Studio. Atomistic simulations performed following\nthe formulated protocol provide valuable insights into the fundamental\nmechanisms of electron-induced precursor fragmentation and the related\nmechanism of nanostructure formation and growth using FEBID, which are\nessential for the further advancement of FEBID-based nanofabrication. The\ndeveloped computational methodology is general and applicable to different\nprecursor molecules, substrate types, irradiation regimes, etc. The methodology\ncan also be adjusted to simulate the nanostructure formation by other\nnanofabrication techniques using electron beams, such as direct electron beam\nlithography. In the present study, the methodology is applied to the IDMD\nsimulation of the FEBID of Pt(PF$_3$)$_4$ - a widely studied precursor molecule\n- on a SiO$_2$ surface. The simulations reveal the processes driving the\ninitial phase of nanostructure formation during FEBID, including nucleation of\nPt atoms, formation of small metal clusters on the surface, followed by their\naggregation and the formation of dendritic platinum nanostructures. The\nanalysis of the simulation results provides space resolved relative metal\ncontent, height and the growth rate of the deposits which represent valuable\nreference data for the experimental characterization of the nanostructures\ngrown by FEBID.", "category": "physics_chem-ph" }, { "text": "Investigating solvent effects on the magnetic properties of molybdate\n ions (MoO$_{4}^{2-}$) with relativistic embedding: We investigate the ability of mechanical and electronic density functional\ntheory (DFT)-based embedding approaches to describe the solvent effects on\nnuclear magnetic resonance (NMR) shielding constants of the $^{95}$Mo nucleus\nin the molybdate ion in aqueous solution. From the description obtained from\ncalculations with two- and four-component relativistic Hamiltonians, we find\nthat for such systems spin-orbit coupling effects are clearly important for\nabsolute shielding values, but for relative quantities a scalar relativistic\ntreatment provides a sufficient estimation of the solvent effects. We find that\nthe electronic contributions to the solvent effects are relatively modest yet\ndecisive to provide a more accurate magnetic response of the system, when\ncompared to reference supermolecular calculations. We analyze the errors in the\nembedding calculations by statistical methods as well as through a real-space\nrepresentation of NMR shielding densities, which are shown to provide a clear\npicture of the physical processes at play.", "category": "physics_chem-ph" }, { "text": "Quantized Auger Recombination of Polaronic Self-trapped Excitons in Bulk\n Iron Oxide: The Auger recombination in bulk semiconductors can depopulate the charge\ncarriers in a non-radiative way, which, fortunately, only has detrimental\nimpact on optoelectronic device performance under the condition of high carrier\ndensity because the restriction arising from concurrent momentum and energy\nconservation limits the Auger rate. Here, we surprisingly found that the Auger\nrecombination in bulk Fe2O3 films was more efficient than narrow-bandgap\nhigh-mobility semiconductors that were supposed to have much higher Auger rate\nconstants than metal oxides. The Auger process in Fe2O3 was ascribed to the\nCoulombically coupled self-trapped excitons (STEs), which was enhanced by the\nrelaxation of momentum conservation because of the strong spatial localization\nof these STEs. Furthermore, due to this localization effect the kinetic traces\nof the STE annihilation for different STE densities exhibited characteristics\nof quantized Auger recombination, and we demonstrated that these traces could\nbe simultaneously modeled by taking into account the quantized Auger rates.", "category": "physics_chem-ph" }, { "text": "A genetic algorithm to build diatomic potentials: Several types of numerical and combinatorial optimization algorithms have\nbeen used as useful tools to minimize functional forms. Generally, when those\nforms are non-linear or occur in problems without a specific optimization\nmethod, stochastic methods based on search algorithms have shown good results\ndue to its smaller susceptibility to be trapped in a local minimum. Besides\nthat, they can be easily implemented to work with other techniques In this\nalgorithms class, the genetic ones have received special attention because they\nare a robust optimization tool. An algorithm can be named genetic when it uses\nsome kind of codification to transform a set of possible solutions of a given\nproblem in a population that will evolve subject to operators inspired, or not,\nby mechanisms of natural selection. In other words, they work with a population\nof solutions to obtain better solutions in the next generation. To do this,\nthey use only information of cost and prize. In this work, we propose a genetic\nalgorithm optimization technique (GAOT) to fit diatomic potential energy\ncurves.In order to show this method, we obtain the analytical functions of the\nH2+ and Li2 systems using the ab initio energy calculations as well as Rydberg\ntrial function. These studies show that the quality of the GAOT fitting is\ncomparable to the best optimization techniques recommended to fit diatomic\nsystems. The introduction of this new technique is important because it arises\nas a new option to fit PES for reactive scattering dynamics.", "category": "physics_chem-ph" }, { "text": "Rotation in liquid $^4$He: Lessons from a toy model: This paper presents an analysis of a model problem, consisting of two\ninteracting rigid rings, for the rotation of molecules in liquid $^4$He. Due to\nBose symmetry, the excitation of the rotor corresponding to a ring of N helium\natoms is restricted to states with integer multiples of N quanta of angular\nmomentum. This minimal model shares many of the same features of the rotational\nspectra that have been observed for molecules in nanodroplets of $\\approx 10^3\n- 10^4$ helium atoms. In particular, this model predicts, for the first time,\nthe very large enhancement of the centrifugal distortion constants that have\nbeen observed experimentally. It also illustrates the different effects of\nincreasing rotational velocity by increases in angular momentum quantum number\nor by increasing the rotational constant of the molecular rotor. It is found\nthat fixed node, diffusion Monte Carlo and a hydrodynamic model provide upper\nand lower bounds on the size of the effective rotational constant of the\nmolecular rotor when coupled to the helium.", "category": "physics_chem-ph" }, { "text": "Efficient computational methods for rovibrational transition rates in\n molecular collisions: Astrophysical modeling of processes in environments that are not in local\nthermal equilibrium requires the knowledge of state-to-state rate coefficients\nof rovibrational transitions in molecular collisions. These rate coefficients\ncan be obtained from coupled-channel (CC) quantum scattering calculations which\nare very demanding, however. Here we present various approximate, but more\nefficient methods based on the coupled-states approximation (CSA) which\nneglects the off-diagonal Coriolis coupling in the scattering Hamiltonian in\nbody-fixed coordinates. In particular, we investigated a method called NNCC\n(nearest-neighbor Coriolis coupling) [D. Yang, X. Hu, D. H. Zhang, and D. Xie,\nJ. Chem. Phys. 148, 084101 (2018)] that includes Coriolis coupling to first\norder. The NNCC method is more demanding than the common CSA method, but still\nmuch more efficient than full CC calculations, and it is substantially more\naccurate than CSA. All of this is illustrated by showing state-to-state cross\nsections and rate coefficients of rovibrational transitions induced in CO$_2$\nby collisions with He atoms. It is also shown that a further reduction of CPU\ntime, practically without loss of accuracy, can be obtained by combining the\nNNCC method with the multi-channel distorted-wave Born approximation (MC-DWBA)\nthat we applied in full CC calculations in a previous paper.", "category": "physics_chem-ph" }, { "text": "Derivation of time-dependent transition probability for\n $2\\mathrm{e}-2\\mathrm{h}$ generation from $1\\mathrm{e}-1\\mathrm{h}$ state in\n the presence of external electromagnetic field: In this work, we investigate the effect of electromagnetic (EM) field on the\ngeneration of 2e-2h states from 1e-2h states. One of the fundamental ways by\nwhich electromagnetic (EM) waves interact with matter is by the generation of\nexcited electronic states. The interaction of EM field with atoms and molecules\nis given by the field-dependent Hamiltonian. Excited states are intrinsically\ntransient in nature because they are not stationary states of the\nfield-dependent Hamiltonian. Consequently, the time-dependent dynamics of\nexcited states depend strongly on the external electromagnetic field. Starting\nwith the 1e-1h excitation in a general many-electron system, the system was\npropagated in time using time-dependent perturbation theory (TDPT). The\nexpression for time-dependent transition probability of\n$(1\\mathrm{e}-1\\mathrm{h}) \\rightarrow (2\\mathrm{e}-2\\mathrm{h})$ was evaluated\nfor a given time $t$ up to second-order in TDPT using diagrammatic techniques.\nThe derivation does not assume any a priori approximations to the\nelectron-electron correlation operator and presents the derivation of a\ncomplete set of contributing diagrams associated with the full configuration\ninteraction wave function. The result from this work show that the calculation\nof time-dependent transition probability can be factored into a\ntime-independent and time-dependent components. This is a significant outcome\nfor efficient computation of the time-dependent transition probability because\nit allows for pre-computation of time-independent components before the start\nof the calculations.", "category": "physics_chem-ph" }, { "text": "Theory of fluid slip in charged capillary nanopores: Based on the capillary pore model (space-charge theory) for combined fluid\nand ion flow through cylindrical nanopores or nanotubes, we derive the\ncontinuum equations modified to include wall slip. We focus on the ionic\nconductance and streaming conductance, cross-coefficients of relevance for\nelectrokinetic energy conversion and electro-osmotic pumping. We combine the\ntheory with a Langmuir-Stern 1-pK charge regulation boundary condition\nresulting in a non-monotonic dependence of the cross-coefficients on salt\nconcentration.", "category": "physics_chem-ph" }, { "text": "Ab initio calculation of real solids via neural network ansatz: Neural networks have been applied to tackle many-body electron correlations\nfor small molecules and physical models in recent years. Here we propose a new\narchitecture that extends molecular neural networks with the inclusion of\nperiodic boundary conditions to enable ab initio calculation of real solids.\nThe accuracy of our approach is demonstrated in four different types of\nsystems, namely the one-dimensional periodic hydrogen chain, the\ntwo-dimensional graphene, the three-dimensional lithium hydride crystal, and\nthe homogeneous electron gas, where the obtained results, e.g. total energies,\ndissociation curves, and cohesive energies, outperform many traditional ab\ninitio methods and reach the level of the most accurate approaches. Moreover,\nelectron densities of typical systems are also calculated to provide physical\nintuition of various solids. Our method of extending a molecular neural network\nto periodic systems can be easily integrated into other neural network\nstructures, highlighting a promising future of ab initio solution of more\ncomplex solid systems using neural network ansatz, and more generally endorsing\nthe application of machine learning in materials simulation and condensed\nmatter physics.", "category": "physics_chem-ph" }, { "text": "Chemical reactions in imperfect cavities: enhancement, suppression, and\n resonance: The use of optical cavities to control chemical reactions has been of great\ninterest recently, following demonstrations of enhancement, suppression, and\nnegligible effects on chemical reaction rates depending on the specific\nreaction and cavity frequency. In this work, we study the reaction rate inside\nimperfect cavities, where we introduce a broadening parameter in the spectral\ndensity to mimic Fabry-P\\'erot cavities. We investigate cavity modifications to\nreaction rates using non-Markovian Langevin dynamics with frictional and random\nforces to account for the presence of imperfect optical cavities. We\ndemonstrate that in the regime of weak solvent and cavity friction, the cavity\ncan enhance chemical reaction rates. On the other hand, in the high friction\nregime, cavities can suppress chemical reactions. Furthermore, we find that the\nbroadening of the cavity spectral density gives rise to blue shifts of the\nresonance conditions and, surprisingly, increases the sharpness of the\nresonance effect.", "category": "physics_chem-ph" }, { "text": "Triangle Counting Rule: An Approach to Forecast the Magnetic Properties\n of Benzenoid Polycyclic Hydrocarbons: Open-shell benzenoid polycyclic hydrocarbons (BPHs) are promising materials\nfor future quantum applications. However, the search and realization of\nopen-shell BPHs with desired properties is a challenging task due to the\ngigantic chemical space of BPHs, requiring new strategies for both theoretical\nunderstanding and experimental advancement. In this work, by building a\nstructure database of BPHs through graphical enumeration, performing\ndata-driven analysis, and combining tight-binding and mean-field Hubbard\ncalculations, we discovered that the number of the internal vertices of the BPH\ngraphs is closely correlated to their open-shell characters. We further\nestablished a series of simple rules, the triangle counting rule (TCR), to\npredict the magnetic ground state of BPHs. These findings not only provide a\ndatabase of open-shell BPHs, but also extend the well-known Lieb's theorem and\nOvchinnikov's rule and provide a straightforward method for designing\nopen-shell carbon nanostructures. These insights may aid in the exploration of\nemerging quantum phases and the development of magnetic carbon materials for\ntechnology applications.", "category": "physics_chem-ph" }, { "text": "A nonorthogonal state-interaction approach for matrix product state wave\n functions: We present a state-interaction approach for matrix product state (MPS) wave\nfunctions in a nonorthogonal molecular orbital basis. Our approach allows us to\ncalculate for example transition and spin-orbit coupling matrix elements\nbetween arbitrary electronic states provided that they share the same\none-electron basis functions and active orbital space, respectively. The key\nelement is the transformation of the MPS wave functions of different states\nfrom a nonorthogonal to a biorthonormal molecular orbital basis representation\nexploiting a sequence of non-unitary transformations following a proposal by\nMalmqvist (Int. J. Quantum Chem. 30, 479 (1986)). This is well-known for\ntraditional wave-function parametrizations but has not yet been exploited for\nMPS wave functions.", "category": "physics_chem-ph" }, { "text": "Black Magic in Gray Titania: Noble-Metal-Free Photocatalytic H2\n Evolution from Hydrogenated Anatase: \"Black\" TiO2 has gained increasing interest because of its outstanding\nproperties and promising applications in a wide range of fields. Among the\noutstanding features of the material is that certain synthesis processes lead\nto the formation of an intrinsic co-catalytic center and thus enable\nnoble-metal free photocatalytic H2 generation. In this work, we report \"grey\nTiO2\" by an appropriate hydrogenation treatment exhibits excellent\nphotocatalytic hydrogen. In this case, by the employment of thermally stable\nand high-surface-area TiO2 nanoparticles as well as mesoporous particles as the\nhydrogenation precursor, the appropriate extent of reduction of TiO2\n(coloration) and the formation of Ti3+ is the key for the efficient\nnoble-metal-free photocatalytic H2 generation. The EPR results reveal that\n\"grey TiO2\" shows stronger Ti3+ feature at g ca. 1.93 than \"black TiO2\"\ncontributing to the intrinsic catalytic center for H2 evolution.", "category": "physics_chem-ph" }, { "text": "Investigation of methane adsorption and its effect on gas transport in\n shale matrix through microscale and mesoscale simulations: Methane adsorption and its effect on fluid flow in shale matrix are\ninvestigated through multi-scale simulation scheme by using molecular dynamics\n(MD) and lattice Boltzmann (LB) methods. Equilibrium MD simulations are\nconducted to study methane adsorption on the organic and inorganic walls of\nnanopores in shale matrix with different pore sizes and pressures. Density and\npressure distributions within the adsorbed layer and the free gas region are\ndiscussed. The illumination of the MD results on larger scale LB simulations is\npresented. Pressure-dependent thickness of adsorbed layer should be adopted and\nthe transport of adsorbed layer should be properly considered in LB\nsimulations. LB simulations, which are based on a generalized Navier-Stokes\nequation for flow through low-permeability porous media with slippage, are\nconducted by taking into consideration the effects of adsorbed layer. It is\nfound that competitive effects of slippage and adsorbed layer exist on the\npermeability of shale matrix, leading to different changing trends of the\napparent permeability.", "category": "physics_chem-ph" }, { "text": "On the thermodynamical analogy in spin-polarized density functional\n theory: The thermodynamical analogy of density functional theory, which is an organic\npart of the spin-independent version of the theory, is reconsidered for its\nspin-polarized generalization in view of the recently uncovered nonuniqueness\nof the external magnetic field B(r) corresponding to a given pair of density\nn(r) and spin density n_s(r). For ground states, the nonuniqueness of B(r)\nimplies the nondifferentiability of the energy functional E[n,n_s] with respect\nto n_s(r). It is shown, on the other hand, that this nonuniqueness allows the\nexistence of the one-sided derivatives of E[n,n_s] with respect to n_s(r).\nAlthough the N-electron ground state can always be obtained from the\nminimization of E[n,n_s] without any constraint on the spin number N_s, the\nLagrange multiplier mu_s associated with the fixation of N_s does not vanish\neven for ground states. Rather, mu_s is identified as the left- or right-side\nderivative of the total energy with respect to N_s. This justifies the\ninterpretation of mu_s as a (spin) chemical potential, which is the cornerstone\nof the thermodynamical analogy.", "category": "physics_chem-ph" }, { "text": "Autobiography of Yoshitaka Tanimura: In this paper, two developments, the theory of hierarchical equations of\nmotion (HEOM) for open quantum dynamics systems and the theory of ultrafast\nnonlinear two-dimensional (2D) spectroscopies, are described, following the\nhistory of their founder. The HEOM was discovered by attempting to derive an\nequation similar to Kuob's stochastic Liouville equation based on the\nsystem-bath Hamiltonian. The theory of 2D spectroscopy was developed in the\nprocess of investigating the effect of quantum coherence on nonlinear\nvibrational spectra based on the Feynman-Vernon influence functional. The paper\nalso describes the development of these two theories for problems such as\nelectron and exciton transfer in photosynthetic systems, quantum statistical\nthermodynamics, and solid-state physics.", "category": "physics_chem-ph" }, { "text": "Analytic treatment of IR-spectroscopy data for double well potential: A theoretical scheme for the analysis of experimental data on IR spectroscopy\nfor a quantum particle in a double well potential (DWP) is suggested. The\nanalysis is based on the trigonometric DWP for which the exact analytic\nsolution of the Schr\\\"odinger equation is available. The corresponding energy\nlevels along with their wave functions are expressed via special functions\nimplemented in {\\sl {Mathematica}} (spheroidal function and its spectrum of\neigenvalues). As a result trigonometric DWP makes the calculation of the energy\nlevels an extremely easy procedure. It contains three parameters allowing one\nto model the most important characteristics of DWP (barrier height and the\ndistance between the minima of the potential) along with the required\nasymmetry. Our approach provides an accurate calculation of the energy spectrum\nfor hydrogen bonds in chromous acid (CrOOH) and potassium dihydrogen phosphate\n(${\\rm{KH_2PO_4}}$) along with their polarizability in agreement with available\nexperimental data.", "category": "physics_chem-ph" }, { "text": "A definitive heat of vaporization of silicon through benchmark ab initio\n calculations on SiF_4: In order to resolve a significant uncertainty in the heat of vaporization of\nsilicon -- a fundamental parameter in gas-phase thermochemistry -- $\\Delta\nH^\\circ_{f,0}$[Si(g)] has been determined from a thermochemical cycle involving\nthe precisely known experimental heats of formation of SiF_4(g) and F(g) and a\nbenchmark calculation of the total atomization energy (TAE_0) of SiF_4 using\ncoupled-cluster methods. Basis sets up to $[8s7p6d4f2g1h]$ on Si and\n$[7s6p5d4f3g2h]$ on F have been employed, and extrapolations for residual basis\nset incompleteness applied. The contributions of inner-shell correlation (-0.08\nkcal/mol), scalar relativistic effects (-1.88 kcal/mol), atomic spin-orbit\nsplitting (-1.97 kcal/mol), and anharmonicity in the zero-point energy (+0.04\nkcal/mol) have all been explicitly accounted for. Our benchmark TAE_0=565.89\n\\pm 0.22 kcal/mol leads to $\\Delta H^\\circ_{f,0}$[Si(g)]=107.15 \\pm 0.38\nkcal/mol ($\\Delta H^\\circ_{f,298}$[Si(g)]=108.19 \\pm 0.38 kcal/mol): between\nthe JANAF/CODATA value of 106.5 \\pm 1.9 kcal/mol and the revised value proposed\nby Grev and Schaefer [J. Chem. Phys. 97, 8389 (1992}], 108.1 \\pm 0.5 kcal/mol.\nThe revision will be relevant for future computational studies on heats of\nformation of silicon compounds.", "category": "physics_chem-ph" }, { "text": "On the importance of experimental details: A Comment on \"Non-Polaritonic\n Effects in Cavity-Modified Photochemistry\": Recently, an article by the Barnes group reported on the experimental study\nof a photoisomerization reaction inside an optical cavity, claiming to\nreproduce previous results by Hutchison et al. and making the point that in\nsuch setups, changes in the absorption of ultraviolet radiation by the\nmolecules in the cavity can lead to modifications in the photochemical reaction\nrate. While Hutchison et al. associated such modifications with the emergence\nof strong light-matter coupling, in their attempt to re-examine these\nexperiments, Barnes et al. did not find any evidence that strong coupling needs\nto be invoked to explain the observed effects. In response to this publication,\nwe herein highlight the main differences between the two experimental studies,\nand explain why the results of Barnes et al. are irrelevant to the former study\nand have no bearing on its conclusions. Specifically, we show that under the\nexperimental conditions used by Hutchison et al. such intensity-modification\neffects are negligible and can therefore be ruled out.", "category": "physics_chem-ph" }, { "text": "Using a multistate Mapping Approach to Surface Hopping to predict the\n Ultrafast Electron Diffraction signal of gas-phase cyclobutanone: Using the recently developed multistate mapping approach to surface hopping\n(multistate MASH) method combined with SA(3)-CASSCF(12,12)/aug-cc-pVDZ\nelectronic structure calculations, the gas-phase isotropic ultrafast electron\ndiffraction (UED) of cyclobutanone is predicted and analyzed. After excitation\ninto the n-3s Rydberg state (S$_2$), cyclobutanone can relax through two\nS$_2$/S$_1$ conical intersections, one characterized by compression of the\n\\ce{CO} bond, the other by dissociation of the $\\mathrm{\\alpha}$-CC bond.\nSubsequent transfer into the ground state (S$_0$) is then achieved via two\nadditional S$_1$/S$_0$ conical intersections that lead to three reaction\npathways: $\\mathrm{\\alpha}$ ring-opening, ethene/ketene production, and \\ce{CO}\nliberation. The isotropic gas-phase UED signal is predicted from the multistate\nMASH simulations, allowing for a direct comparison to experimental data. This\nwork, which is a contribution to the cyclobutanone prediction challenge,\nfacilitates the identification of the main photoproducts in the UED signal and\nthereby emphasizes the importance of dynamics simulations for the\ninterpretation of ultrafast experiments.", "category": "physics_chem-ph" }, { "text": "Free energy along drug-protein binding pathways interactively sampled in\n virtual reality: We describe a two-step approach for combining interactive molecular dynamics\nin virtual reality (iMD-VR) with free energy (FE) calculation to explore the\ndynamics of biological processes at the molecular level. We refer to this\ncombined approach as iMD-VR-FE. Stage one involves using a state-of-the-art\niMD-VR framework to generate a diverse range of protein-ligand unbinding\npathways, benefitting from the sophistication of human spatial and chemical\nintuition. Stage two involves using the iMD-VR-sampled pathways as initial\nguesses for defining a path-based reaction coordinate from which we can obtain\na corresponding free energy profile using FE methods. To investigate the\nperformance of the method, we apply iMD-VR-FE to investigate the unbinding of a\nbenzamidine ligand from a trypsin protein. The binding free energy calculated\nusing iMD-VR-FE is similar for each pathway, indicating internal consistency.\nMoreover, the resulting free energy profiles can distinguish energetic\ndifferences between pathways corresponding to various protein-ligand\nconformations (e.g., helping to identify pathways that are more favourable) and\nenable identification of metastable states along the pathways. The two-step\niMD-VR-FE approach offers an intuitive way for researchers to test hypotheses\nfor candidate pathways in biomolecular systems, quickly obtaining both\nqualitative and quantitative insight.", "category": "physics_chem-ph" }, { "text": "Relativistic coupled-cluster study of BaF in search of $\\mathcal{CP}$\n violation: BaF is one of the potential candidates for the experimental search of the\nelectric dipole moment of the electron (eEDM). The NL-eEDM collaboration is\nbuilding a new experimental set up to measure the eEDM using the BaF molecule\n[The NL-eEDM collaboration, Eur. Phys. J. D (2018) 72: 197]. To analyze the\nresults of such an experiment, one would require the accurate value of the\nmolecular ${\\mathcal{P,T}}$-odd interaction parameters that cannot be measured\nfrom any experiment. In this work, we report the precise value of the\n${\\mathcal{P,T}}$-odd interaction parameters of the BaF molecule obtained from\nthe four-component relativistic coupled-cluster calculations. We also calculate\nthe hyperfine structure (HFS) constants of the same molecule to assess the\nreliability of the reported molecular parameters. The calculated HFS constants\nshow good agreement with the available experimental values. Further, the\nsystematic effects of electron-correlation along with the roles of inner-core\nelectrons and the virtual energy functions in the calculation of the studied\nproperties of BaF are investigated.", "category": "physics_chem-ph" }, { "text": "Chemical bonding in americium oxides: x-ray spectroscopic view: The electronic structure and the chemical state in Am binary oxides and\nAm-doped UO$_2$ were studied by means of x-ray absorption spectroscopy at\nshallow Am core ($4d$ and $5d$) edges. In particular, the Am $5f$ states were\nprobed and the nature of their bonding to the oxygen states was analyzed. The\ninterpretation of the experimental data was supported by the Anderson impurity\nmodel (AIM) calculations which took into account the full multiplet structure\ndue to the interaction between $5f$ electrons as well as the interaction with\nthe core hole. The sensitivity of the branching ratio of the Am $4d_{3/2}$ and\n$4d_{5/2}$ x-ray absorption lines to the chemical state of Am was shown using\nAm binary oxides as reference systems. The observed ratio for Am-doped UO$_2$\nsuggests that at least at low Am concentrations, americium is in the Am(III)\nstate in the UO$_2$ lattice. To confirm the validity of the applied AIM\napproach, the analysis of the Am $4f$ x-ray photoelectron spectra of AmO$_2$\nand Am$_2$O$_3$ was also performed which revealed a good agreement between\nexperiment and calculations. As a whole, AmO$_2$ can be classified as the\ncharge-transfer compound with the $5f$ occupancy ($n_f$) equal to 5.73\nelectrons, while Am$_2$O$_3$ is rather a Mott-Hubbard system with $n_f$=6.05.", "category": "physics_chem-ph" }, { "text": "Fully quantum non-adiabatic dynamics in electronic-nuclear coherent\n state basis: Direct dynamics methods using Gaussian wavepackets have to rely only on local\nproperties, such as gradients and hessians at the center of the wavepacket, so\nas to be compatible with the usual quantum chemistry methods. Matrix elements\nof the potential energy surfaces between wavepackets therefore usually have to\nbe approximated.\n It is shown, that if a modified form of valence bond theory is used instead\nof the usual MO-based theories, the matrix elements can be obtained exactly.\nThis is so because the molecular Hamiltonian only contains the Coulomb\npotential, for which matrix elements between different basis functions\n(consisting of Gaussian nuclear and electronic orbitals) are all well-known. In\nvalence bond theory the self-consistent field calculation can be avoided so\nthat the matrix elements are analytical functions of the nuclear coordinates.\n A method for simulating non-adiabatic quantum dynamics is sketched, where\ncoherent state trajectories are propagated \"on the fly\" on adiabatic potential\nenergy surfaces without making approximations to the matrix elements\nresponsible for the coupling between trajectories.", "category": "physics_chem-ph" }, { "text": "The Tip-Induced Twisted Bilayer Graphene Superlattice on HOPG: Capillary\n Attraction Effect: We use the tip of the scanning tunneling microscope (STM) to manipulate\nsingle weakly bound nanometer-sized sheets on the the highly oriented pyrolytic\ngraphite (HOPG) surface through artifically increasing the tip and sample\ninteraction in humid environment. By this means it is possible to tear apart a\ngraphite sheet againt a step and fold this part onto the HOPG surface and thus\ngenerate the gaphene superlattices with hexagonal symmetry. The tip and sample\nsurface interactions, including the van der Waals force, eletrostatic force and\ncapillary attraction force originating from the Laplace pressure due to the\nformation of a highly curved fluid meniscus connecting the tip and sample, are\ndiscussed in details to understand the fromation mechnism of graphen\nsuperlattice induced by the STM tip. Especially, the capillary force is the key\nrole in manipulating the graphite surface sheet in the hunmidity condition. Our\napproach may provides a simple and feasible route to prepare the controllable\nsuperlattices and graphene nanoribbons but also replenish and find down the\ntheory of generation of graphene superlattice on HOPG surface by the tip.", "category": "physics_chem-ph" }, { "text": "From Peptides to Nanostructures: A Euclidean Transformer for Fast and\n Stable Machine Learned Force Fields: Recent years have seen vast progress in the development of machine learned\nforce fields (MLFFs) based on ab-initio reference calculations. Despite\nachieving low test errors, the reliability of MLFFs in molecular dynamics (MD)\nsimulations is facing growing scrutiny due to concerns about instability over\nextended simulation timescales. Our findings suggest a potential connection\nbetween robustness to cumulative inaccuracies and the use of equivariant\nrepresentations in MLFFs, but the computational cost associated with these\nrepresentations can limit this advantage in practice. To address this, we\npropose a transformer architecture called SO3krates that combines sparse\nequivariant representations (Euclidean variables) with a self-attention\nmechanism that separates invariant and equivariant information, eliminating the\nneed for expensive tensor products. SO3krates achieves a unique combination of\naccuracy, stability, and speed that enables insightful analysis of quantum\nproperties of matter on extended time and system size scales. To showcase this\ncapability, we generate stable MD trajectories for flexible peptides and\nsupra-molecular structures with hundreds of atoms. Furthermore, we investigate\nthe PES topology for medium-sized chainlike molecules (e.g., small peptides) by\nexploring thousands of minima. Remarkably, SO3krates demonstrates the ability\nto strike a balance between the conflicting demands of stability and the\nemergence of new minimum-energy conformations beyond the training data, which\nis crucial for realistic exploration tasks in the field of biochemistry.", "category": "physics_chem-ph" }, { "text": "Iontronic microscopy of a tungsten microelectrode: \"seeing\" ionic\n currents under an optical microscope: Optical methods for monitoring the electrochemical reaction at the interface\nare advantageous because of their table-top setup and ease of integration into\nreactors. Here we apply EDL-modulation microscopy to one of the main components\nof amperometric measurement devices: a microelectrode. We present experimental\nmeasurements of the EDL-modulation contrast from the tip of a tungsten\nmicroelectrode at various electrochemical potentials inside a\nferrocene-dimethanol \\ch{Fe(MeOH)2} solution. By the combination of the\ndark-field scattering microscope and the lock-in detection technique, we\nmeasure the phase and amplitude of local ion-concentration oscillations in\nresponse to an AC potential as the electrode potential is scanned through the\nredox-activity window of the dissolved species. We present the amplitude and\nphase map of this response As such, this method can be used to study the\nspatial and temporal variations of the ion-flux due to an electrochemical\nreaction close to metallic and semiconducting objects of general geometry. We\ndiscuss the advantages and possible extensions of using this microscopy method\nfor wide-field imaging of ionic currents.", "category": "physics_chem-ph" }, { "text": "Nanoscale Patterning of Surface Nanobubbles: Surface nanobubbles forming on hydrophobic surfaces in water present an\nexciting opportunity as potential agents of top-down, bottom-up nanopatterning.\nThe formation and characteristics of surface nanobubbles are strongly\ninfluenced by the physical and chemical properties of the substrate. In this\nstudy, focused ion beam (FIB) milling is used for the first time to spatially\ncontrol the nucleation of surface nanobubbles with 75 nm precision. The\nspontaneous formation of nanobubbles on alternating lines of a self-assembled\nmonolayer (octadecyl trichlorosilane) patterned by FIB is detected by atomic\nforce microscopy. The effect of chemical vs. topographical surface\nheterogeneity on the formation of nanobubbles is investigated by comparing\nsamples with OTS coating applied pre- vs. post-FIB patterning. The results\nconfirm that nanoscale FIB-based patterning can effectively control surface\nnanobubble position by means of chemical heterogeneity. The effect of FIB\nmilling on nanobubble morphology and properties, including contact angle and\ngas oversaturation, is also reported. Molecular dynamics simulations provide\nfurther insight into the effects of FIB amorphization on surface nanobubble\nformation. Combined, experimental and simulation investigations offer insights\nto guide future nanobubble-based patterning using FIB milling.", "category": "physics_chem-ph" }, { "text": "Coulomb explosion imaging of concurrent CH$_{2}$BrI photodissociation\n dynamics: The dynamics following laser-induced molecular photodissociation of gas-phase\nCH$_{2}$BrI at 271.6 nm were investigated by time-resolved Coulomb explosion\nimaging using intense near-IR femtosecond laser pulses. The observed\ndelay-dependent photofragment momenta reveal that CH$_{2}$BrI undergoes C-I\ncleavage, depositing 65.6% of the available energy into internal product\nstates, and that absorption of a second UV photon breaks the C-Br bond of\nCH$_{2}$Br. Simulations confirm that this mechanism is consistent with previous\ndata recorded at 248 nm, demonstrating the sensitivity of Coulomb explosion\nimaging as a real-time probe of chemical dynamics.", "category": "physics_chem-ph" }, { "text": "On the optimal basis set for electron dynamics in strong laser fields:\n The case of molecular ion H$^{+}_2$: A clear understanding of the mechanisms that control the electron dynamics in\nstrong laser field is still a challenge that requires to be interpreted by\nadvanced theory. Development of accurate theoretical and computational methods,\nable to provide a precise treatment of the fundamental processes generated in\nthe strong field regime, is therefore crucial. A central aspect is the choice\nof the basis for the wave-function expansion. Accuracy in describing\nmultiphoton processes is strictly related to the intrinsic properties of the\nbasis, such as numerical convergence, computational cost, and representation of\nthe continuum. By explicitly solving the 1D and 3D time-dependent Schr\\\"odinger\nequation for H$^{+}_{2}$ in presence of an intense electric field, we explore\nthe numerical performance of using a real-space grid, a B-spline basis, and a\nGaussian basis (improved by optimal Gaussian functions for the continuum). We\nanalyze the performance of the three bases for high-harmonic generation and\nabove-threshold ionization for H$^{+}_{2}$. In particular, for high-harmonic\ngeneration, the capability of the basis to reproduce the two-center\ninterference and the hyper-Raman phenomena is investigated.", "category": "physics_chem-ph" }, { "text": "Ab initio calculations to support accurate modelling of the rovibronic\n spectroscopy calculations of vanadium monoxide (VO): Accurate knowledge of the rovibronic near-infrared and visible spectra of\nvanadium monoxide (VO) is very important for studies of cool stellar and hot\nplanetary atmospheres. Here, the required ab initio dipole moment and\nspin-orbit coupling curves for VO are produced. This data forms the basis of a\nnew VO line list considering 13 different electronic states and containing over\n277 million transitions. Open shell transition, metal diatomics are challenging\nspecies to model through ab initio quantum mechanics due to the large number of\nlow-lying electronic states, significant spin-orbit coupling and strong static\nand dynamic electron correlation. Multi-reference configuration interaction\nmethodologies using orbitals from a complete active space self-consistent-field\n(CASSCF) calculation are the standard technique for these systems. We use\ndifferent state-specific or minimal-state CASSCF orbitals for each electronic\nstate to maximise the calculation accuracy. The off-diagonal dipole moment\ncontrols the intensity of electronic transitions. We test finite-field\noff-diagonal dipole moments, but found that (1) the accuracy of the excitation\nenergies were not sufficient to allow accurate dipole moments to be evaluated\nand (2) computer time requirements for perpendicular transitions were\nprohibitive. The best off-diagonal dipole moments are calculated using\nwavefunctions with different CASSCF orbitals.", "category": "physics_chem-ph" }, { "text": "Simulating core electron binding energies of halogenated species\n adsorbed on ice surfaces and in solution with relativistic quantum embedding\n calculations: In this work we investigate the effects of the environment on the X-ray\nphotoelectron spectra of hydrogen chloride and the chloride ions adsorbed on\nice surfaces, as well as of chloride ions in water droplets. In our approach,\nwe combine a density functional theory (DFT) description of the ice surface\nwith that of the halogen species with the recently developed relativistic\ncore-valence separation equation of motion coupled cluster (CVS-EOM-IP-CCSD)\nvia the frozen density embedding formalism (FDE), to determine the K and\nL$_{1,2,3}$ edges of chlorine. Our calculations, which incorporate temperature\neffects through snapshots from classical molecular dynamics simulations, are\nshown to reproduce experimental trends in the change of the core binding\nenergies for Cl$^-$ upon moving from a liquid (water droplets) to an\ninterfacial (ice quasi-liquid layer) environment. Our simulations yield water\nvalence band binding energies in good agreement with experiment, and that vary\nlittle between the droplets and the ice surface. For the halide core binding\nenergies there is an overall trend of overestimating experimental values,\nthough good agreement between theory and experiment is found for Cl$^-$ in\nwater droplets and on ice. For HCl on the other hand there are significant\ndiscrepancies between experimental and calculated core binding energies when we\nconsider structural models which maintain the H-Cl bond more or less intact. An\nanalysis of models that allow for pre-dissociated and dissociated structures\nsuggests that experimentally observed chemical shifts in binding energies\nbetween Cl$^-$ snd HCl would reqire that H$^+$ (in the form of H$_3$O$^+$) and\nCl$^-$ are separated by roughly 4-6 A.", "category": "physics_chem-ph" }, { "text": "Electron--impact resonant vibration excitation cross sections and rate\n coefficients for carbon monoxide: Resonant vibrational and rotation-vibration excitation cross sections for\nelectron-CO scattering are calculated in the 0-10 eV energy range for all 81\nvibrational states of CO, assuming that the excitation occur via the 2{\\Pi}\nshape resonance. Static exchange plus polarization calculations performed using\nthe R-matrix method are used to estimate resonance positions and widths as\nfunctions of internuclear separation. The effects of nuclear motion are\nconsidered using a local complex potential model. Good agreement is obtained\nwith available experimental data on excitation from the vibrational ground\nstate. Excitation rates and cross sections are provided as a functions of the\ninitial CO vibrational state for all ground state vibrational levels.", "category": "physics_chem-ph" }, { "text": "Natural-orbital representation of molecular electronic transitions: This paper aims at introducing the formal foundations of the application of\nreduced density-matrix theory and Green's function theory to the analysis of\nmolecular electronic transitions. For this sake, their mechanics, applied to\nspecific objects containing information related to the passage and the\ninterference between electronic states - the difference and the transition\ndensity operators - are rigorously introduced in a self-contained way. After\nreducing the corresponding $N$-body operators (where $N$ is the number of\nelectrons in the system) using an operator partial-trace procedure, we derive\nthe kernel of the reduced one-body difference and transition density operators,\nas well as the matrix representation of these operators in a finite-dimensional\none-particle-state basis. These derivations are done in first and second\nquantization for the sake of completeness - the two formulations are\nequivalently present in the literature - and because second quantization is\nextensively used in a second part of the paper. Natural orbitals are introduced\nas appropriate bases for reducing the dimensionality of the problem and the\ncomplexity of the analysis of the transition phenomenon. Natural-orbital\nrepresentation of density operators are often used as a tool to characterize\nthe nature of molecular electronic transitions, so we suggest with this\ncontribution to revisit their theoretical foundations in order to better\nunderstand the origin and nature of these tools.", "category": "physics_chem-ph" }, { "text": "Taking the Heat Off of Plasmonic Chemistry: Several chemical reactions catalyzed by plasmonic nanoparticles show enhanced\nrates under visible-light-excitation of the localized surface plasmon resonance\nof the nanoparticles. But it has been argued that there is an associated\nphotothermal effect that can complicate the analysis and/or interpretation of\nthe nature of the role played by plasmon excitation. This Viewpoint discusses\nthis dilemma and provides some best practices for accounting for photothermal\ncontributions in plasmon-excitation-driven chemistry. A classification of\nplasmonic chemistry into plasmonic photocatalysis and plasmonic photosynthesis\nis also proposed. It is argued that photosynthetic reactions, which require a\nGibb's free energy input, constitute an ultimate test of the non-thermal,\nphotochemical action of plasmon excitation.", "category": "physics_chem-ph" }, { "text": "Chemical Environment Adaptive Learning for Optical Band Gap Prediction\n of Doped Graphitic Carbon Nitride Nanosheets: This study presents a novel Machine Learning Algorithm, named Chemical\nEnvironment Graph Neural Network (ChemGNN), designed to accelerate materials\nproperty prediction and advance new materials discovery. Graphitic carbon\nnitride (g-C3N4) and its doped variants have gained significant interest for\ntheir potential as optical materials. Accurate prediction of their band gaps is\ncrucial for practical applications, however, traditional quantum simulation\nmethods are computationally expensive and challenging to explore the vast space\nof possible doped molecular structures. The proposed ChemGNN leverages the\nlearning ability of current graph neural networks (GNNs) to satisfactorily\ncapture the characteristics of atoms' local chemical environment underlying\ncomplex molecular structures. Our benchmark results demonstrate more than 100%\nimprovement in band gap prediction accuracy over existing GNNs on g-C3N4.\nFurthermore, the general ChemGNN model can precisely foresee band gaps of\nvarious doped g-C3N4 structures, making it a valuable tool for performing\nhigh-throughput prediction in materials design and development.", "category": "physics_chem-ph" }, { "text": "A Promising Intersection of Excited-State-Specific Methods from Quantum\n Chemistry and Quantum Monte Carlo: We present a discussion of recent progress in excited-state-specific quantum\nchemistry and quantum Monte Carlo alongside a demonstration of how a\ncombination of methods from these two fields can offer reliably accurate\nexcited state predictions across singly excited, doubly excited, and charge\ntransfer states. Both of these fields have seen important advances supporting\nexcited state simulation in recent years, including the introduction of more\neffective excited-state-specific optimization methods, improved handling of\ncomplicated wave function forms, and ways of explicitly balancing the quality\nof wave functions for ground and excited states. To emphasize the promise that\nexists at this intersection, we provide demonstrations using a combination of\nexcited-state-specific complete active space self-consistent field theory,\nselected configuration interaction, and state-specific variance minimization.\nThese demonstrations show that combining excited-state-specific quantum\nchemistry and variational Monte Carlo can be more reliably accurate than either\nequation of motion coupled cluster theory or multi-reference perturbation\ntheory, and that it can offer new clarity in cases where existing high-level\nmethods do not agree.", "category": "physics_chem-ph" }, { "text": "Mechanical effects of carboxymethylcellulose binder in hard carbon\n electrodes: Electrodes in sodium-ion batteries endure mechanical stress during production\nand application, which can damage these fragile coatings, causing performance\ninefficiencies and early failure. Binder material provides elasticity in\nelectrode composites to resist fracture, but evaluating the effectiveness of\nbinder is complicated by substrate dependency of these films, while\nconventional cell tests are beset by multiple electrochemical variables. This\nwork introduces a practical low-cost indentation test to determine the\nelasticity of hard carbon electrodes containing standard carboxymethylcellulose\nbinder. Using the proposed method, relative elastic moduli of hard carbon\nelectrodes were found to be 0.079 GPa (1% binder), 0.088 GPa (2% binder), 0.105\nGPa (3% binder) and 0.113 GPa (4% binder), which were validated using a\ncomputational model of film deflection to predict mechanical deformation under\nstress. Effects on the electrochemical performance of hard carbon anodes were\nalso demonstrated with impedance spectroscopy and galvanostatic cycling of\nsodium half-cells, revealing 8-9% higher capacity retention of anodes with 4%\nbinder compared with those containing 1% binder. These findings suggest binder\ncontent in hard carbon electrodes should be selected according to requirements\nfor both cycle life and film flexibility during cell manufacturing.", "category": "physics_chem-ph" }, { "text": "Compact and accurate chemical mechanism for methane pyrolysis with PAH\n growth: A reliable and compact chemical mechanism of gas-phase methane pyrolysis\nleading to formation of large polycyclic aromatic hydrocarbon (PAH) molecules\nhas been developed. This model is designed for studies of carbon nanostructure\nsynthesis such as carbon black and graphene flakes, including soot growth\nkinetics. Methane pyrolysis with carbon nanostructure synthesis is a two-stage\nprocess where conversion of CH4 to C2H2 precedes the growth of PAH molecules\nfrom acetylene. We present a single chemical mechanism that accurately\ndescribes both stages. We have constructed a compact and accurate chemical\nmechanism capable of modeling both stages of methane pyrolysis based on the ABF\nmechanism which was expanded with most prominent reaction pathways from the\nmechanism by Tao for small PAH molecules and HACA pathways for larger PAH\nmolecules, up to 37 aromatic rings. The resulting mechanism was validated\nthrough comparison to multiple available sets of experimental data. Good\nagreement with the experimental data for both processes was obtained.\nPerformance of the mechanism was tested for pyrolysis of methane-rich mixtures\nunder long residence times leading to abundant formation of PAH molecules. It\nis shown that the inclusion of larger PAH species (up to A37) in the chemical\nmechanism is important for accurate prediction of the fraction of carbon\nconverted to PAH molecules and, correspondingly, residual fraction of acetylene\nin the mixture.", "category": "physics_chem-ph" }, { "text": "The nonlocal dielectric response of water in nanoconfinement: Recent experiments reporting a very low dielectric permittivity for\nnanoconfined water have renewed the interest to the structure and dielectric\nproperties of water in narrow gaps. Here, we describe such systems with a\nminimal Landau-Ginzburg field-theory composed of a nonlocal bulk-determined\nterm and a local water-surface interaction term. We show how the interplay\nbetween the boundary conditions and intrinsic bulk correlations encodes\ndielectric properties of confined water. Our theoretical analysis is supported\nby molecular dynamics simulations and comparison with the experimental data.", "category": "physics_chem-ph" }, { "text": "Higher Derivative Muffin Tin Orbitals (HDMTO) and Higher Derivative\n Koringa Khon and Rostoker (HDKKR) methods: In this work we introduce a Linearized version of the Koringa Khon and\nRostoker method (LKKR) and show it to be equivalent to the Linearized Muffin\nTin Orbitals method (LMTO). We then present higher derivative versions of both\nmethods, e.g. HDKKR and HDMTO and show them to be partially distinct (not\nequivalent). In particular HDKKR basis set does not have an equivalent ground\nstate for the Khon Sham (KS) Hamiltonian as the HDKKR basis set and has greater\nvariational power than the HDMTO one. Because the KS method, for Density\nFunctional Theory (DFT), is variational HDKKR will give better ground state\nenergies than HDMTO. However HDKKR is much harder to work with then HDMTO\nrequiring much greater computer resources so HDMTO can often be preferred.", "category": "physics_chem-ph" }, { "text": "Evaluating continuum solvation models for the electrode-electrolyte\n interface: challenges and strategies for improvement: Ab initio modeling of electrochemical systems is becoming a key tool for\nunderstanding and predicting electrochemical behavior. Development and careful\nbenchmarking of computational electrochemical methods are essential to ensure\ntheir accuracy. Here, using charging curves for an electrode in the presence of\nan inert aqueous electrolyte, we demonstrate that most continuum models, which\nare parameterized and benchmarked for molecules, anions, and cations in\nsolution, undersolvate metal surfaces, and underestimate the surface charge as\na function of applied potential. We examine features of the electrolyte and\ninterface that are captured by these models, and identify improvements\nnecessary for realistic electrochemical calculations of metal surfaces.\nFinally, we reparameterize popular solvation models using the surface charge of\nAg(100) as a function of voltage to find improved accuracy for metal surfaces\nwithout significant change in utility for molecular and ionic solvation.", "category": "physics_chem-ph" }, { "text": "Quantification of classical and non-classical crystallization pathways\n in calcite precipitation: Crystal precipitation from aqueous solution occurs through multiple pathways.\nBesides the classical ion-by-ion addition, non-classical crystallization\nmechanisms, such as multi-ion polymer and nano-particle attachment, could be of\ngreat significance under certain circumstances. These non-classical\ncrystallization processes have been observed with advanced microscopy, yet\ndetailed quantification of their contribution in mineral precipitation remains\nchallenging. Building from paired Ca and Sr isotope observations, we develop a\nnew theoretical framework to quantify the relative contribution of classical\nand non-classical crystallization pathways on the precipitation of the calcium\ncarbonate mineral calcite, one of the most common precipitates in nature. We\ndemonstrate that the classical (ion-by-ion) crystallization pathway alone is\ninsufficient to account for the observed isotope behaviors and, thus, the\nentire calcite precipitation process. We present a new kinetic surface reaction\nmodel to incorporate the non-classical crystallization pathway. This new model,\nfor the first time, enables the detailed characterization of the roles of\nclassical and non-classical crystallization mechanisms in calcite\nprecipitation. The results suggest that the relative contribution of\nnon-classical crystallization pathways increases with saturation state and can,\nunder high supersaturation levels, be comparable to or greater than\nprecipitation driven by the classical crystallization pathway. The presented\ntheoretical framework readily explains observed trace element partitioning and\nisotope fractionation behaviors during calcite precipitation and can be further\nexpanded onto other mineral systems to gain insights into crystal growth\nmechanisms.", "category": "physics_chem-ph" }, { "text": "Dissolving salt is not equivalent to applying a pressure on water: Salt water is ubiquitous, playing crucial roles in geological and\nphysiological processes. Despite centuries of investigations, whether or not\nwater's structure is drastically changed by dissolved ions is still debated.\nBased on density functional theory, we employ machine learning based molecular\ndynamics to model sodium chloride, potassium chloride, and sodium bromide\nsolutions at different concentrations. The resulting reciprocal-space structure\nfactors agree quantitatively with neutron diffraction data. Here we provide\nclear evidence that the ions in salt water do not distort the structure of\nwater in the same way as neat water responds to elevated pressure. Rather, the\ncomputed structural changes are restricted to the ionic first solvation shells\nintruding into the hydrogen bond network, beyond which the oxygen\nradial-distribution function does not undergo major change relative to neat\nwater. Our findings suggest that the widely cited pressure-like effect on the\nsolvent in Hofmeister series ionic solutions should be carefully revisited.", "category": "physics_chem-ph" }, { "text": "Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic\n Training Protocol for Machine Learning Force Fields: In this study, we introduce a training protocol for developing machine\nlearning force fields (MLFFs), capable of accurately determining energy\nbarriers in catalytic reaction pathways. The protocol is validated on the\nextensively explored hydrogenation of carbon dioxide to methanol over indium\noxide. With the help of active learning, the final force field obtains energy\nbarriers within 0.05 eV of Density Functional Theory. Thanks to the\ncomputational speedup, not only do we reduce the cost of routine in-silico\ncatalytic tasks, but also find a 40\\% reduction in the previously established\nrate-limiting step. Furthermore, we illustrate the importance of\nfinite-temperature effects and compute free energy barriers. The\ntransferability of the protocol is demonstrated on the experimentally relevant,\nyet unexplored, top-layer reduced indium oxide surface. The ability of MLFFs to\nenhance our understanding of extensively studied catalysts underscores the need\nfor fast and accurate alternatives to direct ab-intio simulations.", "category": "physics_chem-ph" }, { "text": "Spherical-harmonic-analysis-based optimization of atomic weighting\n functions for multicenter numerical integration in molecules: The well-known spatial integration schemes in molecular electronic structure\ntheory, immune to cusps and point singularities of some kind at atomic\npositions, use a set of weighting functions to split the integrand into a sum\nof atom-centered parts, each dealt with in its own spherical coordinate system.\nHere, for a given set of integrands in the two-center case, a quality measure\nof the weighting functions is defined to compare, design, and optimize them, it\nis roughly proportional to the average number of angular quadrature points\nneeded to reach a given integration accuracy. A study of Becke's fuzzy\nVorono\\\"i cells has helped to improve their performance by a new modification.\nNew spherically-symmetric unnormalized weighting functions are found in the\nform of a negative power times the negative exponential of the fourth power of\nthe scaled distance to the atomic center, with the parameters related to the\nasymptotic decay of the integrand and the integration accuracy -- these are\nmuch simpler but no less efficient and naturally fit for linear-scaling\ncalculations. Radial distribution of spherical quadrature orders is studied. A\nradial integration scheme of double exponential type is optimized. A symmetric\nanalog of the pseudospectral approximation is used for the seminumerical\nevaluation of two-electron repulsion integrals. Taken together, this allows\nefficient calculation of all molecular integrals with well-controlled accuracy,\nas shown by tests on a set of molecules.", "category": "physics_chem-ph" }, { "text": "The extended star graph as a light-harvesting-complex prototype:\n excitonic absorption speedup by peripheral energy defect tuning: We study the quantum dynamics of a photo-excitation uniformly distributed at\nthe periphery of an extended star network (with $N_B$ branches of length\n$L_B$). More specifically, we address here the question of the energy\nabsorption at the core of the network and how this process can be improved (or\nnot) by the inclusion of peripheral defects with a tunable energy amplitude\n$\\Delta$. Our numerical simulations reveal the existence of optimal value of\nenergy defect $\\Delta^*$ which depends on the network architecture. Around this\nvalue, the absorption process presents a strong speedup (i.e. reduction of the\nabsorption time) provided that $L_B \\leq L_B^*$ with $L_B^* \\approx\n12.5/\\ln(N_B) $. Analytical/numerical developments are then conducted to\ninterpret this feature. We show that the origin of this speedup takes place in\nthe hybridization of two upper-band excitonic eigenstates. This hybridization\nis important when $L_B \\leq L_B^*$ and vanishes almost totally when $L_B >\nL_B^*$. These structural rules we draw here could represent a potential guide\nfor the practical design of molecular nano-network dedicated to the realisation\nof efficient photo-excitation absorption.", "category": "physics_chem-ph" }, { "text": "Artificial Intelligence Assists Discovery of Reaction Coordinates and\n Mechanisms from Molecular Dynamics Simulations: Exascale computing holds great opportunities for molecular dynamics (MD)\nsimulations. However, to take full advantage of the new possibilities, we must\nlearn how to focus computational power on the discovery of complex molecular\nmechanisms, and how to extract them from enormous amounts of data. Both aspects\nstill rely heavily on human experts, which becomes a serious bottleneck when a\nlarge number of parallel simulations have to be orchestrated to take full\nadvantage of the available computing power. Here, we use artificial\nintelligence (AI) both to guide the sampling and to extract the relevant\nmechanistic information. We combine advanced sampling schemes with statistical\ninference, artificial neural networks, and deep learning to discover molecular\nmechanisms from MD simulations. Our framework adaptively and autonomously\ninitializes simulations and learns the sampled mechanism, and is thus suitable\nfor massively parallel computing architectures. We propose practical solutions\nto make the neural networks interpretable, as illustrated in applications to\nmolecular systems.", "category": "physics_chem-ph" }, { "text": "On the Structural Origin of the Catalytic Properties of Inherently\n Strained Ultrasmall Decahedral Gold Nanoparticles: A new mechanism for reactivity of multiply twinned gold nanoparticles\nresulting from their inherently strained structure provides a further\nexplanation of the surprising catalytic activity of small gold nanoparticles.\nAtomic defect structural studies of surface strains and quantitative analysis\nof atomic column displacements in the decahedral structure observed by\naberration corrected transmission electron microscopy reveal an average\nexpansion of surface nearest neighbor distances of 5.6 percent, with many\nstrained by more than 10 percent. Density functional theory calculations of the\nresulting modified gold d-band states predict significantly enhanced activity\nfor carbon monoxide oxidation. The new insights have important implications for\nthe applications of nanoparticles in chemical process technology, including for\nheterogeneous catalysis.", "category": "physics_chem-ph" }, { "text": "O2- Ion Mobility in Dense Ne Gas: the Free Volume Model: We report data of the O2- ion mobility in neon gas over broad density and\ntemperature ranges along with its theoretical description in terms of the\nthermodynamic, free volume model that has successfully been adopted for the\ninterpretation of electron and ion mobility in superfluid and normal helium.\nThe free volume model, which is aimed at computing the free volume accessible\nfor the ion motion, along with the Millikan- Cunningham slip factor correction,\nis able to describe the ion mobility in the crossover region connecting the\ndilute gas regime described by the classical Kinetic Theory to the high density\nregion ruled by the laws of hydrodynamic transport.", "category": "physics_chem-ph" }, { "text": "McMillan-Mayer Theory of Solutions Revisited: Simplifications and\n Extensions: McMillan and Mayer (MM) proved two remarkable theorems in their paper on the\nequilibrium statistical mechanics of liquid solutions. They first showed that\nthe grand canonical partition function for a solution can be reduced to a one\nwith an effectively solute-only form, by integrating out the solvent degrees of\nfreedom. The total effective solute potential in the effective solute grand\npartition function can be decomposed into components which are potentials of\nmean force for isolated groups of one, two, three, etc, solute molecules.\nSecondly, from the first result, now assuming low solute concentration, MM\nderived an expansion for the osmotic pressure in powers of the solute\nconcentration, in complete analogy with the virial expansion of gas pressure in\npowers of the density at low density. The molecular expressions found for the\nosmotic virial coefficients have exactly the same form as the corresponding gas\nvirial coefficients, with potentials of mean force replacing vacuum potentials.\nIn this paper we restrict ourselves to binary liquid solutions with solute\nspecies $A$ and solvent species $B$ and do three things: (a) By working with a\nsemi-grand canonical ensemble (grand with respect to solvent only) instead of\nthe grand canonical ensemble used by MM, and avoiding graphical methods, we\nhave greatly simplified the derivation of the first MM result,(b) by using a\nsimple nongraphical method developed by van Kampen for gases, we have greatly\nsimplified the derivation of the second MM result,i.e.,the osmotic pressure\nvirial expansion; as a by-product, we show the precise relation between MM\ntheory and Widom potential distribution theory, and (c) we have extended MM\ntheory by deriving virial expansions for other solution properties such as the\nenthalpy of mixing. The latter expansion, with changed independent variables\ncorresponding to current experiments, is proving useful.", "category": "physics_chem-ph" }, { "text": "Dielectric matrix formulation of correlation energies in the Random\n Phase Approximation (RPA): inclusion of exchange effects: Starting from the general expression for the ground state correlation energy\nin the adiabatic connection fluctuation dissipation theorem (ACFDT) framework,\nit is shown that the dielectric matrix formulation, which is usually applied to\ncalculate the direct random phase approximation (dRPA) correlation energy, can\nbe used for alternative RPA expressions including exchange effects. Within this\nfamework, the ACFDT analog of the second order screened exchange (SOSEX)\napproximation leads to a logarithmic formula for the correlation energy similar\nto the direct RPA expression. Alternatively, the contribution of the exchange\ncan be included in the kernel used to evaluate the response functions. In this\ncase the use of an approximate kernel is crucial to simplify the formalism and\nto obtain a correlation energy in logarithmic form. Technical details of the\nimplementation of these methods are discussed and it is shown that one can take\nadvantage of density fitting or Cholesky decomposition techniques to improve\nthe computational efficiency; a discussion on the numerical quadrature made on\nthe frequency variable is also provided. A series of test calculations on\natomic correlation energies and molecular reaction energies shows that exchange\neffects are instrumental to improve over direct RPA results.", "category": "physics_chem-ph" }, { "text": "Alchemical perturbation density functional theory (APDFT): We introduce an orbital free electron density functional approximation based\non alchemical perturbation theory. Given convergent perturbations of a suitable\nreference system, the accuracy of popular self-consistent Kohn-Sham density\nfunctional estimates of properties of new molecules can be systematically\nsurpassed---at negligible cost. The associated energy functional is an\napproximation to the integrated energy derivative, requiring only perturbed\nreference electron densities: No self-consistent field equations are necessary\nto estimate energies and electron densities. Electronic ground state properties\nconsidered include covalent bonding potentials, atomic forces, as well as\ndipole and quadropole moments.", "category": "physics_chem-ph" }, { "text": "Ultrafast carbon monoxide photolysis and heme spin-crossover in\n myoglobin via nonadiabatic quantum dynamics: Light absorption of myoglobin triggers diatomic ligand photolysis and spin\ncrossover transition of iron(II) that initiate protein conformational change.\nThe photolysis and spin crossover reactions happen concurrently on a\nfemtosecond timescale. The microscopic origin of these reactions remains\ncontroversial. Here, we apply quantum wavepacket dynamics to elucidate the\nultrafast photochemical mechanism for a heme--carbon monoxide (heme--CO)\ncomplex. We observe coherent oscillations of the Fe-CO bond distance with a\nperiod of 42 fs and an amplitude of $\\sim$1 \\AA{}. These nuclear motions induce\npronounced geometric reorganization, which makes the CO dissociation\nirreversible. The reaction is initially dominated by symmetry breaking\nvibrations inducing an electron transfer from porphyrin to iron. Subsequently,\nthe wavepacket relaxes to the triplet manifold in $\\sim$75 fs and to the\nquintet manifold in $\\sim$430 fs. Our results highlight the central role of\nnuclear vibrations at the origin of the ultrafast photodynamics of\norganometallic complexes.", "category": "physics_chem-ph" }, { "text": "Exploiting machine learning to efficiently predict multidimensional\n optical spectra in complex environments: The excited state dynamics of chromophores in complex environments determine\na range of vital biological and energy capture processes. Time-resolved,\nmultidimensional optical spectroscopies provide a key tool to investigate these\nprocesses. Although theory has the potential to decode these spectra in terms\nof the electronic and atomistic dynamics, the need for large numbers of excited\nstate electronic structure calculations severely limits first principles\npredictions of multidimensional optical spectra for chromophores in the\ncondensed phase. Here, we leverage the locality of chromophore excitations to\ndevelop machine learning models to predict the excited state energy gap of\nchromophores in complex environments for efficiently constructing linear and\nmultidimensional optical spectra. By analyzing the performance of these models,\nwhich span a hierarchy of physical approximations, across a range of\nchromophore-environment interaction strengths, we provide strategies for the\nconstruction of ML models that greatly accelerate the calculation of\nmultidimensional optical spectra from first principles.", "category": "physics_chem-ph" }, { "text": "Analytical impedance of oxygen transport in the channel and gas\n diffusion layer of a PEM fuel cell: Analytical model for impedance of oxygen transport in the gas--diffusion\nlayer (GDL) and cathode channel of a PEM fuel cell is developed. The model is\nbased on transient oxygen mass conservation equations coupled to the proton\ncurrent conservation equation in the catalyst layer. Analytical formula for the\n\"GDL+channel\" impedance is derived assuming that the oxygen and proton\ntransport in the cathode catalyst layer (CCL) are fast. In the Nyquist plot,\nthe resulting impedance consists of two arcs describing oxygen transport in the\nair channel (low-frequency arc) and in the GDL. The characteristic frequency of\nGDL arc depends on the CCL thickness: large CCL thickness strongly lowers this\nfrequency. At small CCL thickness, the high-frequency feature on the arc shape\nforms. This effect is important for identification of peaks in distribution of\nrelaxation times spectra of low--Pt PEMFCs.", "category": "physics_chem-ph" }, { "text": "Generating candidates in global optimization algorithms using\n complementary energy landscapes: Global optimization of atomistic structure rely on the generation of new\ncandidate structures in order to drive the exploration of the potential energy\nsurface (PES) in search for the global minimum energy (GM) structure. In this\nwork, we discuss a type of structure generation, which locally optimizes\nstructures in complementary energy (CE) landscapes. These landscapes are\nformulated temporarily during the searches as machine learned potentials (MLPs)\nusing local atomistic environments sampled from collected data. The CE\nlandscapes are deliberately incomplete MLPs that rather than mimicking every\naspect of the true PES are sought to become much smoother, having only few\nlocal minima. This means that local optimization in the CE landscapes may\nfacilitate identification of new funnels in the true PES. We discuss how to\nconstruct the CE landscapes and we test their influence on global optimization\nof a reduced rutile SnO2(110)-(4x1) surface, and an olivine (Mg2SiO4)4 cluster\nfor which we report a new global minimum energy structure.", "category": "physics_chem-ph" }, { "text": "Hierarchy of equations to calculate the linear spectra of molecular\n aggregates - Time-dependent and frequency domain formulation: In a recent publication [J. Chem. Phys. 142, 034115 (2015)] we have derived a\nhierarchy of coupled differential equations in time domain to calculate the\nlinear optical properties of molecular aggregates. Here we provide details\nabout issues concerning the numerical implementation. In addition we present\nthe corresponding hierarchy in frequency domain.", "category": "physics_chem-ph" }, { "text": "Evidence for weakly bound electrons in non-irradiated alkane crystals.\n The electrons as a probe of structural differences in crystals: It is generally assumed that weakly bound (trapped) electrons in organic\nsolids come only from radiolytical (or photochemical) processes like ionization\ncaused by an excited positron entering the sample. This paper presents an\nevidence for the presence of these electrons in non-irradiated samples of\ndocosane. We argue that these electrons can be located (trapped) either in\ninterlamellar gaps or in spaces made by non-planar conformers. The electrons\nfrom the former ones are bound more weakly than those from the latter ones. The\norigin of Vis absorption for the samples is explained. These spectra can be\nused as a probe indicating differences in the solid structures of hydrocarbons.", "category": "physics_chem-ph" }, { "text": "Quantum Effects on the Free Energy of Ionic Aqueous Clusters Evaluated\n by Non-equilibrium Computational Methods: This paper has been withdrawn by the authors due to a copyright conflict with\nthe Journal of Physical Chemistry B, to which it has been submitted.", "category": "physics_chem-ph" }, { "text": "Arbitrarily Precise Quantum Alchemy: Doping compounds can be considered a perturbation to the nuclear charges in a\nmolecular Hamiltonian. Expansions of this perturbation in a Taylor series, i.e.\nquantum alchemy, has been used in literature to assess millions of derivative\ncompounds at once rather than enumerating them in costly quantum chemistry\ncalculations. So far, it was unclear whether this series even converges for\nsmall molecules, whether it can be used for geometry relaxation and how strong\nthis perturbation may be to still obtain convergent numbers. This work provides\nnumerical evidence that this expansion converges and recovers the\nself-consistent energy of Hartree-Fock calculations. The convergence radius of\nthis expansion is quantified for dimer examples and systematically evaluated\nfor different basis sets, allowing for estimates of the chemical space that can\nbe covered by perturbing one reference calculation alone. Besides electronic\nenergy, convergence is shown for density matrix elements, molecular orbital\nenergies, and density profiles, even for large changes in electronic structure,\ne.g. transforming He$_3$ into H$_6$. Subsequently, mixed alchemical and spatial\nderivatives are used to relax H$_2$ from the electronic structure of He alone,\nhighlighting a path to spatially relaxed quantum alchemy. Finally, the\nunderlying code (APHF) which allows for arbitrary precision evaluation of\nrestricted Hartree-Fock energies and arbitrary-order derivatives is made\navailable to support future method development.", "category": "physics_chem-ph" }, { "text": "Electronic stress tensor analysis of hydrogenated palladium clusters: We study the chemical bonds of small palladium clusters Pd_n (n=2-9)\nsaturated by hydrogen atoms using electronic stress tensor. Our calculation\nincludes bond orders which are recently proposed based on the stress tensor. It\nis shown that our bond orders can classify the different types of chemical\nbonds in those clusters. In particular, we discuss Pd-H bonds associated with\nthe H atoms with high coordination numbers and the difference of H-H bonds in\nthe different Pd clusters from viewpoint of the electronic stress tensor. The\nnotion of \"pseudo-spindle structure\" is proposed as the region between two\natoms where the largest eigenvalue of the electronic stress tensor is negative\nand corresponding eigenvectors forming a pattern which connects them.", "category": "physics_chem-ph" }, { "text": "Modeling surface vibrations and their role in molecular adsorption: a\n generalized Langevin approach: The atomic vibrations of a solid surface can play a significant role in the\nreactions of surface-bound molecules, as well as their adsorption and\ndesorption. Relevant phonon modes can involve the collective motion of atoms\nover a wide array of length scales. In this manuscript, we demonstrate how the\ngeneralized Langevin equation can be utilized to describe these collective\nmotions weighted by their coupling to individual sites. Our approach builds\nupon the generalized Langevin oscillator (GLO) model originally developed by\nTully \\textit{et al.} We extend the GLO by deriving parameters from atomistic\nsimulation data. We apply this approach to study the memory kernel of a model\nplatinum surface and demonstrate that the memory kernel has a bimodal form due\nto coupling to both low-energy acoustic modes and high-energy modes near the\nDebye frequency. The same bimodal form was observed across a wide variety of\nsolids of different elemental compositions, surface structures, and solvation\nstates. By studying how these dominant modes depend on simulation size, we\nargue that the acoustic modes are frozen in the limit of macroscopic lattices.\nBy simulating periodically replicated slabs of various sizes we quantify the\ninfluence of phonon confinement effects in the memory kernel and their\nconcomitant effect on simulated sticking coefficients.", "category": "physics_chem-ph" }, { "text": "On-Surface Pseudo-High Dilution Synthesis of Macrocycles: Principle and\n Mechanism: Macrocycles have attracted much attention due to their specific \"endless\"\ntopology, which results in extraordinary properties compared to related linear\n(open-chain) molecules. However, challenges still remain in their controlled\nsynthesis with well-defined constitution and geometry. Here, we report the\nfirst successful application of the (pseudo-)high dilution method to the\nconditions of on-surface synthesis in ultrahigh vacuum (UHV). This approach\nleads to high yields (up to 84%) of cyclic hyperbenzene ([18]-honeycombene) via\nan Ullmann-type reaction from 4,4\"-dibromo-meta-terphenyl (DMTP) as precursor\non a Ag(111) surface. The mechanism of macrocycle formation was explored in\ndetail using scanning tunneling microscopy (STM) and X-ray photoemission\nspectroscopy (XPS). We propose that hyperbenzene (MTP)6 forms majorly by\nstepwise desilverization of an organometallic (MTP-Ag)6 macrocycle, which\npreforms via cyclisation of (MTP-Ag)6 chains under pseudo-high dilution\ncondition. The high probability of cyclisation on the stage of the\norganometallic phase results from the reversibility of the C-Ag bond. The case\nis different from that in solution, in which cyclisation typically occurs on\nthe stage of covalently bonded open-chain precursor. This difference in the\ncyclisation mechanism on a surface compared to that in solution stems mainly\nfrom the 2D confinement exerted by the surface template, which to a large\nextent prevents the flipping of chain segments necessary for cyclisation.", "category": "physics_chem-ph" }, { "text": "EC-FORC: A New Cyclic Voltammetry Based Method for Examining Phase\n Transitions and Predicting Equilibrium: We propose a new, cyclic-voltammetry based experimental technique that can\nnot only differentiate between discontinuous and continuous phase transitions\nin an adsorbate layer, but also quite accurately recover equilibrium behavior\nfrom dynamic analysis of systems with a continuous phase transition. The\nElectrochemical first-order reversal curve (EC-FORC) diagram for a\ndiscontinuous phase transition (nucleation and growth), such as occurs in\nunderpotential deposition, is characterized by a negative region, while such a\nregion does not exist for a continuous phase transition, such as occurs in the\nelectrosorption of Br on Ag(100). Moreover, for systems with a continuous phase\ntransition, the minima of the individual EC-FORCs trace the equilibrium curve,\neven at very high scan rates. Since obtaining experimental data for the EC-FORC\nmethod would require only a simple reprogramming of the potentiostat used in\nconventional cyclic-voltammetry experiments, we believe that this method has\nsignificant potential for easy, rapid, in-situ analysis of systems undergoing\nelectrochemical deposition.", "category": "physics_chem-ph" }, { "text": "Intermolecular CT excitons enable nanosecond excited-state lifetimes in\n NIR-absorbing non-fullerene acceptors for efficient organic solar cells: State-of-the-art Y6-type molecular acceptors exhibit nanosecond excited-state\nlifetimes despite their low optical gaps (~1.4 eV), thus allowing organic solar\ncells (OSCs) to achieve highly efficient charge generation with extended\nnear-infrared (NIR) absorption range (up to ~1000 nm). However, the precise\nmolecular-level mechanism that enables low-energy excited states in Y6-type\nacceptors to achieve nanosecond lifetimes has remained elusive. Here, we\ndemonstrate that the distinct packing of Y6 molecules in film leads to a strong\nintermolecular charge-transfer (iCT) character of the lowest excited state in\nY6 aggregates, which is absent in other low-gap acceptors such as ITIC. Due to\nstrong electronic couplings between the adjacent Y6 molecules, the iCT-exciton\nenergies are greatly reduced by up to ~0.25 eV with respect to excitons formed\nin separated molecules. Importantly, despite their low energies, the iCT\nexcitons have reduced non-adiabatic electron-vibration couplings with the\nelectronic ground state, thus suppressing non-radiative recombination and\nallowing Y6 to overcome the well-known energy gap law. Our results reveal the\nfundamental relationship between molecular packing and nanosecond excited-state\nlifetimes in NIR-absorbing Y6-type acceptors underlying the outstanding\nperformance of Y6-based OSCs.", "category": "physics_chem-ph" }, { "text": "The hidden hand of lipids in the amyloid cascade: Intrinsically disordered proteins (IDPs), such as amyloid polypeptide (IAPP),\nbeta-amyloid (A\\b{eta}), and {\\alpha}-synuclein are linked to the insurgence of\ntype 2 diabetes, Alzheimer's, and Parkinson's diseases, respectively. Common\nmolecular mechanisms have been explored to elucidate the toxicity pathway of\nthese proteins. For many years, the amyloid hypothesis was believed to explain\nthe toxicity. According to this hypothesis, the misfolding of these proteins\nand the further aggregation into mature and insoluble fibrils rich in the\n\\b{eta}-sheet lead to cell death. However, this theory fails to explain much of\nthe experimental evidence, which led to the hypothesis of soluble\nsmall-oligomer toxicity and pore-like activity. Recently, the lipid-chaperone\nmodel was proposed to explain the effect of lipid compositions on IDPs toxicity\nin vitro. In this work, we summarize the different toxicity models and discuss\nthe possible relevance of the lipid-chaperone model in a biological context,\nsuch as protein overexpression and lipid oxidation. Furthermore, we briefly\nexplore how the model can be incorporated into the framework that explains IDPs\ntoxicity, such as fibril formation and secondary nucleation.", "category": "physics_chem-ph" }, { "text": "Multidimensional X-Ray Spectroscopy of Valence and Core Excitations in\n Cysteine: Several nonlinear spectroscopy experiments which employ broadband x-ray\npulses to probe the coupling between localized core and delocalized valence\nexcitation are simulated for the amino acid cysteine at the K-edges of oxygen\nand nitrogen and the K and L-edges of sulfur. We focus on two dimensional (2D)\nand 3D signals generated by two- and three-pulse stimulated x-ray Raman\nspectroscopy (SXRS) with frequency-dispersed probe. We show how the four-pulse\nx-ray signals\n$\\boldsymbol{k}_\\mathrm{I}=-\\boldsymbol{k}_1+\\boldsymbol{k}_2+\\boldsymbol{k}_3$\nand\n$\\boldsymbol{k}_\\mathrm{II}=\\boldsymbol{k}_1-\\boldsymbol{k}_2+\\boldsymbol{k}_3$\ncan give new 3D insight into the SXRS signals. The coupling between valence-\nand core-excited states can be visualized in three dimensional plots, revealing\nthe origin of the polarizability that controls the simpler pump-probe SXRS\nsignals.", "category": "physics_chem-ph" }, { "text": "The derivative discontinuity of the exchange-correlation functional: The derivative discontinuity is a key concept in electronic structure theory\nin general and density functional theory in particular. The electronic energy\nof a quantum system exhibits derivative discontinuities with respect to\ndifferent degrees of freedom that are a consequence of the integer nature of\nelectrons. The classical understanding refers to the derivative discontinuity\nof the total energy as a function of the total number of electrons ($N$), but\nit can also manifest at constant $N$. Examples are shown in models including\nseveral Hydrogen systems with varying numbers of electrons or nuclear charge\n($Z$), as well as the 1-dimensional Hubbard model (1DHM). Two sides of the\nproblem are investigated: first, the failure of currently used approximate\nexchange-correlation functionals in DFT and, second, the importance of the\nderivative discontinuity in the exact electronic structure of molecules, as\nrevealed by full configuration interaction (FCI). Currently, all approximate\nfunctionals miss the derivative discontinuity, leading to basic errors that can\nbe seen in many ways: from the complete failure to give the total energy of\nH$_2$ and H$_2^+$, to the missing gap in Mott insulators such as stretched\nH$_2$ and the thermodynamic limit of the 1DHM, or a qualitatively incorrect\ndensity in the HZ molecule with two electrons and incorrect electron transfer\nprocesses. Description of the exact particle behavior of electrons is\nemphasized, which is key to many important physical processes in real systems,\nespecially those involving electron transfer, and offers a challenge for the\ndevelopment of new exchange-correlation functionals.", "category": "physics_chem-ph" }, { "text": "Empirical corrections and pair interaction energies in the fragment\n molecular orbital method: The energy and analytic gradient are developed for FMO combined with the\nHartree-Fock method augmented with three empirical corrections (HF-3c). The\nauxiliary basis set approach to FMO is extended to perform pair interaction\nenergy decomposition analysis. The FMO accuracy is evaluated for several\ntypical systems including 3 proteins. Pair interaction energies computed with\ndifferent approaches in FMO are compared for a water cluster and protein-ligand\ncomplexes.", "category": "physics_chem-ph" }, { "text": "Excitonic energy transfer in light-harvesting complexes in purple\n bacteria: Two distinct approaches, the Frenkel-Dirac time-dependent variation and the\nHaken-Strobl model, are adopted to study energy transfer dynamics in\nsingle-ring and double-ring light-harvesting systems in purple bacteria. It is\nfound that inclusion of long-range dipolar interactions in the two methods\nresults in significant increases in intra- or inter-ring exciton transfer\nefficiency. The dependence of exciton transfer efficiency on trapping positions\non single rings of LH2 (B850) and LH1 is similar to that in toy models with\nnearest-neighbor coupling only. However, owing to the symmetry breaking caused\nby the dimerization of BChls and dipolar couplings, such dependence has been\nlargely suppressed. In the studies of coupled-ring systems, both methods reveal\ninteresting role of dipolar interaction in increasing energy transfer\nefficiency by introducing multiple intra/inter-ring transfer paths.\nImportantly, the time scale (~4ps) of inter-ring exciton transfer obtained from\npolaron dynamics is in good agreement with previous studies. In a double-ring\nLH2 system, dipole-induced symmetry breaking leads to global minima and local\nminima of the average trapping time when there is a finite value of non-zero\ndephasing rate, suggesting that environment plays a role in preserving quantum\ncoherent energy transfer. In contrast, dephasing comes into play only when the\nperfect cylindrical symmetry in the hypothetic system is broken. This study has\nrevealed that dipolar interaction between chromophores may play an important\npart in the high energy transfer efficiency in the LH2 system and many other\nnatural photosynthetic systems.", "category": "physics_chem-ph" }, { "text": "Polylogarithmic representation of radiative and thermodynamic properties\n of thermal radiation in a given spectral range: I. Blackbody radiation: Using polylogarithm functions the exact analytical expressions for the\nradiative and thermodynamic properties of blackbody radiation, such as the Wien\ndisplacement law, Stefan-Boltzmann law, total energy density, number density of\nphotons, Helmholtz free energy density, internal energy density, enthalpy\ndensity, entropy density, heat capacity at constant volume, and pressure in the\nfinite range of frequencies are constructed. The obtained expressions allow us\nto tabulate these functions in various finite frequency bands at different\ntemperatures for practical applications. As an example, the radiative and\nthermodynamic functions using experimental data for the monopole spectrum of\nthe Cosmic Microwave Background (CMB) radiation measured by the COBE FIRAS\ninstrument in the 60 - 600 GHz frequency interval at the temperature T = 2.725\nK are calculated. The expressions obtained for the radiative and thermodynamic\nfunctions can be easily presented in wavelength and wavenumber domains.", "category": "physics_chem-ph" }, { "text": "Sensitive Magnetic Control of Ensemble Nuclear Spin Hyperpolarisation in\n Diamond: Dynamic nuclear polarisation, which transfers the spin polarisation of\nelectrons to nuclei, is routinely applied to enhance the sensitivity of nuclear\nmagnetic resonance; it is also critical in spintronics, particularly when spin\nhyperpolarisation can be produced and controlled optically or electrically.\nHere we show the complete polarisation of nuclei located near the\noptically-polarised nitrogen-vacancy (NV) centre in diamond. When approaching\nthe ground-state level anti-crossing condition of the NV electron spins, 13C\nnuclei in the first-shell are polarised in a pattern that depends sensitively\nand sharply upon the magnetic field. Based on the anisotropy of the hyperfine\ncoupling and of the optical polarisation mechanism, we predict and observe a\ncomplete reversal of the nuclear spin polarisation with a few-mT change in the\nmagnetic field. The demonstrated sensitive magnetic control of nuclear\npolarisation at room temperature will be useful for sensitivity-enhanced NMR,\nnuclear-based spintronics, and quantum computation in diamond.", "category": "physics_chem-ph" }, { "text": "Time delay of slow electrons by a diatomic molecule described by\n non-overlapping atomic potentials model: We study the elastic scattering of slow electrons by two-atomic molecule in\nthe frame of non-overlapping atomic potentials model. The molecular continuum\nwave function is represented as a combination of a plane wave and two spherical\ns-waves, generated by the centers of atomic spheres. The asymptotic of this\nfunction determines in closed form the amplitude of elastic electron\nscattering. We show that this amplitude cannot be represented as a series of\nspherical functions. Therefore, it is impossible to use straightly the usual\nS-matrix methods to determine the scattering phases for non-spherical targets.\nWe show that far from molecule the continuum wave function can be presented as\nan expansion in other than spherical orthonormal functions. The coefficients of\nthis expansion determine the molecular scattering phases for non-spherical\nmolecular systems. In such an approach, we calculate the Wigner times delay for\nslow electron scattered by two-atomic target.", "category": "physics_chem-ph" }, { "text": "Infrared spectroscopy of small-molecule endofullerenes: Hydrogen is one of the few molecules which has been incarcerated in the\nmolecular cage of C$_{60}$ and forms endohedral supramolecular complex\nH$_2$@C$_{60}$. In this confinement hydrogen acquires new properties. Its\ntranslational motion becomes quantized and is correlated with its rotations. We\napplied infrared spectroscopy to study the dynamics of hydrogen isotopologs\nH$_2$, D$_2$ and HD incarcerated in C$_{60}$. The translational and rotational\nmodes appear as side bands to the hydrogen vibrational mode in the mid infrared\npart of the absorption spectrum. Because of the large mass difference of\nhydrogen and C$_{60}$ and the high symmetry of C$_{60}$ the problem is\nidentical to a problem of a vibrating rotor moving in a three-dimensional\nspherical potential. The translational motion within the C$_{60}$ cavity breaks\nthe inversion symmetry and induces optical activity of H$_2$. We derive\npotential, rotational, vibrational and dipole moment parameters from the\nanalysis of the infrared absorption spectra. Our results were used to derive\nthe parameters of a pairwise additive five-dimensional potential energy surface\nfor H$_2$@C$_{60}$. The same parameters were used to predict H$_2$ energies\ninside C$_{70}$[Xu et al., J. Chem. Phys., {\\bf 130}, 224306 (2009)]. We\ncompare the predicted energies and the low temperature infrared absorption\nspectra of H$_2$@C$_{70}$.", "category": "physics_chem-ph" }, { "text": "Inelastic low-energy collisions of electrons with HeH$^+$: rovibrational\n excitation and dissociative recombination: Inelastic low-energy (0--1 eV) collisions of electrons with HeH$^+$ cations\nare treated theoretically, with a focus on the rovibrational excitation and\ndissociative recombination (DR) channels. In an application of {\\it ab initio}\nmultichannel quantum defect theory (MQDT), the description of both processes is\nbased on the Born-Oppenheimer quantum defects. The quantum defects were\ndetermined using the R-matrix approach in two different frames of reference:\nthe center-of-charge and the center-of-mass frames. The results obtained in the\ntwo reference systems, after implementing the Fano-Jungen style rovibrational\nframe-transformation technique, shows differences in the rate of convergence\nfor these two different frames of reference. We find good agreement with the\navailable theoretically predicted rotationally inelastic thermal rate\ncoefficients. Our computed DR rate also agrees well with available experimental\nresults. Moreover, several computational experiments shed light on the role of\nrotational and vibrational excitations in the indirect DR mechanism that\ngoverns the low energy HeH$^+$ dissociation process. While the rotational\nexcitation is several orders of magnitude more probable process at the studied\ncollision energies, the closed-channel resonances described by the high-n,\nrotationally excited neutral molecules of HeH contribute very little to the\ndissociation probability. But the situation is very different for resonances\ndefined by the high-n, vibrationally excited HeH molecules, which are found to\ndissociate with approximately 90% probability.", "category": "physics_chem-ph" }, { "text": "Characterizing and optimizing a laser-desorption molecular beam source: The design and characterization of a new laser-desorption molecular beam\nsource, tailored for use in x-ray-free-electron-laser and\nultrashort-pulse-laser imaging experiments, is presented. It consists of a\nsingle mechanical unit containing all source components, including the\nmolecular-beam valve, the sample, and the fiber-coupled desorption laser, which\nis movable in five axes, as required for experiments at central facilities.\nUtilizing strong-field ionization, we characterize the produced molecular beam\nand evaluate the influence of desorption laser pulse energy, relative timing of\nvalve opening and desorption laser, sample bar height, and which part of the\nmolecular packet is probed on the sample properties. Strong-field ionization\nacts as a universal probe and allows to detect all species present in the\nmolecular beam, and hence enables us to analyze the purity of the produced\nmolecular beam, including molecular fragments. We present optimized\nexperimental parameters for the production of the purest molecular beam,\ncontaining the highest yield of intact parent ions, which we find to be very\nsensitive to the placement of the desorbed-molecules plume within the\nsupersonic expansion.", "category": "physics_chem-ph" }, { "text": "From Prescriptive to Predictive: an Interdisciplinary Perspective on the\n Future of Computational Chemistry: Reliable predictions of the behaviour of chemical systems are essential\nacross many industries, from nanoscale engineering over validation of advanced\nmaterials to nanotoxicity assessment in health and medicine. For the future we\ntherefore envision a paradigm shift for the design of chemical simulations\nacross all length scales from a prescriptive to a predictive and quantitative\nscience. This paper presents an integrative perspective about the\nstate-of-the-art of modelling in computational and theoretical chemistry with\nexamples from data- and equation-based models. Extension to include reliable\nrisk assessments and quality control are discussed. To specify and broaden the\nconcept of chemical accuracy in the design cycle of reliable and robust\nmolecular simulations the fields of computational chemistry, physics,\nmathematics, visualisation science, and engineering are bridged. Methods from\nelectronic structure calculations serve as examples to explain how\nuncertainties arise: through assumed mechanisms in form of equations, model\nparameters, algorithms, and numerical implementations. We provide a full\nclassification of uncertainties throughout the chemical modelling cycle and\ndiscuss how the associated risks can be mitigated. Further, we apply our\nstatements to molecular dynamics and partial differential equations based\napproaches. An overview of methods from numerical mathematics and statistics\nprovides strategies to analyse risks and potential errors in the design of new\nmaterials and compounds. We also touch on methods for validation and\nverification. In the conclusion we address cross-disciplinary open challenges.\nIn future the quantitative analysis of where simulations and their prognosis\nfail will open doors towards predictive materials engineering and chemical\nmodelling.", "category": "physics_chem-ph" }, { "text": "Tunneling in a very slow ion-molecule reaction: Quantum tunneling reactions play a significant role in chemistry when\nclassical pathways are energetically forbidden, be it in gas phase reactions,\nsurface diffusion, or liquid phase chemistry. In general, such tunneling\nreactions are challenging to calculate theoretically, given the high\ndimensionality of the quantum dynamics, and also very difficult to identify\nexperimentally. Hydrogenic systems, however, allow for accurate\nfirst-principles calculations. In this way the rate of the gas phase proton\ntransfer tunneling reaction of hydrogen molecules with deuterium anions, H_2 +\nD^- --> H^- + HD, has been calculated, but has so far lacked experimental\nverification. Here we present high-sensitivity measurements of the reaction\nrate carried out in a cryogenic 22-pole ion trap. We observe an extremely low\nrate constant of (5.2 +- 1.6) x 10^(-20) cm^3/s. This measured value agrees\nwith quantum tunneling calculations, serving as a benchmark for molecular\ntheory and advancing the understanding of fundamental collision processes. A\ndeviation of the reaction rate from linear scaling, which is observed at high\nH_2 densities, can be traced back to previously unobserved heating dynamics in\nradiofrequency ion traps.", "category": "physics_chem-ph" }, { "text": "Real-time probing of chirality during a chemical reaction: Chiral molecules interact and react differently with other chiral objects,\ndepending on their handedness. Therefore, it is essential to understand and\nultimately control the evolution of molecular chirality during chemical\nreactions. Although highly sophisticated techniques for the controlled\nsynthesis of chiral molecules have been developed, the observation of chirality\non the natural femtosecond time scale of a chemical reaction has so far\nremained out of reach for isolated molecules. Here, we demonstrate a general\nexperimental technique, based on high-harmonic generation in tailored laser\nfields, and apply it to probe the time evolution of molecular chirality during\nthe photodissociation of 2-iodobutane. These measurements show a change in sign\nand a pronounced increase in the magnitude of the chiral response over the\nfirst 100 fs, followed by its decay within less than 500 fs, revealing the\nphotodissociation to achiral products. The observed time evolution is explained\nin terms of the variation of the electric and magnetic transition-dipole\nmoments between the lowest electronic states of the cation as a function of the\nreaction coordinate. These results open the path to investigations of the\nchirality of molecular reaction pathways, light-induced chirality in chemical\nprocesses and the control of molecular chirality through tailored laser pulses.", "category": "physics_chem-ph" }, { "text": "Specific Na+ and K+ Cation Effects on the Interfacial Water Molecules at\n the Air/Aqueous Salt Solution Interfaces Probed with Non-resonant Second\n Harmonic Generation (SHG): Here we report the polarization dependent non-resonant second harmonic\ngeneration (SHG) measurement of the interfacial water molecules at the aqueous\nsolution of the following salts: NaF, NaCl, NaBr, KF, KCl, and KBr. Through\nquantitative polarization analysis of the SHG data,the orientational parameter\nD value and the relative surface density of the interfacial water molecules at\nthese aqueous solution surfaces were determined. From these results we found\nthat addition of each of the six salts caused increase of the thickness of the\ninterfacial water layer at the surfaces to a certain extent. Noticeably, both\nthe cations and the anions contributed to the changes, and the abilities to\nincrease the thickness of the interfacial water layer were in the following\norder: KBr > NaBr > KCl > NaCl ~ NaF > KF. Since these changes can not be\nfactorized into individual anion and cation contributions, there are possible\nion pairing or association effects, especially for the NaF case. We also found\nthat the orientational parameter D values of the interfacial water molecules\nchanged to opposite directions for the aqueous solutions of the three sodium\nsalts versus the aqueous solutions of the three potassium salts. These findings\nclearly indicated unexpected specific Na+ and K+ cation effects at the aqueous\nsolution surface. These effects were not anticipated from the recent molecular\ndynamics (MD) simulation results, which concluded that the Na+ and K+ cations\ncan be treated as small non-polarizable hard ions and they are repelled from\nthe aqueous interfaces. These results suggest that the electrolyte aqueous\nsolution surfaces are more complex than the currently prevalent theoretical and\nexperimental understandings.", "category": "physics_chem-ph" }, { "text": "The use of industrial molasses waste in the performant synthesis of\n fewlayer graphene (and its Au/Ag nanoparticles nanocomposites):\n Photocatalytic and supercapacitance applications: In view of clean environment, the industry needs to address multiple demands\nat different levels of production and processes via the sustainable approach\nincluding recycling or smart use of produced waste. On the other hand, a\ndevelopment and success of green energy requires the crucial materials\nsynthesized via efficient, sustainable methodology. Herein, we present the\ngreen, simple, easily scalable, fast, and highly efficient synthesis of\nfew-layer graphene (FLG) and its composites with Au and Ag nanoparticles using\na waste. The FLG synthesis based on the exfoliation of graphite occurs in water\nin the presence of industrial co-product, molasses, which next shows also\nperformant reductive properties during Ag and Au NPs formation. The decreased\nsize of NPs deposited on FLG indicates the synergetic effect of molasses and\nFLG, exhibiting the add role of FLG/molasses as metal stabilizer species. The\nNPs/FLG composites 2 are efficient photocatalysts in degradation of organic\ncontaminant, bisphenol (BisA), in the presence of peroxy-monosulfate (PMS)\nactivator. The Au/FLG (PVDF) and Ag/FLG (PVDF) based electrodes reveal as well\nrelatively high gravimetric capacitance, 205 Fg-1 and 729 Fg-1. The presented\napproach is much worthy to be further applied in the synthesis of other layered\nmaterials as well as other non-noble supported metallic systems.", "category": "physics_chem-ph" }, { "text": "Is there a universality of the helix-coil transition in protein models?: The similarity in the thermodynamic properties of two completely different\ntheoretical models for the helix-coil transition is examined critically. The\nfirst model is an all-atomic representation for a poly-alanine chain, while the\nsecond model is a minimal helix-forming model that contains no system\nspecifics. Key characteristics of the helix-coil transition, in particular, the\neffective critical exponents of these two models agree with each other, within\na finite-size scaling analysis.", "category": "physics_chem-ph" }, { "text": "On the unusual Stokes shift in the smallest PPE dendrimer building\n block: Role of the vibronic symmetry on the band origin?: 1,3-bis(phenylethynyl)benzene is the primary chromophore of light-harvesting\npolyphenylene ethynylene (PPE) dendrimers. It is experimentally known to share\nthe same absorption spectrum as its pair of diphenylacetylene (aka. tolane)\nmeta-substituted branches, yet exhibits an unusual Stokes shift of about 2000\ncm$^{-1}$ with respect to its band origin (corresponding to the loss of one\nvibrational quantum within the antisymmetric acetylenic stretching) in its\nemission spectrum. We suggest in the present work the unusual but plausible\ninvolvement of molecular symmetry selection rules in a situation where the\nBorn-Oppenheimer approximation is far to be valid. Our hypothesis is comforted\nwith quantum dynamics (MCTDH) simulations of absorption and emission UV-visible\nspectra based on quantum chemistry (TD-DFT) data and a diabatic vibronic\ncoupling Hamiltonian model.", "category": "physics_chem-ph" }, { "text": "Carrier-envelope phase control over pathway interference in strong-field\n dissociation of H$_2^+$: The dissociation of an H$_2^+$ molecular-ion beam by linearly polarized,\ncarrier-envelope-phase-tagged 5 fs pulses at 4$\\times10^{14} $W/cm$^2$ with a\ncentral wavelength of 730 nm was studied using a coincidence 3D momentum\nimaging technique. Carrier-envelope-phase-dependent asymmetries in the emission\ndirection of H$^+$ fragments relative to the laser polarization were observed.\nThese asymmetries are caused by interference of odd and even photon number\npathways, where net-zero photon and 1-photon interference predominantly\ncontributes at H$^+$+H kinetic energy releases of 0.2 -- 0.45 eV, and\nnet-2-photon and 1-photon interference contributes at 1.65 -- 1.9 eV. These\nmeasurements of the benchmark H$_2^+$ molecule offer the distinct advantage\nthat they can be quantitatively compared with \\textit{ab initio} theory to\nconfirm our understanding of strong-field coherent control via the\ncarrier-envelope phase.", "category": "physics_chem-ph" }, { "text": "Computing the dielectric constant of liquid water at constant dielectric\n displacement: The static dielectric constant of liquid water is computed using classical\nforce field based molecular dynamics simulation at fixed electric displacement\nD. The method to constrain the electric displacement is the finite temperature\nclassical variant of the constant-D method developed by Stengel, Spaldin and\nVanderbilt (Nat. Phys. 2009, 5: 304). There is also a modification of this\nscheme imposing fixed values of the macroscopic field E. The method is applied\nto the popular SPC/E model of liquid water. We compare four different estimates\nof the dielectric constant, two obtained from fluctuations of the polarization\nat D = 0 and E = 0 and two from the variation of polarization with finite D and\nE. It is found that all four estimates agree when properly converged. The\ncomputational effort to achieve convergence varies however, with constant D\ncalculations being substantially more efficient. We attribute this difference\nto the much shorter relaxation time of longitudinal polarization compared to\ntransverse polarization accelerating constant D calculations.", "category": "physics_chem-ph" }, { "text": "State-resolved infrared spectrum of the protonated water dimer:\n Revisiting the characteristic proton transfer doublet peak: The infrared (IR) spectra of protonated water clusters encode precise\ninformation on the dynamics and structure of the hydrated proton. However, the\nstrong anharmonic coupling and quantum effects of these elusive species remain\npuzzling up to the present day. Here, we report unequivocal evidence that the\ninterplay between the proton transfer and the water wagging motions in the\nprotonated water dimer (Zundel ion) giving rise to the characteristic doublet\npeak is both more complex and more sensitive to subtle energetic changes than\npreviously thought. In particular, hitherto overlooked low-intensity satellite\npeaks in the experimental spectrum are now unveiled and mechanistically\nassigned. Our findings rely on the comparison of IR spectra obtained using two\nhighly accurate potential energy surfaces in conjunction with highly accurate\nstate-resolved quantum simulations. We demonstrate that these high-accuracy\nsimulations are important for providing definite assignments of the complex IR\nsignals of fluxional molecules.", "category": "physics_chem-ph" }, { "text": "Dramatic relativistic and magnetic Breit effects for the superheavy\n reaction Og + 3Ts$_2$ -> OgTs$_6$: Prediction of atomization energy and the\n existence of the superheavy octahedral Oganesson hexatennesside OgTs$_6$: Our gargantuan ab initio all-electron fully relativistic Dirac-Fock (DF),\nnonrelativistic (NR) Hartree-Fock(HF) and Dirac-Fock-Breit-Gaunt(DFBG)\nmolecular SCF calculations for the superheavy octahedral Oganesson\nhexatenniside OgTs$_6$ predict atomization energy (Ae) of 9.47, -5.54and 9.37\neV, at the optimized Os-Ts bond distances of 3.35, 3.34 and 3.36 angstroms,\nrespectively. There are dramatic effects of relativity for the atomization\nenergy of OgTs$_6$ (with seven superheavy elements and 820 electrons) of ~ 15.0\neV each at both the DF and DFBG levels of theory, respectively. Our calculated\nenergy of reaction for the titled superheavy reaction Og + 3Ts$_2$ -> OgTs$_6$\nat the DF, NR and DFBG levels of theory is 6.33, 8.81, and 6.26 eV,\nrespectively. Mulliken analysis as implemented in the DIRAC code for our DF and\nNR calculations (using the dyall.ev4z basis) yields the charges Og(+0.60) and\nOg(+0.96), respectively on the central Og atom indicating that our relativistic\nDF calculations predict octahedral OgTs$_6$ to be less ionic. However, due\ncaution must be used to interpret the results of Mulliken's population\nanalysis, which is highly basis set dependent.", "category": "physics_chem-ph" }, { "text": "Challenges with relativistic GW calculations in solids and molecules: For molecules and solids containing heavy elements, accurate electronic\nstructure calculations require accounting not only for electronic correlations\nbut also for relativistic effects. In molecules, relativity can lead to severe\nchanges in the ground-state description. In solids, the interplay between both\ncorrelation and relativity can change the stability of phases or it can lead to\nan emergence of completely new phases. Traditionally, the simplest illustration\nof relativistic effects can be done either by including pseudopotentials in\nnon-relativistic calculations or alternatively by employing large all electron\nbasis sets in relativistic methods. By analyzing different electronic\nproperties (band structure, equilibrium lattice constant and bulk modulus) in\nsemiconductors and insulators, we show that capturing the interplay of\nrelativity and electron correlation can be rather challenging in Green's\nfunction methods. For molecular problems with heavy elements, we also observe\nthat similar problems persist. We trace these challenges to three major\nproblems: deficiencies in pseudopotential treatment as applied to Green's\nfunction methods, the scarcity of accurate and compact all-electron basis-sets\nthat can be converged with respect to the basis-set size, and linear\ndependencies arising in all-electron basis-sets particularly when employing\nGaussian orbitals. Our analysis provides detailed insight into these problems\nand opens a discussion about potential approaches to mitigate them.", "category": "physics_chem-ph" }, { "text": "Radiationless Decay Spectrum of O 1s Double Core Holes in Liquid Water: We present a combined experimental and theoretical investigation of the\nradiationless decay spectrum of an O 1s double core hole in liquid water. Our\nexperiments were carried out using liquid-jet electron spectroscopy from\ncylindrical microjets of normal and deuterated water. The signal of the\ndouble-core-hole spectral fingerprints (hypersatellites) of liquid water was\nclearly identified, with an intensity ratio to Auger decay of singly charged O\n1s of 0.0014(5). We observed a significant isotope effect between liquid H$_2$O\nand D$_2$O. For theoretical modeling, the Auger electron spectrum of the\ncentral water molecule in a water pentamer was calculated using an\nelectronic-structure toolkit combined with molecular-dynamics simulations to\ncapture the influence of molecular rearrangement on the ultra-short lifetime of\nthe double core hole. We obtained the static and dynamic Auger spectra for\nH$_2$O, (H$_2$O)$_5$, D$_2$O, and (D$_2$O)$_5$, instantaneous Auger spectra at\nselected times after core-level ionization, and the symmetrized oxygen-hydrogen\ndistance as a function of time after double core ionization for all four\nprototypical systems. We consider this observation of liquid-water double core\nholes as a new tool to study ultrafast nuclear dynamics.", "category": "physics_chem-ph" }, { "text": "Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in\n multicanonical ensemble: We demonstrate that the multicanonical approach is not restricted to Monte\nCarlo simulations, but can also be applied to simulation techniques such as\nmolecular dynamics, Langevin, and hybrid Monte Carlo algorithms. The\neffectiveness of the methods are tested with an energy function for the protein\nfolding problem. Simulations in the multicanonical ensemble by the three\nmethods are performed for a penta peptide, Met-enkephalin. For each algorithm,\nit is shown that from only one simulation run one can not only find the\nglobal-minimum-energy conformation but also obtain probability distributions in\ncanonical ensemble at any temperature, which allows the calculation of any\nthermodynamic quantity as a function of temperature.", "category": "physics_chem-ph" }, { "text": "Chemical Structure Elucidation from Mass Spectrometry by Matching\n Substructures: Chemical structure elucidation is a serious bottleneck in analytical\nchemistry today. We address the problem of identifying an unknown chemical\nthreat given its mass spectrum and its chemical formula, a task which might\ntake well trained chemists several days to complete. Given a chemical formula,\nthere could be over a million possible candidate structures. We take a data\ndriven approach to rank these structures by using neural networks to predict\nthe presence of substructures given the mass spectrum, and matching these\nsubstructures to the candidate structures. Empirically, we evaluate our\napproach on a data set of chemical agents built for unknown chemical threat\nidentification. We show that our substructure classifiers can attain over 90%\nmicro F1-score, and we can find the correct structure among the top 20\ncandidates in 88% and 71% of test cases for two compound classes.", "category": "physics_chem-ph" }, { "text": "Nonadiabatic Dynamics in Open Quantum-Classical Systems:\n Forward-Backward Trajectory Solution: A new approximate solution to the quantum-classical Liouville equation is\nderived starting from the formal solution of this equation in forward-backward\nform. The time evolution of a mixed quantum-classical system described by this\nequation is obtained in a coherent state basis using the mapping\nrepresentation, which expresses $N$ quantum degrees of freedom in a\n2N-dimensional phase space. The solution yields a simple non-Hamiltonian\ndynamics in which a set of $N$ coherent state coordinates evolve in forward and\nbackward trajectories while the bath coordinates evolve under the influence of\nthe mean potential that depends on these forward and backward trajectories. It\nis shown that the solution satisfies the differential form of the\nquantum-classical Liouville equation exactly. Relations to other mixed\nquantum-classical and semi-classical schemes are discussed.", "category": "physics_chem-ph" }, { "text": "Multiconfigurational Short-Range Density-Functional Theory for\n Open-Shell Systems: Many chemical systems cannot be described by quantum chemistry methods based\non a singlereference wave function. Accurate predictions of energetic and\nspectroscopic properties require a delicate balance between describing the most\nimportant configurations (static correlation) and obtaining dynamical\ncorrelation efficiently. The former is most naturally done through a\nmulticonfigurational (MC) wave function, whereas the latter can be done by,\ne.g., perturbation theory. We have employed a different strategy, namely, a\nhybrid between multiconfigurational wave functions and density-functional\ntheory (DFT) based on range separation. The method is denoted by MC short-range\n(sr) DFT and is more efficient than perturbative approaches as it capitalizes\non the efficient treatment of the (short-range) dynamical correlation by DFT\napproximations. In turn, the method also improves DFT with standard\napproximations through the ability of multiconfigurational wave functions to\nrecover large parts of the static correlation. Until now, our implementation\nwas restricted to closed-shell systems, and to lift this restriction, we\npresent here the generalization of MC-srDFT to open-shell cases. The additional\nterms required to treat open-shell systems are derived and implemented in the\nDALTON program. This new method for open-shell systems is illustrated on\ndioxygen and [Fe(H2O)6]3+.", "category": "physics_chem-ph" }, { "text": "Block2: a comprehensive open source framework to develop and apply\n state-of-the-art DMRG algorithms in electronic structure and beyond: Block2 is an open source framework to implement and perform density matrix\nrenormalization group and matrix product state algorithms. Out-of-the-box it\nsupports the eigenstate, time-dependent, response, and finite-temperature\nalgorithms. In addition, it carries special optimizations for ab initio\nelectronic structure Hamiltonians and implements many quantum chemistry\nextensions to the density matrix renormalization group, such as dynamical\ncorrelation theories. The code is designed with an emphasis on flexibility,\nextensibility, and efficiency, and to support integration with external\nnumerical packages. Here we explain the design principles and currently\nsupported features and present numerical examples in a range of applications.", "category": "physics_chem-ph" }, { "text": "A density functional method for general excited states in atoms: This chapter presents the development of a density functional theory\n(DFT)-based method for accurate, reliable treatment of various resonances in\natoms. Many of these are known to be notorious for their strong correlation,\nproximity to more than one thresholds, degeneracy with more than one minima.\nTherefore these pose unusual challenges to both theoreticians and\nexperimentalists. Our method uses a work-function-based exchange potential in\nconjunction with the popular gradient-corrected Lee-Yang-Parr correlation\nfunctional. The resulting Kohn-Sham equation, in the non-relativistic\nframework, is numerically solved accurately and efficiently by means of a\ngeneralized pseudospectral method through a non-uniform, optimal spatial\ndiscretization. This has been applied to a variety of excited states, such as\nlow and high states; single, double, triple as well as multiple excitations;\nvalence and core excitations; autoionizing states; satellites; hollow and\ndoubly-hollow states; very high-lying Rydberg resonances; etc., of atoms and\nions, with remarkable success. A thorough and systematic comparison with\nliterature data reveals that, for all these systems, the exchange-only results\nare practically of Hartree-Fock quality; while with inclusion of correlation,\nthis offers excellent agreement with available experimental data as well as\nthose obtained from other sophisticated theoretical methods. Properties such as\nindividual state energies, excitation energies, radial densities as well as\nvarious expectation values are studied. This helps us in predicting many states\nfor the first time.", "category": "physics_chem-ph" }, { "text": "Magnetophoresis of nonmagnetic particles in ferrofluids: Ferrofluids containing nonmagnetic particles are called inverse ferrofluids.\nOn the basis of the Ewald-Kornfeld formulation and the Maxwell-Garnett theory,\nwe theoretically investigate the magnetophoretic force exerting on the\nnonmagnetic particles in inverse ferrofluids due to the presence of a\nnonuniform magnetic field, by taking into account the structural transition and\nlong-range interaction. We numerically demonstrate that the force can be\nadjusted by choosing appropriate lattices, volume fractions, geometric shapes,\nand conductivities of the nonmagnetic particles, as well as frequencies of\nexternal magnetic fields.", "category": "physics_chem-ph" }, { "text": "Non-stochastic matrix Schr\u00f6dinger equation for open systems: We propose an extension of the Schr\\\"odinger equation for a quantum system\ninteracting with environment. This equation describes dynamics of auxiliary\nwave-functions $\\mathbf{m}$, from which the system density matrix can be\nreconstructed as $\\hat{\\rho} = \\mathbf{m} \\mathbf{m}^\\dagger$. We formulate a\ncompatibility condition, which ensures that the reconstructed density satisfies\na given quantum master equation for the system density. The resulting\nnon-stochastic evolution equation preserves positive-definiteness of the system\ndensity and is applicable to both Markovian and non-Markovian system-bath\ntreatments. Our formalism also resolves a long-standing problem of energy\nnon-conservation in the time-dependent variational principle applied to mixed\nstates of closed systems.", "category": "physics_chem-ph" }, { "text": "Maximum probability domains for the analysis of the microscopic\n structure of liquids: We introduce the concept of maximum probability domains (MPDs), developed in\nthe context of the analysis of electronic densities, in the study of the\nmicroscopic spatial structures of liquids. The idea of locating a particle in a\nthree dimensional region, by determining the domain where the probability of\nfinding that, and only that, particle is maximum, gives an interesting\ncharacterization of the local structure of the liquid. The optimization\nprocedure, required for the search of the domain of maximum probability, is\ncarried out by the implementation of the level set method. Results for a couple\nof case studies are presented, to illustrate the structure of liquid water at\nambient conditions and upon increasing pressure from the point of view of MPDs\nand to compare the information encoded in the solvation shells of sodium in\nwater with, once again, that extracted from the MPDs.", "category": "physics_chem-ph" }, { "text": "Transition Metal-Tetracyanoquinodimethane Monolayers as Single-Atom\n Catalysts for Electrocatalytic Nitrogen Reduction Reaction: Converting earth-abundant dinitrogen into value-added chemical ammonia is a\nsignificant yet challenging topic. Electrocatalytic nitrogen reduction reaction\n(NRR), compared with conventional Haber-Bosch process, is an energy-saving and\nenvironmentally friendly approach. The major task of electrocatalytic NRR is to\nfind electrocatalysts which can activate dinitrogen effectively and exhibit\nhigh selectivity and stability. Single atom catalysts can act as a good\nsolution. In this work, by means of first-principles density functional theory,\nmolecular dynamics calculations, and a two-step screening process, we confirm\nthat single Sc and Ti atom supported on tetracyanoquinodimethane monolayers\n(Sc,Ti-TCNQ) are excellent candidates for NRR electrocatalysts. N2 adsorption\nand activation are effective due to the acceptance-donation mechanism and\noutstanding electronic structure of TM-TCNQ, and Gibbs free energy diagram\nshows that Sc-TCNQ and Ti-TCNQ exhibit low NRR overpotential of 0.33 and 0.22 V\nthrough enzymatic-consecutive mixed pathway, respectively. In addition,\nselectivity over HER and stability of Sc/Ti-TCNQ monolayers are also validated.\nThis work opens a new avenue for designing novel single atom catalysts for NRR\nas well as other catalytic applications.", "category": "physics_chem-ph" }, { "text": "The water supercooled regime as described by four common water models: The temperature scale of simple water models in general does not coincide\nwith the natural one. Therefore, in order to make a meaningful evaluation of\ndifferent water models a temperature rescaling is necessary. In this paper we\nintroduce a rescaling using the melting temperature and the temperature\ncorresponding to the maximum of the heat capacity to evaluate four common water\nmodels (TIP4P-Ew, TIP4P-2005, TIP5P-Ew and Six-Sites) in the supercooled\nregime. Although all the models show the same general qualitative behavior, the\nTIP5P-Ew appears as the best representation of the supercooled regime when the\nrescaled temperature is used. We also analyze, using thermodynamic arguments,\nthe critical nucleus size for ice growth. Finally, we speculate on the possible\nreasons why atomistic models do not usually crystalize while the coarse grained\nmW model do crystallize.", "category": "physics_chem-ph" }, { "text": "Ab initio methods for polariton chemistry: Polariton chemistry exploits the strong interaction between quantized\nexcitations in molecules and quantized photon states in optical cavities to\naffect chemical reactivity. Molecular polaritons have been experimentally\nrealized by the coupling of electronic, vibrational, and rovibrational\ntransitions to photon modes, which has spurred tremendous theoretical effort to\nmodel and explain how polariton formation can influence chemistry. This\ntutorial review focuses on computational approaches for the electronic strong\ncoupling problem through the combination of familiar techniques from ab initio\nelectronic structure theory and cavity quantum electrodynamics, toward the goal\nof supplying predictive theories for polariton chemistry. Our aim is to\nemphasize the relevant theoretical details with enough clarity for newcomers to\nthe field to follow, and to present simple and practical code examples to\ncatalyze further development work.", "category": "physics_chem-ph" }, { "text": "Complexes of DNA Bases and Small Gold Clusters: DNA base-gold interactions are studied theoretically at the DFT level using\nAu3 and Au4 clusters as simple catalytic models for Au particles. The bonding\nbetween DNA bases and gold clusters occurs via the anchoring of a Au atom to\nthe N or O atoms of the bases. In the most stable planar base-Au3 complexes,\nthe Au-N or Au-O anchor bonds are reinforced by N-H...Au bonds. The mechanism\nof formation of these nonconventional H-bonds is discussed.", "category": "physics_chem-ph" }, { "text": "Fe-carbon nitride 'Core-shell' electrocatalysts for the oxygen reduction\n reaction: In this report, the preparation of Fe-carbon nitride (CN)-based\nelectrocatalysts (ECs) with a 'core-shell' morphology for the oxygen reduction\nreaction (ORR) is described. The ECs consist of spherical XC-72R carbon\nnanoparticles, the 'cores', that are covered by a CN matrix, the 'shell',\nembedding Fe species in 'coordination nests'. The latter is formed by the\npresence of carbon and nitrogen ligands on the surface of the CN matrix, the\n'shell'. Two families of CN-based ECs are prepared, which are grouped on the\nbasis of the concentration of N atoms in the CN 'shell'. Each group comprises\nof both a 'pristine' and an 'activated' EC; the latter is obtained from the\n'pristine' EC by a suitable series of treatments (A) devised to improve the ORR\nperformance. The chemical composition of the CN-based ECs is determined by\nInductively-Coupled Plasma Atomic Emission Spectroscopy (ICP-AES) and\nmicroanalysis. The surface area of the CN-based ECs is determined by nitrogen\nphysisorption techniques, and the surface composition is probed by X-ray\nPhotoelectron Spectroscopy (XPS). The electrochemical performance and reaction\nmechanism of the CN-based ECs in the ORR is investigated in both acid and\nalkaline environments by cyclic voltammetry with the Thin-Film Rotating\nRing-Disk Electrode setup (CV-TF-RRDE). The influence of the preparation\nparameters and of the treatments on the physicochemical properties, the ORR\nperformance, and reaction mechanism is studied in detail. In the alkaline\nenvironment the FeFe2-CNl 900/CA 'core-shell' EC shows a remarkable ORR onset\npotential of 0.908 V vs. RHE which, with respect to the value of 0.946 V vs.\nRHE of the Pt/C ref., classifies the proposed materials as very promising\n'Platinum Group Metal-free' ECs for the ORR.", "category": "physics_chem-ph" }, { "text": "Modified noise kernels in Gaussian process modelling of energy surfaces: We explore the use of non homogenous noise kernels in Gaussian process\nmodelling to improve the potential energy curve models describing stochastic\nelectronic structure data. We use the same noise kernels on energy curves\ndescribing deterministic electronic structure data by creating non-homogenous\nnoise model. We observe, as well as agreement between the noise of the model\nand the stochastic data, a strong regularisation of the curves when using\nartificial noises on deterministic data which improves Gaussian processes in\nthe over fitting regime.", "category": "physics_chem-ph" }, { "text": "Two-particle coalescence conditions revisited: The notion of the n-th order local energy, generated by the n-th power of the\nHamiltonian, has been introduced. The n-th order two-particle coalescence\nconditions have been derived from the requirements that the n-th order local\nenergy at the coalescence point is non-singular and equal to the n-th power of\nthe Hamiltonian eigenvalue. The first condition leads to energy-independent\nconstraints. The second one is state-specific. The analysis has been done using\na radial, one-dimensional, model Hamiltonian. The model is valid in the\nasymptotic region of r ~ 0. The coalescence conditions set the relations\nbetween the expansion coefficients of the radial wave function into a power\nseries with respect to r.", "category": "physics_chem-ph" }, { "text": "Influence of Humidity, Temperature and Radicals on the Formation and\n Thermal Properties of Secondary Organic Aerosol (SOA) from Ozonolysis of\n \u03b2-pinene: The influence of water and radicals on SOAs produced by {\\beta}-pinene\nozonolysis was investigated at 298 and 288 K using a laminar flow reactor. A\nvolatility tandem differential mobility analyzer (VTDMA) was used to measure\nthe evaporation of the SOA, enabling the parameterization of its volatility\nproperties. The parameters extracted included the temperature at which 50% of\nthe aerosol had evaporated (TVFR0.5) and the slope factor (SVFR). An increase\nin SVFR indicates a broader distribution of vapor pressures for the aerosol\nconstituents. Reducing the reaction temperature increased SVFR and decreased\nTVFR0.5 under humid conditions but had less effect on TVFR0.5 under dry\nconditions. In general, higher water concentrations gave lower TVFR0.5 values,\nmore negative SVFR values, and a reduction in total SOA production. The radical\nconditions were changed by introducing OH scavengers to generate systems with\nand without OH radicals and with different [HO2]/[RO2] ratios. Presence of a\nscavenger and lower [HO2]/[RO2] ratio reduced SOA production. Observed changes\nin SVFR values could be linked to the more complex chemistry that occurs in the\nabsence of a scavenger, and indicated that additional HO2 chemistry gives\nproducts with a wider range of vapor pressures. Updates to existing ozonolysis\nmechanisms with routes that describe the observed responses to water and\nradical conditions for monoterpenes with endocyclic and exocyclic double bonds\nare discussed.", "category": "physics_chem-ph" }, { "text": "Excitation energies from G{\u00f6}rling-Levy perturbation theory along the\n range-separated adiabatic connection: A G{\\\"o}rling-Levy (GL)-based perturbation theory along the range-separated\nadiabatic connection is assessed for the calculation of electronic excitation\nenergies. In comparison with the Rayleigh-Schr{\\\"o}dinger (RS)-based\nperturbation theory introduced in a previous work [E. Rebolini, J. Toulouse, A.\nM. Teale, T. Helgaker, A. Savin, Mol. Phys. 113, 1740 (2015)], this GL-based\nperturbation theory keeps the ground-state density constant at each order and\nthus gives the correct ionization energy at each order. Excitation energies up\nto first order in the perturbation have been calculated numerically for the\nhelium and beryllium atoms and the hydrogen molecule without introducing any\ndensity-functional approximations. In comparison with the RS-based perturbation\ntheory, the present GL-based perturbation theory gives much more accurate\nexcitation energies for Rydberg states but similar excitation energies for\nvalence states.", "category": "physics_chem-ph" }, { "text": "Interaction of a Long Alkyl Chain Protic Ionic Liquid and Water: A combined experimental/theoretical approach has been used to investigate the\nrole of water in modifying the microscopic interactions characterizing the\noptical response of butyl-ammonium nitrate (BAN) water solutions. Raman\nspectra, dominated by the signal from the protic ionic liquid, were collected\nas a function of the water content, and the corresponding spatial organization\nof the ionic couples, as well as their local arrangement with water molecules,\nwas studied exploiting classical molecular dynamics calculations. High quality\nspectroscopic data, combined with a careful analysis, revealed that water\naffects the vibrational spectrum BAN in solution: as the water concentration is\nincreased, peaks assigned to stretching modes show a frequency hardening\ntogether with a shape narrowing, whereas the opposite behavior is observed for\npeaks assigned to bending modes. Calculation results clearly show a nanometric\nspatial organization of the ionic couples that is not destroyed on increasing\nthe water content at least within an intermediate range. Our combined results\nshow indeed that small water concentrations even increase the local order.\nWater molecules are located among ionic couples and are closer to the anion\nthan the cation, as confirmed by the computation of the number of H-bonds which\nis greater for water-anion than for water-cation. The whole results set thus\nclarifies the microscopic scenario of the BAN-water interaction and underlines\nthe main role of the extended hydrogen bond network among water molecules and\nnitrate anions.", "category": "physics_chem-ph" }, { "text": "A unified density-matrix functional construction of quantum baths in\n density matrix embedding theory beyond the mean-field approximation: The equivalence in one-electron quantum bath between the practical\nimplementation of density matrix embedding theory (DMET) and the more recent\nHouseholder-transformed density matrix functional embedding theory has been\nshown previously in the standard but special case where the reference full-size\n(one-electron reduced) density matrix, from which the bath is constructed, is\nidempotent [J. Chem. Phys. 157, 214112 (2022)]. We prove mathematically that\nthe equivalence remains valid when the density matrix is not idempotent\nanymore, thus allowing for the construction of correlated (one-electron)\nquantum baths. A density-matrix functional exactification of DMET is derived\nwithin the present unified quantum embedding formalism. Numerical examples\nreveal that the embedding cluster can be quite sensitive to the level of\ndensity-matrix functional approximation used for computing the reference\ndensity matrix.", "category": "physics_chem-ph" }, { "text": "Field-Induced Electron Generation in Water: Solvation Dynamics and\n Many-Body Interactions: The solvated electron represents an elementary quantum system in a liquid\nenvironment. Electrons solvated in water have raised strong interest because of\ntheir prototypical properties, their role in radiation chemistry, and their\nrelevance for charge separation and transport. Nonequilibrium dynamics of\nphotogenerated electrons in water occur on ultrafast time scales and include\ncharge transfer, localization, and energy dissipation processes. We present new\ninsight in the role of fluctuating electric fields of the liquid for generating\nelectrons in presence of an external terahertz field and address polaronic\nmany-body properties of solvated electrons. The article combines a review of\nrecent results from experiment and theory with a discussion of basic electric\ninteractions of electrons in water.", "category": "physics_chem-ph" }, { "text": "Graph-based Quantum Response Theory and Shadow Born-Oppenheimer\n Molecular Dynamics: Graph-based linear scaling electronic structure theory for quantum-mechanical\nmolecular dynamics simulations is adapted to the most recent shadow potential\nformulations of extended Lagrangian Born-Oppenheimer molecular dynamics,\nincluding fractional molecular-orbital occupation numbers, which enables stable\nsimulations of sensitive complex chemical systems with unsteady charge\nsolutions. The proposed formulation includes a preconditioned Krylov subspace\napproximation for the integration of the extended electronic degrees of\nfreedom, which requires quantum response calculations for electronic states\nwith fractional occupation numbers. For the response calculations we introduce\na graph-based canonical quantum perturbation theory that can be performed with\nthe same natural parallelism and linear scaling complexity as the graph-based\nelectronic structure calculations for the unperturbed ground state. The\nproposed techniques are particularly well-suited for semi-empirical electronic\nstructure theory and the methods are demonstrated using self-consistent charge\ndensity-functional tight-binding (SCC-DFTB) theory, both for the acceleration\nof self-consistent field calculations and for quantum molecular dynamics\nsimulations. The graph-based techniques combined with the semi-empirical theory\nenable stable simulations of large, complex chemical systems, including\ntens-of-thousands of atoms.", "category": "physics_chem-ph" }, { "text": "Precision measurement of the rotational energy-level structure of the\n three-electron molecule He$_2^+$: The term values of all rotational levels of the\n$^4$He${_2}^+\\,X^+\\,^2\\Sigma_u^+\\,(\\nu^+=0)$ ground vibronic state with\nrotational quantum number $N^+\\le 19$ have been determined with an accuracy of\n8 x 10$^{-4}$ cm$^{-1}$ ($\\sim{25}$ MHz) by MQDT-assisted Rydberg spectroscopy\nof metastable He$_2^*$. Comparison of these term values with term values\nrecently calculated ab initio by Tung et al. [J. Chem. Phys. 136, 104309\n(2012)] reveal discrepancies that rapidly increase with increasing rotational\nquantum number and reach values of 0.07 cm$^{-1}$ ($\\sim{2.1}$ GHz) at\n$N^+=19$.", "category": "physics_chem-ph" }, { "text": "Excited electronic states from a variational approach based on\n symmetry-projected Hartree--Fock configurations: Recent work from our research group has demonstrated that symmetry-projected\nHartree--Fock (HF) methods provide a compact representation of molecular ground\nstate wavefunctions based on a superposition of non-orthogonal Slater\ndeterminants. The symmetry-projected ansatz can account for static correlations\nin a computationally efficient way. Here we present a variational extension of\nthis methodology applicable to excited states of the same symmetry as the\nground state. Benchmark calculations on the C$_2$ dimer with a modest basis\nset, which allows comparison with full configuration interaction results,\nindicate that this extension provides a high quality description of the\nlow-lying spectrum for the entire dissociation profile. We apply the same\nmethodology to obtain the full low-lying vertical excitation spectrum of\nformaldehyde, in good agreement with available theoretical and experimental\ndata, as well as to a challenging model $C_{2v}$ insertion pathway for BeH$_2$.\nThe variational excited state methodology developed in this work has two\nremarkable traits: it is fully black-box and will be applicable to fairly large\nsystems thanks to its mean-field computational cost.", "category": "physics_chem-ph" }, { "text": "Enabling Heterogeneous Catalysis to Achieve Carbon Neutrality:\n Directional Catalytic Conversion of CO$_2$ into Carboxylic Acids: The increase in anthropogenic carbon dioxide (CO$_2$) emissions has\nexacerbated the deterioration of the global environment, which should be\ncontrolled to achieve carbon neutrality. Central to the core goal of achieving\ncarbon neutrality is the utilization of CO$_2$ under economic and sustainable\nconditions. Recently, the strong need for carbon neutrality has led to a\nproliferation of studies on the direct conversion of CO$_2$ into carboxylic\nacids, which could effectively alleviate CO$_2$ emissions and create high-value\nchemicals. The purpose of this review is to present the application prospects\nof carboxylic acids and the basic principles of CO$_2$ conversion into\ncarboxylic acids through photo-, electric-, and thermal catalysis. Special\nattention is focused on the regulation strategy of the activity of abundant\ncatalysts at the molecular level, inspiring the preparation of high-performance\ncatalysts. In addition, theoretical calculation, advanced technologies, and\nnumerous typical examples are introduced to elaborate on the corresponding\nprocess and influencing factors of catalytic activity. Finally, challenges and\nprospects are provided for the future development of this field. It is hoped\nthat this review contributes to a deeper understanding of the conversion of\nCO$_2$ into carboxylic acids and inspires more innovative breakthroughs", "category": "physics_chem-ph" }, { "text": "Ring-polymer instanton theory of electron transfer in the nonadiabatic\n limit: We take the golden-rule instanton method derived in the previous paper\n[arXiv:1509.04919] and reformulate it using a ring-polymer approach. This gives\nequations which can be used to compute the rates of electron-transfer reactions\nin the nonadiabatic (golden-rule) limit numerically within a semiclassical\napproximation. The multidimensional ring-polymer instanton trajectories are\nobtained efficiently by minimization of the action. In this form, comparison\nwith Wolynes' quantum instanton method [P. G. Wolynes, J. Chem. Phys. 87, 6559\n(1987)] is possible and we show that our semiclassical approach is the\nsteepest-descent limit of this method. We discuss advantages and disadvantages\nof both methods and give examples of where the new approach is more accurate.", "category": "physics_chem-ph" }, { "text": "Improved laser-distillation method for complete enantio-conversion of\n chiral mixtures: Laser-assisted enantio-conversion is an ambitious issue related to chiral\nmolecules in the atomic, molecular, and optical physics. The theoretical\nlaser-distillation method had been proposed to realize enantio-conversion based\non a four-level double-$\\Delta$ model of two degenerated chiral ground states\nand two achiral excited states. Here, we re-investigate and improve the\nlaser-distillation method so that a chiral mixture can be converted to an\nenantiopure sample of the desired chirality, i.e., complete enantio-conversion,\nwhich has not been discussed in the previous theoretical works of the\nlaser-distillation method. Since the undesired chirality may be inefficient or\neven cause serious side effects in pharmacology, our work plays as an important\nimprovement to the original theoretical works of the laser-assisted\nenantio-conversion.", "category": "physics_chem-ph" }, { "text": "A Universal Density Matrix Functional from Molecular Orbital-Based\n Machine Learning: Transferability across Organic Molecules: We address the degree to which machine learning can be used to accurately and\ntransferably predict post-Hartree-Fock correlation energies. Refined strategies\nfor feature design and selection are presented, and the molecular-orbital-based\nmachine learning (MOB-ML) method is applied to several test systems.\nStrikingly, for the MP2, CCSD, and CCSD(T) levels of theory, it is shown that\nthe thermally accessible (350 K) potential energy surface for a single water\nmolecule can be described to within 1 millihartree using a model that is\ntrained from only a single reference calculation at a randomized geometry. To\nexplore the breadth of chemical diversity that can be described, MOB-ML is also\napplied to a new dataset of thermalized (350 K) geometries of 7211 organic\nmodels with up to seven heavy atoms. In comparison with the previously reported\n$\\Delta$-ML method, MOB-ML is shown to reach chemical accuracy with three-fold\nfewer training geometries. Finally, a transferability test in which models\ntrained for seven-heavy-atom systems are used to predict energies for\nthirteen-heavy-atom systems reveals that MOB-ML reaches chemical accuracy with\n36-fold fewer training calculations than $\\Delta$-ML (140 versus 5000 training\ncalculations).", "category": "physics_chem-ph" }, { "text": "Symmetric Post-Transition-State Bifurcation Reactions with Berry\n Pseudo-Magnetic Fields: We investigate how the Berry force (i.e. the pseudo-magnetic force operating\non nuclei as induced by electronic degeneracy and spin-orbit coupling (SOC))\nmight modify a post-transition state bifurcation (PTSB) reaction path and\naffect product selectivity for situations when multiple products share the same\ntransition state. To estimate the magnitude of this effect, Langevin dynamics\nare performed on a model system with a valley-ridge inflection (VRI) point in\nthe presence of a magnetic field (that mimics the Berry curvature). We also\ndevelop an analytic model for such selectivity that depends on key parameters\nsuch as the surface topology, the magnitude of the Berry force, and the nuclear\nfriction. Within this dynamical model, static electronic structure calculations\n(at the level of generalized Hartree-Fock with spin-orbit coupling (GHF+SOC)\ntheory) suggest that electronic-spin induced Berry force effects may indeed\nlead to noticeable changes in methoxy radical isomerization.", "category": "physics_chem-ph" }, { "text": "Converging High-Level Coupled-Cluster Energetics via Adaptive Selection\n of Excitation Manifolds Driven by Moment Expansions: A novel approach to rapidly converging high-level coupled-cluster (CC)\nenergetics in an automated fashion is proposed. The key idea is an adaptive\nselection of the excitation manifolds defining higher-than-two-body components\nof the cluster operator inspired by the CC($P$;$Q$) moment expansions. The\nusefulness of the resulting methodology is illustrated by molecular examples\nwhere the goal is to recover the electronic energies obtained using the CC\nmethod with a full treatment of singly, doubly, and triply excited clusters\n(CCSDT) when the noniterative triples corrections to CCSD fail.", "category": "physics_chem-ph" }, { "text": "Prediction of many-electron wavefunctions using atomic potentials: For a given many-electron molecule, it is possible to define a corresponding\none-electron Schr\\\"odinger equation, using potentials derived from simple\natomic densities, whose solution predicts fairly accurate molecular orbitals\nfor single- and multi-determinant wavefunctions for the molecule. The energy is\nnot predicted and must be evaluated by calculating Coulomb and exchange\ninteractions over the predicted orbitals. Potentials are found by minimizing\nthe energy of predicted wavefunctions. There exist slightly less accurate\naverage potentials for first-row atoms that can be used without modification in\ndifferent molecules. For a test set of molecules representing different bonding\nenvironments, these average potentials give wavefunctions with energies that\ndeviate from exact self-consistent field or configuration interaction energies\nby less than 0.08 eV and 0.03 eV per bond or valence electron pair,\nrespectively.", "category": "physics_chem-ph" }, { "text": "Doped rare gas clusters up to completion of first solvation shell,\n CO2-(Rg)n, n = 3-17, Rg = Ar, Kr, Xe: Spectra of rare gas atom clusters containing a single carbon dioxide molecule\nare observed using a tunable mid-infrared (4.3 micron) source to probe a pulsed\nslit jet supersonic expansion. There are relatively few previous detailed\nexperimental results on such clusters. The assigned clusters include CO2-Arn\nwith n = 3, 4, 6, 9, 10, 11, 12, 15, and 17, as well as CO2-Krn and -Xen with n\n= 3, 4, and 5. Each spectrum has (at least) partially resolved rotational\nstructure, and each yields precise values for the shift of the CO2 vibrational\nfrequency (nu3) induced by the nearby rare gas atoms, together with one or more\nrotational constants. These results are compared with theoretical predictions.\nThe more readily assigned CO2-Arn species tend to be those with symmetric\nstructures, and CO2-Ar17 represents completion of a highly symmetric (D5h)\nsolvation shell. Those not assigned (e.g. n = 7, 13) are probably also present\nin the observed spectra, but with band structures which are not well-resolved\nand thus not recognizable. The spectra of CO2-Ar9, -Ar15, and -Ar17 suggest the\npresence of sequences involving very low frequency (~2 cm-1) cluster\nvibrational modes, an interpretation which should be amenable to theoretical\nconfirmation (or rejection).", "category": "physics_chem-ph" }, { "text": "Anomalous Effects in Air While Cooling Water: Water is a unique compound with many anomalies and properties not fully\nunderstood. Designing an experiment in the laboratory to study such anomalies,\nwe set up a series of experiments where a tube was placed inside a sealed\ncontainer with thermocouples attached to the outer surface of the tube and in\nthe air adjacent to the tube. Alternately, deionized water and other compounds\nwere added to the tube and cooled to freezing. Several of the thermocouples\nsuspended in the air and adjacent to the tube showed thermal oscillations as\nthe overall temperature of the container was decreasing. The temperature of the\nthermocouples increased and decreased in a sinusoidal way during part of the\ncool down to freezing. Thermal oscillations as large as 3 degrees Celsius were\nrecorded with typical frequencies of about 5 oscillations per minute.", "category": "physics_chem-ph" }, { "text": "Ultrafast dephasing in hydrogen-bonded pyridine-water mixtures: Hydrogen-bonded mixtures with varying concentration are a complicated\nnetworked system that demands a detection technique with both time and\nfrequency resolutions. Hydrogen-bonded pyridine-water mixtures are studied by a\ntime-frequency resolved coherent Raman spectroscopic technique. Femtosecond\nbroadband dual-pulse excitation and delayed picosecond probing provide\nsub-picosecond time resolution in the mixtures temporal evolution. For\ndifferent pyridine concentrations in water, asymmetric blue versus red shifts\n(relative to pure pyridine spectral peaks) were observed by simultaneously\nrecording both the coherent anti-Stokes and Stokes Raman spectra. Macroscopic\ncoherence dephasing times for the perturbed pyridine ring modes were observed\nin ranges of 0.9 - 2.6 picoseconds for both 18 and 10 cm-1 broad probe pulses.\nFor high pyridine concentrations in water, an additional spectral broadening\n(or escalated dephasing) for a triangular ring vibrational mode was observed.\nThis can be understood as a result of ultrafast collective emissions from\ncoherently excited ensemble of pairs of pyridine molecules bound to water\nmolecules.", "category": "physics_chem-ph" }, { "text": "The proton momentum distribution in strongly H-bonded phases of water; a\n critical test of electrostatic models: Water is often viewed as a collection of monomers interacting\nelectrostatically with each other. We compare the water proton momentum\ndistributions from recent neutron scattering data with those calculated from\ntwo electronic structure based models. We find that below 500 K the\nelectrostatic models are not able to even qualitatively account for the sizable\nvibrational zero-point contribution to the enthalpy of vaporization. This\ndiscrepancy is evidence that the change in the proton well upon solvation\ncannot be entirely explained by electrostatic effects alone.", "category": "physics_chem-ph" }, { "text": "Corrosion studies on Fe-30Mn-1C alloy in chloridecontaining solutions\n with view to biomedical application: Austenitic Fe-30Mn-1C (FeMnC) is a prospective biodegradable implant material\ncombining high mechanical integrity with adequate corrosion rates. The fast\nsolidified TWIP alloy, its constituents and 316L stainless steel were\nelectrochemically analysed in various electrolytes at 37 {\\deg}C under laminar\nflow. Potentiodynamic polarization tests were conducted in Trisbuffered\nsimulated body fluid (SBF), in Tris-buffered saline (TBS) and in 150 mM - 0.15\nmM NaCl solutions (pH 7.6, 10, 5, 2) to study initial corrosion stages. Active\ndissolution of FeMnC is revealed in all electrolytes and is discussed on basis\nof the Fe and Mn behaviour plus is compared to that of 316L. The role of Tris\n(Tris(hydroxymethyl)aminomethane) as organic buffer for SBFs is critically\nassessed, particularly with view to the sensitivity of Fe. SEM studies of FeMnC\ncorroded in NaCl revealed preferential dissolution along Mn-rich grain boundary\nregions. Static immersion tests of FeMnC in SBF with surface and solution\nanalyses (SEM/EDX, XPS, ICP-OES) indicated that dissolution processes interfere\nwith the formation of permeable surface coatings comprising hydroxides and\nsalts.", "category": "physics_chem-ph" }, { "text": "Spin-Lattice Relaxation in Metal-Organic Platinum(II) Complexes: The dynamics of spin-lattice relaxation (slr) of metal-organic Pt(II)\ncompounds is studied. Often, such systems are characterized by pronounced\nzero-field splittings (zfs) of the lowest-lying triplets. Previous expressions\nfor the Orbach slr process do not allow to treat such splitting patterns\nproperly. We discuss the behavior of a modified Orbach expression for a model\nsystem and present results of a fit of the temperature dependence of the\nspin-lattice relaxation rate of Pt(2-thpy)$_2$ based on the modified\nexpression.", "category": "physics_chem-ph" }, { "text": "A New Type of Two-photon Forward Radiation in Pure Liquids: Unexpected spectral features are observed in the two photon spectrum of the\npure water in the forward direction when an 80 femtosecond laser pulse is\nfocused at 10^10Wcm-2 or less. Such intensity is much lower than the breakdown\nor stimulated threshold of the liquid water. The two broad features are about\n2700cm-1 and 5000cm-1 red shifted from the hyper-Rayleigh wavelength,\nrespectively, and they are quadratic with the laser intensity. They do not\nmatch the known Raman or hyper-Raman frequencies of water, and they are both\ncentered at a narrow angle in the forward direction. Several other liquids also\nexhibited similar but molecular specific spectral features.", "category": "physics_chem-ph" }, { "text": "Two-dimensional partial covariance mass spectrometry for the top-down\n analysis of intact proteins: Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the\ninherent fluctuations of fragment ion abundances across a series of tandem mass\nspectra, to identify correlated pairs of fragment ions produced along the same\nfragmentation pathway of the same parent (e.g. peptide) ion. Here, we apply\n2D-PC-MS to the analysis of intact protein ions in a standard linear ion trap\nmass analyzer, using the fact that the fragment-fragment correlation signals\nare much more specific to bio-molecular sequence than 1D MS/MS signals at the\nsame mass accuracy and resolution. We show that from the distribution of\nsignals on a 2D-PC-MS map it is possible to extract the charge state of both\nparent and fragment ions without resolving the isotopic envelope. Furthermore,\nthe 2D map of fragment-fragment correlations naturally reveals the secondary\ndecomposition pathways of the fragment ions. We access this spectral\ninformation using an adapted version of the Hough transform. We demonstrate the\nsuccessful identification of highly charged, intact protein molecules without\nthe need for high mass resolution. Using this technique we also perform the in\nsilico deconvolution of the overlapping fragment ion signals from two\nco-isolated and co-fragmented intact protein molecules, demonstrating a viable\nnew method for the concurrent mass spectrometric identification of a mixture of\nintact protein ions from the same fragment ion spectrum.", "category": "physics_chem-ph" }, { "text": "On detailed balance in nonadiabatic dynamics: From spin spheres to\n equilibrium ellipsoids: Trajectory-based methods that propagate classical nuclei on multiple quantum\nelectronic states are often used to simulate nonadiabatic processes in the\ncondensed phase. A long-standing problem of these methods is their lack of\ndetailed balance, meaning that they do not conserve the equilibrium\ndistribution. In this article, we investigate ideas for how to restore detailed\nbalance in mixed quantum--classical systems by tailoring the previously\nproposed spin-mapping approach to thermal equilibrium. We find that adapting\nthe spin magnitude can recover the correct long-time populations but is\ninsufficient to conserve the full equilibrium distribution. The latter can\nhowever be achieved by a more flexible mapping of the spin onto an ellipsoid,\nwhich is constructed to fulfill detailed balance for arbitrary potentials. This\nellipsoid approach solves the problem of negative populations that has plagued\nprevious mapping approaches and can therefore be applied also to strongly\nasymmetric and anharmonic systems. Because it conserves the thermal\ndistribution, the method can also exploit efficient sampling schemes used in\nstandard molecular dynamics, which drastically reduces the number of\ntrajectories needed for convergence. The dynamics does however still have\nmean-field character, as is observed most clearly by evaluating reaction rates\nin the golden-rule limit. This implies that although the ellipsoid mapping\nprovides a rigorous framework, further work is required to find an accurate\nclassical-trajectory approximation that captures more properties of the true\nquantum dynamics.", "category": "physics_chem-ph" }, { "text": "Machine learning potentials for complex aqueous systems made simple: Simulation techniques based on accurate and efficient representations of\npotential energy surfaces are urgently needed for the understanding of complex\naqueous systems such as solid-liquid interfaces. Here, we present a machine\nlearning framework that enables the efficient development and validation of\nmodels for complex aqueous systems. Instead of trying to deliver a\nglobally-optimal machine learning potential, we propose to develop models\napplicable to specific thermodynamic state points in a simple and user-friendly\nprocess. After an initial ab initio simulation, a machine learning potential is\nconstructed with minimum human effort through a data-driven active learning\nprotocol. Such models can afterwards be applied in exhaustive simulations to\nprovide reliable answers for the scientific question at hand. We showcase this\nmethodology on a diverse set of aqueous systems with increasing degrees of\ncomplexity. The systems chosen here comprise bulk water with different ions in\nsolution, water on a titanium dioxide surface, as well as water confined in\nnanotubes and between molybdenum disulfide sheets. Highlighting the accuracy of\nour approach with respect to the underlying ab initio reference, the resulting\nmodels are evaluated in detail with an automated validation protocol that\nincludes structural and dynamical properties and the precision of the force\nprediction of the models. Finally, we demonstrate the capabilities of our\napproach for the description of water on the rutile titanium dioxide (110)\nsurface to analyze the structure and mobility of water on this surface. Such\nmachine learning models provide a straightforward and uncomplicated but\naccurate extension of simulation time and length scales for complex systems.", "category": "physics_chem-ph" }, { "text": "Path integral molecular dynamics with surface hopping for thermal\n equilibrium sampling of nonadiabatic systems: In this work, a novel ring polymer representation for multi-level quantum\nsystem is proposed for thermal average calculations. The proposed presentation\nkeeps the discreteness of the electronic states: besides position and momentum,\neach bead in the ring polymer is also characterized by a surface index\nindicating the electronic energy surface. A path integral molecular dynamics\nwith surface hopping (PIMD-SH) dynamics is also developed to sample the\nequilibrium distribution of ring polymer configurational space. The PIMD-SH\nsampling method is validated theoretically and by numerical examples.", "category": "physics_chem-ph" }, { "text": "The Combined Influence of Nuclear Quantum Effects and van der Waals\n Interactions on the Structure of Ambient Water: Path-integral molecular dynamics simulations based on density functional\ntheory employing exchange-correlation density functionals capable of treating\nnonlocal van der Waals (vdW) interactions self-consistently provide a\nremarkably accurate description of ambient water. Moreover, they suggest that\nwater's structure may be impacted by a combined influence between nuclear\nquantum effects and vdW interactions. The latter strongly favor the formation\nof a high-density liquid, whereas the inclusion of the former mitigates this by\ndecreasing the mean hydrogen-bond (H-bond) distance. Examining the structure of\nwater reveals that while the major fraction of molecules do in fact exhibit the\ntraditional picture of near-tetrahedral coordination, the liquid considerably\nsofter than previously simulations have suggested, including a much lower\nproportion of molecules double-donating H-bonds as well as a much larger\ndistribution of their angles.", "category": "physics_chem-ph" }, { "text": "Chemical Reactivity Studies by the Natural-Orbital-Functional\n 2nd-Order-Moller-Plesset (NOF-MP2) method. Water Dehydrogenation by the\n Scandium Cation: The reliability of the recently proposed natural orbital functional\nsupplemented with second-order M{\\o}ller-Plesset calculations, (NOF-MP2), has\nbeen assessed for the mechanistic studies of elementary reactions of transition\nmetal compounds by investigating the dehydrogenation of water by the scandium\ncation. Both high- and low-spin state potential energy surfaces have been\nsearched thoroughly. Special attention has been paid to the assessment of the\ncapability of the NOF-MP2 method to describe the strong, both static and\ndynamic, electron correlation effects on the reactivity of Sc+(3D,1D) with\nwater. In agreement with experimental observations, our calculations correctly\npredict that the only exothermic products are the lowest-lying ScO+(1\\Sigma)\nand H2(1\\Sigma_g+) species. Nevertheless, an in-depth analysis of the reaction\npaths leading to several additional products was carried out, including the\ncharacterization of various minima and several key transition states. Our\nresults have been compared with the highly accurate multiconfigurational\nsupplemented with quasi degenerate perturbation theory, MCQDPT,\nwavefunction-type calculations, and with the available experimental data. It is\nobserved that NOF-MP2 is able to give a satisfactorily quantitative agreement,\nwith a performance on par with that of the MCQDPT method.", "category": "physics_chem-ph" }, { "text": "Mechanism of CO-oxidation on Pd/CeO2(100): The unique surface-structure\n of CeO2(100) and the role of peroxide: Understanding the atomic mechanism of low-temperature CO oxidation on a\nheterogeneous catalyst is challenging. We performed density functional theory\n(DFT) calculations to identify the surface structure and reaction mechanism\nresponsible for low-temperature CO oxidation on Pd/CeO2 (100) surfaces. DFT\ncalculations reveal the formation of a unique zigzag chain structure by the\noxygen and Ce atoms of the topmost surface of CeO2(100) with Pd atoms located\nbetween the zigzag chains. O2 adsorbed on such Pd atoms is stable in the\npresence of CO but plays a very important role in lowering the activation\nbarrier for low-temperature CO oxidation by forming a square-planar PdO4\nstructure and facilitating further O2 adsorption. In-situ Raman spectroscopy\nstudies confirm the adsorbed oxygen species to be peroxides. The calculated\nactivation barrier for CO oxidation, based on the mechanism suggested by these\nunique structures and peroxides, is 31.2 kJ/mol, in excellent agreement with\nour experimental results.", "category": "physics_chem-ph" }, { "text": "Combining Machine Learning and Spectroscopy to Model Reactive Atom +\n Diatom Collisions: The prediction of product translational, vibrational, and rotational energy\ndistributions for arbitrary initial conditions for reactive atom+diatom\ncollisions is of considerable practical interest in atmospheric re-entry. Due\nto the large number of accessible states, determination of the necessary\ninformation from explicit (quasi-classical or quantum) dynamics studies is\nimpractical. Here, a machine-learned (ML) model based on translational energy\nand product vibrational states assigned from a spectroscopic, ro-vibrational\ncoupled energy expression based on the Dunham expansion is developed and tested\nquantitatively. All models considered in this work reproduce final state\ndistributions determined from quasi-classical trajectory (QCT) simulations with\n$R^2 \\sim 0.98$. As a further validation, thermal rates determined from the\nmachine-learned models agree with those from explicit QCT simulations and\ndemonstrate that the atomistic details are retained by the machine learning\nwhich makes them suitable for applications in more coarse-grained simulations.\nMore generally, it is found that ML is suitable for designing robust and\naccurate models from mixed computational/experimental data which may also be of\ninterest in other areas of the physical sciences.", "category": "physics_chem-ph" }, { "text": "Similarity transformed equation of motion coupled cluster theory\n revisited: a benchmark study of valence excited states: The similarity transformed equation of motion coupled cluster (STEOM-CC)\nmethod is benchmarked against CC3 and EOM-CCSDT-3 for a large test set of\nvalence excited states of organic molecules studied by Schreiber et al. [M.\nSchreiber, M.R. Silva-Junior, S.P. Sauer, and W. Thiel, J. Chem. Phys.\n$\\textbf{128}$, 134110 (2008)]. STEOM-CC is found to behave quite\nsatisfactorily and provides significant improvement over EOM-CCSD, CASPT2 and\nNEVPT2 for singlet excited states, lowering standard deviations of these\nmethods by almost a factor of 2. Triplet excited states are found to be\ndescribed less accurately, however. Besides the parent version of STEOM-CC,\nadditional variations are considered. STEOM-D includes a perturbative\ncorrection from doubly excited determinants. The novel STEOM-H ($\\omega$)\napproach presents a sophisticated technique to render the STEOM-CC transformed\nHamiltonian hermitian. In STEOM-PT, the expensive CCSD step is replaced by\nmany-body second-order perturbation theory (MBPT(2)), while extended STEOM\n(EXT-STEOM) provides access to doubly excited states. To study orbital\ninvariance in STEOM, we investigate orbital rotation in the STEOM-ORB approach.\nComparison of theses variations of STEOM for the large test set provides a\ncomprehensive statistical basis to gauge the usefulness of these approaches.", "category": "physics_chem-ph" }, { "text": "Towards a fully size-consistent method of increments: The method of increments (MoI) allows one to successfully calculate cohesive\nenergies of bulk materials with high accuracy, but it encounters difficulties\nwhen calculating whole dissociation curves. The reason is that its standard\nformalism is based on a single Hartree-Fock (HF) configuration whose orbitals\nare localized and used for the many-body expansion. Therefore, in those\nsituations where HF does not allow a size-consistent description of the\ndissociation, the MoI cannot yield proper results either. Herein we address the\nproblem by employing a size-consistent multiconfigurational reference for the\nMoI formalism. This leads to a matrix equation where a coupling derived by the\nreference itself is employed. In principle, such approach allows one to\nevaluate approximate values for the ground as well as excited states energies.\nWhile the latter are accurate close to the avoided crossing only, the ground\nstate results are very promising for the whole dissociation curve, as shown by\nthe comparison with density matrix renormalization group (DMRG) benchmarks. We\ntested this two-state constant-coupling (TSCC)-MoI on beryllium rings of\ndifferent sizes and studied the error introduced by the constant coupling.", "category": "physics_chem-ph" }, { "text": "Variational Monte Carlo on a Budget -- Fine-tuning pre-trained Neural\n Wavefunctions: Obtaining accurate solutions to the Schr\\\"odinger equation is the key\nchallenge in computational quantum chemistry. Deep-learning-based Variational\nMonte Carlo (DL-VMC) has recently outperformed conventional approaches in terms\nof accuracy, but only at large computational cost. Whereas in many domains\nmodels are trained once and subsequently applied for inference, accurate DL-VMC\nso far requires a full optimization for every new problem instance, consuming\nthousands of GPUhs even for small molecules. We instead propose a DL-VMC model\nwhich has been pre-trained using self-supervised wavefunction optimization on a\nlarge and chemically diverse set of molecules. Applying this model to new\nmolecules without any optimization, yields wavefunctions and absolute energies\nthat outperform established methods such as CCSD(T)-2Z. To obtain accurate\nrelative energies, only few fine-tuning steps of this base model are required.\nWe accomplish this with a fully end-to-end machine-learned model, consisting of\nan improved geometry embedding architecture and an existing SE(3)-equivariant\nmodel to represent molecular orbitals. Combining this architecture with\ncontinuous sampling of geometries, we improve zero-shot accuracy by two orders\nof magnitude compared to the state of the art. We extensively evaluate the\naccuracy, scalability and limitations of our base model on a wide variety of\ntest systems.", "category": "physics_chem-ph" }, { "text": "Electron Scattering from Gaseous Ocs($^1\u03a3$): Comparing Computed\n Angular Distributions and Elastic Cross Sections with Experiments: Differential cross sections are computed for the title polar molecule using\nstatic interaction, exchange forces and correlation-polarisation effects as\ndescribed in detail in the main text. The dipole effect is also reported via\nthe dipole Born correction procedure and the final angular distributions are\ncompared with existing experimental data. The shape and location of the\nprominent low-energy resonance are computed and compared with experiments. The\ncomparison shows that the present treatment of the interaction forces and of\nthe quantum dynamics can indeed afford good agreement between measured and\ncomputed quantities for a multielectron target as OCS.", "category": "physics_chem-ph" }, { "text": "The MD17 Datasets from the Perspective of Datasets for Gas-Phase \"Small\"\n Molecule Potentials: There has been great progress in developing methods for machine-learned\npotential energy surfaces. There have also been important assessments of these\nmethods by comparing so-called learning curves on datasets of electronic\nenergies and forces, notably the MD17 database. The dataset for each molecule\nin this database generally consists of tens of thousands of energies and forces\nobtained from DFT direct dynamics at 500 K. We contrast the datasets from this\ndatabase for three \"small\" molecules, ethanol, malonaldehyde, and glycine, with\ndatasets we have generated with specific targets for the PESs in mind: a\nrigorous calculation of the zero-point energy and wavefunction, the tunneling\nsplitting in malonaldehyde and in the case of glycine a description of all\neight low-lying conformers. We found that the MD17 datasets are too limited for\nthese targets. We also examine recent datasets for several PESs that describe\nsmall-molecule but complex chemical reactions. Finally, we introduce a new\ndatabase, \"QM-22\", which contains datasets of molecules ranging from 4 to 15\natoms that extend to high energies and a large span of configurations.", "category": "physics_chem-ph" }, { "text": "Invariance of experimental observables with respect to coarse-graining\n in standard and many-body dissipative particle dynamics: Dissipative particle dynamics (DPD) is a well-established mesoscale\nsimulation method. However, there have been long-standing ambiguities regarding\nthe dependence of its (purely repulsive) force field parameter on temperature\nas well as the variation of the resulting experimental observables, such as\ndiffusivity or surface tension, with coarse-graining (CG) degree. Here, we\nrevisit the role of the CG degree and rederive the temperature dependence in\nstandard DPD simulations. Consequently, we derive a scaling of the input\nvariables that renders the system properties invariant with respect to CG\ndegree, and illustrate the versatility of the method by computing the surface\ntensions of binary solvent mixtures. We then extend this procedure to many-body\ndissipative particle dynamics (MDPD) and, by computing surface tensions of the\nsame mixtures at a range of CG degrees, demonstrate that this newer method,\nwhich has not been widely applied so far, is also capable of simulating complex\nfluids of practical interest.", "category": "physics_chem-ph" }, { "text": "Exploring molecular dynamics with forces from n-body potentials using\n Matlab: We present methods for exploratory studies of molecular dynamics using\nMATLAB. Such methods are not suitable for large scale applications, but they\ncan be used for developement and testing of new types of interactions and other\naspects of the simulations, or simply for instruction and education purposes.\nWe also present exploration of forces obtained from 3-body potentials in\nMolecular Dynamics in this framework. The methods are based on use of matrices\nand multidimensional arrays for which MATLAB has a set of both linear algebra\nbased as well as element-wise operations. Applications to three-body\ninteractions are the main aspect of this work, but extension to any general\nform of n-body interactions is also discussed. The methods discussed can be\nalso applied without any change using the latest versions of the package GNU\nOCTAVE as a replacement for MATLAB. The code examples are listed in some\ndetail, a full package of the MATLAB and OCTAVE codes is available for\ndownload.", "category": "physics_chem-ph" }, { "text": "Effect of Low Oxygen Annealing on Photoelectrochemical Water Splitting\n Properties of $\u03b1$-Fe$_2$O$_3$: Photoelectrochemical (PEC) water splitting is a promising method for\nconversing solar energy into chemical energy stored in the form of hydrogen.\nNanostructured hematite ($\\alpha$-Fe$_2$O$_3$) is one of the most attractive\nmaterials for highly efficient charge carrier generation and collection due to\nits large specific surface area and shortening minority carrier diffusion\nlength required to reach the surface. In the present work, PEC water splitting\nperformance of $\\alpha$-Fe$_2$O$_3$ prepared by anodization of thin iron layers\non an FTO glass and subsequent annealing in low O$_2$-Ar ambient with only\n0.03% O$_2$ was investigated. The key finding is that annealing the anodic\nnanostructures with low oxygen concentration provides a strongly enhanced PEC\nperformance compared with classic air annealing. The photocurrent of the former\nat 1.5 V vs. RHE results in 1.1 mA/cm2, being 11 times higher than that of the\nlatter. The enhancement of the PEC performance for $\\alpha$-Fe$_2$O$_3$\nannealed in low oxygen atmosphere can be attributed to controlled morphology,\nSn doping, and introduction of oxygen vacancies, which contribute to the\nenhancement of the hole flux from the photogenerated site to the reactive\nsurface and additionally lead to an enhanced hole transfer at the interface\nbetween the $\\alpha$-Fe$_2$O$_3$ and the electrolyte. From the obtained\nresults, it is evident that low oxygen annealing is a surprisingly effective\nmethod of defect engineering and optimizing $\\alpha$-Fe$_2$O$_3$ electrodes for\na maximized PEC water splitting performance.", "category": "physics_chem-ph" }, { "text": "A Review of Experimental Solubilities and a General Correlation between\n the Temperature-Dependent Solubility and Solute and Solvent Molar Masses for\n Binary n-Alkane Mixtures: The solubility of a \"heavy\" alkane (solute) in a \"light\" alkane (solvent) is\ngenerally temperature dependent. Moreover, it is determined by the molar masses\nof the solute and solvent. In the current paper, published solubility data for\nbinary normal-alkane mixtures is reviewed (solid-liquid equilibrium). A total\nof 43 unique solute-solvent data-sets, obtained from a total of 24 published\nexperimental studies, are collected and presented in a systematic manner. Based\non thermodynamic considerations and the experimental data, it is demonstrated\nthat there is a log-linear relationship between the solubility and the\ntemperature in the dilute range. Linear regression is employed to 1) obtain\ndata-set-specific solubility-temperature best-fit parameters and 2) obtain a\ngeneral correlation between the solubility and the solvent and solute molar\nmasses and the temperature. Finally, it is demonstrated that the developed\ncorrelation carries predictive power even for multi-component mixtures by\nutilizing solvent and solute average molar masses.", "category": "physics_chem-ph" }, { "text": "Two-orders of magnitude improvement detection limit of lateral flow\n assays using isotachophoresis: Lateral flow (LF) immunoassays are one of the most prevalent point-of-care\n(POC) diagnostics due to their simplicity, low cost, and robust operation. A\ncommon criticism of LF tests is that they have poor detection limits compared\nto analytical techniques, like ELISA, which confines their application as a\ndiagnostic tool. The low detection limit of LF assays and associated long\nequilibration times is due to kinetically limited surface reactions that result\nfrom low target concentrations. Here we use isotachophoresis (ITP), a powerful\nelectrokinetic preconcentration and separation technique, to focus target\nanalytes into a thin band and transport them to the LF capture line resulting\nis a dramatic increase in the surface reaction rate and equilibrium binding. We\nshow that ITP is able to improve limit of detection (LOD) of LF assays by\n400-fold for 90 second assay time and by 160-fold for a longer 5 minutes time\nscale. ITP-enhanced LF (ITP-LF) also shows up to 30% target extraction from 100\nuL of the sample, while conventional LF captures less than 1% of the target.\nITP improves LF assay LOD to the level of some lab based immunoassays, such as\nELISA, and may provide sufficient analytical sensitivity for application to a\nbroader range of analytes and diseases that require higher sensitivity and\nlower detection limits.", "category": "physics_chem-ph" }, { "text": "Ab initio study of charge doping effect on 1D polymerization of C60: We study the interplay between charge doping and intermolecular distance in\nthe polymerization of C60 fullerene chains by means of density functional\ntheory (DFT)-based first principle calculations. The potential energy surface\nanalysis shows that both the equilibrium intermolecular distance of the\nunpolymerized system and the polymerization energy barrier are inversely\nproportional to the electron doping of the system. We analyze the origin of\nthis charge-induced polymerization effect by studying the behavior of the\nsystem's wavefunctions around the Fermi level and the structural modifications\nof the molecules as a function of two variables: the distance between the\ncenters of the molecules and the number of electrons added to the system.", "category": "physics_chem-ph" }, { "text": "Resetting Metadynamics: Metadynamics is a powerful method to accelerate molecular dynamics\nsimulations, but its efficiency critically depends on the identification of\ncollective variables that capture the slow modes of the process. Unfortunately,\ncollective variables are usually not known a priori, and finding them can be\nvery challenging. We recently presented a collective variables-free approach to\nenhanced sampling using stochastic resetting. Here, we combine the two methods\nfor the first time, showing that it can lead to greater acceleration than\neither of them separately. We also demonstrate that resetting Metadynamics\nsimulations performed with suboptimal collective variables can lead to speedups\ncomparable with those obtained with optimal collective variables. Therefore,\nthe application of stochastic resetting can be an alternative to the\nchallenging task of improving suboptimal collective variables, at almost no\nadditional computational cost. Finally, we propose a method to extract unbiased\nmean first-passage times from Metadynamics simulations with resetting,\nresulting in an improved tradeoff between speedup and accuracy. This work opens\nthe way for combining stochastic resetting with other enhanced sampling methods\nto accelerate a broad range of molecular simulations.", "category": "physics_chem-ph" }, { "text": "Influence of molecular shape on self-diffusion under severe confinement:\n A molecular dynamics study: We have investigated the effect of molecular shape and charge asymmetry on\nthe translation dynamics of confined hydrocarbon molecules having different\nshapes but similar kinetic diameters, inside ZSM-5 pores using molecular\ndynamics simulations. The mean square displacement of propane, acetonitrile,\nacetaldehyde, and acetone in ZSM-5 exhibit two different regimes - ballistic\nand diffusive/sub-diffusive. All the molecules except propane exhibit\nsub-diffusive motion at time scales greater than 1 ps. The intermediate\nscattering functions reveal that there is a considerable rotational-\ntranslational coupling in the motion of all the molecules, due to the strong\ngeometrical restriction imposed by ZSM-5. Overall the difference in shape and\nasymmetry in charge imposes severe restriction inside the ZSM-5 channels for\nall the molecules to different extents. Further, the behavior of molecules\nconfined in ZSM-5 in the present study, quantified wherever possible, is\ncompared to their behavior in bulk or in other porous media reported in\nliterature.", "category": "physics_chem-ph" }, { "text": "Exciton Localization in Extended \u03c0-electron Systems: Comparison of\n Linear and Cyclic Structures: We employ five {\\pi}-conjugated model materials of different molecular shape\n--- oligomers and cyclic structures --- to investigate the extent of exciton\nself-trapping and torsional motion of the molecular framework following optical\nexcitation. Our studies combine steady-state and transient fluorescence\nspectroscopy in the ensemble with measurements of polarization anisotropy on\nsingle molecules, supported by Monte Carlo simulations. The dimer exhibits a\nsignificant spectral red-shift within $\\sim$ 100 ps after photoexcitation which\nis attributed to torsional relaxation. This relaxation mechanism is inhibited\nin the structurally rigid macrocyclic analogue. However, both systems show a\nhigh degree of exciton localization but with very different consequences: while\nin the macrocycle the exciton localizes randomly on different parts of the\nring, scrambling polarization memory, in the dimer, localization leads to a\ndeterministic exciton position with luminescence characteristics of a dipole.\nMonte Carlo simulations allow us to quantify the structural difference between\nthe emitting and absorbing units of the {\\pi}-conjugated system in terms of\ndisorder parameters.", "category": "physics_chem-ph" }, { "text": "Correlation-Driven Phenomena in Periodic Molecular Systems from\n Variational Two-electron Reduced Density Matrix Theory: Correlation-driven phenomena in molecular periodic systems are challenging to\npredict computationally not only because such systems are periodically infinite\nbut also because they are typically strongly correlated. Here we generalize the\nvariational two-electron reduced density matrix (2-RDM) theory to compute the\nenergies and properties of strongly correlated periodic systems. The 2-RDM of\nthe unit cell is directly computed subject to necessary $N$-representability\nconditions such that the unit-cell 2-RDM represents at least one $N$-electron\ndensity matrix. Two canonical but non-trivial systems, periodic metallic\nhydrogen chains and periodic acenes, are treated to demonstrate the\nmethodology. We show that, while single-reference correlation theories do not\ncapture the strong (static) correlation effects in either of these molecular\nsystems, the periodic variational 2-RDM theory predicts the Mott\nmetal-to-insulator transition in the hydrogen chains and the length-dependent\npolyradical formation in acenes. For both hydrogen chains and acenes the\nperiodic calculations are compared with previous non-periodic calculations with\nthe results showing a significant change in energies and increase in the\nelectron correlation from the periodic boundary conditions. The 2-RDM theory,\nwhich allows for much larger active spaces than are traditionally possible, is\napplicable to studying correlation-driven phenomena in general periodic\nmolecular solids and materials.", "category": "physics_chem-ph" }, { "text": "Overlapped Embedded Fragment Stochastic Density Functional Theory for\n Covalently Bonded Materials: The stochastic density functional theory (DFT) [Phys. Rev. Lett. 111, 106402\n(2013)] is a valuable linear scaling approach to Kohn-Sham DFT that does not\nrely on the sparsity of the density matrix. Linear (and often sub-linear)\nscaling is achieved by introducing a controlled statistical error in the\ndensity, energy and forces. The statistical error (noise) is proportional to\nthe inverse square root of the number of stochastic orbitals and thus decreases\nslowly, however, by dividing the system to fragments that are embedded\nstochastically, the statistical error can be reduced significantly. This has\nbeen shown to provide remarkable results for non-covalently bonded systems,\nhowever, the application to covalently bonded systems had limited success,\nparticularly for delocalized electrons. Here, we show that the statistical\nerror in the density correlates with both the density and the density matrix of\nthe system and propose a new fragmentation scheme that elegantly interpolates\nbetween overlapped fragments. We assess the performance of the approach for\nbulk silicon of varying supercell sizes (up to $N_{e}=16384$ electrons) and\nshow that overlapped fragments reduce significantly the statistical noise even\nfor systems with a delocalized density matrix.", "category": "physics_chem-ph" }, { "text": "DSDP: A Blind Docking Strategy Accelerated by GPUs: Virtual screening, including molecular docking, plays an essential role in\ndrug discovery. Many traditional and machine-learning based methods are\navailable to fulfil the docking task. The traditional docking methods are\nnormally extensively time-consuming, and their performance in blind docking\nremains to be improved. Although the runtime of docking based on machine\nlearning is significantly decreased, their accuracy is still limited. In this\nstudy, we take the advantage of both traditional and machine-learning based\nmethods, and present a method Deep Site and Docking Pose (DSDP) to improve the\nperformance of blind docking. For the traditional blind docking, the entire\nprotein is covered by a cube, and the initial positions of ligands are randomly\ngenerated in the cube. In contract, DSDP can predict the binding site of\nproteins and provide an accurate searching space and initial positions for the\nfurther conformational sampling. The docking task of DSDP makes use of the\nscore function and a similar but modified searching strategy of AutoDock Vina,\naccelerated by implementation in GPUs. We systematically compare its\nperformance with the state-of-the-art methods, including Autodock Vina, GNINA,\nQuickVina, SMINA, and DiffDock. DSDP reaches a 29.8% top-1 success rate (RMSD <\n2 {\\AA}) on an unbiased and challenging test dataset with 1.2 s wall-clock\ncomputational time per system. Its performances on DUD-E dataset and the\ntime-split PDBBind dataset used in EquiBind, TankBind, and DiffDock are also\neffective, presenting a 57.2% and 41.8% top-1 success rate with 0.8 s and 1.0 s\nper system, respectively.", "category": "physics_chem-ph" }, { "text": "QED-SCF, MCSCF and Coupled-cluster Methods in Quantum Chemistry: We investigate the method to combine the techniques of quantum chemisty with\nQED. In our theory, we treat the N-electron system and the Dirac sea on an\nequal footing; we regard both of them as the dynamical degrees of freedom of a\nmany-body system. After the introduction of our QED-SCF method, the QED-SCF\nsolutions are classified into several classes on the basis of group-theoretical\noperations such as time reversal, parity and O(3) rotational symmetry. The\nnatural orbitals of general QED-SCF solutions are determined by diagonalizing\nthe first order density matrix. Thus, we obtain the possibility to treat the\nsystem under strong QED effect by the methods of quantum chemistry, such as\nQED-MCSCF and QED-coupled-cluster approaches.", "category": "physics_chem-ph" }, { "text": "Spectroscopic Interpretation: The High Vibrations of CDBrClF: We extract the dynamics implicit in an algebraic fitted model Hamiltonian for\nthe deuterium chromophore's vibrational motion in the molecule CDBrClF. The\noriginal model has 4 degrees of freedom, three positions and one representing\ninterbond couplings. A conserved polyad allows in a semiclassical approach the\nreduction to 3 degrees of freedom. For most quantum states we can identify the\nunderlying motion that when quantized gives the said state. Most of the\nclassifications, identifications and assignments are done by visual inspection\nof the already available wave function semiclassically transformed from the\nnumber representation to a representation on the reduced dimension toroidal\nconfiguration space corresponding to the classical action and angle variables.\nThe concentration of the wave function density to lower dimensional subsets\ncentered on idealized simple lower dimensional organizing structures and the\nbehavior of the phase along such organizing centers already reveals the atomic\nmotion. Extremely little computational work is needed.", "category": "physics_chem-ph" }, { "text": "Coarse-Graining Auto-Encoders for Molecular Dynamics: Molecular dynamics simulations provide theoretical insight into the\nmicroscopic behavior of materials in condensed phase and, as a predictive tool,\nenable computational design of new compounds. However, because of the large\ntemporal and spatial scales involved in thermodynamic and kinetic phenomena in\nmaterials, atomistic simulations are often computationally unfeasible.\nCoarse-graining methods allow simulating larger systems, by reducing the\ndimensionality of the simulation, and propagating longer timesteps, by\naveraging out fast motions. Coarse-graining involves two coupled learning\nproblems; defining the mapping from an all-atom to a reduced representation,\nand the parametrization of a Hamiltonian over coarse-grained coordinates.\nMultiple statistical mechanics approaches have addressed the latter, but the\nformer is generally a hand-tuned process based on chemical intuition. Here we\npresent Autograin, an optimization framework based on auto-encoders to learn\nboth tasks simultaneously. Autograin is trained to learn the optimal mapping\nbetween all-atom and reduced representation, using the reconstruction loss to\nfacilitate the learning of coarse-grained variables. In addition, a\nforce-matching method is applied to variationally determine the coarse-grained\npotential energy function. This procedure is tested on a number of model\nsystems including single-molecule and bulk-phase periodic simulations.", "category": "physics_chem-ph" }, { "text": "Reactive atomistic simulations of Diels-Alder-type reactions:\n Conformational and dynamic effects in the polar cycloaddition of\n 2,3-dibromobutadiene radical ions with maleic anhydride: The kinetics, dynamics and conformational specificities for the ionic\nDiels-Alder reaction (polar cycloaddition) of maleic anhydride with\n2,3-dibromobutadiene radical ions have been studied theoretically using\nmultisurface adiabatic reactive molecular dynamics. A competition of concerted\nand stepwise reaction pathways was found and both the s-cis and s-trans\nconformers of of the diene are reactive. The analysis of the minimum dynamic\npath of the reaction indicates that both, rotations and vibrations of the\nreactant molecules are important for driving the system towards the transition\nstate. The rates were computed as $k = 5.1 \\times 10^{-14}$ s$^{-1}$ for the\ns-cis and $k = 3.8 \\times 10^{-14}$ s$^{-1}$ for the s-trans conformer of\n2,3-dibromobutadiene at an internal temperature of 300 K. The present results\nare to be contrasted with the neutral variant of the title system in which only\nthe gauche conformer of the diene was found to undergo a considerably slower,\nconcerted and mostly synchronous reaction driven by the excitation of\nrotations. The results presented here inform detailed experimental studies of\nthe dynamics of polar cycloadditions under single-collision conditions in the\ngas phase.", "category": "physics_chem-ph" }, { "text": "Exploring a dynamical path for C$_2$H$^-$ and NCO$^-$ formation in dark\n molecular clouds: This paper deals with the possible formation of two molecular anions often\nconsidered likely components in the physical environments of the Interstellar\nMedium ( ISM) : $\\mathrm{C_2H^-}$ and $\\mathrm{NCO^-}$. They are both discussed\nhere by computationally following the radiative association (RA) mechanism\nstarting from $\\mathrm{C_2^-}$, $\\mathrm{H}$, $\\mathrm{NC^-}$ and $\\mathrm{O}$\nas partners. The corresponding RA total cross sections produced by the\ncalculations are in turn employed to generate the overall association rates\nover the relevant range of temperatures. The latter are found to be in line\nwith other molecular ions formed by RA but not large enough to uniquivocally\nsuggest this path as the main route to the anions formation in the ISM. Other\npossible paths of formation are also analysed and discussed. The presence of\nresonant structures during the association dynamics for both systems is found\nby the calculations and their consequences are discussed in some detail in the\npresent study.", "category": "physics_chem-ph" }, { "text": "Identification of Ultrafast Photophysical Pathways in Photoexcited\n Organic Heterojunctions: The exciton dissociation and charge separation occurring on subpicosecond\ntime scales following the photoexcitation are studied in a model donor/acceptor\nheterojunction using a fully quantum approach. Higher-than-LUMO acceptor\norbitals which are energetically aligned with the donor LUMO orbital\nparticipate in the ultrafast interfacial dynamics by creating photon-absorbing\ncharge-bridging states in which charges are spatially separated and which can\nbe directly photoexcited. Along with the states brought about by\nsingle-particle resonances, the two-particle (exciton) mixing gives rise to\nbridge states in which charges are delocalized. Bridge states open up a number\nof photophysical pathways that indirectly connect the initial donor states with\nstates of spatially separated charges and compete with the efficient\nprogressive deexcitation within the manifold of donor states. The diversity and\nefficiency of these photophysical pathways depend on a number of factors, such\nas the precise energy alignment of exciton states, the central frequency of the\nexcitation, and the strength of carrier-phonon interaction.", "category": "physics_chem-ph" }, { "text": "Accurate DOSY measure of out-of-equilibrium systems by permutated DOSY\n (p-DOSY): NMR spectroscopy is an excellent tool for monitoring in-situ chemical\nreactions. In particular, DOSY measurement is well suited to characterize\ntransient species by the determination of their sizes. However, here we bring\nto light a difficulty in the DOSY experiments performed in out-of-equilibrium\nsystems. On such a system, the evolution of the concentration of species\ninterferes with the measurement process, and creates a bias on the diffusion\ncoefficient determination that may lead to erroneous interpretations.\n We show that a random permutation of the series of gradient strengths used\nduring the DOSY experiment allows to average out this bias. This approach, that\nwe name p-DOSY does not require changes in the the pulse sequences nor in the\nprocessing software, and restores completely the full accuracy of the measure.\nThis technique is demonstrated on the monitoring of the anomerization reaction\nof \\alpha- to \\beta-glucose.", "category": "physics_chem-ph" }, { "text": "Homonuclear J-Coupling Spectroscopy at Low Magnetic Fields using\n Spin-Lock Induced Crossing: Nuclear magnetic resonance (NMR) spectroscopy usually requires high magnetic\nfields to create spectral resolution among different proton species. At low\nfields, chemical shift dispersion is insufficient to separate the species, and\nthe spectrum exhibits just a single line. In this work, we demonstrate that\nspectra can nevertheless be acquired at low field using a novel pulse sequence\ncalled spin-lock induced crossing (SLIC). This probes energy level crossings\ninduced by a weak spin-locking pulse and produces a unique J-coupling spectrum\nfor most organic molecules. Unlike other forms of low-field J-coupling\nspectroscopy, our technique does not require the presence of heteronuclei and\ncan be used for most compounds in their native state. We performed SLIC\nspectroscopy on a number of small molecules at 276 kHz and 20.8 MHZ, and we\nshow that SLIC spectra can be simulated in good agreement with measurements.", "category": "physics_chem-ph" }, { "text": "Signatures of Exciton Delocalization and Exciton-Exciton Annihilation in\n Fluorescence-Detected Two-Dimensional Coherent Spectroscopy: We present calculations of the fluorescence-detected coherent two-dimensional\n(F-2DES) spectra of a molecular heterodimer. We compare how the F-2DES\ntechnique differs from the standard coherently detected two-dimensional (2DES)\nspectroscopy in measuring exciton delocalization. We analyze which processes\ncontribute to cross-peaks in the zero-waiting-time spectra obtained by the two\nmethods. Based strictly on time-dependent perturbation theory, we study how in\nboth methods varying degree of cancellation between perturbative contributions\ngives rise to cross-peaks, and identify exciton annihilation and exciton\nrelaxation contributions to the cross-peak in the zero-waiting-time F-2DES. We\npropose that time-gated fluorescence detection can be used to isolate the\nannihilation contribution to F-2DES both to retrieve information equivalent to\n2DES spectroscopy and to study annihilation contribution itself.", "category": "physics_chem-ph" }, { "text": "A mathematical and computational review of Hartree-Fock SCF methods in\n Quantum Chemistry: We present here a review of the fundamental topics of Hartree-Fock theory in\nQuantum Chemistry. From the molecular Hamiltonian, using and discussing the\nBorn-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock\nequations for the electronic problem. Special emphasis is placed in the most\nrelevant mathematical aspects of the theoretical derivation of the final\nequations, as well as in the results regarding the existence and uniqueness of\ntheir solutions. All Hartree-Fock versions with different spin restrictions are\nsystematically extracted from the general case, thus providing a unifying\nframework. Then, the discretization of the one-electron orbitals space is\nreviewed and the Roothaan-Hall formalism introduced. This leads to a exposition\nof the basic underlying concepts related to the construction and selection of\nGaussian basis sets, focusing in algorithmic efficiency issues. Finally, we\nclose the review with a section in which the most relevant modern developments\n(specially those related to the design of linear-scaling methods) are commented\nand linked to the issues discussed. The whole work is intentionally\nintroductory and rather self-contained, so that it may be useful for non\nexperts that aim to use quantum chemical methods in interdisciplinary\napplications. Moreover, much material that is found scattered in the literature\nhas been put together here to facilitate comprehension and to serve as a handy\nreference.", "category": "physics_chem-ph" }, { "text": "Optimized FTO seeding enables the growth of high efficient Ta-doped\n TiO$_2$ nanorod photoanodes: Tantalum doped rutile nanorods were hydrothermally grown on FTO substrates\nusing a new seeding approach. This approach allows the incorporation of high\nconcentrations of up to 4.8 at% tantalum as active doping and results in a\nsignificant enhancement of photoelectrochemical water splitting rate (1.8\nmA/cm2 at a potential of +1.5 V vs RHE) which corresponds to ca. 1%\nphotocurrent conversion efficiency under AM 1.5, 100 mW/cm2 simulated sunlight\nirradiation.", "category": "physics_chem-ph" }, { "text": "Density-Wavefunction Mapping in Degenerate Current-Density-Functional\n Theory: We show that the particle density, $\\rho(\\mathbf{r})$, and the paramagnetic\ncurrent density, $\\mathbf{j}^{p}(\\mathbf{r})$, are not sufficient to determine\nthe set of degenerate ground-state wave functions. This is a general feature of\ndegenerate systems where the degenerate states have different angular momenta.\nWe provide a general strategy for constructing Hamiltonians that share the same\nground state density, yet differ in degree of degeneracy. We then provide a\nfully analytical example for a noninteracting system subject to electrostatic\npotentials and uniform magnetic fields. Moreover, we prove that when\n$(\\rho,\\mathbf{j}^p)$ is ensemble $(v,\\mathbf{A})$-representable by a mixed\nstate formed from $r$ degenerate ground states, then any Hamiltonian\n$H(v',\\mathbf{A}')$ that shares this ground state density pair must have at\nleast $r$ degenerate ground states in common with $H(v,\\mathbf{A})$. Thus, any\nset of Hamiltonians that shares a ground-state density pair\n$(\\rho,\\mathbf{j}^p)$ by necessity has at least have one joint ground state.", "category": "physics_chem-ph" }, { "text": "Geometric dependencies of vibronically mediated excitation transfer in\n rylene dyads: We study the excitation transfer in various geometric arrangements of rylene\ndimers using absorption, fluorescence and transient absorption spectra.\nPolarization and detection frequency dependencies of transient absorption track\nthe interplay of transfer and vibrational relaxation within the dyads. We have\nresolved microscopic parametrization of intermolecular coupling between rylenes\nand reproduced transport data. Dynamical sampling of molecular geometries\ncaptures thermal fluctuations for Quantum Chemical estimate of couplings for\northogonally arranged dyad, where static estimates vanish and normal mode\nanalysis of fluctuations underestimates them by an order of magnitude.\nNonperturbative accounts for the modulation of transport by strongly coupled\nanharmonic vibrational modes is provided by a vibronic dimer model. Vibronic\ndynamics is demonstrated to cover both the F\\\"{o}rster transport regime of\northogonally arranged dyads and the strong coupling regime of parallel\nchromophores and allows us to model signal variations along the detection\nfrequency.", "category": "physics_chem-ph" }, { "text": "Electrostatic cooling in Ion-Exchange Membranes: In ion-exchange membrane processes, ions and water flow under the influence\nof gradients in hydrostatic pressure, ion chemical potential, and electrical\npotential (voltage), leading to solvent flow, ionic fluxes and ionic current.\nAt the outer surfaces of the membranes, electrical double layers (EDLs) are\nformed (Donnan layers). When a current flows through the membrane, we argue\nthat besides Joule heating in the bulk of the membrane and in the electrolyte\noutside the membrane, there is also electrostatic heating and cooling in the\nEDLs. In addition, when fluid flows through a charged membrane, at the outsides\nof the membrane there is pressure-related heating or cooling due to the osmotic\nand hydrostatic pressure differences across the EDLs.", "category": "physics_chem-ph" }, { "text": "Aging Feynman-Kac Equation: Aging, the process of growing old or maturing, is one of the most widely seen\nnatural phenomena in the world. For the stochastic processes, sometimes the\ninfluence of aging can not be ignored. For example, in this paper, by analyzing\nthe functional distribution of the trajectories of aging particles performing\nanomalous diffusion, we reveal that for the fraction of the occupation time\n$T_+/t$ of strong aging particles, $\\langle (T^+(t)^2)\\rangle=\\frac{1}{2}t^2$\nwith coefficient $\\frac{1}{2}$, having no relation with the aging time $t_a$\nand $\\alpha$ and being completely different from the case of weak (none) aging.\nIn fact, we first build the models governing the corresponding functional\ndistributions, i.e., the aging forward and backward Feynman-Kac equations; the\nabove result is one of the applications of the models. Another application of\nthe models is to solve the asymptotic behaviors of the distribution of the\nfirst passage time, $g(t_a,t)$. The striking discovery is that for weakly aging\nsystems, $g(t_a,t)\\sim t_a^{\\frac{\\alpha}{2}}t^{-1-\\frac{\\alpha}{2}}$, while\nfor strongly aging systems, $g(t_a,t)$ behaves as $ t_a^{\\alpha-1}t^{-\\alpha}$.", "category": "physics_chem-ph" }, { "text": "Water as a Levy rotor: A probability density function describing the angular evolution of a\nfixed-length atom-atom vector as a L\\'{e}vy rotor is derived containing just\ntwo dynamical parameters: the L\\'{e}vy parameter $\\alpha$ and a rotational time\nconstant $\\tau$. A L\\'{e}vy parameter $\\alpha\\!<\\!2$ signals anomalous\n(non-Brownian) motion. A molecular dynamics simulation of water at 298\\,K\nvalidates the probability density function for the intra-molecular $^1$H--$^1$H\ndynamics of water. The rotational dynamics of water is found to be\napproximately Brownian at sub-picosecond time intervals but becomes\nincreasingly anomalous at longer times due to hydrogen-bond breaking and\nreforming. The rotational time constant lies in the range $8 \\! < \\! \\tau \\! <\n\\! 11$\\,ps. The L\\'{e}vy rotor model is used to estimate the intra-molecular\ncontribution to the longitudinal nuclear-magnetic-resonance relaxation rate\n$R_{1,{\\rm intra}}$ due to dipolar $^1$H--$^1$H interactions. It is found that\n$R_{1,{\\rm intra}}$ contributes $65\\,\\pm 7$\\% to the overall relaxation rate of\nwater at room temperature.", "category": "physics_chem-ph" }, { "text": "The near-infrared spectrum of ethynyl radical: Transient diode laser absorption spectroscopy has been used to measure three\nstrong vibronic bands in the near infrared spectrum of the C$_2$H, ethynyl,\nradical not previously observed in the gas phase. The radical was produced by\nultraviolet excimer laser photolysis of either acetylene or\n(1,1,1)-trifluoropropyne in a slowly flowing sample of the precursor diluted in\ninert gas, and the spectral resolution was Doppler-limited. The character of\nthe upper states was determined from the rotational and fine structure in the\nobserved spectra and assigned by measurement of ground state rotational\ncombination differences. The upper states include a $^2\\Sigma ^+$ state at 6696\ncm$^{-1}$, a second $^2\\Sigma ^+$ state at 7088 cm$^{-1}$, and a $^2\\Pi$ state\nat 7110 cm$^{-1}$. By comparison with published calculations (R. Tarroni and S.\nCarter, \\textit{J. Chem. Phys} \\textbf{119}, 12878 (2003) and \\textit{Mol.\nPhys}. \\textbf{102}, 2167 (2004)), the vibronic character of these levels was\nalso assigned. The observed states contain both $X^2\\Sigma^+$ and $A^2\\Pi$\nelectronic character. Several local rotational level perturbations were\nobserved in the excited states. Kinetic measurements of the time-evolution of\nthe ground state populations following collisional relaxation and reactive loss\nof the radicals formed in a hot, non-thermal, population distribution were made\nusing some of the strong rotational lines observed. The case of C$ _{2} $H may\nbe a good place to investigate the behavior at intermediate pressures of inert\ncolliders, where the competition between relaxation and reaction can be tuned\nand observed to compare with master equation models, rather than deliberately\nsuppressed to measure thermal rate constants.", "category": "physics_chem-ph" }, { "text": "Investigation of the Effects of Biodiesel Produced from Crambe\n Abyssinica Plant on Combustion, Engine Performance and Exhaust Emissions: In this study, biodiesel fuel produced from crambe abyssinica plant using KOH\nand NaOH catalysts was mixed with standard diesel fuel and the effects on\nengine performance, combustion and emission were experimentally investigated.\nStandard diesel fuel and 6 different fuel mixtures were tested at 3.75, 7.5,\n11.25 and 15 Nm engine loads. During the experiment, in-cylinder pressure data\nwere specified depending on crank angle for each test fuel and engine load. In\naddition, measurements of HC, NOx, CO and smoke emissions were carried out.\nWith the obtained experimental data, parameters such as heat release rate,\ncombustion stages, thermal efficiency, indicated mean effective pressure\n(imep), ignition delay (ID), ringing intensity (RI) and specific fuel\nconsumptions (SFC) were calculated and evaluated in MATLAB/Simulink\nenvironment. The same concentrated crambe abyssinica with NaOH catalyst (CAN)\nblended fuel series has been found to have a lower BSFC value at all engine\nloads than the crambe abyssinica with KOH catalyst (CAK) blended fuel series.\nIt was concluded that the highest thermal efficiency values were achieved with\nCAK B25 mixed fuel under all engine load conditions. It was concluded that the\nusage of standard diesel fuel is more prone to knock than other blends.", "category": "physics_chem-ph" }, { "text": "Exploring the top and bottom of the quantum control landscape: A controlled quantum system possesses a search landscape defined by the\ntarget physical objective as a function of the controls. This paper focuses on\nthe landscape for the transition probability Pif between the states of a finite\nlevel quantum system. Traditionally, the controls are applied fields; here we\nextend the notion of control to also include the Hamiltonian structure, in the\nform of time independent matrix elements. Level sets of controls that produce\nthe same transition probability value are shown to exist at the bottom Pif =\n0.0 and top Pif = 1.0 of the landscape with the field and/or Hamiltonian\nstructure as controls. We present an algorithm to continuously explore these\nlevel sets starting from an initial point residing at either extreme value of\nPif . The technique can also identify control solutions that exhibit the\ndesirable properties of (a) robustness at the top and (b) the ability to\nrapidly rise towards an optimal control from the bottom. Numerical simulations\nare presented to illustrate the varied control behavior at the top and bottom\nof the landscape for several simple model systems.", "category": "physics_chem-ph" }, { "text": "Selective gas capture via kinetic trapping: Conventional approaches to the capture of CO_2 by metal-organic frameworks\nfocus on equilibrium conditions, and frameworks that contain little CO_2 in\nequilibrium are often rejected as carbon-capture materials. Here we use a\nstatistical mechanical model, parameterized by quantum mechanical data, to\nsuggest that metal-organic frameworks can be used to separate CO_2 from a\ntypical flue gas mixture when used under {\\em nonequilibrium} conditions. The\norigin of this selectivity is an emergent gas-separation mechanism that results\nfrom the acquisition by different gas types of different mobilities within a\ncrowded framework. The resulting distribution of gas types within the framework\nis in general spatially and dynamically heterogeneous. Our results suggest that\nrelaxing the requirement of equilibrium can substantially increase the\nparameter space of conditions and materials for which selective gas capture can\nbe effected.", "category": "physics_chem-ph" }, { "text": "Influence of Ti$_3^+$ Defect-type on Heterogeneous Photocatalytic H$_2$\n Evolution Activity of TiO$_2$: Reduced titanium dioxide has recently attracted large attention, particularly\nfor its unique co-catalyst-free H$_2$ heterogeneous photocatalytic application.\nThe enhanced photocatalytic activity of the reduced TiO$_2$ was previously\nascribed to the introduction of point crystal defects (mainly Ti$_3^+$\ncenters), which result in the formation of intrinsic co-catalytic centers and\nenhanced visible light absorption. In this work, we systematically investigate\nthe effect of different defects in the TiO$_{2-x}$ lattice on photocatalytic\nH$_2$ evolution. To introduce different types of defects, thermal annealing in\nair (oxidative), Ar (inert), Ar/H$_2$ (reducing), and H$_2$ (reducing)\natmospheres were performed on commercially available anatase nanopowder. Then,\nthe powders were characterized by scanning electron microscopy (SEM), X-ray\ndiffraction (XRD) and high-resolution transmission electron microscopy (HR-TEM)\nto clarify the effect of treatment on material properties. Furthermore, the\ndefect types were characterized by electron paramagnetic resonance (EPR)\nspectroscopy. We show that thermal annealing in different atmospheres can form\ndifferent amounts of different defect types in the TiO$_2$ structure. The\nhighest photocatalytic activation is achieved by annealing the anatase powder\nin a reducing atmosphere for an appropriate temperature/annealing time. By\ncombining the results from H$_2$ generation and EPR analysis we show that the\nsimultaneous presence of two types of defects, i.e. surface exposed Ti$_3^+$\nand lattice embedded Ti$_3^+$ centers, in an optimum low concentration, is the\ndetermining factor for an optimized photocatalytic H$_2$ evolution rate. In\nfact, annealing anatase powder under the so-reported optimized conditions in\nreducing atmosphere leads to the generation of a considerable amount of H$_2$,\nwith rates as high as 338 $\\mu$molh-1g-1.", "category": "physics_chem-ph" }, { "text": "Quantum hardware calculations of the activation and dissociation of\n nitrogen on iron clusters and surfaces: Catalytic processes are vital in the chemical industry, with\nnitrogen-to-ammonia conversion being a major industrial process. Designing\ncatalysts relies on computational chemistry methods like Density Functional\nTheory (DFT), which have limitations in accuracy, especially for complex\nmaterials. Quantum computing advancements offer promise for precise ab-initio\nmethods. We introduce a hybrid quantum-classical workflow to model chemical\nreactions on surfaces, demonstrated on nitrogen activation and dissociation on\nsmall Fe clusters and an iron surface. We decoupled key electronic structures\nusing CASSCF, translated them into qubits, and estimated energies with quantum\nand classical simulations, showing potential for quantum computing in catalysis\nresearch as technology scales up.", "category": "physics_chem-ph" }, { "text": "A near infrared line list for \\NH: Analysis of a Kitt Peak spectrum\n after 35 years: A Fourier Transform (FT) absorption spectrum of room temperature NH3 in the\nregion 7400 - 8600 cm-1 is analysed using a variational line list and ground\nstate energies determined using the MARVEL procedure. The spectrum was measured\nby Dr Catherine de Bergh in 1980 and is available from the Kitt Peak data\ncenter. The centers and intensities of 8468 ammonia lines were retrieved using\na multiline fitting procedure. 2474 lines are assigned to 21 bands providing\n1692 experimental energies in the range 7000 - 9000 cm-1. The spectrum was\nassigned by the joint use of the BYTe variational line list and combination\ndifferences. The assignments and experimental energies presented in this work\nare the first for ammonia in the region 7400 - 8600 cm-1, considerably\nextending the range of known vibrational-excited states", "category": "physics_chem-ph" }, { "text": "Isolated vibrational wavepackets in D2+: Defining superposition\n conditions and wavepacket distinguishability: Tunnel ionization of room-temperature D$_2$ in an ultrashort (12 femtosecond)\nnear infra-red (800 nm) pump laser pulse excites a vibrational wavepacket in\nthe D2+ ions; a rotational wavepacket is also excited in residual D2 molecules.\nBoth wavepacket types are collapsed a variable time later by an ultrashort\nprobe pulse. We isolate the vibrational wavepacket and quantify its evolution\ndynamics through theoretical comparison. Requirements for quantum computation\n(initial coherence and quantum state retrieval) are studied using this\nwell-defined (small number of initial states at room temperature, initial\nwavepacket spatially localized) single-electron molecular prototype by\ntemporally stretching the pump and probe pulses.", "category": "physics_chem-ph" }, { "text": "Temperature dependence in fast-atom diffraction at surfaces: Grazing incidence fast atom diffraction at crystal surfaces (GIFAD or FAD)\nhas demonstrated coherent diffraction both at effective energies close to one\neV ($\\lambda_\\perp\\approx$ 14 pm for He) and at elevated surface temperatures\noffering high topological resolution and real time monitoring of growth\nprocesses. This is explained by a favorable Debye-Waller factor specific to the\nmultiple collision regime of grazing incidence. This paper presents the first\nextensive evaluation of the temperature behavior between 177 and 1017 K on a\nLiF surface. Similarly to diffraction at thermal energies, an exponential\nattenuation of the elastic intensity is observed but the maximum coherence is\nhardly limited by the attraction forces. It is more influenced by the surface\nstiffness and appears very sensitive to surface defects.", "category": "physics_chem-ph" }, { "text": "Valorization of biodigestor plant waste in electrodes for\n supercapacitors and microbial fuel cells: This study aims at demonstrating that wastes from anaerobic biodigester\nplants can be effectively valorized as functional materials to be implemented\nin technologies that enable efficient energy management and water treatment,\ntherefore simultaneously addressing the Water-Energy-Waste Nexus challenges.\nLignin, the main solid residue of the biodigester plant, has been valorized\ninto activated biochar with a mild activation agent, like KHCO3, to produce\nelectrode of supercapacitors and microbial fuel cells. In addition, the same\nsludge that is the liquid effluent of the biodigester plant has been exploited\nas inoculum and electrolyte for the MFC. The lignin derived carbons obtained at\nlignin/KHCO3 mass ratios of 1:0.5 (LAC-0.5) and 1:2 (LAC-2) comprised of\nmesopores and micropores displaying BETs of 1558 m2/g and 1879 m2/g,\nrespectively. LAC-2 carbon exhibited a superior specific capacitance of 114 F/g\nin 2.5 M KNO3 with respect to LAC-0.5. A supercapacitor with LAC-2 electrodes\nwas built displaying specific energy specific power up to 10 Wh/kg and 6.9\nkW/kg, respectively. Durability tests showed that the device was able to\nmaintain a capacitance retention of 84.5% after 15,000 charge-discharge cycles.\nThe lignin-derived carbons were also studied as electrocatalysts for ORR in a\nneutral medium. The LAC-2 showed higher ORR electrocatalytic activity than\nLAC-0.5. The interconnected porous network and the high surface area made the\nlignin-derived porous carbons suitable electrode materials for dual\napplications. The feasibility of the use of LAC 2 carbon incorporated in an air\nbreathing cathode for MFC applications is also reported.", "category": "physics_chem-ph" }, { "text": "Occupied-orbital fast multipole method for efficient exact exchange\n evaluation: We present an efficient algorithm for computing the exact exchange\ncontributions in the Hartree-Fock and hybrid density functional theory models\non the basis of the fast multipole method (FMM). Our algorithm is based on the\nobservation that FMM with hierarchical boxes can be efficiently used in the\nexchange matrix construction, when at least one of the indices of the exchange\nmatrix is constrained to be an occupied orbital. Timing benchmarks are\npresented for alkane chains (C400H802 and C150H302), a graphene sheet\n(C150H30), a water cluster [(H2O)100], and a protein Crambin\n(C202H317O64N55S6). The computational cost of the far-field exchange evaluation\nfor Crambin is roughly 3% that of a self-consistent field iteration when the\nmultipoles up to rank 2 are used.", "category": "physics_chem-ph" }, { "text": "Rovibrational Internal Energy Transfer and Dissociation of\n High-Temperature Oxygen Mixture: This work constructs a rovibrational state-to-state model for the\n$\\text{O}_2$+$\\text{O}_2$ system leveraging high-fidelity potential energy\nsurfaces and quasi-classical trajectory calculations. The model is used to\ninvestigate internal energy transfer and non-equilibrium reactive processes in\ndissociating environment using a master equation approach, whereby the kinetics\nof each internal rovibrational state is explicitly computed. To cope with the\nexponentially large number of elementary processes that characterize reactive\nbimolecular collisions, the internal states of the collision partner are\nassumed to follow a Boltzmann distribution at a prescribed internal\ntemperature. This procedure makes the problem tractable, reducing the\ncomputational cost to a comparable scale with the $\\text{O}_2$+O system. The\nconstructed rovibrational-specific kinetic database covers the temperature\nrange of 7500-20000 K. The analysis of the energy transfer and dissociation\nprocess in isochoric and isothermal conditions reveals that significant\ndepartures from the equilibrium Boltzmann distribution occur during the energy\ntransfer and dissociation phase. Comparing the population distribution of the\n$\\text{O}_2$ molecules against the $\\text{O}_2$+O demonstrates a more\nsignificant extent of non-equilibrium characterized by a more diffuse\ndistribution whereby the vibrational strands are more clearly identifiable.\nThis is partly due to a less efficient mixing of the rovibrational states,\nwhich results in more diffuse rovibrational distributions in the\nquasi-steady-state distribution. The master equation analysis for the combined\n$\\text{O}_3$+$\\text{O}_4$ system reveals that the $\\text{O}_2$+$\\text{O}_2$\ngoverns the early stage of energy transfer, while the $\\text{O}_2$+O takes\ncontrol of the dissociation dynamics. The findings will provide strong physical\nfoundations for future development of oxygen chemistry.", "category": "physics_chem-ph" }, { "text": "Nonlinear Model of non-Debye Relaxation: We present a simple nonlinear relaxation equation which contains the Debye\nequation as a particular case. The suggested relaxation equation results in\npower-law decay of fluctuations. This equation contains a parameter defining\nthe frequency dependence of the dielectric permittivity similarly to the\nwell-known one-parameter phenomenological equations of Cole-Cole, Davidson-Cole\nand Kohlrausch-Williams-Watts. Unlike these models, the obtained dielectric\npermittivity (i) obeys to the Kramers-Kronig relation; (ii) has proper\nbehaviour at large frequency; (iii) its imaginary part, conductivity, shows a\npower-law frequency dependence \\sigma ~ \\omega^n where n<1 corresponds to\nempirical Jonscher's universal relaxation law while n>1 is also observed in\nseveral experiments. The nonlinear equation proposed may be useful in various\nfields of relaxation theory.", "category": "physics_chem-ph" }, { "text": "Ultrafast adsorbate excitation probed with sub-ps resolution XAS: We use a pump-probe scheme to measure the time evolution of the C K-edge\nX-ray absorption spectrum (XAS) from CO/Ru(0001) after excitation by an\nultrashort high-intensity optical laser pulse. Due to the short duration of the\nX-ray probe pulse and precise control of the pulse delay, the\nexcitation-induced dynamics during the first ps after the pump can be resolved\nwith unprecedented time resolution. By comparing with theoretical (DFT)\nspectrum calculations we find high excitation of the internal stretch and\nfrustrated rotation modes occurring within 200 fs of laser excitation, as well\nas thermalization of the system in the ps regime. The ~100 fs initial\nexcitation of these CO vibrational modes is not readily rationalized by\ntraditional theories of nonadiabatic coupling of adsorbates to metal surfaces,\ne. g. electronic frictions based on first order electron-phonon coupling or\ntransient population of adsorbate resonances. We suggest that coupling of the\nadsorbate to non-thermalized electron-hole pairs is responsible for the\nultrafast initial excitation of the modes.", "category": "physics_chem-ph" }, { "text": "Revealing the Physico-Chemical Basis of Organic Solid-Solid Wetting\n Deposition: Casimir-Like Forces, Hydrophobic Collapse, and the Role of the\n Zeta Potential: Supramolecular self-assembly at the solid-solid interface enables the\ndeposition and monolayer formation of insoluble organic semiconductors under\nambient conditions. The underlying process, termed as the Organic Solid-Solid\nWetting Deposition (OSWD), generates two-dimensional adsorbates directly from\ndispersed three-dimensional organic crystals. This straightforward process has\nimportant implications in various fields of research and technology, such as in\nthe domains of low-dimensional crystal engineering, the chemical doping and\nband-gap engineering of graphene, and in the area of field-effect transistor\nfabrication. However, till date, lack of an in-depth understanding of the\nphysico-chemical basis of the OSWD prevented the identification of important\nparameters, essential to achieve a better control of the growth of monolayers\nand supramolecular assemblies with defined structures, sizes, and coverage\nareas. Here we propose a detailed model for the OSWD, derived from experimental\nand theoretical results that have been acquired by using the organic\nsemiconductor quinacridone as an example system. The model reveals the vital\nrole of the zeta potential and includes Casimir-like fluctuation-induced forces\nand the effect of dewetting in hydrophobic nano-confinements. Based on our\nresults, the OSWD of insoluble organic molecules can hence be applied to\nenvironmental friendly and low-cost dispersing agents, such as water. In\naddition, the model substantially enhances the ability to control the OSWD in\nterms of adsorbate structure and substrate coverage.", "category": "physics_chem-ph" }, { "text": "Intermolecular Coulombic decay by concerted transfer of energy from\n photoreceptors to a reaction center: Molecular mechanisms that enable concerted transfer of energy from several\nphotoacceptors to a distinct reaction center are most desirable for the\nutilization of light-energy. Here we show that intermolecular Coulombic decay,\na channel which enables non-local disposal of energy in photoexcited molecules,\noffers an avenue for such a novel energy-transfer mechanism. On irradiation of\npyridine-argon gas mixture at 266 nm and at low laser intensities, we observed\na surprisingly dominant formation of argon cations. Our measurements on the\nlaser-power dependence of the yield of the Ar cations reveal that\nintermolecular Coulombic interactions concertedly localize the excitation\nenergy of several photoexcited pyridines at the argon reaction center and\nionize it. The density of the reaction center offers an efficient handle to\noptimize this concerted energy-transfer. This mechanism paves the way for a new\n$\\pi$-molecular light-harvesting system, and can also contribute to\nbiomolecular stability against photodamage.", "category": "physics_chem-ph" }, { "text": "Asymmetric supercapacitors: optical and thermal effects when active\n carbon electrodes are embedded with nano-scale semiconductor dots: Optical and thermal effects in asymmetric supercapacitors, whose\nactive-carbon (AC) electrodes were embedded with nano-Si (n-Si) quantum dots\n(QD), are reported. We describe two structures: (1) p-n like, obtained by using\na polyethylimine (PEI) binder for the n-like electrode and a\npolyvinylpyrrolidone (PVP) binder for the p-like electrode; (2) a single\ncomponent binder, poly(methyl methacrylate) (PMMA). In general, AC appears\nblack to the naked eye and one may assume that it acts as a black body\nabsorber, namely, indiscriminately absorbing all light spectra. Yet, on top of\na flat lossy spectra, AC (from two manufacturers) exhibited two distinct\nabsorption bands: one in the blue (~ 400 nm) and the other one in the near IR\n(~ 840 nm). The n-Si material accentuated the absorption in the blue and\nbleached the IR absorption. Both bands contributed to capacitance increase: (a)\nwhen using aqueous solution and a PMMA binder, the optical related increased\ncapacitance was 20% at low n-Si concentration and more than 100% for a high\nconcentration dose; (b) when using IL electrolyte, the large, thermal\ncapacitance increase (of ca 40%) was comparable to the optical effect (of ca\n42%) and hence was assigned as an optically-induced thermal effect. The\nexperimental data point to an optically induced capacitance increase even in\nthe absence of the n-Si dots; this could be attributed to the absorption of AC\nin the blue.", "category": "physics_chem-ph" }, { "text": "High-Level Coupled-Cluster Energetics by Monte Carlo Sampling and Moment\n Expansions: Further Details and Comparisons: We recently proposed a novel approach to converging electronic energies\nequivalent to high-level coupled-cluster (CC) computations by combining the\ndeterministic CC($P$;$Q$) formalism with the stochastic configuration\ninteraction (CI) and CC Quantum Monte Carlo (QMC) propagations. This article\nextends our initial study [J. E. Deustua, J. Shen, and P. Piecuch, Phys. Rev.\nLett. 119, 223003 (2017)], which focused on recovering the energies obtained\nwith the CC method with singles, doubles, and triples (CCSDT) using the\ninformation extracted from full CI QMC and CCSDT-MC, to the CIQMC approaches\ntruncated at triples and quadruples. It also reports our first semi-stochastic\nCC($P$;$Q$) calculations aimed at converging the energies that correspond to\nthe CC method with singles, doubles, triples, and quadruples (CCSDTQ). The\nability of the semi-stochastic CC($P$;$Q$) formalism to recover the CCSDT and\nCCSDTQ energies, even when electronic quasi-degeneracies and triply and\nquadruply excited clusters become substantial, is illustrated by a few\nnumerical examples, including the F-F bond breaking in ${\\rm F}_{2}$, the\nautomerization of cyclobutadiene, and the double dissociation of the water\nmolecule.", "category": "physics_chem-ph" }, { "text": "An efficient implementation of the localized operator partitioning\n method for electronic energy transfer: The localized operator partitioning method [Y. Khan and P. Brumer, J. Chem.\nPhys. 137, 194112 (2012)] rigorously defines the electronic energy on any\nsubsystem within a molecule and gives a precise meaning to the subsystem ground\nand excited electronic energies, which is crucial for investigating electronic\nenergy transfer from first principles. However, an efficient implementation of\nthis approach has been hindered by complicated one- and two-electron integrals\narising in its formulation. Using a resolution of the identity in the\ndefinition of partitioning we reformulate the method in a computationally\nefficient manner that involves standard one- and two-electron integrals. We\napply the developed algorithm to the 9-((1-naphthyl)-methyl)-anthracene (A1N)\nmolecule by partitioning A1N into anthracenyl and CH2-naphthyl groups as\nsubsystems, and examine their electronic energies and populations for several\nexcited states using Configuration Interaction Singles method. The implemented\napproach shows a wide variety of different behaviors amongst the excited\nelectronic states.", "category": "physics_chem-ph" }, { "text": "Application of Neural Network Algorithm in Propylene Distillation: Artificial neural network modeling does not need to consider the mechanism.\nIt can map the implicit relationship between input and output and predict the\nperformance of the system well. At the same time, it has the advantages of\nself-learning ability and high fault tolerance. The gas-liquid two phases in\nthe rectification tower conduct interphase heat and mass transfer through\ncountercurrent contact. The functional relationship between the product\nconcentration at the top and bottom of the tower and the process parameters is\nextremely complex. The functional relationship can be accurately controlled by\nartificial neural network algorithms. The key components of the propylene\ndistillation tower are the propane concentration at the top of the tower and\nthe propylene concentration at the bottom of the tower. Accurate measurement of\nthem plays a key role in increasing propylene yield in ethylene production\nenterprises. This article mainly introduces the neural network model and its\napplication in the propylene distillation tower.", "category": "physics_chem-ph" }, { "text": "Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics,\n and Long-Time Dynamics Computations: We present a ``coarse molecular dynamics'' approach and apply it to studying\nthe kinetics and thermodynamics of a peptide fragment dissolved in water. Short\nbursts of appropriately initialized simulations are used to infer the\ndeterministic and stochastic components of the peptide motion parametrized by\nan appropriate set of coarse variables. Techniques from traditional numerical\nanalysis (Newton-Raphson, coarse projective integration) are thus enabled;\nthese techniques help analyze important features of the free-energy landscape\n(coarse transition states, eigenvalues and eigenvectors, transition rates,\netc.). Reverse integration of (irreversible) expected coarse variables backward\nin time can assist escape from free energy minima and trace low-dimensional\nfree energy surfaces. To illustrate the ``coarse molecular dynamics'' approach,\nwe combine multiple short (0.5-ps) replica simulations to map the free energy\nsurface of the ``alanine dipeptide'' in water, and to determine the ~ 1/(1000\nps) rate of interconversion between the two stable configurational basins\ncorresponding to the alpha-helical and extended minima.", "category": "physics_chem-ph" }, { "text": "Linear nonequilibrium thermodynamics of reversible periodic processes\n and chemical oscillations: Onsager's phenomenological equations successfully describe irreversible\nthermodynamic processes. They assume a symmetric coupling matrix between\nthermodynamic fluxes and forces. It is easily shown that the antisymmetric part\nof a coupling matrix does not contribute to dissipation. Therefore, entropy\nproduction is exclusively governed by the symmetric matrix even in the presence\nof antisymmetric terms. In this work we focus on the antisymmetric\ncontributions which describe isentropic oscillations and well-defined equations\nof motion. The formalism contains variables that are equivalent to momenta, and\ncoefficients that are analogous to an inertial mass. We apply this formalism to\nsimple problems such as an oscillating piston and the oscillation in an\nelectrical LC-circuit. We show that isentropic oscillations are possible even\nclose to equilibrium in the linear limit and one does not require far-from\nequilibrium situations. One can extend this formalism to other pairs of\nvariables, including chemical systems with oscillations. In isentropic\nthermodynamic systems all extensive and intensive variables including\ntemperature can display oscillations reminiscent of adiabatic waves.", "category": "physics_chem-ph" }, { "text": "Many-body quantum chemistry for the electron gas: convergent\n perturbative theories: We investigate the accuracy of a number of wavefunction based methods at the\nheart of quantum chemistry for metallic systems. Using Hartree-Fock as a\nreference, perturbative (M{\\o}ller-Plesset, MP) and coupled cluster (CC)\ntheories are used to study the uniform electron gas model. Our findings suggest\nthat non-perturbative coupled cluster theories are acceptable for modelling\nelectronic interactions in metals whilst perturbative coupled cluster theories\nare not. Using screened interactions, we propose a simple modification to the\nwidely-used coupled-cluster singles and doubles plus perturbative triples\nmethod (CCSD(T)) that lifts the divergent behaviour and is shown to give very\naccurate correlation energies for the homogeneous electron gas.", "category": "physics_chem-ph" }, { "text": "Extended Donnan model for ion partitioning in charged nanopores: Membranes consist of pores and the walls of these pores are often charged. In\ncontact with an aqueous solution, the pores fill with water and ions migrate\nfrom solution into the pores until chemical equilibrium is reached. The\ndistribution of ions between outside and pore solution is governed by a balance\nof chemical potential, and the resulting model is called a Donnan theory, or\nDonnan equation. Including a partitioning coefficient that does not depend on\nsalt concentration results in an extended Donnan equation `of the first kind'.\nRecently, an electrostatic model was proposed for ions in a pore based on the\narrangement of ions around strands of polymer charge, including also ion\nactivity coefficients in solution. That framework leads to an extended Donnan\nequation `of the second kind', which has extra factors depending on ion\nconcentrations in the pores and salt concentration in solution. In the present\nwork, we set up another Donnan model of the second kind by evaluating the\nCoulombic interactions of ions in a cylindrical pore, including the interaction\nof ions with the charged pore walls and between the ions. We assume that\ncounterions are near the pore wall while coions distribute over the center\nregion. Starting from a complete analysis, we arrive at an elegant expression\nfor the chemical potential of ions in such a pore. This expression depends on\ncoion concentration, pore size, and other geometrical factors, but there is no\nadditional dependence on counterion concentration and charge density. This\nmodel predicts the Coulombic contribution to the chemical potential in the pore\nto be small, much smaller than predicted by the electrostatic model from\nliterature. Instead, we predict that up to around 1 M salt concentration,\nactivity effects of ions in solution are more important.", "category": "physics_chem-ph" }, { "text": "Testing entropy production hypotheses in non-linear steady states: In the last few decades, some hypotheses for entropy production (EP)\nprinciples have been forwarded as possible candidates for organizational\nprinciples in non-linear non- equilibrium systems. Two important hypotheses\nwill be studied: the maximum entropy production (MaxEP) principle that claims\nthat the selected steady state has the highest EP, and the gradient response\nprinciple that claims that the EP of the selected steady state (maximally)\nincreases when the external thermodynamic driving force increases. We will\nformulate these hypotheses more rigorously and present a simple chemical\nreaction model to test these hypotheses. With the help of this model, we will\nclearly demonstrate that there are different MaxEP hypotheses being discussed\nin the literature and we will look at some parts in the literature where these\ndifferences are not always clarified. Furthermore, our chemical model will be a\ngeneral counter example to all of these MaxEP and gradient response hypotheses.", "category": "physics_chem-ph" }, { "text": "A Blessing and a Curse: How a Supercapacitor's Large Capacitance Causes\n its Slow Charging: The development of novel electrolytes and electrodes for supercapacitors is\nhindered by a gap of several orders of magnitude between experimentally\nmeasured and theoretically predicted charging timescales. Here, we propose an\nelectrode model, containing many parallel stacked electrodes, that explains the\nslow charging dynamics of supercapacitors. At low applied potentials, the\ncharging behavior of this model is described well by an equivalent circuit\nmodel. Conversely, at high potentials, charging dynamics slow down and evolve\non two relaxation time scales: a generalized $RC$ time and a diffusion time,\nwhich, interestingly, become similar for porous electrodes. The charging\nbehavior of the stack-electrode model presented here helps to understand the\ncharging dynamics of porous electrodes and qualitatively agrees with\nexperimental time scales measured with porous electrodes.", "category": "physics_chem-ph" }, { "text": "Image Super-resolution Inspired Electron Density Prediction: Drawing inspiration from the domain of image super-resolution, we view the\nelectron density as a 3D grayscale image and use a convolutional residual\nnetwork to transform a crude and trivially generated guess of the molecular\ndensity into an accurate ground-state quantum mechanical density. We find that\nthis model outperforms all prior density prediction approaches. Because the\ninput is itself a real-space density, the predictions are equivariant to\nmolecular symmetry transformations even though the model is not constructed to\nbe. Due to its simplicity, the model is directly applicable to unseen molecular\nconformations and chemical elements. We show that fine-tuning on limited new\ndata provides high accuracy even in challenging cases of exotic elements and\ncharge states. Our work suggests new routes to learning real-space physical\nquantities drawing from the established ideas of image processing.", "category": "physics_chem-ph" }, { "text": "Non-Newtonian behavior and molecular structure of Cooee bitumen under\n shear flow: a non-equilibrium molecular dynamics study: The rheology and molecular structure of a model bitumen (Cooee bitumen) under\nshear are investigated in the non-Newtonian regime using non-equilibrium\nmolecular dynamics simulations. The shear viscosity, normal stress differences\nand pressure of the bitumen mixture are computed at different shear rates and\ndifferent temperatures. The model bitumen is shown to be a shear-thinning fluid\nat all temperatures. In addition, the Cooee model is able to reproduce\nexperimental results showing the formation of nanoaggregates composed of stacks\nof flat aromatic molecules in bitumen. These nanoaggregates are immersed in a\nsolvent of saturated hydrocarbon molecules. At a fixed temperature, the\nshear-shinning behavior is related to the inter- and intramolecular alignment\nof the solvent molecules, but also to the decrease of the average size of the\nnanoaggregates at high shear rates. The variation of the viscosity with\ntemperature at different shear rates is also related to the size and relative\ncomposition of the nanoaggregates. The slight anisotropy of the whole sample\ndue to the nanoaggregates is considered and quantified. Finally, the position\nof bitumen mixtures in the broad literature of complex systems such as\ncolloidal suspensions, polymer solutions and associating polymer networks is\ndiscussed.", "category": "physics_chem-ph" }, { "text": "Tutorial review of Reverse Osmosis and Electrodialysis: Reverse osmosis (RO) and electrodialysis (ED) are the two most important\nmembrane technologies for water desalination and treatment. Their desalination\nand transport mechanisms are very different, but on closer look also have many\nsimilarities. In this tutorial review we describe state-of-the-art theory for\nboth processes focusing on simple examples that are helpful for the\nnon-specialist and for classroom teaching. We describe relevant theory for ion\nand water transport and the coupling with theory for chemical and mechanical\nequilibrium on membrane/solution interfaces. For RO of neutral solutes, we\nexplain the solution-friction (SF) model which is closely related to the\nclassical sieving or pore flow model. The SF model includes advection,\ndiffusion, and solute partitioning, and leads to simple relationships for the\ncoupled fluxes of water and solutes (and thus for solute retention as well),\nalso when a diffusion boundary layer is included in the model. Subsequently\nthis theory is extended to describe RO for symmetric salt solutions with\ncharged membranes. For the desalination of salt solutions, both for RO and ED\nwe present two-dimensional module-scale calculations which lead to a\ncharacteristic curve that determines optimum operational conditions based on a\nsimple cost calculation that offsets energy and material costs. We discuss the\ntwo-fluid model (TFM) that comprehensively describes ion and water flow both in\nRO and ED, and we explain how this theory also accurately describes osmosis\nexperiments where water and ions run in opposite directions through a membrane.\nFinally, we present results of optimization studies of the combination of\nmultiple modules for RO and ED, and we evaluate the relevance of concentration\npolarization by using a 3D model for cross-current flow in an ED module.", "category": "physics_chem-ph" }, { "text": "First principles molecular dynamics without self-consistent field\n optimization: We present a first principles molecular dynamics approach that is based on\ntime-reversible ex- tended Lagrangian Born-Oppenheimer molecular dynamics\n[Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent\nfield optimization. The optimization-free dynamics keeps the computational cost\nto a minimum and typically provides molecular trajectories that closely follow\nthe exact Born-Oppenheimer potential energy surface. Only one single\ndiagonalization and Hamiltonian (or Fockian) costruction are required in each\nintegration time step. The proposed dy- namics is derived for a general\nfree-energy potential surface valid at finite electronic temperatures within\nhybrid density functional theory. Even in the event of irregular functional\nbehavior that may cause a dynamical instability, the optimization-free limit\nrepresents an ideal starting guess for force calculations that may require a\nmore elaborate iterative electronic ground state optimization. Our\noptimization-free dynamics thus represents a flexible theoretical framework for\na broad and general class of ab initio molecular dynamics simulations.", "category": "physics_chem-ph" }, { "text": "On the theory of proton solid echo in polymer melts: Based on a modified Anderson-Weiss approximation (N. Fatkullin, A.\nGubaidullin, C. Mattea, S.Stapf, J. Chem. Phys. 137 (2012), 224907) an improved\ntheory of proton spin solid echo in polymer melts is formulated, taking into\naccount contribution from intermolecular magnetic dipole-dipole interactions.\nThe solid echo build-up function defined by the relation , where , and are the\nrespective signals arising from ( ),( ) and ( ) spin echo experiments, where is\nan operator rotating the spin system on the angle relatively axis , is\ninvestigated. It is shown that the intermolecular part of this function at\nshort times , where is a characteristic time for flip-flop transitions between\nproton spins, contains information about the relative mean squared\ndisplacements of polymer segments at different macromolecules, opening up a new\nopportunity for obtaining information about polymer dynamics in the millisecond\nregime.", "category": "physics_chem-ph" }, { "text": "Active learning of Boltzmann samplers and potential energies with\n quantum mechanical accuracy: Extracting consistent statistics between relevant free-energy minima of a\nmolecular system is essential for physics, chemistry and biology. Molecular\ndynamics (MD) simulations can aid in this task but are computationally\nexpensive, especially for systems that require quantum accuracy. To overcome\nthis challenge, we develop an approach combining enhanced sampling with deep\ngenerative models and active learning of a machine learning potential (MLP). We\nintroduce an adaptive Markov chain Monte Carlo framework that enables the\ntraining of one Normalizing Flow (NF) and one MLP per state. We simulate\nseveral Markov chains in parallel until they reach convergence, sampling the\nBoltzmann distribution with an efficient use of energy evaluations. At each\niteration, we compute the energy of a subset of the NF-generated configurations\nusing Density Functional Theory (DFT), we predict the remaining configuration's\nenergy with the MLP and actively train the MLP using the DFT-computed energies.\nLeveraging the trained NF and MLP models, we can compute thermodynamic\nobservables such as free-energy differences or optical spectra. We apply this\nmethod to study the isomerization of an ultrasmall silver nanocluster,\nbelonging to a set of systems with diverse applications in the fields of\nmedicine and catalysis.", "category": "physics_chem-ph" }, { "text": "Enhancing automated reaction discovery with boxed molecular dynamics in\n energy space: The rare event acceleration method BXDE is interfaced in the present work\nwith the automated reaction discovery method AutoMeKin. To test the efficiency\nof the combined AutoMeKin-BXDE procedure, the ozonolysis of a-pinene is studied\nin comparison with standard AutoMeKin. AutoMeKin-BXDE locates intermediates and\ntransition states that are more densely connected with each other and\napproximately 50 kcal/mol more stable than those found with standard AutoMeKin.\nOther than the different density of edges between the nodes, both networks are\nscale-free and display small-world properties, mimicking the network of organic\nchemistry. Finally, while AutoMeKin-BXDE finds more transition states than\nthose previously reported for O3 + a-pinene, the standard procedure fails to\nlocate some of the previously published reaction pathways using the same\nsimulation time of 2.5 ns. In summary, the mixed procedure is very promising\nand clearly outperforms the standard simulation algorithms implemented in\nAutoMeKin. BXDE will be available in the next release of AutoMekin.", "category": "physics_chem-ph" }, { "text": "Enhancing Reduced Density Matrix Functional Theory Calculations by\n Coupling Orbital and Occupation Optimizations: Reduced density matrix functional theory (RDMFT) calculations are usually\nimplemented in a decoupled manner, where the orbital and occupation\noptimizations are repeated alternately. Although the unitary optimization\nmethod and the recently developed explicit-by-implicit (EBI) method in Su group\nperform well for the optimizations of orbitals and occupations, respectively,\nthe decoupled optimization methods often suffer from slow convergence and\nrequire dozens of alternations between the orbital and occupation\noptimizations. To address this issue, this work proposes a coupled optimization\nmethod that combines unitary and EBI optimizations to update orbitals and\noccupations simultaneously at each step. To achieve favorable convergence in\ncoupled optimization using a simple first-order algorithm, an effective and\nefficient preconditioner and line search are further introduced. The\nsuperiority of the new method is demonstrated through numerous tests on\ndifferent molecules, random initial guesses, different basis sets and different\nfunctionals. It outperforms all decoupled optimization methods in terms of\nconvergence speed, convergence results and convergence stability. Even a large\nsystem like $\\mathrm{C_{60}}$ can converge to $10^{-8}$ au in 154 iterations,\nwhich shows that the coupled optimization method can make RDMFT more practical\nand facilitate its wider application and further development.", "category": "physics_chem-ph" }, { "text": "Lambda-type sharp rise in the widths of Raman and infra-red line shape\n near the Widom line in super-critical water above its gas-liquid critical\n temperature: A lambda-type divergent rise of Raman linewidth of liquid nitrogen near its\ncritical temperature has been a subject of many discussions in the past[1-5].\nHere we explore the possibility of such an anomaly in infra-red and Raman\nspectroscopy of super-critical water (SCW) by varying the density across the\nWidom line just above its critical temperature. Vibrational phase relaxation is\nexpected to be a sensitive probe of fluid dynamics. We carry out computer\nsimulations of two different model potentials (SPC/E and TIP4P/2005) to obtain\nthe necessary time correlation functions. An additional feature of this work is\na quantum chemical calculation of the anharmonicity parameter that largely\ncontrols frequency fluctuations. We find a sharp rise in the vibrational\nrelaxation rate (or the line widths) for both the models as we travel across\nthe Widom line. The rise is noticeably less sharp in water than in nitrogen. We\nattribute this difference to the faster relaxation rate in water. We\ndemonstrate that the anomalous rise is due to sharp increase in the mean square\nfrequency fluctuation and not due to any dynamical critical slowing down\nbecause the time constant of the normalized frequency-frequency time\ncorrelation functions show lack of any noticeable change as we move across the\nWidom line. We present an explanation of the observed results using the mode\ncoupling theory of liquid dynamics.", "category": "physics_chem-ph" }, { "text": "Fast periodic Gaussian density fitting by range separation: We present an efficient implementation of periodic Gaussian density fitting\n(GDF) using the Coulomb metric. The three-center integrals are divided into two\nparts by range-separating the Coulomb kernel, with the short-range part\nevaluated in real space and the long-range part in reciprocal space. With a few\nalgorithmic optimizations, we show that this new method -- which we call\nrange-separated GDF (RSGDF) -- scales sublinearly to linearly with the number\nof $k$-points for small to medium-sized $k$-point meshes that are commonly used\nin periodic calculations with electron correlation. Numerical results on a few\nthree-dimensional solids show about $10$-fold speedups over the previously\ndeveloped GDF with little precision loss. The error introduced by RSGDF is\nabout $10^{-5}~E_{\\textrm{h}}$ in the converged Hartree-Fock energy with\ndefault auxiliary basis sets and can be systematically reduced by increasing\nthe size of the auxiliary basis with little extra work.\n [The article has been accepted by The Journal of Chemical Physics.]", "category": "physics_chem-ph" }, { "text": "Impact of environmentally induced fluctuations on quantum mechanically\n mixed electronic and vibrational pigment states in photosynthetic energy\n transfer and 2D electronic spectra: Recently, nuclear vibrational contribution signatures in 2D electronic\nspectroscopy have attracted considerable interest, in particular as regards\ninterpretation of the oscillatory transients observed in light-harvesting\ncomplexes. These transients have dephasing times that persist for much longer\nthan theoretically predicted electronic coherence lifetime. As a plausible\nexplanation for this long-lived spectral beating in 2D electronic spectra,\nquantum-mechanically mixed electronic and vibrational states (vibronic\nexcitons) were proposed by Christensson et al. [J. Phys. Chem. B 116, 7449\n(2012)] and have since been explored. In this work, we address a dimer which\nproduces little beating of electronic origin in the absence of vibronic\ncontributions, and examine the impact of protein-induced fluctuations upon\nelectronic-vibrational quantum mixtures by calculating the electronic energy\ntransfer dynamics and 2D electronic spectra in a numerically accurate manner.\nIt is found that, at cryogenic temperatures, the electronic-vibrational quantum\nmixtures are rather robust, even under the influence of the fluctuations and\ndespite the small Huang-Rhys factors of the Franck-Condon active vibrational\nmodes. This results in long-lasting beating behavior of vibrational origin in\nthe 2D electronic spectra. At physiological temper- atures, however, the\nfluctuations eradicate the mixing and, hence, the beating in the 2D spectra\ndisappears. Further, it is demonstrated that such electronic-vibrational\nquantum mixtures do not necessarily play a significant role in electronic\nenergy trans- fer dynamics, despite contributing to the enhancement of\nlong-lived quantum beating in 2D electronic spectra, contrary to speculations\nin recent publications.", "category": "physics_chem-ph" }, { "text": "Potential of an ionic impurityin a large $^4$He cluster: This paper presents an analysis of the motion of an impurity ion in a\nnanometer scale $^4$He cluster. Due to induction forces, ions are strongly\nlocalized near the center of the cluster, with a root mean squared thermal\ndisplacements of only a few \\AA. The trapping potential is found to be nearly\nharmonic, with a frequency of 2.3(1.0) GHz for a positive (negative) ion in a\nHe cluster of radius 5 nm. The anharmonicity is small and positive (energy\nincreases slightly faster than linear with quantum number). It is suggested\nthat by using frequency sweep microwave radiation, it should be possible to\ndrive the ion center of mass motion up to high quantum numbers, allowing the\nstudy of the critical velocity as a function of cluster size.", "category": "physics_chem-ph" }, { "text": "Elimination of the Translational Kinetic Energy Contamination in\n pre-Born-Oppenheimer Calculations: In this paper we present a simple strategy for the elimination of the\ntranslational kinetic energy contamination of the total energy in\npre-Born--Oppenheimer calculations carried out in laboratory-fixed Cartesian\ncoordinates (LFCCs). The simple expressions for the coordinates and the\noperators are thus preserved throughout the calculations, while the\nmathematical form and the parametrisation of the basis functions are chosen so\nthat the translational and rotational invariances are respected. The basis\nfunctions are constructed using explicitly correlated Gaussian functions (ECGs)\nand the global vector representation. First, we observe that it is not possible\nto parametrise the ECGs so that the system is at rest in LFCCs and at the same\ntime the basis functions are square-integrable with a non-vanishing norm. Then,\nwe work out a practical strategy to circumvent this problem by making use of\nthe properties of the linear transformation between the LFCCs and\ntranslationally invariant and center-of-mass Cartesian coordinates as well as\nthe transformation properties of the corresponding basis function parameter\nmatrices. By exploiting these formal mathematical relationships we can identify\nand separate the translational contamination terms in the matrix representation\nof the kinetic energy operator in the LFCC formalism. We present numerical\nexamples for the translational contamination and its elimination for the two\nlowest rotational energy levels of the singlet hydrogen molecule, corresponding\nto para- and ortho-H2, respectively, treated as four-particle quantum systems.", "category": "physics_chem-ph" }, { "text": "Explicitly correlated double hybrid DFT: a comprehensive analysis of the\n basis set convergence on the GMTKN55 database: Double-hybrid density functional theory (DHDFT) offers a pathway to\naccuracies approaching composite wavefunction approaches like G4 theory.\nHowever, the GLPT2 (G{\\\"o}rling 2nd order perturbation theory) term causes them\nto partially inherit the slow $\\propto L^{-3}$ (with $L$ the maximum angular\nmomentum) basis set convergence of correlated wavefunction methods. This could\npotentially be remedied by introducing F12 explicit correlation: we investigate\nthe basis set convergence of both DHDFT and DHDFT-F12 for the large and\nchemically diverse GMTKN55 (general main-group thermochemistry, kinetics, and\nnoncovalent interactions) benchmark suite. The B2GP-PLYP-D3(BJ) and\nrevDSD-PBEP86-D4 double hybrid density functionals (DHDFs) are investigated as\ntest cases, together with orbital basis sets as large as aug-cc-pV5Z and F12\nbasis sets as large as cc-pV(Q+d)Z-F12. We show that F12 greatly accelerates\nbasis set convergence of DHDFs, to the point that even the modest cc-pVDZ-F12\nbasis set is closer to the basis set limit than cc-pV(Q+d)Z or def2-QZVPP in\norbital-based approaches, and in fact comparable in quality to cc-pV(5+d)Z.\nSomewhat surprisingly, aug-cc-pVDZ-F12 is not required even for the anionic\nsubsets. In conclusion, DHDF-F12/VDZ-F12 eliminates concerns about basis set\nconvergence in both the development and application of double-hybrid\nfunctionals. Mass storage and I/O bottlenecks for larger systems can be\ncircumvented by localized pair natural orbital approximations, which also\nexhibit much gentler system size scaling.", "category": "physics_chem-ph" }, { "text": "Deep learning path-like collective variable for enhanced sampling\n molecular dynamics: Several enhanced sampling techniques rely on the definition of collective\nvariables to effectively explore free energy landscapes. Existing variables\nthat describe the progression along a reactive pathway offer an elegant\nsolution but face a number of limitations. In this paper, we address these\nchallenges by introducing a new path-like collective variable called the\n`Deep-locally-non-linear-embedding', which is inspired by principles of the\nlocally linear embedding technique and is trained on a reactive trajectory. The\nvariable mimics the ideal reaction coordinate by automatically generating a\nnon-linear combination of features through a differentiable generalized\nautoencoder that combines a neural network with a continuous k-nearest-neighbor\nselection. Among the key advantages of this method is its capability to\nautomatically choose the metric for searching neighbors and to learn the path\nfrom state A to state B without the need to handpick landmarks a priori. We\ndemonstrate the effectiveness of DeepLNE by showing that the progression along\nthe path variable closely approximates the ideal reaction coordinate in toy\nmodels such as the M\\\"uller-Brown-potential and alanine dipeptide. We then use\nit in molecular dynamics simulations of an RNA tetraloop, where we highlight\nits capability to accelerate transitions and converge the free energy of\nfolding.", "category": "physics_chem-ph" }, { "text": "Dealing with the exponential wall in electronic structure calculations: An alternative to Density Functional Theory are wavefunction based electronic\nstructure calculations for solids. In order to perform them the Exponential\nWall (EW) problem has to be resolved. It is caused by an exponential increase\nof the number of configurations with increasing electron number N. There are\ndifferent routes one may follow. One is to characterize a many-electron\nwavefunction by a vector in Liouville space with a cumulant metric rather than\nin Hilbert space. This removes the EW problem. Another is to model the solid by\nan {\\it impurity} or {\\it fragment} embedded in a {\\it bath} which is treated\nat a much lower level than the former. This is the case in Density Matrix\nEmbedding Theory (DMET) or Density Embedding Theory (DET). The latter are\nclosely related to a Schmidt decomposition of a system and to the determination\nof the associated entanglement. We show here the connection between the two\napproaches. It turns out that the DMET (or DET) has an identical active space\nas a previously used Local Ansatz, based on a projection and partitioning\napproach. Yet, the EW problem is resolved differently in the two cases. By\nstudying a $H_{10}$ ring these differences are analyzed with the help of the\nmethod of increments.", "category": "physics_chem-ph" }, { "text": "Correlated Particle Motion and THz Spectral Response of Supercritical\n Water: Molecular dynamics simulations of supercritical water reveal distinctly\ndifferent distance-dependent modulations of dipolar response and correlations\nin particle motion compared to ambient conditions. The strongly perturbed\nH-bond network of water at supercritical conditions allows for considerable\ntranslational and rotational freedom of individual molecules. These changes\ngive rise to substantially different infrared spectra and vibrational density\nof states at THz frequencies for densities above and below the Widom line that\nseparates percolating liquid-like and clustered gas-like supercritical water.", "category": "physics_chem-ph" }, { "text": "Collision statistics of clusters: From Poisson model to Poisson mixtures: Clusters traverse a gas and collide with gas particles. The gas particles are\nadsorbed and the clusters become hosts. If the clusters are size selected, the\nnumber of guests will be Poisson distributed. We review this by showcasing four\nlaboratory procedures that all rely on the validity of the Poisson model. The\neffects of a statistical distribution of the cluster sizes in a beam of\nclusters are discussed. We derive the average collision rates. Additionally, we\npresent Poisson mixture models that involve also standard deviations. We derive\nthe collision statistics for common size distributions of hosts and also for\nsome generalizations thereof. The models can be applied to large noble gas\nclusters traversing doping gas. While outlining how to fit a generalized\nPoisson to the statistics, we still find even these Poisson models to be often\ninsufficient.", "category": "physics_chem-ph" }, { "text": "Fingerprints of antiaromaticity in the negative ion (Li$_3$Al$_4$)$^-$\n via an ab initio quantum-chemical study of the equilibrium structure of the\n inhomogeneous electron liquid: Fingerprints of antiaromaticity in the negative ion (Li$_3$Al$_4$)$^-$, this\nspecies being realizable via a laser vaporization technique, are revealed by\nmeans of an \\emph{ab initio} quantum-chemical investigation. First, the\nground-state equilibrium geometry of this ion is predicted. Also, for the\ncorresponding inhomogeneous electron liquid, the characteristics of the HOMO\nare studied, both for the square and the rectangular Al$_4$ geometry in two\nlow-lying isomers of the negative ion. There is no particular sensitivity to\nthe change in geometry of the Al$_4$ configuration. Therefore, we have\ncalculated theoretically chemical shifts (NICS), which contain remarkable\nfingerprints of antiaromaticity. As to future directions, some comments are\nadded in relation to the Shannon entropy.", "category": "physics_chem-ph" }, { "text": "Paramagnetic NMR chemical shift in a spin state subject to zero-field\n splitting: We derive a general formula for the paramagnetic NMR nuclear shielding tensor\nof an open-shell molecule in a pure spin state, subject to a zero-field\nsplitting (ZFS). Our findings are in contradiction with a previous proposal. We\npresent a simple application of the newly derived formula to the case of a\ntriplet ground state split by an easy-plane ZFS spin Hamiltonian. When $kT$ is\nmuch smaller than the ZFS gap, thus a single non-degenerate level is thermally\npopulated, our approach correctly predicts a temperature-independent\nparamagnetic shift, while the previous theory leads to a Curie temperature\ndependence.", "category": "physics_chem-ph" }, { "text": "Significant Conditions on the Two-electron Reduced Density Matrix from\n the Constructive Solution of N-representability: We recently presented a constructive solution to the N-representability\nproblem of the two-electron reduced density matrix (2-RDM)---a systematic\napproach to constructing complete conditions to ensure that the 2-RDM\nrepresents a realistic N-electron quantum system [D. A. Mazziotti, Phys. Rev.\nLett. 108, 263002 (2012)]. In this paper we provide additional details and\nderive further N-representability conditions on the 2-RDM that follow from the\nconstructive solution. The resulting conditions can be classified into a\nhierarchy of constraints, known as the (2,q)-positivity conditions where the q\nindicates their derivation from the nonnegativity of q-body operators. In\naddition to the known T1 and T2 conditions, we derive a new class of\n(2,3)-positivity conditions. We also derive 3 classes of (2,4)-positivity\nconditions, 6 classes of (2,5)-positivity conditions, and 24 classes of\n(2,6)-positivity conditions. The constraints obtained can be divided into two\ngeneral types: (i) lifting conditions, that is conditions which arise from\nlifting lower (2,q)-positivity conditions to higher (2,q+1)-positivity\nconditions and (ii) pure conditions, that is conditions which cannot be derived\nfrom a simple lifting of the lower conditions. All of the lifting conditions\nand the pure (2,q)-positivity conditions for q>3 require tensor decompositions\nof the coefficients in the model Hamiltonians. Subsets of the new\nN-representability conditions can be employed with the previously known\nconditions to achieve polynomially scaling calculations of ground-state\nenergies and 2-RDMs of many-electron quantum systems even in the presence of\nstrong electron correlation.", "category": "physics_chem-ph" }, { "text": "Coordinate Descent Full Configuration Interaction for Excited States: An efficient excited state method, named xCDFCI, in the configuration\ninteraction framework, is proposed. xCDFCI extends the unconstrained nonconvex\noptimization problem in coordinate descent full configuration\ninteraction~(CDFCI) to a multicolumn version, for low-lying excited states\ncomputation. The optimization problem is addressed via a tailored coordinate\ndescent method. In each iteration, a determinant is selected based on an\napproximated gradient, and coefficients of all states associated with the\nselected determinant are updated. A deterministic compression is applied to\nlimit memory usage. We test xCDFCI applied to H2O and N2 molecules under the\ncc-pVDZ basis set. For both systems, five low-lying excited states in the same\nsymmetry sector are calculated together with the ground state. xCDFCI also\nproduces accurate binding curves of carbon dimer in the cc-pVDZ basis with\nchemical accuracy, where the ground state and four excited states in the same\nsymmetry sector are benchmarked.", "category": "physics_chem-ph" }, { "text": "Inverse Quantum Chemistry: Concepts and Strategies for Rational Compound\n Design: The rational design of molecules and materials is becoming more and more\nimportant. With the advent of powerful computer systems and sophisticated\nalgorithms, quantum chemistry plays an important role in rational design. While\ntraditional quantum chemical approaches predict the properties of a predefined\nmolecular structure, the goal of inverse quantum chemistry is to find a\nstructure featuring one or more desired properties. Herein, we review inverse\nquantum chemical approaches proposed so far and discuss their advantages as\nwell as their weaknesses.", "category": "physics_chem-ph" }, { "text": "Neural network Gaussian processes as efficient models of potential\n energy surfaces for polyatomic molecules: Kernel models of potential energy surfaces (PES) for polyatomic molecules are\noften restricted by a specific choice of the kernel function. This can be\navoided by optimizing the complexity of the kernel function. For regression\nproblems with very expensive data, the functional form of the model kernels can\nbe optimized in the Gaussian process (GP) setting through compositional\nfunction search guided by the Bayesian information criterion. However, the\ncompositional kernel search is computationally demanding and relies on greedy\nstrategies, which may yield sub-optimal kernels. An alternative strategy of\nincreasing complexity of GP kernels treats a GP as a Bayesian neural network\n(NN) with a variable number of hidden layers, which yields NNGP models. Here,\nwe present a direct comparison of GP models with composite kernels and NNGP\nmodels for applications aiming at the construction of global PES for polyatomic\nmolecules. We show that NNGP models of PES can be trained much more efficiently\nand yield better generalization accuracy without relying on any specific form\nof the kernel function. We illustrate that NNGP models trained by distributions\nof energy points at low energies produce accurate predictions of PES at high\nenergies. We also illustrate that NNGP models can extrapolate in the input\nvariable space by building the free energy surface of the Heisenberg model\ntrained in the paramagnetic phase and validated in the ferromagnetic phase. By\nconstruction, composite kernels yield more accurate models than kernels with a\nfixed functional form. Therefore, by illustrating that NNGP models outperform\nGP models with composite kernels, our work suggests that NNGP models should be\na preferred choice of kernel models for PES.", "category": "physics_chem-ph" }, { "text": "Interdigitated ring electrodes: Theory and experiment: The oxidation of potassium ferrocyanide, K_4Fe(CN)_6, in aqueous solution\nunder fully supported conditions is carried out at interdigitated band and ring\nelectrode arrays, and compared to theoretical models developed to simulate the\nprocesses. Simulated data is found to fit well with experimental results using\nliterature values of diffusion coefficients for Fe(CN)_6^(4-) and\nFe(CN)_6^(3-). The theoretical models are used to compare responses from\ninterdigitated band and ring arrays, and the size of ring array required to\napproximate the response to a linear band array is investigated. An equation is\ndeveloped for the radius of ring required for a pair of electrodes in a ring\narray to give a result with 5% of a pair of electrodes in a band array. This\nequation is found to be independent of the scan rate used over six orders of\nmagnitude.", "category": "physics_chem-ph" }, { "text": "Time-resolved broadband Raman spectroscopies; A unified six-wave-mixing\n representation: Excited-state vibrational dynamics in molecules can be studied by an\nelectronically off-resonant Raman process induced by a probe pulse with\nvariable delay with respect to an actinic pulse. We establish the connection\nbetween several variants of the technique that involve either spontaneous or\nstimulated Raman detection and different pulse configurations. By using loop\ndiagrams in the frequency domain we show that all signals can be described as\nsix wave mixing which depend on the same four point molecular correlation\nfunctions involving two transition dipoles and two polarizabilities and\naccompanied by a different gating. Simulations for the stochastic\ntwo-state-jump model illustrate the origin of the absorptive and dispersive\nfeatures observed experimentally.", "category": "physics_chem-ph" }, { "text": "Validating Fewest-Switches Surface Hopping in the Presence of Laser\n Fields: The capability of fewest-switches surface hopping (FSSH) to describe\nnon-adiabatic dynamics of small and medium sized molecules under explicit\nexcitation with external fields is evaluated. Different parameters in FSSH and\ncombinations thereof are benchmarked against multi-configurational time\ndependent Hartree (MCTDH) reference calculations using SO$_2$ and\n2-thiocytosine as model, yet realistic, molecular systems. Qualitatively, we\nfind that FSSH is able to reproduce the trends in the MCTDH dynamics with (and\nwithout) an explicit external field; however, no set of FSSH parameters is\nideal. An adequate treatment of the overcoherence in FSSH is identified as the\ndriving factor to improve the description of the excitation process with\nrespect to the MCTDH reference. Here two corrections were tested, the\naugmented-FSSH (AFSSH) and the energy-based decoherence correction. A\ndependence on the employed basis is detected for the AFSSH algorithm,\nperforming better when spin-orbit and external laser field couplings are\ntreated as off-diagonal elements instead of projecting them onto the diagonal\nof the Hamilton operator. In the presence of an electric field, the excited\nstate dynamics was found to depend strongly on the vector used to rescale the\nkinetic energy along after a transition between surfaces. For SO$_2$,\nrecurrence of the excited wave packet throughout the duration of the applied\nlaser pulse is observed for long laser pulses (>100~fs), resulting in\nadditional interferences not captured by FSSH and only visible in variational\nmulti-configurational Gaussian when utilizing a large amount of gaussian basis\nfunctions. This feature essentially vanishes when going towards larger\nmolecules, such as 2-thiocytosine, where this effect is barely visible in a\nlaser pulse with a full width at half maximum of 200~fs.", "category": "physics_chem-ph" }, { "text": "Coupling, lifetimes and \"strong coupling\" maps for single molecules at\n plasmonic interfaces: The interaction between excited states of a molecule and excited states of\nmetal nanostructure (e.g. plasmons) leads to hybrid states with modified\noptical properties. When plasmon resonance is swept through molecular\ntransition frequency an avoided crossing may be observed, which is often\nregarded as a signature of strong coupling between plasmons and molecules. Such\nstrong coupling is expected to be realized when $2|U|/{\\hbar\\Gamma}>1$, where\n$U$ and ${\\Gamma}$ are the molecule-plasmon coupling and the spectral width of\nthe optical transition respectively. Because both $U$ and ${\\Gamma}$ strongly\nincrease with decreasing distance between a molecule and a plasmonic structure\nit is not obvious that this condition can be satisfied for any molecule-metal\nsurface distance. In this work we investigate the behavior of $U$ and\n${\\Gamma}$ for several geometries. Surprisingly, we find that if the only\ncontributions to ${\\Gamma}$ are lifetime broadenings associated with the\nradiative and nonradiative relaxation of a single molecular vibronic\ntransition, including effects on molecular radiative and nonradiative lifetimes\ninduced by the metal, the criterion $2|U|/{\\hbar\\Gamma}>1$ is easily satisfied\nby many configurations irrespective of the metal-molecule distance. This\nimplies that the Rabi splitting can be observed in such structures if other\nsources of broadening are suppressed. Additionally, when the molecule-metal\nsurface distance is varied keeping all other molecular and metal parameters\nconstant, this behavior is mitigated due to the spectral shift associated with\nthe same molecule-plasmon interaction, making the observation of Rabi splitting\nmore challenging.", "category": "physics_chem-ph" }, { "text": "A theory of phonon induced friction on molecular adsorbates: In this manuscript, we provide a general theory for how surface phonons\ncouple to molecular adsorbates. Our theory maps the extended dynamics of a\nsurface's atomic vibrational motions to a generalized Langevin equation, and by\ndoing so captures these dynamics in a single quantity: the non-Markovian\nfriction. The different frequency components of this friction are the phonon\nmodes of the surface slab weighted by their coupling to the adsorbate degrees\nof freedom. Using this formalism, we demonstrate that physisorbed species\ncouple primarily to acoustic phonons while chemisorbed species couple to\ndispersionless local vibrations. We subsequently derive equations for\nphonon-adjusted reaction rates using transition state theory and demonstrate\nthat these corrections improve agreement with experimental results for CO\ndesorption rates from Pt(111).", "category": "physics_chem-ph" }, { "text": "A room temperature CO$_2$ line list with ab initio computed intensities: Atmospheric carbon dioxide concentrations are being closely monitored by\nremote sensing experiments which rely on knowing line intensities with an\nuncertainty of 0.5% or better. We report a theoretical study providing\nrotation-vibration line intensities substantially within the required accuracy\nbased on the use of a highly accurate {\\it ab initio} dipole moment surface\n(DMS). The theoretical model developed is used to compute CO$_2$ intensities\nwith uncertainty estimates informed by cross comparing line lists calculated\nusing pairs of potential energy surfaces (PES) and DMS's of similar high\nquality. This yields lines sensitivities which are utilized in reliability\nanalysis of our results. The final outcome is compared to recent accurate\nmeasurements as well as the HITRAN2012 database. Transition frequencies are\nobtained from effective Hamiltonian calculations to produce a comprehensive\nline list covering all $^{12}$C$^{16}$O$_2$ transitions below 8000 cm$^{-1}$\nand stronger than 10$^{-30}$ cm / molecule at $T=296$~K", "category": "physics_chem-ph" }, { "text": "On the vibron dressing in the $\u03b1$--helicoidal macromolecular chains: We present a study of the physical properties of the vibrational excitation\nin $\\alpha$--helicoidal macromolecular chains, caused by the interaction with\nacoustical and optical phonon modes. The influence of the temperature and the\nbasic system parameters on the vibron dressing has been analyzed by employing\nthe simple mean--field approach based on the variational extension of the\nLang--Firsov unitary transformation. Applied approach predicts a region in\nsystem parameter space where one takes place an abrupt transition from\npartially dressed (light and mobile) to fully dressed (immobile) vibron states.\nWe found that the boundary of this region depends on system temperature and\ntype of bond among structural elements in the macromolecular chain.", "category": "physics_chem-ph" }, { "text": "Wavepacket control and simulation protocol for entangled\n two-photon-absorption of molecules: Quantum light spectroscopy, providing novel molecular information\nnon-accessible by classical light, necessitates new computational tools when\napplied for complex molecular systems. We introduce two computational protocols\nfor the molecular nuclear wave packet dynamics interacting with an entangled\nphoton pair to produce the entangled two-photon absorption signal. The first\ninvolves summing over transition pathways in a temporal grid defined by two\nlight-matter interaction times accompanied by the field correlation functions\nof quantum light. The signal is obtained by averaging over the two-time\ndistribution characteristic of the entangled photon state. The other protocol\ninvolves a Schmidt decomposition of the entangled light and requires summing\nover the Schmidt modes. We demonstrate how photon entanglement can be used to\ncontrol and manipulate the two-photon excited nuclear wave packets in a\ndisplaced harmonic oscillator model.", "category": "physics_chem-ph" }, { "text": "Predicted Land\u00e9 $g$-factors for open shell diatomic molecules: The program {\\sc Duo} (Yurchenko {\\it et al.}, Computer Phys. Comms., 202\n(2016) 262) provides direct solutions of the nuclear motion Schr\\\"odinger\nequation for the (coupled) potential energy curves of open shell diatomic\nmolecules. Wavefunctions from {\\sc Duo} are used to compute Land\\'e $g$-factors\nvalid for weak magnetic fields, the results are compared with the idealized\npredictions of both Hund's case (a) and Hund's case (b) coupling schemes. Test\ncalculations are performed for AlO, NO, CrH and C$_2$. The computed $g_J$'s\nboth provide a sensitive test of the underlying spectroscopic model used to\nrepresent the system and an indication of whether states of the molecule are\nwell-represented by the either of the Hund's cases considered. The computation\nof Land\\'e $g$-factors is implemented as a standard option in the latest\nrelease of {\\sc Duo}.", "category": "physics_chem-ph" }, { "text": "A joint theoretical and experimental study of phenylene-acetylene\n molecular wires: The excited state electronic structure of $\\pi$ conjugated\nphenylene-acetylene oligomers is calculated using time-dependent density\nfunctional theory (TD-DFT) approaches. The theoretical fluorescence spectra are\nanalyzed in terms of Frank-Condon active nuclear normal modes and shown to\ncompare well with experiment. Theoretical and experimental results for the\noptical absorption and emission spectra of these molecules indicate that the\nconjugation length can be significantly reduced by conformational rotations\nabout the triple-bonded carbon links. This has serious implications on the\nelectronic functionalities of polyphenylene-acetylene based molecular wires and\ntheir possible use as charge/energy conduits in nano-assemblies.", "category": "physics_chem-ph" }, { "text": "De novo Design of Polymer Electrolytes with High Conductivity using\n GPT-based and Diffusion-based Generative Models: Solid polymer electrolytes hold significant promise as materials for\nnext-generation batteries due to their superior safety performance, enhanced\nspecific energy, and extended lifespans compared to liquid electrolytes.\nHowever, the material's low ionic conductivity impedes its commercialization,\nand the vast polymer space poses significant challenges for the screening and\ndesign. In this study, we assess the capabilities of generative artificial\nintelligence (AI) for the de novo design of polymer electrolytes. To optimize\nthe generation, we compare different deep learning architectures, including\nboth GPT-based and diffusion-based models, and benchmark the results with\nhyperparameter tuning. We further employ various evaluation metrics and\nfull-atom molecular dynamics simulations to assess the performance of different\ngenerative model architectures and to validate the top candidates produced by\neach model. Out of only 45 candidates being tested, we discovered 17 polymers\nthat achieve superior ionic conductivity better than any other polymers in our\ndatabase, with some of them doubling the conductivity value. In addition, by\nadopting a pretraining and fine-tuning methodology, we significantly improve\nthe efficacy of our generative models, achieving quicker convergence, enhanced\nperformance with limited data, and greater diversity. Using the proposed\nmethod, we can easily generate a large number of novel, diverse, and valid\npolymers, with a chance of synthesizability, enabling us to identify promising\ncandidates with markedly improved efficiency.", "category": "physics_chem-ph" }, { "text": "An experimental and theoretical investigation of the C(1D) + D2 reaction: In a previous joint experimental and theoretical study of the barrierless\nchemical reaction C(1D) + H2 at low temperatures (300-50 K) [K. M. Hickson,\nJ.-C. Loison, H. Guo, Y. V. Suleimanov, J. Phys. Chem. Lett., 2015, 6, 4194.],\nexcellent agreement was found between experimental thermal rate constants and\ntheoretical estimates based on ring polymer molecular dynamics (RPMD) over the\ntwo lowest singlet potential energy surfaces (PESs). Here, we extend this work\nto one of its deuterated counterparts, C(1D) + D2, over the same temperature\nrange. Experimental and RPMD results are in very good agreement when\ncontributions from both PESs to this chemical reaction are included in the RPMD\nsimulations. The deviation between experiment and the RPMD calculations does\nnot exceed 25 % and both results exhibit a slight negative temperature\ndependence. The first excited 1A\" PES plays a more important role than the\nground 1A' PES as the temperature is decreased, similar to our previous studies\nof the C(1D) + H2 reaction but with a more pronounced effect. The small\ndifferences in temperature dependence between the earlier and present\nexperimental studies of C(1D) + H2/D2 reactions are discussed in terms of the\nuse of non-equilibrium populations of ortho/para-H2/D2. We argue that RPMD\nprovides a very convenient and reliable tool to study low-temperature chemical\nreactions.", "category": "physics_chem-ph" }, { "text": "Binding of muonated hydrogen molecules on the occasionof the\n Born-Oppenheimer approximation 90th anniversary: The stability of four fermionic particles with unit charge, of which, two are\npositively, and two negatively charged, is discussed. Except for using the\nsimplest approximation of a single Gaussian orbital per particle, the problem\nis exactly solved variationally and, by varying the masses to simulate\nmolecular di-hydrogen, mono-muonated di-hydrogen and di-muonated di-hydrogen,\nemployed to illustrate the celebrated Born-Oppenheimer approximation on the\noccasion of its 90th anniversary. It is suggested that it is valid only for\ndi-hydrogen.", "category": "physics_chem-ph" }, { "text": "Interaction of Polar and Nonpolar Organic Pollutants with Soil Organic\n Matter: Sorption Experiments and Molecular Dynamics Simulation: The fate of organic pollutants in the environment is influenced by several\nfactors including the type and strength of their interactions with soil\ncomponents especially SOM. However, a molecular level answer to the question\nHow organic pollutants interact with SOM? is lacking. In order to explore\nmechanisms of this interaction, we have developed a new SOM model followed by\ncarrying out molecular dynamics (MD) simulations in parallel with sorption\nexperiments. The new SOM model comprises free SOM functional groups (carboxylic\nacid and naphthalene) as well as SOM cavities (with two different sizes),\nrepresenting the soil voids, containing the same SOM functional groups. To\nexamine the effect of the hydrophobicity on the interaction, the organic\npollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar)\nwere considered. The experimental and the theoretical outcomes explored four\nmajor points regarding sorption of SAA and HCB on soil. 1. The interaction\ndepends on the SOM chemical composition more than the SOM content. 2. The\ninteraction causes a site-specific adsorption on the soil surfaces. 3. Sorption\nhysteresis occurs, which can be explained by inclusion of these pollutants\ninside soil voids. 4. It was observed that the hydrophobic HCB is adsorbed on\nsoil stronger than the hydrophilic SAA. Moreover, the theoretical results\nshowed that HCB forms stable complexes with all SOM models in the aqueous\nsolution while most of SAA complexes are accompanied by dissociation. The\nSOM-cavity modeling showed a significant effect on binding of organic\npollutants to SOM.", "category": "physics_chem-ph" }, { "text": "Variational versus perturbative relativistic energies for small and\n light atomic and molecular systems: Variational and perturbative relativistic energies are computed and compared\nfor two-electron atoms and molecules with low nuclear charge numbers. In\ngeneral, good agreement of the two approaches is observed. Remaining deviations\ncan be attributed to higher-order relativistic, also called non-radiative\nquantum electrodynamics (QED), corrections of the perturbative approach that\nare automatically included in the variational solution of the no-pair\nDirac$-$Coulomb$-$Breit (DCB) equation to all orders of the $\\alpha$\nfine-structure constant. The analysis of the polynomial $\\alpha$ dependence of\nthe DCB energy makes it possible to determine the leading-order relativistic\ncorrection to the non-relativistic energy to high precision without\nregularization. Contributions from the Breit$-$Pauli Hamiltonian, for which\nexpectation values converge slowly due the singular terms, are implicitly\nincluded in the variational procedure. The $\\alpha$ dependence of the no-pair\nDCB energy shows that the higher-order ($\\alpha^4 E_\\mathrm{h}$) non-radiative\nQED correction is 5 % of the leading-order ($\\alpha^3 E_\\mathrm{h}$)\nnon-radiative QED correction for $Z=2$ (He), but it is 40 % already for $Z=4$\n(Be$^{2+}$), which indicates that resummation provided by the variational\nprocedure is important already for intermediate nuclear charge numbers.", "category": "physics_chem-ph" }, { "text": "Molecular chirality and its monitoring by ultrafast X-ray pulses: Major advances in X-ray sources including the development of circularly\npolarized and orbital angular momentum pulses make it possible to probe matter\nchirality at unprecedented energy regimes and with Angstr\\\"om and femtosecond\nspatiotemporal resolutions. We survey the theory of stationary and\ntime-resolved nonlinear chiral measurements that can be carried out in the\nX-ray regime using tabletop X-ray sources or large scale (XFEL, synchrotron)\nfacilities. A variety of possible signals and their information content are\nsurveyed.", "category": "physics_chem-ph" }, { "text": "Interpretation of van der Waals density functionals: The nonlocal correlation energy in the van der Waals density functional\n(vdW-DF) method [Phys. Rev. Lett. 92, 246401 (2004); Phys. Rev. B 76, 125112\n(2007); Phys. Rev. B 89, 035412 (2014)] can be interpreted in terms of a\ncoupling of zero-point energies of characteristic modes of semilocal\nexchange-correlation (xc) holes. These xc holes reflect the internal functional\nin the framework of the vdW-DF method [Phys. Rev. B 82, 081101(2010)]. We\nexplore the internal xc hole components, showing that they share properties\nwith those of the generalized-gradient approximation. We use these results to\nillustrate the nonlocality in the vdW-DF description and analyze the vdW-DF\nformulation of nonlocal correlation.", "category": "physics_chem-ph" }, { "text": "Predicting the Oxidation States of Mn ions in the Oxygen Evolving\n Complex of Photosystem II Using Supervised and Unsupervised Machine Learning: Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL)\nsources enabled the imaging of the catalytic intermediates of the oxygen\nevolution reaction of Photosystem II. However, due to the incoherent transition\nof the S-states, the resolved structures are a convolution from different\ncatalytic states. Here, we train Decision Tree Classifier and K-mean clustering\nmodels on Mn compounds obtained from the Cambridge Crystallographic Database to\npredict the S-state of the X-ray, XFEL, and CryoEm structures by predicting the\nMn's oxidation states in the oxygen evolving complex (OEC). The model agrees\nmostly with the XFEL structures in the dark S1 state. However, significant\ndiscrepancies are observed for the excited XFEL states (S2, S3, and S0) and the\ndark states of the X-ray and CryoEm structures. Furthermore, there is a\nmismatch between the predicted S-states within the two monomers of the same\ndimer, mainly in the excited states. The model suggests that improving the\nresolution is crucial to precisely resolve the geometry of the illuminated\nS-states to overcome the noncoherent S-state transition. In addition,\nsignificant radiation damage is observed in X-ray and CryoEM structures,\nparticularly at the dangler Mn center (Mn4). Our model represents a valuable\ntool for investigating the electronic structure of the catalytic metal cluster\nof PSII to understand the water splitting mechanism.", "category": "physics_chem-ph" }, { "text": "Nonadiabatic instanton rate theory beyond the golden-rule limit: Fermi's golden rule describes the leading-order behaviour of the reaction\nrate as a function of the diabatic coupling. Its asymptotic $(\\hbar \\rightarrow\n0)$ limit is the semiclassical golden-rule instanton rate theory, which\nrigorously approximates nuclear quantum effects, lends itself to efficient\nnumerical computation and gives physical insight into reaction mechanisms.\nHowever the golden rule by itself becomes insufficient as the strength of the\ndiabatic coupling increases, so higher-order terms must be additionally\nconsidered. In this work we give a first-principles derivation of the\nnext-order term beyond the golden rule, represented as a sum of three\ncomponents. Two of them lead to new instanton pathways that extend the\ngolden-rule case and, among other factors, account for the effects of\nrecrossing on the full rate. The remaining component derives from the\nequilibrium partition function and accounts for changes in potential energy\naround the reactant and product wells due to diabatic coupling. The new\nsemiclassical theory demands little computational effort beyond a golden-rule\ninstanton calculation. It makes it possible to rigorously assess the accuracy\nof the golden-rule approximation and sets the stage for future work on general\nsemiclassical nonadiabatic rate theories.", "category": "physics_chem-ph" }, { "text": "High Sensitivity real-time VOCs monitoring in air through FTIR\n Spectroscopy using a Multipass Gas Cell Setup: Human exposure to Volatile Organic Compounds (VOCs) and their presence in\nindoor and working environments is recognized as a serious health risk, causing\nimpairment of varying severity. Different detecting systems able to monitor\nVOCs are available in the market, however they have significant limitations for\nboth sensitivity and chemical discrimination capability. During the last years\nwe studied systematically the use of Fourier Transform Infrared Spectroscopy\n(FTIR) spectroscopy as an alternative, powerful tool for quantifying VOCs in\nair. We calibrated the method for a set of compounds (styrene, acetone, ethanol\nand isopropanol) by using both laboratory and portable infrared spectrometers.\nThe aim was to develop a new, real time and highly sensitive sensor system for\nVOCs monitoring. In this paper, we improve the setup performance testing the\nfeasibility of using a multipass cell with the aim of extending the sensitivity\nof this sensor system down to the part per milion (ppb) level. Considering that\nmultipass cells are now available also for portable instruments, this study\nopens the road for the design of new high-resolution devices for environmental\nmonitoring.", "category": "physics_chem-ph" }, { "text": "Measuring molecular parity nonconservation using nuclear magnetic\n resonance spectroscopy: The weak interaction does not conserve parity and therefore induces energy\nshifts in chiral enantiomers that should in principle be detectable in\nmolecular spectra. Unfortunately, the magnitude of the expected shifts are\nsmall and in spectra of a mixture of enantiomers, the energy shifts are not\nresolvable. We propose a nuclear magnetic resonance (NMR) experiment in which\nwe titrate the chirality (enantiomeric excess) of a solvent and measure the\ndiasteriomeric splitting in the spectra of a chiral solute in order to search\nfor an anomalous offset due to parity nonconservation (PNC). We present a\nproof-of-principle experiment in which we search for PNC in the\n\\textsuperscript{13}C resonances of small molecules, and use the\n\\textsuperscript{1}H resonances, which are insensitive to PNC, as an internal\nreference. We set a new constraint on molecular PNC in \\textsuperscript{13}C\nchemical shifts at a level of $10^{-5}$\\,ppm, and provide a discussion of\nimportant considerations in the search for molecular PNC using NMR\nspectroscopy.", "category": "physics_chem-ph" }, { "text": "Comment on 'Energy partitioning schemes: a dilemma' [I. Mayer, Faraday\n Discuss., (2007) 135, 439]: A study of some decomposition schemes of the molecular energy into one- and\ntwo-center contributions published in the above mentioned journal highlights\nthe importance of a 'dilemma' raised in such decompositions. Even more, it has\nbeen recently assigned a prominent role in the promotion energy mechanism. This\ncritical comment clarifies the validity of such a 'dilemma'.", "category": "physics_chem-ph" }, { "text": "Unitary coupled-cluster based self-consistent polarization propagator\n theory: a quadratic unitary coupled-cluster singles and doubles scheme: The development of a quadratic unitary coupled-cluster singles and doubles\n(qUCCSD) based self-consistent polarization propagator method is reported. We\npresent a simple strategy for truncating the commutator expansion of the UCC\ntransformed Hamiltonian $\\bar{H}$. The qUCCSD method for the electronic\nground-state includes up to double commutators for the amplitude equations and\nup to cubic commutators for the energy expression. The qUCCSD excited-state\neigenvalue equations include up to double commutators for the singles-singles\nblock of $\\bar{H}$, single commutators for the singles-doubles and\ndoubles-singles blocks, and the bare Hamiltonian for the doubles-doubles block.\nBenchmark qUCCSD calculations of the ground-state properties and excitation\nenergies for representative molecules demonstrate significant improvement of\nthe accuracy and robustness over the previous UCC3 scheme derived using\nM{\\o}ller-Plesset perturbation theory.", "category": "physics_chem-ph" }, { "text": "Refinement of molecular dynamics ensembles using experimental data and\n flexible forward models: A novel method combining maximum entropy principle, the Bayesian-inference of\nensembles approach, and the optimization of empirical forward models is\npresented. Here we focus on the Karplus parameters for RNA systems, which\nrelate the dihedral angles of $\\gamma$, $\\beta$, and the dihedrals in the sugar\nring to the corresponding $^3J$-coupling signal between coupling protons.\nExtensive molecular simulations are performed on a set of RNA tetramers and\nhexamers and combined with available nucleic-magnetic-resonance data. Within\nthe new framework, the sampled structural dynamics can be reweighted to match\nexperimental data while the error arising from inaccuracies in the forward\nmodels can be corrected simultaneously and consequently does not leak into the\nreweighted ensemble. Carefully crafted cross-validation procedure and\nregularization terms enable obtaining transferable Karplus parameters. Our\napproach identifies the optimal regularization strength and new sets of Karplus\nparameters balancing good agreement between simulations and experiments with\nminimal changes to the original ensemble.", "category": "physics_chem-ph" }, { "text": "Dynamical Consequences of Time-Reversal Symmetry for Systems with Odd\n Number of Electrons: Conical Intersections, Semiclassical Dynamics, and\n Topology: In this manuscript we identify the main differences between the effects of\nKramers symmetry on the systems with even and odd number of electrons, the ways\nhow the aforementioned symmetry affects the structure of the Conical Seams\n(CSs), and how it shows up in semiclassical propagation of nuclear wavepackets,\ncrossing the CSs. We identify the topological invariants, associated with CSs,\nin three cases: even and odd number of electrons with time-reversal symmetry,\nas well as absence of the latter. We obtain asymptotically exact semiclassical\nanalytical solutions for wavepackets scattered on a CS for all three cases,\nidentify topological features in a non-trivial shape of the scattered\nwavepacket, and connect them to the topological invariants, associated with\nCSs. We argue that, due to robustness of topology, the non-trivial wavepacket\nstructure is a topologically protected evidence of a wavepacket having passed\nthrough a CS, rather than a feature of a semiclassical approximation.", "category": "physics_chem-ph" }, { "text": "Cavity Click Chemistry: Cavity-Catalyzed Azide-Alkyne Cycloaddition: Click chemistry, which refers to chemical reactions that are fast, selective,\nand with high product yields, has become a powerful approach in organic\nsynthesis and chemical biology. Due to the cytotoxicity of the transition\nmetals employed in click chemistry reactions, a search for novel metal-free\nalternatives continues. Herein we demonstrate that an optical cavity can be\nutilized as a metal-free alternative in click chemistry cycloaddition reaction\nbetween cyanoacetylene and formylazide using the quantum electrodynamics\ncoupled cluster (QED-CC) method. We show that by changing the molecular\norientation with respect to the polarization of the cavity mode(s), the\nreaction can be selectively catalyzed to form a major 1,4-disubstituted or\n1,5-disubstituted product. This work highlights that a cavity has the same\neffect on the investigated cycloaddition as the transition metal catalysts\ntraditionally employed in click chemistry reactions. We expect our findings to\nfurther stimulate research in cavity-assisted click chemistry reactions.", "category": "physics_chem-ph" }, { "text": "A Simple 'Range Extender' for Basis Set Extrapolation Methods for MP2\n and Coupled Cluster Correlation Energies: We discuss the interrelations between various basis set extrapolation\nformulas and show that for the nZaPa and aug-cc-pVnZ basis set formulas, for\nn=4--6 their behavior closely resembles the Petersson (L+a)^{-3} formula with a\nshift a specific to the basis set family and level of theory. This is\nfunctionally equivalent to the Pansini-Varandas extrapolation for large L. This\nnaturally leads to a simple way to extend these extrapolations to n=7 and\nhigher. The formula is validated by comparison with newly optimized\nextrapolation factors for the AV{6,7}Z basis set pairs and literature values\nfor {6,7}ZaPa. For L\\geq5, the CCSD extrapolations of both the Schwenke and\nVarandas type are functionally equivalent to E(L)=E_\\infty+A.(L-0.30)^{-3},\ni.e., E(\\infty)=E(L)+[E(L)-E(L-1)]/([(L-0.30)/(L-1.30)]^3-1)", "category": "physics_chem-ph" }, { "text": "Kinetic correlation functionals from the entropic regularisation of the\n strictly-correlated electrons problem: We investigate whether the entropic regularisation of the\nstrictly-correlated-electrons problem can be used to build approximations for\nthe kinetic correlation energy functional at large coupling strengths and, more\ngenerally, to gain new insight in the problem of describing and understanding\nstrong correlation within Density Functional Theory.", "category": "physics_chem-ph" }, { "text": "Core Excitations with Excited State Mean Field and Perturbation Theory: We test the efficacy of excited state mean field theory and its\nexcited-state-specific perturbation theory on the prediction of K-edge\npositions and X-ray peak separations. We find that the mean field theory is\nsurprisingly accurate, even though it contains no accounting of differential\nelectron correlation effects. In the perturbation theory, we test multiple\ncore-valence separation schemes and find that, with the mean field theory\nalready so accurate, electron-counting biases in one popular separation scheme\nbecome a dominant error when predicting K-edges. Happily, these appear to be\nrelatively easy to correct for, leading to a perturbation theory for K-edge\npositions that is lower scaling and more accurate than coupled cluster theory\nand competitive in accuracy with recent high-accuracy results from restricted\nopen-shell Kohn Sham theory. For peak separations, our preliminary data show\nexcited state mean field theory to be exceptionally accurate, but more\nextensive testing will be needed to see how it and its perturbation theory\ncompare to coupled cluster peak separations more broadly.", "category": "physics_chem-ph" }, { "text": "The influence of charge ordering in the microscopic structure of\n monohydroxy alcohols: While radiation scattering data provides insight inside the microstructure of\nliquids, the Debye relation relating the scattering intensity $I(k)$ to the\natom-atom structure factors $S_{ab}(k)$ shows that, ultimately, it is these\nindividual structure correlation functions which contain the relevant\ninformation about the micro-structure. However, these quantities are not\nobservables, except in few cases where one can invert the Debye relation in\norder to obtain the structure functions. In the majority of other cases, the\nneed for model dependent computer simulations is unavoidable. The resulting\ncalculations reveal that the scattering pre-peak is the result of cancellations\nbetween positive pre-peaks and negative anti-peaks contributions from the\natom-atom structure factors. What of systems where this cancellation is such\nthat it entirely suppresses the scattering pre-peak? One would be tempted to\nfalsely conclude that there is no uderlying micro-heterogeneity. Hence, the\nstructure functions appear as hidden variables, and it is important to\nunderstand the relation between their features and the micro-structure of the\nsystem. Through the computer simulation study of various mono-ols, ranging from\nmethanol to 1-nonanol, as well as the branched octanols, we show how the\nfeatures of the atom-atom pair correlation function $g_{ab}(r)$ affect that of\nthe structure factors $S_{ab}(k)$, and reveal that the micro-structure is\nultimately the result of the charge ordering between different atoms in the\nsystem.", "category": "physics_chem-ph" }, { "text": "Approximating First Hitting Point Distribution in Milestoning for Rare\n Event Kinetics: Milestoning is an efficient method for rare event kinetics calculation using\nshort trajectory parallelization. Mean first passage time (MFPT) is the key\nkinetic output of Milestoning, whose accuracy crucially depends the initial\ndistribution of the short trajectory ensemble. The true initial distribution,\ni.e., first hitting point distribution (FHPD), has no analytic expression in\nthe general case. Here, we introduce two algorithms, local passage time\nweighted Milestoning (LPT-M) and Bayesian inference Milestoning (BI-M), to\naccurately and efficiently approximate FHPD for systems at equilibrium\ncondition. Starting from sampling Boltzmann distribution on milestones, we\ncalculate the proper weighting factor for the short trajectory ensemble. The\nmethods are tested on two model examples for illustration purpose. Both methods\nimprove significantly over the widely used classical Milestoning method in\nterms of the accuracy of MFPT. In particular, BI-M covers the directional\nMilestoning method as a special case in the deterministic Hamiltonian dynamics.\nLPT-M is especially advantageous in terms of computational costs and robustness\nwith respect to the increasing number of intermediate milestones. Furthermore,\na locally iterative correction algorithm for non-equilibrium stationary FHPD is\ndeveloped for exact MFPT calculation, which can be combined with LPT-M/BI-M and\nis much cheaper than the exact Milestoning method.", "category": "physics_chem-ph" }, { "text": "Topical Issue \"Dynamics of Systems on the Nanoscale (2021)\". Editorial: Exploration of the structure formation and dynamics of animate and inanimate\nmatter on the nanometer scale is a highly interdisciplinary field of rapidly\nemerging research. It is relevant for various molecular and nanoscale systems\nof different origins and compositions and concerns numerous phenomena\noriginating from physics, chemistry, biology, and materials science. This\ntopical issue presents a collection of research papers devoted to different\naspects of the Dynamics of Systems on the Nanoscale. Some of the contributions\ndiscuss specific applications of the research results in several modern and\nemerging technologies, such as controlled nanofabrication with charged particle\nbeams or the design and practical realization of novel gamma-ray crystal-based\nlight sources. Most works presented in this topical issue were reported at the\njoint Sixth International Conference \"Dynamics of Systems on the Nanoscale\" and\nthe tenth International Symposium \"Atomic Cluster Collisions\" (DySoN-ISACC\n2021), which were held in Santa Margherita Ligure, Italy, in October 2021.", "category": "physics_chem-ph" }, { "text": "Deep Learning for Optoelectronic Properties of Organic Semiconductors: Atomistic modeling of energetic disorder in organic semiconductors (OSCs) and\nits effects on the optoelectronic properties of OSCs requires a large number of\nexcited-state electronic-structure calculations, a computationally daunting\ntask for many OSC applications. In this work, we advocate the use of deep\nlearning to address this challenge and demonstrate that state-of-the-art deep\nneural networks (DNNs) are capable of predicting the electronic properties of\nOSCs at an accuracy comparable with the quantum chemistry methods used for\ngenerating training data. We extensively investigate the performances of four\nrecent DNNs (deep tensor neural network, SchNet, message passing neural\nnetwork, and multilevel graph convolutional neural network) in predicting\nvarious electronic properties of an important class of OSCs, i.e.,\noligothiophenes (OTs), including their HOMO and LUMO energies, excited-state\nenergies and associated transition dipole moments. We find that SchNet shows\nthe best performance for OTs of different sizes (from bithiophene to\nsexithiophene), achieving average prediction errors in the range of 20-80meV\ncompared to the results from (time-dependent) density functional theory. We\nshow that SchNet also consistently outperforms shallow feed-forward neural\nnetworks, especially in difficult cases with large molecules or limited\ntraining data. We further show that SchNet could predict the transition dipole\nmoment accurately, a task previously known to be difficult for feed-forward\nneural networks, and we ascribe the relatively large errors in transition\ndipole prediction seen for some OT configurations to the charge-transfer\ncharacter of their excited states. Finally, we demonstrate the effectiveness of\nSchNet by modeling the UV-Vis absorption spectra of OTs in dichloromethane and\na good agreement is observed between the calculated and experimental spectra.", "category": "physics_chem-ph" }, { "text": "Geminal-based strategies for modeling large building blocks of organic\n electronic materials: We elaborate on unconventional electronic structure methods based on geminals\nand their potential to advance the rapidly developing field of organic\nphotovoltaics (OPV). Specifically, we focus on the computational advantages of\ngeminal-based methods over standard approaches and identify the critical\naspects of OPV development. Examples are reliable and efficient computations of\norbital energies, electronic spectra, and van-der-Waals interactions.\nGeminal-based models can also be combined with quantum embedding techniques and\na quantum information analysis of orbital interactions to gain a fundamental\nunderstanding of the electronic structures and properties of realistic OPV\nbuilding blocks. Furthermore, other organic components present in, for\ninstance, dye-sensitized solar cells (DSSC) represent another promising scope\nof application. Finally, we provide numerical examples predicting the\nproperties of a small building block of OPV components and two carbazole-based\ndyes proposed as possible DSSC sensitizers.", "category": "physics_chem-ph" }, { "text": "Electronic Spectra of Ytterbium Fluoride from Relativistic Electronic\n Structure Calculations: We report an investigation of the low-lying excited states of the YbF\nmolecule--a candidate molecule for experimental measurements of the electron\nelectric dipole moment--with 2-component based multi-reference configuration\ninteraction (MRCI), equation of motion coupled cluster (EOM-CCSD) and the\nextrapolated intermediate Hamiltonian Fock-space coupled cluster (XIHFS-CCSD).\nSpecifically, we address the question of the nature of these low-lying states\nin terms of configurations containing filled or partially-filled Yb $4f$\nshells. We show that while it does not appear possible to carry out\ncalculations with both kinds of configurations contained in the same active\nspace, reliable information can be extracted from different sectors of Fock\nspace--that is, by performing electron attachment and detachment IHFS-CCSD and\nEOM-CCSD calculation on the closed-shell YbF$^+$ and YbF$^-$ species,\nrespectively. From these we observe $\\Omega = 1/2, 3/2$ states that arise from\nthe $4f^{13}\\sigma_{6s}^2$, $4f^{14}5d$/$6p$, and $4f^{13}5d\\sigma_{6s}$\nconfigurations appear in the same energy range around the ground-state\nequilibrium geometry and they are therefore able to interact. As these states\nare generated from different sectors of Fock space, they are almost orthogonal\nand provide complementary descriptions of parts of the excited state manifold.\nTo obtain a comprehensive picture, we introduce a simple adiabatization model\nto extract energies of interacting $\\Omega = 1/2, 3/2$ states that can be\ncompared to experimental observations.", "category": "physics_chem-ph" }, { "text": "Toward a complete and comprehensive cross section database for electron\n scattering from NO using machine learning: We review experimental and theoretical cross sections for electron scattering\nin nitric oxide (NO) and form a comprehensive set of plausible cross sections.\nTo assess the accuracy and self-consistency of our set, we also review electron\nswarm transport coefficients in pure NO and admixtures of NO in Ar, for which\nwe perform a multi-term Boltzmann equation analysis. We address observed\ndiscrepancies with these experimental measurements by training an artificial\nneural network to solve the inverse problem of unfolding the underlying\nelectron-NO cross sections, while using our initial cross section set as a base\nfor this refinement. In this way, we refine a suitable quasielastic momentum\ntransfer cross section, a dissociative electron attachment cross section and a\nneutral dissociation cross section. We confirm that the resulting refined cross\nsection set has an improved agreement with the experimental swarm data over\nthat achieved with our initial set. We also use our refined data base to\ncalculate electron transport coefficients in NO, across a large range of\ndensity-reduced electric fields from 0.003 Td to 10,000 Td.", "category": "physics_chem-ph" }, { "text": "Comment on \"Communication: Simple and accurate uniform electron gas\n correlation energy for the full range of densities\" [J. Chem. Phys. 145,\n 021101 (2016)]: A simple expression for the uniform electron gas (UEG) correlation energy,\nrecently presented in Ref. [J. Chem. Phys. 145, 021101 (2016)], deviates from\nthe reference quantum Monte-Carlo (QMC) data at large r_s. We propose to define\none of the parameters from a requirement to match the large-rs QMC data.\nFunctional with the new parameter provides much better agreement with the QMC\ndata at large r_s without deterioration of the functional quality at small and\nintermediate r_s.", "category": "physics_chem-ph" }, { "text": "Inelastic scattering of electrons in water from first principles: cross\n sections and inelastic mean free path for use in Monte Carlo track-structure\n simulations of biological damage: Modelling the inelastic scattering of electrons in water is fundamental,\ngiven their crucial role in biological damage. In Monte Carlo track-structure\ncodes used to assess biological damage, the energy loss function, from which\ncross sections are extracted, is derived from different semi-empirical optical\nmodels. Only recently, first ab-initio results for the energy loss function and\ncross-sections in water became available. For benchmarking purpose, in this\nwork, we present ab-initio linear-response time-dependent density functional\ntheory calculations of the energy loss function of liquid water. We calculated\nthe inelastic scattering cross sections, inelastic mean free paths, and\nelectronic stopping powers and compared our results with recent calculations\nand experimental data showing a good agreement. In addition, we provide an\nin-depth analysis of the contributions of different molecular orbitals,\nspecies, and orbital angular momenta to the total energy loss function.\nMoreover, we present single-differential cross sections computed for each\nmolecular orbital channel, which should prove useful for Monte-Carlo\ntrack-structure simulations.", "category": "physics_chem-ph" }, { "text": "Subspace methods for the simulation of molecular response properties on\n a quantum computer: We explore Davidson methods for obtaining excitation energies and other\nlinear response properties within quantum self-consistent linear response\n(q-sc-LR) theory. Davidson-type methods allow for obtaining only a few selected\nexcitation energies without explicitly constructing the electronic Hessian\nsince they only require the ability to perform Hessian-vector multiplications.\nWe apply the Davidson method to calculate the excitation energies of hydrogen\nchains (up to H$_{10}$) and analyze aspects of statistical noise for computing\nexcitation energies on quantum simulators. Additionally, we apply Davidson\nmethods for computing linear response properties such as static\npolarizabilities for H$_2$, LiH, H$_2$O, OH$^-$, and NH$_3$, and show that\nunitary coupled cluster outperforms classical projected coupled cluster for\nmolecular systems with strong correlation. Finally, we formulate the Davidson\nmethod for damped (complex) linear response, with application to the nitrogen\nK-edge X-ray absorption of ammonia, and the $C_6$ coefficients of H$_2$, LiH,\nH$_2$O, OH$^-$, and NH$_3$.", "category": "physics_chem-ph" }, { "text": "Wave function methods for canonical ensemble thermal averages in\n correlated many-fermion systems: We present a wave function representation for the canonical ensemble thermal\ndensity matrix by projecting the thermofield double state against the desired\nnumber of particles. The resulting canonical thermal state obeys an imaginary\ntime-evolution equation. Starting with the mean-field approximation, where the\ncanonical thermal state becomes an antisymmetrized geminal power wave function,\nwe explore two different schemes to add correlation: by number-projecting a\ncorrelated grand-canonical thermal state, and by adding correlation to the\nnumber-projected mean-field state. As benchmark examples, we use\nnumber-projected configuration interaction and an AGP-based perturbation theory\nto study the Hydrogen molecule in a minimal basis and the six-site Hubbard\nmodel.", "category": "physics_chem-ph" }, { "text": "Mean first-passage times for solvated LiCN isomerization at intermediate\n to high temperatures: The behavior of a particle in a solvent has been framed using stochastic\ndynamics since the early theory of Kramers. A particle in a chemical reaction\nreacts slower in a diluted solvent because of the lack of energy transfer via\ncollisions. The flux-over-population reaction rate constant rises with\nincreasing density before falling again for very dense solvents. This Kramers\nturnover is observed in this paper at intermediate and high temperatures in the\nbackward reaction of the LiNC $\\rightleftharpoons$ LiCN isomerization via\nLangevin dynamics and mean first-passage times (MFPTs). It is in good agreement\nwith the Pollak-Grabert-H\\\"anggi (PGH) reaction rates at lower temperatures.\nFurthermore, we find a square root behavior of the reaction rate at high\ntemperatures and have made direct comparisons of the methods in the\nintermediate- and high- temperature regimes; all suggesting increased ranges in\naccuracy of both the PGH and MFPT approaches.", "category": "physics_chem-ph" }, { "text": "Structure and dynamics of the interface between a binary hard-sphere\n crystal of NaCl type and its coexisting binary fluid: Molecular dynamics simulations are performed to study the [100] and [111]\norientations of the crystal-melt interface between an ordered two-component\nhard sphere with a NaCl structure and its coexisting binary hard-sphere fluid.\nThe diameter ratio of the two types of hard spheres making up the mixture is\ntaken to be 0.414. This work complements our earlier interface simulations [J.\nChem. Phys.116, 3410] for the same diameter ratio at lower pressures where the\nsmaller component is immiscible in the solid and the fluid mixture coexists\nwith a pure FCC crystal of large particles. Density profiles and diffusion\ncoefficient profiles are presented for the AB interfacial system. We find that\nfor this system, the transition from crystal-like to fluid-like behavior of\nboth the density and diffusion constant profiles occurs over a narrower region\nthan that seen in our previous studies [J. Chem. Phys. 116, 3410] of the\nFCC/binary fluid system. But similar to what was found in the FCC/binary fluid\ninterface the transition region for the large particle diffusion constant is\nshifted about the size of the large particles toward the fluid phase relative\nto that for the small particles.", "category": "physics_chem-ph" }, { "text": "Transition-Based Constrained DFT for the Robust and Reliable Treatment\n of Excitations in Supramolecular Systems: Despite the variety of available computational approaches, state-of-the-art\nmethods for calculating excitation energies such as time-dependent density\nfunctional theory (TDDFT), are computationally demanding and thus limited to\nmoderate system sizes. Here, we introduce a new variation of constrained DFT\n(CDFT), wherein the constraint corresponds to a particular transition (T), or\ncombination of transitions, between occupied and virtual orbitals, rather than\na region of the simulation space as in traditional CDFT. We compare T-CDFT with\nTDDFT and $\\Delta$SCF results for the low lying excited states (S$_{1}$ and\nT$_{1}$) of a set of gas phase acene molecules and OLED emitters, as well as\nwith reference results from the literature. At the PBE level of theory, T-CDFT\noutperforms $\\Delta$SCF for both classes of molecules, while also proving to be\nmore robust. For the local excitations seen in the acenes, T-CDFT and TDDFT\nperform equally well. For the charge-transfer (CT)-like excitations seen in the\nOLED molecules, T-CDFT also performs well, in contrast to the severe energy\nunderestimation seen with TDDFT. In other words, T-CDFT is equally applicable\nto both local excitations and CT states, providing more reliable excitation\nenergies at a much lower computational cost than TDDFT. T-CDFT is designed for\nlarge systems and has been implemented in the linear scaling BigDFT code. It is\ntherefore ideally suited for exploring the effects of explicit environments on\nexcitation energies, paving the way for future simulations of excited states in\ncomplex realistic morphologies, such as those which occur in OLED materials.", "category": "physics_chem-ph" }, { "text": "Understanding and Improving the Efficiency of Full Configuration\n Interaction Quantum Monte Carlo: Within Full Configuration Interaction Quantum Monte Carlo, we investigate how\nthe statistical error behaves as a function of the parameters which control the\nstochastic sampling. We define the inefficiency as a measure of the statistical\nerror per particle sampling the space and per timestep and show there is a\nsizeable parameter regime where this is minimised. We find that this\ninefficiency increases sublinearly with Hilbert space size and can be reduced\nby localising the canonical Hartree--Fock molecular orbitals, suggesting that\nthe choice of basis impacts the method beyond that of the sign problem.", "category": "physics_chem-ph" }, { "text": "Machine learning at the atomic-scale: Statistical learning algorithms are finding more and more applications in\nscience and technology. Atomic-scale modeling is no exception, with machine\nlearning becoming commonplace as a tool to predict energy, forces and\nproperties of molecules and condensed-phase systems. This short review\nsummarizes recent progress in the field, focusing in particular on the problem\nof representing an atomic configuration in a mathematically robust and\ncomputationally efficient way. We also discuss some of the regression\nalgorithms that have been used to construct surrogate models of atomic-scale\nproperties. We then show examples of how the optimization of the\nmachine-learning models can both incorporate and reveal insights onto the\nphysical phenomena that underlie structure-property relations.", "category": "physics_chem-ph" }, { "text": "Time-dependent coupled cluster with orthogonal adaptive basis functions:\n General formalism and application to the vibrational problem: We derive equations of motion for bivariational wave functions with\northogonal adaptive basis sets and specialize the formalism to the coupled\ncluster ansatz. The equations are related to the biorthogonal case in a\ntransparent way, and similarities and differences are analyzed. We show that\nthe amplitude equations are identical in the orthogonal and biorthogonal\nformalisms, while the linear equations that determined the basis set time\nevolution differ by symmetrization. Applying the orthogonal framework to the\nnuclear dynamics problem, we introduce and implement the orthogonal\ntime-dependent modal vibrational coupled cluster (oTDMVCC) method and benchmark\nit against exact reference results for four triatomic molecules as well as a 5D\ntrans-bithiophene model. We confirm numerically that the biorthogonal TDMVCC\nhierarchy converges to the exact solution, while oTDMVCC does not. The\ndifferences between TDMVCC and oTDMVCC are found to be small for three of the\nfive cases, but we also identify one case where the formal deficiency of the\noTDMVCC approach results in clear and visible errors relative to the exact\nresult. For the remaining example, oTDMVCC exhibits rather modest but visible\nerrors.", "category": "physics_chem-ph" }, { "text": "Entangled system-and-environment dynamics: Phase-space dissipaton theory: Dissipaton-equation-of-motion (DEOM) theory [Y. J. Yan, J. Chem. Phys. 140,\n054105 (2014)] is an exact and nonperturbative many-particle method for open\nquantum systems. The existing dissipaton algebra treats also the dynamics of\nhybrid bath solvation coordinates. The dynamics of conjugate momentums remain\nto be addressed within the DEOM framework. In this work, we establish this\nmissing ingredient, the dissipaton algebra on solvation momentums, with\nrigorous validations against necessary and sufficient criteria. The resulted\nphase-space DEOM theory will serve as a solid ground for further developments\nof various practical methods toward a broad range of applications. We\nillustrate this novel dissipaton algebra with the phase-space DEOM-evaluation\non heat current fluctuation.", "category": "physics_chem-ph" }, { "text": "Accurate electronic excitations for two alkali-halide systems obtained\n by density-functional theory and verified by multi-configuration\n self-consistent field calculations: Use of density-functional theory in a $\\Delta$self-consistent field framework\nresult in both the ground- and two lowest electronicly excited states of the\nNaCl and LiCl. The accuracy of this method is confirmed using a\nmulti-configuration self-consistent field method to obtain the same states. The\noverall good agreement between the calculated ground and excited\npotential-energy surfaces speaks promising for the computationally simple\n$\\Delta$self-consistent field method.", "category": "physics_chem-ph" }, { "text": "Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid\n Densities and Static Dielectric Constants from the ThermoML Data Archive: Atomistic molecular simulations are a powerful way to make quantitative\npredictions, but the accuracy of these predictions depends entirely on the\nquality of the forcefield employed. While experimental measurements of\nfundamental physical properties offer a straightforward approach for evaluating\nforcefield quality, the bulk of this information has been tied up in formats\nthat are not machine-readable. Compiling benchmark datasets of physical\nproperties from non-machine-readable sources require substantial human effort\nand is prone to accumulation of human errors, hindering the development of\nreproducible benchmarks of forcefield accuracy. Here, we examine the\nfeasibility of benchmarking atomistic forcefields against the NIST ThermoML\ndata archive of physicochemical measurements, which aggregates thousands of\nexperimental measurements in a portable, machine-readable, self-annotating\nformat. As a proof of concept, we present a detailed benchmark of the\ngeneralized Amber small molecule forcefield (GAFF) using the AM1-BCC charge\nmodel against measurements (specifically bulk liquid densities and static\ndielectric constants at ambient pressure) automatically extracted from the\narchive, and discuss the extent of available data. The results of this\nbenchmark highlight a general problem with fixed-charge forcefields in the\nrepresentation low dielectric environments such as those seen in binding\ncavities or biological membranes.", "category": "physics_chem-ph" }, { "text": "Pair-correlated product speed and angular distributions for the\n OH+CH4/CD4 reactions: Further remarks on their classical trajectory\n calculations in a quantum spirit: Ten years ago, Liu and co-workers measured pair-correlated product speed and\nangular distributions for the OH+CH4/CD4 reactions at the collision energy of ~\n10 kcal/mol [B. Zhang, W. Shiu, J. J. Lin and K. Liu, J. Chem. Phys 122, 131102\n(2005); B. Zhang, W. Shiu and K. Liu, J. Phys. Chem. A 2005, 109, 8989].\nRecently, two of us could semi-quantitatively reproduce these measurements by\nperforming full-dimensional classical trajectory calculations in a quantum\nspirit on an ab-initio potential energy surface of their own [J.\nEspinosa-Garcia and J. C. Corchado, Theor Chem Acc, 2015, 134, 6 ; J. Phys.\nChem. B, Article ASAP, DOI: 10.1021/acs.jpcb.5b04290]. The goal of the present\nwork is to show that these calculations can be significantly improved by adding\na few more constraints to better comply with the experimental conditions.\nOverall, the level of agreement between theory and experiment is remarkable\nconsidering the large dimensionality of the processes under scrutiny.", "category": "physics_chem-ph" }, { "text": "Non-Collinearity in Small Magnetic Cobalt-Benzene Molecules: Organometallic clusters based on transition metal atoms are interesting\nbecause possible applications in spintronics and quantum information. In\naddition to the enhanced magnetism at the nanoscale, the organic ligands may\nprovide a natural shield again unwanted magnetic interactions with the matrices\nrequired for applications. Here we show that the organic ligands may lead to\nnon-collinear magnetic order as well as the expected quenching of the magnetic\nmoments. We use different density functional theory (DFT) methods to study the\nexperimentally relevant three cobalt atoms surrounded by benzene rings\n(Co$_3$Bz$_3$). We found that the benzene rings induce a ground state with\nnon-collinear magnetization, with the magnetic moments localized on the cobalt\ncenters and lying on the plane formed by the three cobalt atoms. We further\nanalyze the magnetism of such a cluster using an anisotropic Heisenberg model\nwhere the involved parameters are obtained by a comparison with the DFT\nresults. These results may also explain the recent observation of null magnetic\nmoment of Co$_3$Bz$_3^+$. Moreover, we propose an additional experimental\nverification based on electron paramagnetic resonance.", "category": "physics_chem-ph" }, { "text": "Imaging ultrafast molecular wavepackets with a single chirped UV pulse: We show how to emulate a conventional pump-probe scheme using a single\nfrequency-chirped ultrashort UV pulse to obtain a time-resolved image of\nmolecular ultrafast dynamics. The chirp introduces a spectral phase in time\nthat encodes the delay between the pump and the probe frequencies contained in\nthe pulse. By comparing the results of full dimensional ab initio calculations\nfor the H$^+_2$ molecule with those of a simple sequential model, we\ndemonstrate that, by tuning the chirp parameter, two-photon energy-differential\nionization probabilities directly map the wave packet dynamics generated in the\nmolecule. As a result, one can also achieve a significant amount of control of\nthe total ionization yields, with a possible enhancement by more than an order\nof magnitude.", "category": "physics_chem-ph" }, { "text": "Developing an aqueous approach for synthesizing Au and M@Au (M = Pd,\n CuPt) hybrid nanostars with plasmonic properties: Anisotropic Au nanoparticles show unique localized surface plasmon resonance\n(LSPR) properties, which make it attractive in optical, sensing, and biomedical\napplications. In this contribution, we report a general and facile strategy\ntowards aqueous synthesis of Au and M@Au (M = Pd, CuPt) hybrid nanostars by\nreducing HAuCl4 with ethanolamine in the presence of cetyltrimethylammonium\nbromide (CTAB). According to electron microscopic observation and spectral\nmonitoring, we found that the layered epitaxial growth mode (i.e., Frank-van\nder Merwe mechanism) contributes to the enlargement of the core, while, the\nrandom attachment of Au nanoclusters onto the cores accounts for the formation\nof the branches. Both of them are indispensable for the formation of the\nnanostars. The LSPR properties of the Au nanoparticles have been well\ninvestigated with morphology control via precursor amount and growth\ntemperature. The Au nanostars showed improved surface-enhanced Raman\nspectroscopy (SERS) performance for rhodamine 6G due to their sharp edges and\ntips, which were therefore confirmed as good SERS substrate to detect trace\namount of molecules.", "category": "physics_chem-ph" }, { "text": "Application of a symmetry-adapted algebraic model to the vibratioinal\n spectrum of methane: The stretching and bending vibrations of methane are studied in the framework\nof a symmetry-adapted algebraic model. The model is based on the realization of\nthe one-dimensional Morse potential in terms of a $U(2)$ algebra. For the 44\nobserved energies we obtain a fit with a r.m.s. deviation of 1.16 cm$^{-1}$\nwhich is an order of magnitude more accurate than previous algebraic\ncalculations.", "category": "physics_chem-ph" }, { "text": "Integer Discontinuity of Density Functional Theory: Density functional approximations to the exchange-correlation energy of\nKohn-Sham theory, such as the local density approximation and generalized\ngradient approximations, lack the well-known integer discontinuity, a feature\nthat is critical to describe molecular dissociation correctly. Moreover,\nstandard approximations to the exchange-correlation energy also fail to yield\nthe correct linear dependence of the ground-state energy on the number of\nelectrons when this is a non-integer number obtained from the grand canonical\nensemble statistics. We present a formal framework to restore the integer\ndiscontinuity of any density functional approximation. Our formalism derives\nfrom a formula for the exact energy functional and a new constrained search\nfunctional that recovers the linear dependence of the energy on the number of\nelectrons.", "category": "physics_chem-ph" }, { "text": "A nonlinear equation for ionic diffusion in a strong binary electrolyte: The problem of the one dimensional electro-diffusion of ions in a strong\nbinary electrolyte is considered. In such a system the solute dissociates\ncompletely into two species of ions with unlike charges. The mathematical\ndescription consists of a diffusion equation for each species augmented by\ntransport due to a self consistent electrostatic field determined by the\nPoisson equation. This mathematical framework also describes other important\nproblems in physics such as electron and hole diffusion across semi-conductor\njunctions and the diffusion of ions in plasmas. If concentrations do not vary\nappreciably over distances of the order of the Debye length, the Poisson\nequation can be replaced by the condition of local charge neutrality first\nintroduced by Planck. It can then be shown that both species diffuse at the\nsame rate with a common diffusivity that is intermediate between that of the\nslow and fast species (ambipolar diffusion). Here we derive a more general\ntheory by exploiting the ratio of Debye length to a characteristic length scale\nas a small asymptotic parameter. It is shown that the concentration of either\nspecies may be described by a nonlinear integro-differential equation which\nreplaces the classical linear equation for ambipolar diffusion but reduces to\nit in the appropriate limit. Through numerical integration of the full set of\nequations it is shown that this nonlinear equation provides a better\napproximation to the exact solution than the linear equation it replaces.", "category": "physics_chem-ph" }, { "text": "State-Specific Coupled-Cluster Methods for Excited States: We reexamine $\\Delta$CCSD, a state-specific coupled-cluster (CC) with single\nand double excitations (CCSD) approach that targets excited states through the\nutilization of non-Aufbau determinants. This methodology is particularly\nefficient when dealing with doubly excited states, a domain where the standard\nequation-of-motion CCSD (EOM-CCSD) formalism falls short. Our goal here is to\nevaluate the effectiveness of $\\Delta$CCSD when applied to other types of\nexcited states, comparing its consistency and accuracy with EOM-CCSD. To this\nend, we report a benchmark on excitation energies computed with the\n$\\Delta$CCSD and EOM-CCSD methods, for a set of molecular excited-state\nenergies that encompasses not only doubly excited states but also\ndoublet-doublet transitions and (singlet and triplet) singly-excited states of\nclosed-shell systems. In the latter case, we rely on a minimalist version of\nmultireference CC known as the two-determinant CCSD method to compute the\nexcited states. Our dataset, consisting of 276 excited states stemming from the\n\\textsc{quest} database [V\\'eril \\textit{et al.}, \\textit{WIREs Comput. Mol.\nSci.} \\textbf{2021}, 11, e1517], provides a significant base to draw general\nconclusions concerning the accuracy of $\\Delta$CCSD. Except for the\ndoubly-excited states, we found that $\\Delta$CCSD underperforms EOM-CCSD. For\ndoublet-doublet transitions, the difference between the mean absolute errors\n(MAEs) of the two methodologies (of \\SI{0.10}{\\eV} and \\SI{0.07}{\\eV}) is less\npronounced than that obtained for singly-excited states of closed-shell systems\n(MAEs of \\SI{0.15}{\\eV} and \\SI{0.08}{\\eV}). This discrepancy is largely\nattributed to a greater number of excited states in the latter set exhibiting\nmulticonfigurational characters, which are more challenging for $\\Delta$CCSD.", "category": "physics_chem-ph" }, { "text": "Markov models from the Square Root Approximation of the Fokker-Planck\n equation: calculating the grid-dependent flux: Molecular dynamics are extremely complex, yet understanding the slow\ncomponents of their dynamics is essential to understanding their macroscopic\nproperties. To achieve this, one models the molecular dynamics as a stochastic\nprocess and analyses the dominant eigenfunctions of the associated\nFokker-Planck operator, or of closely related transfer operators. So far, the\ncalculation of the discretized operators requires extensive molecular dynamics\nsimulations. The Square-root approximation of the Fokker-Planck equation is a\nmethod to calculate transition rates as a ratio of the Boltzmann densities of\nneighboring grid cells times a flux, and can in principle be calculated without\na simulation. In a previous work we still used molecular dynamics simulations\nto determine the flux. Here, we propose several methods to calculate the exact\nor approximate flux for various grid types, and thus estimate the rate matrix\nwithout a simulation. Using model potentials we test computational efficiency\nof the methods, and the accuracy with which they reproduce the dominant\neigenfunctions and eigenvalues. For these model potentials, rate matrices with\nup to $\\mathcal{O}(10^6)$ states can be obtained within seconds on a single\nhigh-performance compute server if regular grids are used.", "category": "physics_chem-ph" }, { "text": "Enrichment of nuclear spin isomers by molecular coherent control: Enrichment of nuclear spin isomers of molecules by infrared radiation\nresonant to molecular rovibrational transition is considered. Special attention\nis given to the enrichment by light-induced crossing of far separated ortho and\npara states.", "category": "physics_chem-ph" }, { "text": "Role of Self-Assembled Monolayers on Improved Electrical Stability of\n Amorphous In-Ga-Zn-O Thin-Film Transistors: Self-assembled monolayers (SAMs) have been used to improve both the positive\nand negative bias-stress stability of amorphous indium gallium zinc oxide\n(IGZO) bottom gate thin film transistors (TFTs). N-hexylphosphonic acid (HPA)\nand fluorinated hexylphosphonic acid (FPA) SAMs adsorbed on IGZO back channel\nsurfaces were shown to significantly reduce bias stress turn-on voltage shifts\ncompared to IGZO back channel surfaces with no SAMs. FPA was found to have a\nlower surface energy and lower packing density than HPA, as well as lower bias\nstress turn-on voltage shifts. The improved stability of IGZO TFTs with SAMs\ncan be primarily attributed to a reduction in molecular adsorption of\ncontaminants on the IGZO back channel surface and minimal trapping states\npresent with phosphonic acid binding to the IGZO surface.", "category": "physics_chem-ph" }, { "text": "Triplet Rydberg states of aluminum monofluoride: Aluminum monofluoride (AlF) is a suitable molecule for laser cooling and\ntrapping. Such experiments require an extensive spectroscopic characterization\nof the electronic structure. Two of the theoretically predicted higher lying\ntriplet states of AlF, the counterparts of the well-characterized D$^1\\Delta$\nand E$^1\\Pi$ states, had experimentally not been identified yet. We here report\non the characterization of the d$^3\\Pi$ ($v=0-6$) and e$^3\\Delta$ ($v=0-2$)\nstates, confirming the predicted energetic ordering of these states (J. Chem.\nPhys. 88 (1988) 5715-5725), as well as of the f$^3\\Sigma^+$ ($v=0-2$) state.\nThe transition intensity of the d$^3\\Pi, v=3$ $-$ a$^3\\Pi, v=3$ band is\nnegligibly small. This band gets its weak, unexpected rotational structure via\nintensity borrowing from the nearby e$^3\\Delta, v=2$ $-$ a$^3\\Pi, v=3$ band,\nmade possible via spin-orbit and spin-rotation interaction between the d$^3\\Pi$\nand e$^3\\Delta$ states. This interaction affects the equilibrium rotational\nconstants in both states; their deperturbed values yield equilibrium\ninternuclear distances that are consistent with the observations. We determine\nthe ionization potential of AlF to be 78492(1) cm$^{-1}$ by ionization from the\nd$^3\\Pi$ state.", "category": "physics_chem-ph" }, { "text": "M\u00f6ssbauer, nuclear inelastic scattering and density functional studies\n on the second metastable state of Na2[Fe(CN)5NO]$\\cdot$2H2O: The structure of the light-induced metastable state SII of\nNa2[Fe(CN)5NO]$\\cdot$2H2O 14 was investigated by transmission M\\\"ossbauer\nspectroscopy (TMS) in the temperature range 15 between 85 and 135 K, nuclear\ninelastic scattering (NIS) at 98 K using synchrotron 16 radiation and density\nfunctional theory (DFT) calculations. The DFT and TMS results 17 strongly\nsupport the view that the NO group in SII takes a side-on molecular orientation\n18 and, further, is dynamically displaced from one eclipsed, via a staggered,\nto a second 19 eclipsed orientation. The population conditions for generating\nSII are optimal for 20 measurements by TMS, yet they are modest for\naccumulating NIS spectra. Optimization 21 of population conditions for NIS\nmeasurements is discussed and new NIS experiments on 22 SII are proposed.", "category": "physics_chem-ph" }, { "text": "Steric effects in the dynamics of electrolytes at large applied\n voltages: I. Double-layer charging: The classical Poisson-Boltzmann (PB) theory of electrolytes assumes a dilute\nsolution of point charges with mean-field electrostatic forces. Even for very\ndilute solutions, however, it predicts absurdly large ion concentrations\n(exceeding close packing) for surface potentials of only a few tenths of a\nvolt, which are often exceeded, e.g. in microfluidic pumps and electrochemical\nsensors. Since the 1950s, several modifications of the PB equation have been\nproposed to account for the finite size of ions in equilibrium, but in this\ntwo-part series, we consider steric effects on diffuse charge dynamics (in the\nabsence of electro-osmotic flow). In this first part, we review the literature\nand analyze two simple models for the charging of a thin double layer, which\nmust form a condensed layer of close-packed ions near the surface at high\nvoltage. A surprising prediction is that the differential capacitance typically\nvaries non-monotonically with the applied voltage, and thus so does the\nresponse time of an electrolytic system. In PB theory, the capacitance blows up\nexponentially with voltage, but steric effects actually cause it to decrease\nabove a threshold voltage where ions become crowded near the surface. Other\nnonlinear effects in PB theory are also strongly suppressed by steric effects:\nThe net salt adsorption by the double layers in response to the applied voltage\nis greatly reduced, and so is the tangential \"surface conduction\" in the\ndiffuse layer, to the point that it can often be neglected compared to bulk\nconduction (small Dukhin number).", "category": "physics_chem-ph" }, { "text": "Ion Transport through Short Nanopores Modulated by Charged Exterior\n Surfaces: Short nanopores find extensive applications capitalizing on their high\nthroughput and detection resolution. Ionic behaviors through long nanopores are\nmainly determined by charged inner-pore walls. When pore lengths decrease to\nsub-200 nm, charged exterior surfaces provide considerable modulation to ion\ncurrent. We find that the charge status of inner-pore walls affects the\nmodulation of ion current from charged exterior surfaces. For 50-nm-long\nnanopores with neutral inner-pore walls, charged exterior surfaces on the\nvoltage (surfaceV) and ground (surfaceG) sides enhance and inhibit ion\ntransport by forming ion enrichment and depletion zones inside nanopores,\nrespectively. For nanopores with both charged inner-pore and exterior surfaces,\ncontinuous electric double layers enhance ion transport through nanopores\nsignificantly. The charged surfaceV results in higher ion current by\nsimultaneously weakening ion depletion at pore entrances and enhancing the\nintra-pore ion enrichment. The charged surfaceG expedites the exit of ions from\nnanopores, resulting in a decrease in ion enrichment at pore exits. Through\nadjustment in the width of charged-ring regions near pore boundaries, the\neffective charged width of the charged exterior is explored at ~20nm. Our\nresults may provide a theoretical guide for further optimizing the performance\nof nanopore-based applications, like seawater desalination, biosensing, and\nosmotic energy conversion.", "category": "physics_chem-ph" }, { "text": "Contrasting Mechanisms for Photodissociation of Methyl Halides Adsorbed\n on Thin Films of C$_6$H$_6$ and C$_6$F$_6$: The mechanisms for photodissociation of methyl halides (CH$_3$X, X= Cl, Br,\nI) have been studied for these molecules when adsorbed on thin films of\nC$_6$H$_6$ or C$_6$F$_6$ on copper single crystals, using time-of-flight\nspectroscopy with 248nm and 193nm light. For CH$_3$Cl and CH$_3$Br monolayers\nadsorbed on C$_6$H$_6$, two photodissociation pathways can be identified:\nneutral photodissociation similar to the gas-phase, and a dissociative electron\nattachment (DEA) pathway due to photoelectrons from the metal. The same methyl\nhalides adsorbed on a C$_6$F$_6$ thin film display only neutral\nphotodissociation, with the DEA pathway entirely absent due to intermolecular\nquenching via a LUMO-derived electronic band in the C$_6$F$_6$ thin film. For\nCH$_3$I adsorbed on a C$_6$F$_6$ thin film, illumination with 248nm light\nresults in CH$_3$ photofragments departing due to neutral photodissociation via\nthe A-band absorption. When CH$_3$I monolayers on C$_6$H$_6$ thin films are\nilluminated at the same wavelength, additional new photodissociation pathways\nare observed that are due to absorption in the molecular film with energy\ntransfer leading to dissociation of the CH$_3$I molecules adsorbed on top. The\nproposed mechanism for this photodissociation is via a charge-transfer complex\nfor the C$_6$H$_6$ layer and adsorbed CH$_3$I.", "category": "physics_chem-ph" }, { "text": "Multireference Algebraic Diagrammatic Construction Theory for Excited\n States: Extended Second-Order Implementation and Benchmark: We present an implementation and benchmark of new approximations in\nmultireference algebraic diagrammatic construction theory for simulations of\nneutral electronic excitations and UV/Vis spectra of strongly correlated\nmolecular systems (MR-ADC). Following our work on the first-order MR-ADC\napproximation [J. Chem. Phys. 2018, 149, 204113], we report the strict and\nextended second-order MR-ADC methods (MR-ADC(2) and MR-ADC(2)-X) that combine\nthe description of static and dynamic electron correlation in the ground and\nexcited electronic states without relying on state-averaged reference\nwavefunctions. We present an extensive benchmark of the new MR-ADC methods for\nexcited states in several small molecules, including the carbon dimer,\nethylene, and butadiene. Our results demonstrate that for weakly-correlated\nelectronic states the MR-ADC(2) and MR-ADC(2)-X methods outperform the\nthird-order single-reference ADC approximation and are competitive with the\nresults from equation-of-motion coupled cluster theory. For states with\nmultireference character, the performance of the MR-ADC methods is similar to\nthat of an N-electron valence perturbation theory. In contrast to conventional\nmultireference perturbation theories, the MR-ADC methods have a number of\nattractive features, such as a straightforward and efficient calculation of\nexcited-state properties and a direct access to excitations outside of the\nfrontier (active) orbitals.", "category": "physics_chem-ph" }, { "text": "Modulation effects within the mean-field theory of electrolyte solutions: The consequences of source charge and surface modulation are studied within\nthe framework of the Poisson-Boltzmann theory of electrolyte solutions. Through\na consideration of various examples, it is found that inherent modulation can\nlead to both like-charge attraction and overcharging effects.", "category": "physics_chem-ph" }, { "text": "Electron correlation by polarization of interacting densities: Coulomb interactions that occur in electronic structure calculations are\ncorrelated by allowing basis function components of the interacting densities\nto polarize, thereby reducing the magnitude of the interaction. Exchange\nintegrals of molecular orbitals are not correlated. The modified Coulomb\ninteractions are used in single-determinant or configuration interaction\ncalculations. The objective is to account for dynamical correlation effects\nwithout explicitly introducing higher spherical harmonic functions into the\nmolecular orbital basis. Molecular orbital densities are decomposed into a\ndistribution of spherical components that conserve the charge and each of the\ninteracting components is considered as a two-electron wavefunction embedded in\nthe system acted on by an average field Hamiltonian plus . A method of avoiding\nredundancy is described. Applications to atoms, negative ions and molecules\nrepresenting different types of bonding and spin states are discussed.", "category": "physics_chem-ph" }, { "text": "Machine Learning Wavefunction: This chapter introduces the main ideas and the most important methods for\nrepresenting the electronic wavefunction through machine learning models. The\nwavefunction of a N-electron system is an incredibly complicated mathematical\nobject, and models thereof require enough flexibility to properly describe the\ncomplex interactions between the particles, but at the same time a sufficiently\ncompact representation to be useful in practice. Machine learning techniques\noffer an ideal mathematical framework to satisfy these requirements, and\nprovide algorithms for their optimization in both supervised and unsupervised\nfashions. In this chapter, various examples of machine learning wavefunctions\nare presented and their strengths and weaknesses with respect to traditional\nquantum chemical approaches are discussed; first in theory, and then in\npractice with two case studies.", "category": "physics_chem-ph" }, { "text": "A Robust and Unified Solution for Choosing the Phases of Adiabatic\n States as a Function of Geometry: Extending Parallel Transport Concepts to\n the cases of Trivial & Near Trivial Crossings: We investigate a simple and robust scheme for choosing the phases of\nadiabatic electronic states smoothly (as a function of geometry) so as to\nmaximize the performance of ab initio non-adiabatic dynamics methods. Our\napproach is based upon consideration of the overlap matrix ($\\mathbf{U}$)\nbetween basis functions at successive points in time and selecting the phases\nso as to minimize the matrix norm of $\\log(\\mathbf{U})$. In so doing, one can\nextend the concept of parallel transport to cases with sharp curve crossings.\nWe demonstrate that this algorithm performs well under extreme situations where\ndozens of states cross each other either through trivial crossings (where there\nis zero effective diabatic coupling), or through nontrivial crossings (when\nthere is a nonzero diabatic coupling), or through a combination of both. In all\ncases, we compute the time-derivative coupling matrix elements (or equivalently\nnon-adiabatic derivative coupling matrix elements) that are as smooth as\npossible. Our results should be of interest to all who are interested in either\nnon-adiabatic dynamics, or more generally, parallel transport in large systems.", "category": "physics_chem-ph" }, { "text": "A derivation of a microscopic entropy and time irreversibility from the\n discreteness of time: All of the basic microsopic physical laws are time reversible. In contrast,\nthe second law of thermodynamics, which is a macroscopic physical\nrepresentation of the world, is able to describe irreversible processes in an\nisolated system through the change of entropy S larger than 0. It is the\nattempt of the present manuscript to bridge the microscopic physical world with\nits macrosocpic one with an alternative approach than the statistical mechanics\ntheory of Gibbs and Boltzmann. It is proposed that time is discrete with\nconstant step size. Its consequence is the presence of time irreversibility at\nthe microscopic level if the present force is of complex nature (i.e. not\nconst). In order to compare this discrete time irreversible mechamics (for\nsimplicity a classical, single particle in a one dimensional space is selected)\nwith its classical Newton analog, time reversibility is reintroduced by scaling\nthe time steps for any given time step n by the variable sn leading to the\nNose-Hoover Lagrangian. The corresponding Nose-Hoover Hamiltonian comprises a\nterm Ndf *kB*T*ln(sn) (with kB the Boltzmann constant, T the temperature, and\nNdf the number of degrees of freedom) which is defined as the microscopic\nentropy Sn at time point n multiplied by T. Upon ensemble averaging this\nmicroscopic entropy Sn in equilibrium for a system which does not have fast\nchanging forces approximates its macroscopic counterpart known from\nthermodynamics. The presented derivation with the resulting analogy between the\nensemble averaged microscopic entropy and its thermodynamic analog suggests\nthat the original description of the entropy by Boltzmann and Gibbs is just an\nensemble averaging of the time scaling variable sn which is in equilibrium\nclose to 1, but that the entropy term itself has its root not in statistical\nmechanics but rather in the discreteness of time.", "category": "physics_chem-ph" }, { "text": "Transient response of an electrolyte to a thermal quench: We study the transient response of an electrolytic cell subject to a small,\nsuddenly applied temperature increase at one of its two bounding electrode\nsurfaces. An inhomogeneous temperature profile then develops, causing, via the\nSoret effect, ionic rearrangements towards a state of polarized ionic charge\ndensity $q$ and local salt density $c$. For the case of equal cationic and\nanionic diffusivities, we derive analytical approximations to $q, c$, and the\nthermovoltage $V_{T}$ for early ($t\\ll\\tau_{T}$) and late ($t\\gg\\tau_{T}$)\ntimes as compared to the relaxation time $\\tau_{T}$ of the temperature. We\nchallenge the conventional wisdom that the typically large Lewis number, the\nratio $a/D$ of thermal to ionic diffusivities, of most liquids implies a\nquickly reached steady-state temperature profile onto which ions relax slowly.\nThough true for the evolution of $c$, it turns out that $q$ (and $V_{T}$) can\nrespond much faster. Particularly when the cell is much bigger than the Debye\nlength, a significant portion of the transient response of the cell falls in\nthe $t\\ll\\tau_{T}$ regime, for which our approximated $q$ (corroborated by\nnumerics) exhibits a density wave that has not been discussed before in this\ncontext. For electrolytes with unequal ionic diffusivities, $V_{T}$ exhibits a\ntwo-step relaxation process, in agreement with experimental data of Bonetti et\nal. [J. Chem. Phys. 142, 244708 (2015)].", "category": "physics_chem-ph" }, { "text": "Polariton Enhanced Free Charge Carrier Generation in Donor-Acceptor\n Cavity Systems by a Second-Hybridization Mechanism: Cavity quantum electrodynamics has been studied as a potential approach to\nmodify free charge carrier generation in donor-acceptor heterojunctions because\nof the delocalization and controllable energy level properties of hybridized\nlight-matter states known as polaritons. However, in many experimental systems,\ncavity coupling decreases charge separation. Here, we theoretically study the\nquantum dynamics of a coherent and dissipative donor-acceptor cavity system, to\ninvestigate the dynamical mechanism and further discover the conditions under\nwhich polaritons may enhance free charge carrier generation. We use open\nquantum system methods based on single-pulse pumping to find that polaritons\nhave the potential to connect excitonic states and charge separated states,\nfurther enhancing free charge generation on an ultrafast timescale of several\nhundred femtoseconds. The mechanism involves that polaritons with proper energy\nlevels allow the exciton to overcome the high Coulomb barrier induced by\nelectron-hole attraction. Moreover, we propose that a second-hybridization\nbetween a polariton state and dark states with similar energy enables the\nformation of the hybrid charge separated states that are optically active.\nThese two mechanisms lead to a maximum of 50% enhancement of free charge\ncarrier generation on a short timescale. However, our simulation reveals that\non the longer timescale of picoseconds, internal conversion and cavity loss\ndominate and suppress free charge carrier generation, reproducing the\nexperimental results. Thus, our work shows that polaritons can affect the\ncharge separation mechanism and promote free charge carrier generation\nefficiency, but predominantly on a short timescale after photoexcitation.", "category": "physics_chem-ph" }, { "text": "Variational solution of congruent transformed Hamiltonian for\n many-electron systems using full configuration interaction calculation: The congruent transformation of the electronic Hamiltonian is developed to\naddress the electron correlation problem in many-electron systems. The central\nstrategy presented in this method is to perform transformation on the\nelectronic Hamiltonian for approximate removal of the Coulomb singularity. The\nprinciple difference between the present method and the transcorrelated method\nof Handy and Boys is that the congruent transformation preserves the Hermitian\nproperty of the Hamiltonian. The congruent transformation is carried out using\nexplicitly correlated functions and the optimum correlated transform\nHamiltonian is obtained by performing a search over a set of transformation\nfunctions. The ansatz of the transformation functions are selected to\nfacilitate analytical evaluation of all the resulting integrals. The ground\nstate energy is obtained variationally by performing a full configuration\ninteraction (FCI) calculation on the congruent transformed Hamiltonian.\nComputed results on well-studied benchmark systems show that for the identical\nbasis functions, the energy from the congruent transformed Hamiltonian is\nsignificantly lower than the conventional FCI calculations. Since the number of\nconfiguration state functions in the FCI calculation increases rapidly with the\nsize of the 1-particle basis set, the results indicate that the congruent\ntransformed Hamiltonian provides a viable alternative to obtain FCI quality\nenergy using a smaller underlying 1-particle basis set.", "category": "physics_chem-ph" }, { "text": "Directional States of Symmetric-Top Molecules Produced by Combined\n Static and Radiative Electric Fields: We show that combined electrostatic and radiative fields can greatly amplify\nthe directional properties, such as axis orientation and alignment, of\nsymmetric top molecules. In our computational study, we consider all four\nsymmetry combinations of the prolate and oblate inertia and polarizability\ntensors, as well as the collinear and perpendicular (or tilted) geometries of\nthe two fields. In, respectively, the collinear or perpendicular fields, the\noblate or prolate polarizability interaction due to the radiative field forces\nthe permanent dipole into alignment with the static field. Two mechanisms are\nfound to be responsible for the amplification of the molecules' orientation,\nwhich ensues once the static field is turned on: (a) permanent-dipole coupling\nof the opposite-parity tunneling doublets created by the oblate polarizability\ninteraction in collinear static and radiative fields; (b) hybridization of the\nopposite parity states via the polarizability interaction and their coupling by\nthe permanent dipole interaction to the collinear or perpendicular static\nfield. In perpendicular fields, the oblate polarizability interaction, along\nwith the loss of cylindrical symmetry, is found to preclude the wrong-way\norientation, causing all states to become high-field seeking with respect to\nthe static field. The adiabatic labels of the states in the tilted fields\ndepend on the adiabatic path taken through the parameter space comprised of the\npermanent and induced-dipole interaction parameters and the tilt angle between\nthe two field vectors.", "category": "physics_chem-ph" }, { "text": "Fourier expansions for the potentials of lattices of charge: We apply the Poisson sum rule to obtain formal expressions for the Fourier\ncoefficients of the potential of a lattice of generalized charge. Each\ngeneralized charge is assumed to contribute to the potential a term which\ndepends only on the vector displacement from the charge's location. The\ncoefficients are explicitly calculated for Coulomb and Yukawa-type individual\nparticle potentials. The potentials of finite and disordered lattices are also\nbriefly considered.", "category": "physics_chem-ph" }, { "text": "Topological Studies related to Molecular Systems formed soon after the\n Big Bang: HeH2+ as the Precursor for HeH+: In the early universe, following the nucleosynthesis, conditions were right\nfor recombination processes to take place yielding neutral atoms H, He and Li.\nThe understanding so far in astrophysics is that the first molecule to be\nformed was HeH+ by radiative association (He + H+ -> HeH+ + h(nu) and He+ + H\n-> HeH+ + h(nu). The recent report by Guesten et al (Nature, 568, 357, 2019) of\ndetection of HeH+ in planetary Nebula NGC 7027 confirms its presence, but it\ndoes not conclusively prove the origin of this species. To create molecules\nfrom free moving quasi-ions surrounded by an electronic cloud, the\nBorn-Oppenheimer-Huang (BOH) theory furnishes two kinds of forces, namely, one\nthat results from the Potential Energy Surfaces (PESs) and the other from\nNon-Adiabatic Coupling Terms (NACTs). Whereas the PESs are known to manage slow\nmoving quasi-ions the NACTs, with their, frequently, infinitely large values at\nthe vicinity of the singularities can control the fast moving quasi-ions. To\nachieve that the BOH equation indicates that the NACTs are affecting the fast\nmoving quasi-ions directly and if they are attributed with dissipative features\nor in other words to behave as a Friction Force they indeed could serve (like\nany other ordinary friction) as moderators for the fast atomic(ionic) species.\nIt is proposed in the present paper that the triatomic HeH2+ was the precursor\nto HeH+ and it could have been formed by the (He, H, H)+ nuclei coming together\nunder the electron cloud, facilitated by the NACTs between different electronic\nstates acting as an astronomical friction force. This is possible because of\nthe singularities in the NACTs for triatomic systems and NOT for diatomic\nsystems. Although the existence of HeH2+ was established in the laboratory in\n1996, it has not been detected in the interstellar media so far. But, there is\nno reason why it cannot be detected in near future.", "category": "physics_chem-ph" }, { "text": "Solvent Effects on Extractant Conformational Energetics in Liquid-Liquid\n Extraction: A Simulation Study of Molecular Solvents and Ionic Liquids: Extractant design in liquid-liquid extraction (LLE) is a research frontier of\nmetal ion separations that typically focuses on the direct extractant-metal\ninteractions. However, a more detailed understanding of energetic drivers of\nseparations beyond primary metal coordination is often lacking, including the\nrole of solvent in the extractant phase. In this work, we propose a new\nmechanism for enhancing metal-complexant energetics with nanostructured\nsolvents. Using molecular dynamics simulations with umbrella sampling, we find\nthat the organic solvent can reshape the energetics of the extractant's\nintramolecular conformational landscape. We calculate free energy profiles of\ndifferent conformations of a representative bidentate extractant,\nn-octyl(phenyl)-N,N-diisobutyl carbamoyl methyl phosphinoxide (CMPO), in four\ndifferent solvents: dodecane, tributyl phosphate (TBP), and dry and wet ionic\nliquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide\n([EMIM][Tf_2N]). By promoting reorganization of the extractant molecule into\nits binding conformation, our findings reveal how particular solvents can\nameliorate this unfavorable step of the metal separation process. In\nparticular, the charge alternating nanodomains formed in ILs substantially\nreduce the free energy penalty associated with extractant reorganization.\nImportantly, using alchemical free energy calculations, we find that this\nstabilization persists even when we explicitly include the extracted cation.\nThese findings provide insight into the energic drivers of metal ion\nseparations and potentially suggest a new approach to designing effective\nseparations using a molecular-level understanding of solvent effects.", "category": "physics_chem-ph" }, { "text": "Tailoring the Acidity of Liquid Media with Ionizing Radiation --\n Rethinking the Acid-Base Correlation Beyond pH: Advanced in situ techniques based on electrons and X-rays are increasingly\nused to gain insights into fundamental materials dynamics in liquid media. Yet,\nionizing radiation changes the solution chemistry. In this work, we show that\nionizing radiation decouples the acidity from autoprotolysis. Consequently, pH\nis insufficient to capture the acidity of water-based systems under\nirradiation. Via radiolysis simulations, we provide a more conclusive\ndescription of the acid-base interplay. Finally, we demonstrate that acidity\ncan be tailored by adjusting the dose rate and adding pH-irrelevant species.\nThis opens up a huge parameter landscape for studies involving ionizing\nradiation.", "category": "physics_chem-ph" }, { "text": "Automated Discovery of Elementary Chemical Reaction Steps Using Freezing\n String and Berny Optimization Methods: We present a simple protocol which allows fully automated discovery of\nelementary chemical reaction steps using in cooperation single- and\ndouble-ended transition-state optimization algorithms - the freezing string and\nBerny optimization methods, respectively. To demonstrate the utility of the\nproposed approach, the reactivity of several systems of combustion and\natmospheric chemistry importance is investigated. The proposed algorithm\nallowed us to detect without any human intervention not only \"known\" reaction\npathways, manually detected in the previous studies, but also new, previously\n\"unknown\", reaction pathways which involve significant atom rearrangements. We\nbelieve that applying such a systematic approach to elementary reaction path\nfinding will greatly accelerate the possibility of discovery of new chemistry\nand will lead to more accurate computer simulations of various chemical\nprocesses.", "category": "physics_chem-ph" }, { "text": "Regression-clustering for Improved Accuracy and Training Cost with\n Molecular-Orbital-Based Machine Learning: Machine learning (ML) in the representation of molecular-orbital-based (MOB)\nfeatures has been shown to be an accurate and transferable approach to the\nprediction of post-Hartree-Fock correlation energies. Previous applications of\nMOB-ML employed Gaussian Process Regression (GPR), which provides good\nprediction accuracy with small training sets; however, the cost of GPR training\nscales cubically with the amount of data and becomes a computational bottleneck\nfor large training sets. In the current work, we address this problem by\nintroducing a clustering/regression/classification implementation of MOB-ML. In\na first step, regression clustering (RC) is used to partition the training data\nto best fit an ensemble of linear regression (LR) models; in a second step,\neach cluster is regressed independently, using either LR or GPR; and in a third\nstep, a random forest classifier (RFC) is trained for the prediction of cluster\nassignments based on MOB feature values. Upon inspection, RC is found to\nrecapitulate chemically intuitive groupings of the frontier molecular orbitals,\nand the combined RC/LR/RFC and RC/GPR/RFC implementations of MOB-ML are found\nto provide good prediction accuracy with greatly reduced wall-clock training\ntimes. For a dataset of thermalized geometries of 7211 organic molecules of up\nto seven heavy atoms, both implementations reach chemical accuracy (1 kcal/mol\nerror) with only 300 training molecules, while providing 35000-fold and\n4500-fold reductions in the wall-clock training time, respectively, compared to\nMOB-ML without clustering. The resulting models are also demonstrated to retain\ntransferability for the prediction of large-molecule energies with only\nsmall-molecule training data. Finally, it is shown that capping the number of\ntraining datapoints per cluster leads to further improvements in prediction\naccuracy with negligible increases in wall-clock training time.", "category": "physics_chem-ph" }, { "text": "Chemical Reactions under Nanoconfinement: Unravelling Equilibrium\n Constant Equations: Equilibrium Constant Differential Equations (ECDE) are derived for several\nnanoconfined elemental bimolecular reactions in the frameworks of statistical\nmechanics and the ideal gas model. The ECDEs complement the well-known\nequilibrium-constant ordinary equations that are used for macroscopic systems.\nSolving the ECDE numerically or analytically furnishes the average reaction\nextent, as well as its variance and skewness. This original\ntheoretical-computational methodology fills the gap in studies of nanochemical\nequilibrium providing a consistent and convenient alternative to derivations\nbased on direct employment of the canonical partition-functions. Whereas the\nlatter become more complex and time-consuming with increased number of\nmolecules, the ECDE-based computations are equally efficient for small as well\nas large numbers of nanoconfined reacting molecules. The ECDE methodology\nintroduced here is confirmed by a complete agreement with partition-function\ncomputations. In addition, the new approach is applied to nanoconfined\nadsorption.", "category": "physics_chem-ph" }, { "text": "A tutorial review: probing molecular structure and dynamics with CEI and\n LIED: Knowledge of the molecular structure is key to understanding the function of\nparticipating molecules in photo-induced chemical reactions. Visualizing the\nnuclear dynamics of a photochemical reaction requires an ultrafast measurement\ntechnique that can identify the location of atoms in molecules with atomic\n{\\AA}ngstrom spatial resolution evolving on the nuclear (i.e. hundreds of\nfemtosecond) timescale. Coulomb explosion imaging (CEI) and laser-induced\nelectron diffraction (LIED) offer the required sub-{\\AA}ngstrom spatial and\ntens of femtosecond temporal resolution to track in real-time changes in the\nmolecular structure. In this tutorial review, details of the tools, analysis\nprocedures, exemplary previous results and future perspectives of both CEI and\nLIED techniques are described.", "category": "physics_chem-ph" }, { "text": "Characterization of AlW oxide coatings on aluminum formed by pulsed\n direct current plasma electrolytic oxidation at ultralow duty cycles: The growth of thin oxide coatings on the aluminum substrate in water-based\nsodium tungstate electrolyte by plasma electrolytic oxidation (PEO) is\ndiscussed and experimentally illustrated. The growth is carried out using a\ndistinctive ultra-low duty cycle pulsed direct current (DC) power supply.\nDuring the PEO processing elements present in micro-discharges are identified\nusing standard optical emission spectroscopy (OES) technique. The spectral line\nshape analysis of the first two hydrogen Balmer lines shows the presence of two\ntypes of micro-discharges. Obtained coatings are also characterized with\nrespect to their morphology and chemical and phase composition. It is shown\nthat coatings are composed of Al, O, and W, featuring low roughness and\nporosity. Partial crystallization of the coatings resulted in identification of\nWO3, W3O8, and gamma-Al2O3 crystalline phases.", "category": "physics_chem-ph" }, { "text": "Chemical reactions of conformationally selected molecules in a beam with\n Coulomb-crystallized ions: Many molecules exhibit multiple conformers that often easily interconvert\nunder thermal conditions. Therefore, single conformations are difficult to\nisolate which renders the study of their distinct chemical reactivities\nchallenging. We have recently reported a new experimental method for the\ncharacterization of conformer-specific effects in chemical reactions [Y. P.\nChang et al., Science 342, 98 (2013)]. Different conformers are spatially\nseparated using inhomogeneous electric fields and reacted with a Coulomb\ncrystal of cold, spatially localized ions in a trap. As a first application, we\nstudied reactions between the two conformers of 3-aminophenol and Ca$^+$. We\nobserved a twofold larger rate constant for the $cis$ compared to the $trans$\nconformer which was rationalized in terms of the differences in the long-range\nion-molecule interactions. The present article provides a detailed description\nof the new method and a full account of the experimental results as well as the\naccompanying theoretical calculations.", "category": "physics_chem-ph" }, { "text": "Conformer-specific Chemistry Imaged in Real Space and Time: Conformational isomers or conformers of molecules play a decisive role in\nchemistry and biology. However, experimental methods to investigate chemical\nreaction dynamics are typically not conformer-sensitive. Here, we report on a\ngas-phase megaelectronvolt ultrafast electron diffraction investigation of\n{\\alpha}-phellandrene undergoing an electrocyclic ring-opening reaction. We\ndirectly image the evolution of a specific set of {\\alpha}-phellandrene\nconformers into the product isomer predicted by the Woodward-Hoffmann rules in\nreal space and time. Our experimental results are in quantitative agreement\nwith nonadiabatic quantum molecular dynamics simulations, which provide\nunprecedented detail of how conformation influences time scale and quantum\nefficiency of photoinduced ring-opening reactions. Due to the prevalence of\nlarge numbers of conformers in organic chemistry, our findings impact our\ngeneral understanding of reaction dynamics in chemistry and biology.", "category": "physics_chem-ph" }, { "text": "Theory on polarization-averaged core-level molecular-frame photoelectron\n angular distributions: II. Extracting the X-ray induced fragmentation\n dynamics of carbon monoxide dication from forward and backward intensities: Recent developments of high-reputation-rate X-ray free electron lasers\n(XFELs) such as European XFEL and LSCS-II, combined with coincidence\nmeasurements at the COLTRIMS-Reaction Microscope, is now opening a door to\nrealize a long-standing dream to create molecular movies of photo-induced\nchemical reactions of gas-phase molecules. In this paper, we theoretically\npropose a new method to experimentally visualize dissociation of diatomic\nmolecules via time-resolved polarization-averaged molecular-frame photoelectron\nangular distributions (PA-MFPADs) measurements using the COLTRIMs--Reaction\nMicroscope and two-color XFEL pump-probe set-up. The first and second order\nscattering theories with the Muffin-tin approximation give us simple EXAFS type\nformula for the forward and backward scattering peaks in the PA-MFPADs\nstructure. This formula acts as an experimentally applicable \"bond length\nruler\" by adjusting only three semi-empirical parameters from the time-resolved\nmeasurements. The accuracy and applicability of a new ruler equation are\nnumerically examined against the PA-MFPADs of CO2+ calculated by\nFull-potential multiple scattering theory as a function of the C-O bond length\nreported in the preceding work. The bond lengths retrieved from the PA-MFPADs\nvia the EXAFS formula well reproduce the original C-O bond lengths used in the\nreference ab-initio PA-MFPADs with accuracy of 0.1 {\\AA}. We expect that\ntime-resolved PA-MFPADs will be a new attractive tool to make molecular movies\nvisualizing intramolecular reactions.", "category": "physics_chem-ph" }, { "text": "Without Spectroscopy at the Beginning, Catalysis Research Proceeded in\n the Wrong Direction for More Than 100 Years: A study by infrared spectroscopy of the physisorbed region of catalysis\ndemonstrated that the intermediates of catalysis exist on the surface as a two\ndimensional gas. Data in the Atomic Energy Level tables show that of the\nthousands of positive ions tabulated only approximately one hundred have the\nlow-lying excited states that produce surface electric fields with a fractional\ncharge. The specific catalyst for a reaction has the electric field with the\nfractional charge which when imparted to the two reactants changes the\nfrequency of the fields at the sites of reaction on each so that they are\nharmonically equal, that is their ratio is a power of two. When the two\nreactants meet in the electric field of the catalyst resonance occurs. It is\nduring resonance that electrons are shared, paired and exchanged and bonds are\nbroken and made. This analysis of catalysis explains the most extraordinary\nobservation that a catalyst is Not consumed when used because the catalyst is\nthe electric fields. These discoveries are applied to explain such diverse\nreactions as the oxidation and chlorination of carbon monoxide and the\ndestruction of nitric oxide in automobile exhaust. The use of electric fields\nto produce reactions may have application not only in chemistry but in biology\nand mechanics as well.", "category": "physics_chem-ph" }, { "text": "Infinite-order perturbative treatment for quantum evolution with\n exchange: Many important applications in biochemistry, materials science, and catalysis\nsit squarely at the interface between quantum and statistical mechanics:\ncoherent evolution is interrupted by discrete events, such as binding of a\nsubstrate or isomerization. Theoretical models for such dynamics usually\ntruncate the incorporation of these events to the linear-response limit, thus\nrequiring small step sizes. Here, we completely re-assess the foundations of\nchemical exchange models and redesign a master equation treatment accurate to\nall orders in perturbation theory. The net result is an astonishingly simple\ncorrection to the traditional picture which vastly improves convergence with no\nincreased computational cost. We demonstrate that this approach accurately and\nefficiently extracts physical parameters from highly complex experimental data,\nsuch as coherent hyperpolarization dynamics in magnetic resonance, and is\napplicable to a wide range of other systems.", "category": "physics_chem-ph" }, { "text": "Electron Photodetachment from Aqueous Anions. II. Ionic Strength Effect\n on Geminate Recombination Dynamics and Quantum Yield for Hydrated Electron: In concentrated solutions of NaClO4 and Na2SO4, the quantum yield for free\nelectron generated by detachment from photoexcited anions (such as I-, OH-,\nClO^4-, and [SO3]^2-) linearly decreases by 6-12% per 1 M ionic strength. In 9\nM sodium perchlorate solution, this quantum yield decreases by roughly an order\nof magnitude. Ultrafast kinetic studies of 200 nm photon induced electron\ndetachment from Br-, HO- and [SO3]^2- suggest that the prompt yield of\nthermalized electron does not change in these solutions; rather, the ionic\nstrength effect originates in more efficient recombination of geminate pairs.\nWithin the framework of the recently proposed mean force potential (MFP) model\nof charge separation dynamics in such photosystems, the observed changes are\ninterpreted as an increase in the short-range attractive potential between the\ngeminate partners. Association of sodium cation(s) with the electron and the\nparent anion is suggested as the most likely cause for the observed\nmodification of the MFP. Electron thermalization kinetics suggest that the\ncation associated with the parent anion (by ion pairing and/or ionic atmosphere\ninteraction) is passed to the detached electron in the course of the\nphotoreaction. The precise atomic-level mechanism for the ionic strength effect\nis presently unclear; any further advance is likely to require the development\nof an adequate quantum molecular dynamics model.", "category": "physics_chem-ph" }, { "text": "ExoMol molecular line lists -- XLIII: Rovibronic molecular line list the\n low-lying two states of NaO: The sodium monoxide radical (NaO) is observed in night glow in the Earth's\nmesosphere and likely has astronomical importance. This study concerns the\noptical transitions within the ground X $^2\\Pi$ state and to the very low-lying\n($T_{\\textrm e}\\approx 2000$ cm$^{-1}$) excited A $^2\\Sigma^+$ state. A line\nlist consisting of rovibronic term values, allowed electric dipole transitions,\nEinstein coefficients, and partition functions for varying temperature are\nproduced due to a variational solution of the coupled-channel Schr\\\"{o}dinger\nequations using the program \\Duo. MRCI \\textit{ab initio} calculations\ncharacterising the potential energy curves of the both states, spin-orbit and\n$L$-uncoupling non-adiabatic matrix elements, as well as permanent and\ntransition dipole moments were integral in formation of the final\ndeperturbation model. \\textit{Ab initio} potential energy curves are\nrepresented in the analytical Extended-Morse-Oscillator form and refined, along\nwith the spin-orbit and $L$-uncoupling functions, by least-squares fitting to\nthe available spectroscopic data. The input experimental data consisted of pure\nrotational transitions within the fine structure components of the X $^2\\Pi$\nstate for $v''\\in [0,3]$ vibrational levels as well as the rovibronic A\n$^2\\Sigma^+(v'=0) \\leftarrow$ X $^2\\Pi(v''=0)$ transitions, both with limited\ncoverage over rotational excitation. The lack of data detailing the vibrational\nstructure of the X and A states prompts a request for further experimental\nstudy of higher excited levels which would provide a robust spectroscopic\nmodel. The NaO NaOUCMe line list is available via www.exomol.com and the CDS\ndatabase.", "category": "physics_chem-ph" }, { "text": "Uncertainty quantification for predictions of atomistic neural networks: The value of uncertainty quantification on predictions for trained neural\nnetworks (NNs) on quantum chemical reference data is quantitatively explored.\nFor this, the architecture of the PhysNet NN was suitably modified and the\nresulting model was evaluated with different metrics to quantify calibration,\nquality of predictions, and whether prediction error and the predicted\nuncertainty can be correlated. The results from training on the QM9 database\nand evaluating data from the test set within and outside the distribution\nindicate that error and uncertainty are not linearly related. The results\nclarify that noise and redundancy complicate property prediction for molecules\neven in cases for which changes - e.g. double bond migration in two otherwise\nidentical molecules - are small. The model was then applied to a real database\nof tautomerization reactions. Analysis of the distance between members in\nfeature space combined with other parameters shows that redundant information\nin the training dataset can lead to large variances and small errors whereas\nthe presence of similar but unspecific information returns large errors but\nsmall variances. This was, e.g., observed for nitro-containing aliphatic chains\nfor which predictions were difficult although the training set contained\nseveral examples for nitro groups bound to aromatic molecules. This underlines\nthe importance of the composition of the training data and provides chemical\ninsight into how this affects the prediction capabilities of a ML model.\nFinally, the approach put forward can be used for information-based improvement\nof chemical databases for target applications through active learning\noptimization.", "category": "physics_chem-ph" }, { "text": "Equivariant representations for molecular Hamiltonians and N-center\n atomic-scale properties: Symmetry considerations are at the core of the major frameworks used to\nprovide an effective mathematical representation of atomic configurations that\nis then used in machine-learning models to predict the properties associated\nwith each structure. In most cases, the models rely on a description of\natom-centered environments, and are suitable to learn atomic properties, or\nglobal observables that can be decomposed into atomic contributions. Many\nquantities that are relevant for quantum mechanical calculations, however --\nmost notably the single-particle Hamiltonian matrix when written in an\natomic-orbital basis -- are not associated with a single center, but with two\n(or more) atoms in the structure. We discuss a family of structural descriptors\nthat generalize the very successful atom-centered density correlation features\nto the N-centers case, and show in particular how this construction can be\napplied to efficiently learn the matrix elements of the (effective)\nsingle-particle Hamiltonian written in an atom-centered orbital basis. These\nN-centers features are fully equivariant -- not only in terms of translations\nand rotations, but also in terms of permutations of the indices associated with\nthe atoms -- and are suitable to construct symmetry-adapted machine-learning\nmodels of new classes of properties of molecules and materials.", "category": "physics_chem-ph" }, { "text": "Observation of Concerted and Stepwise Multiple Dechlorination Reactions\n of Perchlorethylene in Electron Ionization Mass Spectrometry According to\n Measured Chlorine Isotope Effects: Dechlorinated fragmental ions of organochlorines can be commonly found on\nelectron ionization-mass spectrometry (EI-MS). Yet it is still unclear whether\nmultiple dechlorination reactions taking place in EI-MS are concerted or\nstepwise. This study investigated the concertedness of the multiple\ndechlorination reactions of perchlorethylene (PCE) in EI-MS in light of the\nobserved chlorine isotope effects during different dechlorination reactions\nalong with the detected MS signal intensities. The fluctuant isotope ratios\namong different ions revealed that the observed multiple dechlorinated\nreactions in the EI-DFS-HRMS were stepwise. And the changing trends of isotope\nratios of the ions detected by EI-qMS might suggest that the observed multiple\ndechlorination reactions in this MS were concerted. Mechanisms for these\nconcerted/stepwise multiple dechlorination reactions are tentatively\ninterpreted. Besides the evidence of isotope effects, according to the\nquasi-equilibrium theory, the MS signal intensities also suggested that the\nmultiple dechlorination reactions in the EI-HRMS were likely stepwise, while\nthose in the EI-qMS might be concerted. The distance from the ionization region\nto the mass analyzer entrance in an MS may be a critical factor affecting the\ndechlorination reactions of ions flying over this distance. This distance in\nthe EI-qMS is significantly shorter than that in the EI-HRMS. Thus, the main\ndetected ions in the EI-qMS might be generated during the ionization and\nin-source fragmentation processes, while the main ions detected in the EI-HRMS\nmight be produced during the fragmentation of precursor ions flying over the\ndistance. We deduce that the main dechlorination reactions in the ionization\nregion were concerted, while those taking place during the flight of precursor\nions over the distance from the ionization region to the mass analyzer entrance\nwere stepwise.", "category": "physics_chem-ph" }, { "text": "Treatments of the exchange energy in density-functional theory: Following a recent work [Gal, Phys. Rev. A 64, 062503 (2001)], a simple\nderivation of the density-functional correction of the Hartree-Fock equations,\nthe Hartree-Fock-Kohn-Sham equations, is presented, completing an integrated\nview of quantum mechanical theories, in which the Kohn-Sham equations, the\nHartree-Fock-Kohn-Sham equations and the ground-state Schrodinger equation\nformally stem from a common ground: density-functional theory, through its\nEuler equation for the ground-state density. Along similar lines, the Kohn-Sham\nformulation of the Hartree-Fock approach is also considered. Further, it is\npointed out that the exchange energy of density-functional theory built from\nthe Kohn-Sham orbitals can be given by degree-two homogeneous N-particle\ndensity functionals (N=1,2,...), forming a sequence of degree-two homogeneous\nexchange-energy density functionals, the first element of which is minus the\nclassical Coulomb-repulsion energy functional.", "category": "physics_chem-ph" }, { "text": "A theory of inductive loops in electrochemical impedance spectroscopy: We demonstrate that failure of time-invariance assumption in the modeling of\nelectrochemical systems by equivalent circuits can lead to the formation of low\nfrequency \"inductive loops\" that manifest themselves as positive imaginary\nparts of the impedance function. Assuming that the properties of the equivalent\ncircuits change slowly in time we perform an asymptotic analysis and obtain a\nnew integral representation of the impedance function that reduces to the\nstandard one at high frequencies, while exhibiting inductive loops at low\nfrequencies.", "category": "physics_chem-ph" }, { "text": "Density Functional Model for Nondynamic and Strong Correlation: A single-term density functional model for nondynamic and strong correlation\nis presented, based on single-determinant Kohn-Sham density functional theory.\nIt is derived from modeling the adiabatic connection and contains only two\nnonlinear empirical parameters. Preliminary tests show that the model recovers\nmajority of nondynamic correlation during a molecular dissociation and at the\nsame time performs reasonably for atomization energies. It demonstrates the\nfeasibility of developing DFT functionals for nondynamic and strong correlation\nwithin the single-determinant KS scheme.", "category": "physics_chem-ph" }, { "text": "A DFT-based Tight-Binding Approach to the Self-consistent Description of\n Molecule Metal-Nanoparticle Interactions: The interaction within a hybrid system consisting of a spherical metal\nnanoparticle and a nearby organic dye molecule is formulated in a combined\nquantum-classical approach. Whereas the nanoparticle's polarization field is\ntreated in classical multipole form, the electronic charge density of the\nmolecule is described quantum mechanically. An efficient solution of the\nresulting self-consistency problem becomes possible by using the discrete\nrepresentation of the charge density in terms of atom-centered Mulliken charges\nwithin the density functional theory-based tight binding (DFTB) approach.\nResults for two different dye molecules are presented, which focus on the\ndependence of the interaction on the nanoparticle's radius, the distance\nbetween nanoparticle and molecule and their mutual orientation.", "category": "physics_chem-ph" }, { "text": "Detailed Thermal Characterization on a 48V Lithium-Ion Battery Pack\n during Charge-Discharge Cycles: This study experimentally investigates the temperature distribution and\nbehavior of a 48V Lithium-Ion (Li-ion) battery pack during two charge-discharge\ncycles using 25 thermocouples. Results indicate that better convective heat\ntransfer occurs at the external surfaces of the pack, while middle cells reach\nmaximum temperatures. Differences are also observed in the behavior of the\nthree modules. The discharge cycle shows a temperature rise of 5.8{\\deg}C with\na pack temperature gradient increasing from 1.3{\\deg}C to 2.7{\\deg}C. The study\nhighlights the importance of assessing the thermal behavior of each module and\nthe complexity of the Li-ion battery pack system. Findings on the battery\ncells, modules, and pack in the same study can provide valuable insights for\ndesigning efficient cooling systems for Li-ion battery packs.", "category": "physics_chem-ph" }, { "text": "Double Core Hole Valence-to-Core X-ray Emission Spectroscopy: A\n Theoretical Exploration Using Time-Dependent Density Functional Theory: With the help of newly developed X-ray free-electron laser (XFEL) sources,\ncreating double core holes simultaneously at the same or different atomic sites\nin a molecule has now become possible. Double core hole (DCH) X-ray emission is\na new form of X-ray nonlinear spectroscopy that can be studied with a XFEL.\nHere we computationally explore the metal K-edge valence-to-core (VtC) X-ray\nemission spectroscopy (XES) of metal/metal and metal/ligand double core hole\nstates in a series of transition metal complexes with time-dependent density\nfunctional theory. The simulated DCH VtC-XES signals are compared with\nconventional single core hole (SCH) XES signals. The energy shifts and\nintensity changes of the DCH emission lines with respect to the corresponding\nSCH-XES features are fingerprints of the coupling between the second core hole\nand the occupied orbitals around the DCHs that contain important chemical\nbonding information of the complex. The core hole localization effect on DCH\nVtC-XES is also briefly discussed. We theoretically demonstrate that DCH XES\nprovides subtle information on the local electronic structure around metal\ncenters in transition metal complexes beyond conventional linear XES. Our\npredicted changes from calculations between SCH-XES and DCH-XES features should\nbe detectable with modern XFEL sources.", "category": "physics_chem-ph" }, { "text": "Boltzmann-conserving classical dynamics in quantum time-correlation\n functions: Matsubara dynamics: We show that a single change in the derivation of the linearized\nsemiclassical-initial value representation (LSC-IVR or classical Wigner\napproximation) results in a classical dynamics which conserves the quantum\nBoltzmann distribution. We rederive the (standard) LSC-IVR approach by writing\nthe (exact) quantum time-correlation function in terms of the normal modes of a\nfree ring-polymer (i.e. a discrete imaginary-time Feynman path), taking the\nlimit that the number of polymer beads $N \\to \\infty$, such that the lowest\nnormal-mode frequencies take their Matsubara values. The change we propose is\nto truncate the quantum Liouvillian, not explicitly in powers of $\\hbar^2$ at\n$\\hbar^0$ (which gives back the standard LSC-IVR approximation), but in the\nnormal-mode derivatives corresponding to the lowest Matsubara frequencies. The\nresulting Matsubara dynamics is inherently classical (since all terms\n$\\mathcal{O}\\left(\\hbar^{2}\\right)$ disappear from the Matsubara Liouvillian in\nthe limit $N \\to \\infty$), and conserves the quantum Boltzmann distribution\nbecause the Matsubara Hamiltonian is symmetric with respect to imaginary-time\ntranslation. Numerical tests show that the Matsubara approximation to the\nquantum time-correlation function converges with respect to the number of\nmodes, and gives better agreement than LSC- IVR with the exact quantum result.\nMatsubara dynamics is too computationally expensive to be applied to complex\nsystems, but its further approximation may lead to practical methods.", "category": "physics_chem-ph" }, { "text": "VO2 Phase Change Electrodes in Li-ion Batteries: Use of electrode materials that show phase change behavior and hence drastic\nchanges in electrochemical activity during operation, have not been explored\nfor Li-ion batteries. Here we demonstrate the vanadium oxide (VO2) cathode that\nundergoes metal-insulator transition due to first-order structural phase\ntransition at accessible temperature of 68{\\deg}C for battery operation. Using\na suitable electrolyte operable across the phase transition range and\ncompatible with vanadium oxide cathodes, we studied the effect of electrode\nstructure change on lithium insertion followed by the electrochemical\ncharacteristics above and below the phase transition temperature. The\nhigh-temperature VO2 phase shows significantly improved capacitance, enhanced\ncurrent rate capabilities, improved electrical conductivity and lithium-ion\ndiffusivity compared to the insulating low temperature phase. This opens up new\navenues for electrode designs, allowing manipulation of electrochemical\nreactions around phase transition temperatures, and in particular enhancing\nelectrochemical properties at elevated temperatures contrary to existing\nclasses of battery chemistries that lead to performance deterioration at\nelevated temperatures.", "category": "physics_chem-ph" }, { "text": "Paired Ru-O-Mo ensemble for efficient and stable alkaline hydrogen\n evolution reaction: Electrocatalytic hydrogen evolution reaction (HER) in alkaline media is a\npromising electrochemical energy conversion strategy. Ruthenium (Ru) is an\nefficient catalyst with a desirable cost for HER, however, the sluggish H2O\ndissociation process, due to the low H2O adsorption on its surface, currently\nhampers the performances of this catalyst in alkaline HER. Herein, we\ndemonstrate that the H2O adsorption improves significantly by the construction\nof Ru-O-Mo sites. We prepared Ru/MoO2 catalysts with Ru-O-Mo sites through a\nfacile thermal treatment process and assessed the creation of Ru-O-Mo\ninterfaces by transmission electron microscope (TEM) and extended X-ray\nabsorption fine structure (EXAFS). By using Fourier-transform infrared\nspectroscopy (FTIR) and H2O adsorption tests, we proved Ru-O-Mo sites have\ntenfold stronger H2O adsorption ability than that of Ru catalyst. The catalysts\nwith Ru-O-Mo sites exhibited a state-of-the-art overpotential of 16 mV at 10 mA\ncm-2 in 1 M KOH electrolyte, demonstrating a threefold reduction than the\nprevious bests of Ru (59 mV) and commercial Pt (31 mV) catalysts. We proved the\nstability of these performances over 40 hours without decline. These results\ncould open a new path for designing efficient and stable catalysts.", "category": "physics_chem-ph" }, { "text": "The Structural Fate of Individual Multicomponent Metal-Oxide\n Nanoparticles in Polymer Nanoreactors: Multicomponent nanoparticles can be synthesized with either homogeneous or\nphase-segregated architectures depending on the synthesis conditions and\nelements incorporated. To understand the parameters that determine their\nstructural fate, multicomponent metal-oxide nanoparticles consisting of\ncombinations of Co, Ni, and Cu were synthesized via scanning probe block\ncopolymer lithography and characterized using correlated electron microscopy.\nThese studies revealed that the miscibility, ratio of the metallic components,\nand the synthesis temperature determine the crystal structure and architecture\nof the nanoparticles. A Co-Ni-O system forms a rock salt structure largely due\nto the miscibility of CoO and NiO, while Cu-Ni-O, which has large miscibility\ngaps, forms either homogeneous oxides, heterojunctions, or alloys depending on\nthe annealing temperature and composition. Moreover, a higher ordered\nstructure, Co-Ni-Cu-O, was found to follow the behavior of lower ordered\nsystems.", "category": "physics_chem-ph" }, { "text": "Nonlinear Light Absorption in Many-Electron Systems Excited by an\n Instantaneous Electric Field: A Non-Perturbative Approach: We study light absorption in many-electron interacting systems beyond the\nlinear regime by using a {\\em single} broadband impulse of an electric field in\nthe instantaneous limit. We determine non-pertubatively the absorption cross\nsection from the Fourier transform of the time-dependent induced dipole moment,\nwhich can be obtained from the time evolution of the wavefunction. We discuss\nthe dependence of the resulting cross section on the magnitude of the impulse\nand we highlight the advantages of this method in comparison with perturbation\ntheory working on a one-dimensional model system for which numerically exact\nsolutions are accessible. Thus we demonstrate that the considered non\npertubative approach provides us with an effective tool for investigating\nfluence-dependent nonlinear optical excitations.", "category": "physics_chem-ph" }, { "text": "A study of accurate exchange-correlation functionals through adiabatic\n connection: A systematic way of improving exchange-correlation energy functionals of\ndensity functional theory has been to make them satisfy more and more exact\nrelations. Starting from the initial GGA functionals, this has culminated into\nthe recently proposed SCAN(Strongly constrained and appropriately normed)\nfunctional that satisfies several known constraints and is appropriately\nnormed. The ultimate test for the functionals developed is the accuracy of\nenergy calculated by employing them. In this paper, we test these\nexchange-correlation functionals -the GGA hybrid functionals B3LYP and PBE0,\nand the meta-GGA functional SCAN- from a different perspective. We study how\naccurately these functionals reproduce the exchange-correlation energy when\nelectron-electron interaction is scaled as scaling parameter times Vee with\nthis parameter varying between 0 and 1. Our study reveals interesting\ncomparison between these functionals and the associated difference Tc between\nthe interacting and the non-interacting kinetic energy for the same density.", "category": "physics_chem-ph" }, { "text": "Discrete Thermodynamics of 2-level Laser - Why Not and When Yes: The paper explores a possible application of the discrete thermodynamics to a\n2-level laser. The model accounts for the laser openness to incoming pumping\npower and coming out energy with the emitted light. As an open system, a laser\nshould be in open equilibrium with thermodynamic forces, related to both energy\nflows. Conditions of equilibria are expressed by a logistic map with specially\ndeveloped dynamic inverse pitchfork bifurcation diagrams for graphical\npresentation of the solutions. The graphs explicitly confirm the triggering\nnature of a laser where bistability is manifested by pitchfork ground and laser\nbranches, with the relative population equilibrium values close to 1 and 0\ncorrespondingly. Simulation was run for a 2-level laser emitting light from far\ninfrared to short wave UV. A newly discovered feature of such a laser is the\nline spectrum of up and down transitions of the laser excitable dwellers,\noccurring between the laser and the ground pitchfork branches beyond\nbifurcation point. The density of the spectra lines tangibly increases as the\nbranches approach their limits. Transitions of both types are overlapping in\nopposite phases. This effect is a new confirmation of the Einstein's\nprohibition on practical realization of a 2-level laser. Wide enough gaps\nbetween the lines of the spectra were also discovered in this research. The\ngaps are shielding the light irradiation and may be considered as potential\nareas of control over the 2-level laser emissions.", "category": "physics_chem-ph" }, { "text": "Simple eigenvalue-self-consistent $\\bar\u0394GW_{0}$: We derive a general form of eigenvalue self-consistency for $GW_{0}$ in the\ntime domain and use it to obtain a simplified postprocessing eigenvalue\nself-consistency, which we label $\\bar{\\Delta}GW_{0}$. The method costs the\nsame as a one-shot $G_{0}W_{0}$ when the latter gives the full frequency-domain\n(or time-domain) matrix element of the self-energy. The accuracy of\n$\\bar{\\Delta}GW_{0}$ increases with system size, as demonstrated here by\ncomparison to other $GW$ self-consistency results and to CCSD(T) predictions.\nWhen combined with the large-scale stochastic $G_{0}W_{0}$ formulation\n$\\bar{\\Delta}GW_{0}$ is applicable to very large systems, as exemplified by\nperiodic supercells of semiconductors and insulators with 2048 valence\nelectrons. For molecules the error of our eventual partially self-consistent\napproach starts at about 0.2eV for small molecules and decreases to 0.05eV for\nlarge ones, while for the periodic solids studied here the mean-absolute-error\nis only 0.03eV.", "category": "physics_chem-ph" }, { "text": "Coupled charge and energy transfer dynamics in light harvesting\n complexes from a hybrid hierarchical equations of motion approach: We describe a method for simulating exciton dynamics in protein-pigment\ncomplexes, including effects from charge transfer as well as fluorescence. The\nmethod combines the hierarchical equations of motion, which are used to\ndescribe quantum dynamics of excitons, and the Nakajima-Zwanzig quantum master\nequation, which is used to describe slower charge transfer processes. We study\nthe charge transfer quenching in light harvesting complex II, a protein\npostulated to control non-photochemcial quenching in many plant species. Using\nour hybrid approach, we find good agreement between our calculation and\nexperimental measurements of the excitation lifetime. Furthermore our\ncalculations reveal that the exciton energy funnel plays an important role in\ndetermining quenching efficiency, a conclusion we expect to extend to other\nproteins that perform protective excitation quenching. This also highlights the\nneed for simulation methods that properly account for the interplay of exciton\ndynamics and charge transfer processes.", "category": "physics_chem-ph" }, { "text": "(4,4')-Bipyridine in Vacuo and in Solvents: A Quantum Chemical Study of\n a Prototypical Floppy Molecule From a Molecular Transport Perspective: We report results of quantum chemical calculations for the neutral and\nanionic species of (4,4{'})-bipyridine (44BPY), a prototypical molecule with a\nfloppy degree of freedom, placed in vacuo and in solvents. In addition to\nequilibrium geometries and vibrational frequencies and spectra, we present\nadiabatic energy curves for the vibrational modes with significant\nintramolecular reorganization upon charge transfer. Special attention is paid\nto the floppy strongly anharmonic degree of freedom of 44BPY, which is related\nto the most salient structural feature, namely the twist angle $\\theta$ between\nthe two pyridine rings. The relevance of the present results for molecular\ntransport will be emphasized. We show that the solvent acts as an effective\ngate electrode and propose a scissor operator to account for solvent effects on\nmolecular transport. Our result on the conductance $G$ vs. $\\cos^2\\theta$ is\nconsistent with a significant transmission in perpendicular conformation\nindicated by previous microscopic analysis.", "category": "physics_chem-ph" }, { "text": "Physics-informed Neural-Network Software for Molecular Dynamics\n Applications: We have developed a novel differential equation solver software called PND\nbased on the physics-informed neural network for molecular dynamics simulators.\nBased on automatic differentiation technique provided by Pytorch, our software\nallows users to flexibly implement equation of atom motions, initial and\nboundary conditions, and conservation laws as loss function to train the\nnetwork. PND comes with a parallel molecular dynamics (MD) engine in order for\nusers to examine and optimize loss function design, and different conservation\nlaws and boundary conditions, and hyperparameters, thereby accelerate the\nPINN-based development for molecular applications.", "category": "physics_chem-ph" }, { "text": "Collisional excitation of NH3 by atomic and molecular hydrogen: We report extensive theoretical calculations on the rotation-inversion\nexcitation of interstellar ammonia (NH3) due to collisions with atomic and\nmolecular hydrogen (both para- and ortho-H2). Close-coupling calculations are\nperformed for total energies in the range 1-2000 cm-1 and rotational cross\nsections are obtained for all transitions among the lowest 17 and 34\nrotation-inversion levels of ortho- and para-NH3, respectively. Rate\ncoefficients are deduced for kinetic temperatures up to 200 K. Propensity rules\nfor the three colliding partners are discussed and we also compare the new\nresults to previous calculations for the spherically symmetrical He and para-H2\nprojectiles. Significant differences are found between the different sets of\ncalculations. Finally, we test the impact of the new rate coefficients on the\ncalibration of the ammonia thermometer. We find that the calibration curve is\nonly weakly sensitive to the colliding partner and we confirm that the ammonia\nthermometer is robust.", "category": "physics_chem-ph" }, { "text": "A new \"gold standard\": perturbative triples corrections in unitary\n coupled cluster theory and prospects for quantum computing: A major difficulty in quantum simulation is the adequate treatment of a large\ncollection of entangled particles, synonymous with electron correlation in\nelectronic structure theory, with coupled cluster (CC) theory being the leading\nframework in dealing with this problem. Augmenting computationally affordable\nlow-rank approximations in CC theory with a perturbative account of higher-rank\nexcitations is a tractable and effective way of accounting for the missing\nelectron correlation in those approximations. This is perhaps best exemplified\nby the \"gold standard\" CCSD(T) method, which bolsters the baseline CCSD with\neffects of triple excitations using considerations from many-body perturbation\ntheory (MBPT). Despite this established success, such a synergy between MBPT\nand the unitary analog of CC theory (UCC) has not been explored. In this work,\nwe propose a similar approach wherein converged UCCSD amplitudes, which can be\nobtained on a quantum computer, are leveraged by a classical computer to\nevaluate energy corrections associated with triple excitations - leading to the\nUCCSD[T] and UCCSD(T*) methods. The rationale behind these choices is shown to\nbe rigorous by studying the properties of finite-order UCC energy functionals.\nAlthough our efforts do not support the addition of the fifth-order\ncontribution as in the (T) correction, comparisons are nevertheless made using\na hybrid UCCSD(T) approach. We assess the performance of these approaches on a\ncollection of small molecules, and demonstrate the benefits of harnessing the\ninherent synergy between MBPT and UCC theories.", "category": "physics_chem-ph" }, { "text": "Projected Density Matrix Embedding Theory with Applications to the\n Two-Dimensional Hubbard Model: Density matrix embedding theory (DMET) is a quantum embedding theory for\nstrongly correlated systems. From a computational perspective, one bottleneck\nin DMET is the optimization of the correlation potential to achieve\nself-consistency, especially for heterogeneous systems of large size. We\npropose a new method, called projected density matrix embedding theory\n(p-DMET), which achieves self-consistency without needing to optimize a\ncorrelation potential. We demonstrate the performance of p-DMET on the\ntwo-dimensional Hubbard model.", "category": "physics_chem-ph" }, { "text": "Chemical bond analysis for the entire periodic table: Energy\n Decomposition and Natural Orbitals for Chemical Valence in the Four-Component\n Relativistic Framework: Chemical bonding is a ubiquitous concept in chemistry and it provides a\ncommon basis for experimental and theoretical chemists to explain and predict\nthe structure, stability and reactivity of chemical species. Among others, the\nEnergy Decomposition Analysis (EDA, also known as the Extended Transition State\nmethod) in combination with Natural Orbitals for Chemical Valence (EDA-NOCV) is\na very powerful tool for the analysis of the chemical bonds based on a charge\nand energy decomposition scheme within a common theoretical framework. While\nthe approach has been applied in a variety of chemical contexts, the current\nimplementations of the EDA-NOCV scheme include relativistic effects only at\nscalar level, so simply neglecting the spin-orbit coupling effects and de facto\nlimiting its applicability. In this work, we extend the EDA-NOCV method to the\nrelativistic four-component Dirac-Kohn-Sham theory that variationally accounts\nfor spin-orbit coupling. Its correctness and numerical stability have been\ndemonstrated in the case of simple molecular systems, where the relativistic\neffects play a negligible role, by comparison with the implementation available\nin the ADF modelling suite (using the non-relativistic Hamiltonian and the\nscalar ZORA approximation). As an illustrative example we analyse the\nmetal-ethylene coordination bond in the group 6-element series\n(CO)$_5$TM-C$_2$H$_4$, with TM =Cr, Mo, W, Sg, where relativistic effects are\nlikely to play an increasingly important role as one moves down the group. The\nmethod provides a clear measure (also in combination with the CD analysis) of\nthe donation and back-donation components in coordination bonds, even when\nrelativistic effects, including spin-orbit coupling, are crucial for\nunderstanding the chemical bond involving heavy and superheavy atoms.", "category": "physics_chem-ph" }, { "text": "Nonadiabatic semiclassical dynamics in the mixed quantum-classical\n initial value representation: We extend the Mixed Quantum-Classical Initial Value Representation (MQC-IVR),\na semiclassical method for computing real-time correlation functions, to\nelectronically nonadiabatic systems using the Meyer-Miller-Stock-Thoss (MMST)\nHamiltonian to treat electronic and nuclear degrees of freedom (dofs) within a\nconsistent dynamic framework. We introduce an efficient symplectic integration\nscheme, the MInt algorithm, for numerical time-evolution of the nuclear and\nelectronic phase space variables as well as the Monodromy matrix, under the\nnon-separable MMST Hamiltonian. We then calculate the probability of\ntransmission through a curve-crossing in model two-level systems and show that\nin the quantum limit MQC-IVR is in good agreement with the exact quantum\nresults, whereas in the classical limit the method yields results in keeping\nwith mean-field approaches like the Linearized Semiclassical IVR. Finally,\nexploiting the ability of MQC-IVR to quantize different dofs to different\nextents, we present a detailed study of the extents to which quantizing the\nnuclear and electronic dofs improves numerical convergence properties without\nsignificant loss of accuracy.", "category": "physics_chem-ph" }, { "text": "A computational approach to calculate the heat of transport of aqueous\n solutions: Thermal gradients induce concentration gradients in alkali halide solutions,\nand the salt migrates towards hot or cold regions depending on the average\ntemperature of the solution. This effect has been interpreted using the heat of\ntransport, which provides a route to rationalize thermophoretic phenomena.\nEarly theories provide estimates of the heat of transport at infinite dilution.\nThese values are used to interpret thermodiffusion (Soret) and thermoelectric\n(Seebeck) effects. However, accessing heats of transport of individual ions at\nfinite concentration remains an outstanding question both theoretically and\nexperimentally. Here we discuss a computational approach to calculate heats of\ntransport of aqueous solutions at finite concentrations, and apply our method\nto study lithium chloride solutions at concentrations $>0.5$~M. The heats of\ntransport are significantly different for Li$^+$ and Cl$^-$ ions, unlike what\nis expected at infinite dilution. We find theoretical evidence for the\nexistence of minima in the Soret coefficient of LiCl, where the magnitude of\nthe heat of transport is maximized. The Seebeck coefficient obtained from the\nionic heats of transport varies significantly with temperature and\nconcentration. We identify thermodynamic conditions leading to a maximization\nof the thermoelectric response of aqueous solutions.", "category": "physics_chem-ph" }, { "text": "Properties of modified periodic one-dimensional hopping model: One-dimensional hopping model is useful to describe the motion of microscopic\nparticle in thermal noise environment, such as motor proteins. Recent\nexperiments about the new generation of light-driven rotary molecular motors\nfound that, the motor in state i can jump forward to state i+1 or i+2, or\nbackward to state i-1 or i-2 directly. In this paper, such modified periodic\none-dimensional hopping model of arbitrary period N is studied mathematically.\nThe mean velocity, effective diffusion constant, and mean dwell time in one\nsingle cycle are obtained. Corresponding results are illustrated and verified\nby being applied to a type of synthetic rotary molecular motors.", "category": "physics_chem-ph" }, { "text": "Ab initio study and assignment of electronic states in molecular RaCl: Radium compounds have attracted recently considerable attention due to both\ndevelopment of experimental techniques for high-precision laser spectroscopy of\nmolecules with short-lived nuclei and amenability of certain radium compounds\nfor direct cooling with lasers. Currently, radium monofluoride (RaF) is one of\nthe most studied molecules among the radium compounds, both theoretically and\nrecently also experimentally. Complementary studies of further diatomic radium\nderivatives are highly desired to assess the influence of chemical substitution\non diverse molecular parameters, especially on those connected with laser\ncooling, such as vibronic transition probabilities, and those related to\nviolations of fundamental symmetries. In this article high-precision \\emph{ab\ninitio} studies of electronic and vibronic levels of diatomic radium\nmonochloride (RaCl) are presented. Recently developed approaches for treating\nelectronic correlation with Fock-space coupled cluster methods are applied for\nthis purpose. Theoretical results are compared to an early experimental\ninvestigation by Lagerqvist and used to partially reassign the experimentally\nobserved transitions and molecular electronic levels of RaCl. Effective\nconstants of $\\mathcal{P}$-odd hyperfine interaction $W_{\\rm{a}}$ and\n$\\mathcal{P,T}$-odd scalar-pseudoscalar nucleus-electron interaction\n$W_{\\rm{s}}$ in the ground electronic state of RaCl are estimated within the\nframework of a quasirelativistic Zeroth-Order Regular Approximation approach\nand compared to parameters in RaF and RaOH.", "category": "physics_chem-ph" }, { "text": "Stretched chemical bonds in Si6H6: A transition from ring currents to\n localized pi-electrons?: Motivated by solid-state studies on the cleavage force in Si, and the\nconsequent stretching of chemical bonds, we here study bond stretching in the,\nas yet unsynthesized, free space molecule Si6H6. We address the question as to\nwhether substantial bond stretching (but constrained to uniform scaling on all\nbonds) can result in a transition from ring current behaviour, characteristic\nsay of benzene at its equilibrium geometry, to localized pi-electrons on Si\natoms. Some calculations are also recorded on dissociation into 6 SiH radicals.\nWhile the main studies have been carried out by unrestricted Hartree-Fock (HF)\ntheory, the influence of electron correlation has been examined using two forms\nof density functional theory. Planar Si6H6 treated by HF is bound to be\nunstable, not all vibrational frequencies being real. Some buckling is then\nallowed, which results in real frequencies and stability. Evidence is then\nprovided that the non-planar structure, as the Si-Si distance is increased,\nexhibits pi-electron localization in the range 1.2-1.5 times the equilibrium\ndistance.", "category": "physics_chem-ph" }, { "text": "Are Heptazine-Based Organic Light-Emitting Diode (OLED) Chromophores\n Thermally Activated Delayed Fluorescence (TADF) or Inverted Singlet-Triplet\n (IST) Systems?: Two chromophores derived from heptazine, HAP-3MF and HAP-3TPA, were\nsynthesized and tested as emitters in light-emitting diodes (OLEDs) by Adachi\nand coworkers. Both emitters were shown to exhibit quantum efficiencies which\nexceed the theoretical maximum of conventional fluorescent OLEDs. The enhanced\nemission efficiency was explained by the mechanism of thermally activated\ndelayed fluorescence (TADF). In the present work, the electronic excitation\nenergies and essential features of the topography of the excited-state\npotential-energy surfaces of HAP-3MF and HAP-3TPA have been investigated with a\nwave-function based ab initio method (ADC(2)). It is found that HAP-3MF is an\ninverted singlet-triplet (IST) system, that is, the energies of the S1and\nT1states are robustly inverted in violation of Hund's multiplicity rule.\nNotably, HAP-3MF presumably is the first IST emitter which was implemented in\nan OLED device. In HAP-3TPA, on the other hand, the vertical excitation\nenergies of the S1 and T1 states are essentially degenerate. The excited states\nexhibit vibrational stabilization energies of similar magnitude along different\nrelaxation coordinates, resulting in adiabatic excitation energies which also\nare nearly degenerate. HAP-3TPA is found to be a chromophore at the borderline\nof TADF and IST systems. The spectroscopic data reported by Adachi and\ncoworkers forHAP-3MF and HAP-3TPA are analysed in the light of these\ncomputational results.", "category": "physics_chem-ph" }, { "text": "Donnan Equilibrium Revisited: Coupling between Ion Concentrations,\n Osmotic Pressure, and Donnan Potential: This paper discusses the little-known fact that Donnan's equilibrium criteria\nestablished over 100 years ago neglected the coupling between ion\nconcentrations and the osmotic pressure. Such coupling can be treated based on\ngeneral thermodynamic considerations including the solvent equilibrium, leading\nto a membrane potential that consists of not only the classical Donnan\npotential term but also an additional term due to the osmotic pressure, and the\nexistence of a membrane potential even when the impermeable species are not\ncharged. This coupled treatment is in conflict with the well-established\nPoisson-Boltzmann equation and Nernst-Planck equation, but is consistent with\nthe extension of these equations including the solvent effects by Freise and\nSchlogl, enables us to view the electrical double layer equilibrium as Donnan\nequilibrium.", "category": "physics_chem-ph" }, { "text": "Identification of the Molecule-Metal Bonding Geometries of Molecular\n Nanowires: Molecular nanowires in which a single molecule bonds chemically to two metal\nelectrodes and forms a stable electrically conducting bridge between them have\nbeen studied intensively for more than a decade. However the experimental\ndetermination of the bonding geometry between the molecule and electrodes has\nremained elusive. Here we demonstrate by means of ab initio calculations that\ninelastic tunneling spectroscopy (IETS) can determine these geometries. We\nidentify the bonding geometries at the gold-sulfur interfaces of\npropanedithiolate molecules bridging gold electrodes that give rise to the\nspecific IETS signatures that were observed in recent experiments.", "category": "physics_chem-ph" }, { "text": "General phenomenology of ionization from aligned molecular ensembles: Single and multi-photon ionization of aligned molecular ensembles is\nexamined, with a particular focus on the link between the molecular axis\ndistribution and observable in various angle-integrated and angle-resolved\nmeasurements. To maintain generality the problem is treated geometrically, with\nthe aligned ensemble cast in terms of axis distribution moments, and the\nresponse of observables in terms of couplings to these moments. Within this\nformalism the angular momentum coupling is treated analytically, allowing for\ngeneral characteristics - independent of the details of the ionization dynamics\nof a specific molecule - to be determined. Limiting cases are explored in order\nto provide a phenomenology which should be readily applicable to a range of\nexperimental measurements, and illustrate how observables can be sensitive to\nfine details of the alignment, i.e. higher-order moments of the axis\ndistribution, which are often neglected in experimental studies. We hope that\nthis detailed and comprehensive treatment will bridge the gap between existing\ntheoretical and experimental works, and provide both quantitative physical\ninsights and a useful general phenomenology for researchers working with\naligned molecular ensembles.", "category": "physics_chem-ph" }, { "text": "Enhancing Autoignition Characteristics: A Framework to Discover Fuel\n Additives and Making Predictions Using Machine Learning: Combustion process can become more energy efficient and environment friendly\nif used with appropriate fuel additive. Discovery of fuel additive can be\naccelerated by applying hybrid approach of using of chemical kinetics and\nMachine Learning (ML). In this work, we present a framework that takes the\nrobustness of Machine Learning and accuracy of chemical kinetics to predict the\neffect of fuel additive on autoignition process. We present a case of making\npredictions for Ignition Delay Time (IDT) of biofuel n-butanol ($C_4H_9OH$)\nwith several fuel additives. The proposed framework was able to predict IDT of\nautoignition with high accuracy when used with unseen additives. This framework\nhighlights the potential of ML to exploit chemical mechanisms in exploring and\ndeveloping the fuel additives to obtain the desirable autoignition\ncharacteristics.", "category": "physics_chem-ph" }, { "text": "Real-time polarimetry of hyperpolarized $^{13}$C nuclear spins using an\n atomic magnetometer: We introduce a method for non-destructive quantification of nuclear spin\npolarization, of relevance to hyperpolarized spin tracers widely used in\nmagnetic resonance from spectroscopy to in vivo imaging. In a bias field of\naround 30 nT we use a high-sensitivity miniaturized $^{87}$Rb vapor\nmagnetometer to measure the field generated by the sample, as it is driven by a\nwindowed dynamical decoupling pulse sequence that both maximizes the nuclear\nspin lifetime and modulates the polarization for easy detection. We demonstrate\nthe procedure applied to a 0.08 M hyperpolarized [1--$^{13}$C]-pyruvate\nsolution produced by dissolution dynamic nuclear polarization, measuring\npolarization repeatedly during natural decay at Earth's field. Application to\nreal-time quality monitoring of hyperpolarized substances is discussed.", "category": "physics_chem-ph" }, { "text": "Experiments and Modeling of the Autoignition of Methylcyclohexane at\n High Pressure: New experimental data are collected for methyl-cyclohexane (MCH) autoignition\nin a heated rapid compression machine (RCM). Three mixtures of MCH/O2/N2/Ar at\nequivalence ratios of $\\phi$=0.5, 1.0, and 1.5 are studied and the ignition\ndelays are measured at compressed pressure of 50 bar and for compressed\ntemperatures in the range of 690-900 K. By keeping the fuel mole fraction in\nthe mixture constant, the order of reactivity, in terms of inverse ignition\ndelay, is measured to be $\\phi$=0.5 > $\\phi$=1.0 > $\\phi$=1.5, demonstrating\nthe dependence of the ignition delay on oxygen concentration. In addition, an\nexisting model for the combustion of MCH is updated with new reaction rates and\npathways, including substantial updates to the low-temperature chemistry. The\nnew model shows good agreement with the overall ignition delays measured in\nthis study, as well as the ignition delays measured previously in the\nliterature using RCMs and shock tubes. This model therefore represents a strong\nimprovement compared to the previous version, which uniformly over-predicted\nthe ignition delays. Chemical kinetic analyses of the updated mechanism are\nalso conducted to help understand the fuel decomposition pathways and the\nreactions controlling the ignition. Combined, these results and analyses\nsuggest that further investigation of several of the low-temperature fuel\ndecomposition pathways is required.", "category": "physics_chem-ph" }, { "text": "Investigation of the exchange-correlation potential of functionals based\n on the adiabatic connection interpolation: We have studied the correlation potentials produced by various adiabatic\nconnection models (ACM) for several atoms and molecules. The results have been\ncompared to accurate reference potentials (coupled cluster and quantum Monte\nCarlo results) as well as to state-of-the-art ab initio DFT approaches. We have\nfound that all the ACMs yield correlation potentials that exhibit a correct\nbehavior, quite resembling scaled second-order G\\\"orling-Levy (GL2) potentials,\nand including most of the physically meaningful features of the accurate\nreference data. The behavior and contribution of the strong-interaction limit\npotentials has also been investigated and discussed.", "category": "physics_chem-ph" }, { "text": "Biexcitons are bound in CsPbBr3 Perovskite Nanocrystals: We study the energetics of quasi-particle excitations in CsPbBr3 perovskite\nnanocrystals using path integral molecular dynamics simulations. Employing\ndetailed molecular models, we elucidate the interplay of anharmonic lattice\ndegrees of freedom, dielectric confinement, and electronic correlation on\nexciton and biexciton binding energies over a range of nanocrystal sizes. We\nfind generally good agreement with some experimental observations on binding\nenergies, and additionally explain the observed size dependent Stokes shift.\nThe explicit model calculations are compared to simplified approximations to\nrationalize the lattice contributions to binding. We find that polaron\nformation significantly reduces exciton binding energies, whereas these effects\nare negligible for biexciton interactions. While experimentally, the binding\nenergy of biexcitons is uncertain, based on our study we conclude that\nbiexcitons are bound in CsPbBr3.", "category": "physics_chem-ph" }, { "text": "Multilayer multi-configuration time-dependent Hartree method:\n implementation and applications to a Henon-Heiles Hamiltonian and to pyrazine: The multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method is\ndiscussed and a fully general implementation for any number of layers based on\nthe recursive ML-MCTDH algorithm given by Manthe [J. Chem. Phys. {\\bf 128},\n164116 (2008)] is presented. The method is applied first to a generalized\nHenon-Heiles (HH) Hamiltonian. For 6D HH the overhead of ML-MCTDH makes the\nmethod slower than MCTDH, but for 18D HH ML-MCTDH starts to be competitive. We\nreport as well 1458D simulations of the HH Hamiltonian using a seven layer\nscheme. The photoabsorption spectrum of pyrazine computed with the 24D\nHamiltonian of Raab {\\em et. al.} [J. Chem. Phys. {\\bf 110}, 936 (1999)]\nprovides a realistic molecular test case for the method. Quick and small\nML-MCTDH calculations needing a fraction of the time and resources of reference\nMCTDH calculations provide already spectra with all the correct features.\nAccepting slightly larger deviations, the calculation can be accelerated to\ntake only 7 minutes. When pushing the method towards convergence, results of\nsimilar quality than the best available MCTDH benchmark, which is based on a\nwavepacket with $4.6\\times 10^7$ time-dependent coefficients, are obtained with\na much more compact wavefunction consisting of only $4.5\\times 10^5$\ncoefficients and requiring a shorter computation time.", "category": "physics_chem-ph" }, { "text": "The i-V curve curve characteristics of burner-stabilized premixed\n flames: detailed and reduced models: The i-V curve describes the current drawn from a flame as a function of the\nvoltage difference applied across the reaction zone. Since combustion\ndiagnostics and flame control strategies based on electric fields depend on the\namount of current drawn from flames, there is significant interest in modeling\nand understanding i-V curves. We implement and apply a detailed model for the\nsimulation of the production and transport of ions and electrons in one\ndimensional premixed flames. An analytical reduced model is developed based on\nthe detailed one, and analytical expressions are used to gain insight into the\ncharacteristics of the i-V curve for various flame configurations. In order for\nthe reduced model to capture the spatial distribution of the electric field\naccurately, the concept of a dead zone region, where voltage is constant, is\nintroduced, and a suitable closure for the spatial extent of the dead zone is\nproposed and validated. The results from the reduced modeling framework are\nfound to be in good agreement with those from the detailed simulations. The\nsaturation voltage is found to depend significantly on the flame location\nrelative to the electrodes, and on the sign of the voltage difference applied.\nFurthermore, at sub-saturation conditions, the current is shown to increase\nlinearly or quadratically with the applied voltage, depending on the flame\nlocation. These limiting behaviors exhibited by the reduced model elucidate the\nfeatures of i-V curves observed experimentally. The reduced model relies on the\nexistence of a thin layer where charges are produced, corresponding to the\nreaction zone of a flame. Consequently, the analytical model we propose is not\nlimited to the study of premixed flames, and may be applied easily to others\nconfigurations, e.g. nonpremixed counterflow flames.", "category": "physics_chem-ph" }, { "text": "A comparative study of solvent dynamics in Choline Bromide aqueous\n solution using combination of neutron scattering technique and molecular\n dynamics simulation: A comparative study between Choline and Tetra-methyl ammonium bromide is\npresented here. Choline which is a crucial component for our dietary\nrequirements causes many diseases if there is deficiency. We used combined\napproach of all-atom molecular dynamics simulation coupled with neutron\nscattering technique to study mainly the solvent behavior in this study. There\nis follow up work where we discussed about the solute dynamical behavior.", "category": "physics_chem-ph" }, { "text": "Self-consistent double-hybrid density-functional theory using the\n optimized-effective-potential method: We introduce an orbital-optimized double-hybrid (DH) scheme using the\noptimized-effective-potential (OEP) method. The orbitals are optimized using a\nlocal potential corresponding to the complete exchange-correlation energy\nexpression including the second-order M{{\\o}}ller-Plesset (MP2) correlation\ncontribution. We have implemented a one-parameter version of this OEP-based\nself-consistent DH scheme using the BLYP density-functional approximation and\ncompared it to the corresponding non-self-consistent DH scheme for calculations\non a few closed-shell atoms and molecules. While the OEP-based self-consistency\ndoes not provide any improvement for the calculations of ground-state total\nenergies and ionization potentials, it does improve the accuracy of electron\naffinities and restores the meaning of the LUMO orbital energy as being\nconnected to a neutral excitation energy. Moreover, the OEP-based\nself-consistent DH scheme provides reasonably accurate exchange-correlation\npotentials and correlated densities.", "category": "physics_chem-ph" }, { "text": "A missing high-spin molecule in the family of cyano-bridged heptanuclear\n heterometal complexes, [(LCuII)6FeIII(CN)6]3+, and its CoIII and CrIII\n analogues, accompanied in the crystal by a novel octameric water cluster: Three isostructural cyano-bridged heptanuclear complexes,\n[{CuII(saldmen)(H2O)}6{MIII(CN)6}](ClO4)3$\\cdotp$8H2O (M = FeIII 2; CoIII, 3;\nCrIII 4), have been obtained by reacting the binuclear copper(II) complex,\n[Cu2(saldmen)2(mu-H2O)(H2O)2](ClO4)2$\\cdotp$2H2O 1, with K3[Co(CN)6],\nK4[Fe(CN)6], and, respectively, K3[Cr(CN)6] (Hsaldmen is the Schiff base\nresulted from the condensation of salicylaldehyde with\nN,N-dimethylethylenediamine). A unique octameric water cluster, with\nbicyclo[2,2,2]octane-like structure, is sandwiched between the heptanuclear\ncations in 2, 3 and 4. The cryomagnetic investigations of compounds 2 and 4\nreveal ferromagnetic couplings of the central FeIII or CrIII ions with the CuII\nions (JCuFe = +0.87 cm-1, JCuCr = +30.4 cm-1). The intramolecular Cu-Cu\nexchange interaction in 3, across the diamagnetic cobalt(III) ion, is -0.3\ncm-1. The solid-state1H-NMR spectra of compounds 2 and 3 have been\ninvestigated.", "category": "physics_chem-ph" }, { "text": "Rate of Convergence of Phase Field Equations in Strongly Heterogeneous\n Media towards their Homogenized Limit: We study phase field equations based on the diffuse-interface approximation\nof general homogeneous free energy densities showing different local minima of\npossible equilibrium configurations in perforated/porous domains. The study of\nsuch free energies in homogeneous environments found a broad interest over the\nlast decades and hence is now widely accepted and applied in both science and\nengineering. Here, we focus on strongly heterogeneous materials with\nperforations such as porous media. To the best of our knowledge, we present a\ngeneral formal derivation of upscaled phase field equations for arbitrary free\nenergy densities and give a rigorous justification by error estimates for a\nbroad class of polynomial free energies. The error between the effective\nmacroscopic solution of the new upscaled formulation and the solution of the\nmicroscopic phase field problem is of order $\\epsilon^1/2$ for a material given\ncharacteristic heterogeneity $\\epsilon$. Our new, effective, and reliable\nmacroscopic porous media formulation of general phase field equations opens new\nmodelling directions and computational perspectives for interfacial transport\nin strongly heterogeneous environments.", "category": "physics_chem-ph" }, { "text": "Critical analysis of data concerning Saccharomyces cerevisiae free-cell\n proliferations and fermentations assisted by magnetic and electromagnetic\n fields: The review analyses studies on magnetically assisted proliferations and batch\nfermentations with Saccharomyces cerevisiae yeasts. The results available in\nthe literature are contradictory and show two tendencies: magnetic field\nsuppression of the cell growth and positive effects in batch fermentation with\nincreasing both biomass and metabolite production. The amount of data analyzed\nallows several concepts existing in the literature to be outlined and\ncritically commented. Further, a new concept of magnetically induced\nmicro-dynamos, recently conceived, is developed towards a unified explanation\nof the results provided by proliferation and batch fermentation experiments", "category": "physics_chem-ph" }, { "text": "Reactive Vortexes in a Naturally Activated Process: Non-Diffusive\n Rotational Fluxes at Transition State Uncovered by Persistent Homology: Dynamics of reaction coordinates during barrier-crossing are key to\nunderstand activated processes in complex systems such as proteins. The default\nassumption from Kramers physical intuition is that of a diffusion process.\nHowever, the dynamics of barrier-crossing in natural complex molecules are\nlargely unexplored. Here we investigate the transition dynamics of\nalanine-dipeptide isomerization, the simplest complex system with a large\nnumber of non-reaction coordinates that can serve as an adequate thermal bath\nfeeding energy into the reaction coordinates. We separate conformations along\nthe time axis and construct the dynamic probability surface of reaction. We\nquantify its topological structure and rotational flux using persistent\nhomology and differential form. Our results uncovered a region with strong\nreactive vortex in the configuration-time space, where the highest probability\npeak and the transition state ensemble are located. This reactive region\ncontains strong rotational fluxes: Most reactive trajectories swirl multiple\ntimes around this region in the subspace of the two most-important reaction\ncoordinates. Furthermore, the rotational fluxes result from cooperative\nmovement along the isocommitter surfaces and orthogonal barrier-crossing.\nOverall, our findings offer a first glimpse into the reactive vortex regions\nthat characterize the non-diffusive dynamics of barrier-crossing of a naturally\noccurring activation process.", "category": "physics_chem-ph" }, { "text": "Systematically Improvable Generalization of Self-Interaction Corrected\n Density Functional Theory: Perdew-Zunger self-interaction correction (PZSIC) reintroduces an exact\nconstraint to approximate density functional theory (DFT), but can\nparadoxically degrade performance and is not systematically improvable. We use\nthe Adiabatic Projection formalism to derive PZSIC in terms of a reference\nsystem experiencing only electron self-interaction. Generalization introduces\ncorrelation into the reference system, systematically bridging from PZSIC to\nexact wavefunction theory. Minimal active spaces resolve the PZSIC paradox,\naccurately treating near-equilibrium and strongly-correlated systems.", "category": "physics_chem-ph" }, { "text": "Singlet-Triplet Energy Gaps of Organic Biradicals and Polyacenes with\n Auxiliary-Field Quantum Monte Carlo: The energy gap between the lowest-lying singlet and triplet states is an\nimportant quantity in chemical photocatalysis, with relevant applications\nranging from triplet fusion in optical upconversion to the design of organic\nlight-emitting devices. The ab initio prediction of singlet-triplet (ST) gaps\nis challenging due to the potentially biradical nature of the involved states,\ncombined with the potentially large size of relevant molecules. In this work,\nwe show that phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) can\naccurately predict ST gaps for chemical systems with singlet states of highly\nbiradical nature, including a set of 13 small molecules and the ortho-, meta-,\nand para-isomers of benzyne. With respect to gas-phase experiments, ph-AFQMC\nusing CASSCF trial wavefunctions achieves a mean averaged error of ~1 kcal/mol.\nFurthermore, we find that in the context of a spin-projection technique,\nph-AFQMC using unrestricted single-determinant trial wavefunctions, which can\nbe readily obtained for even very large systems, produces equivalently high\naccuracy. We proceed to show that this scalable methodology is capable of\nyielding accurate ST gaps for all linear polyacenes for which experimental\nmeasurements exist, i.e. naphthalene, anthracene, tetracene, and pentacene. Our\nresults suggest a protocol for selecting either unrestricted Hartree-Fock or\nKohn-Sham orbitals for the single-determinant trial wavefunction, based on the\nextent of spin-contamination. These findings pave the way for future\ninvestigations of specific photochemical processes involving large molecules\nwith substantial biradical character.", "category": "physics_chem-ph" }, { "text": "Observation and calculation of the quasi-bound rovibrational levels of\n the electronic ground state of H$_2^+$: Although the existence of quasi-bound rotational levels of the $X^+ \\\n^2\\Sigma_g^+$ ground state of H$_2^+$ has been predicted a long time ago, these\nstates have never been observed. Calculated positions and widths of quasi-bound\nrotational levels located close to the top of the centrifugal barriers have not\nbeen reported either. Given the role that such states play in the recombination\nof H(1s) and H$^+$ to form H$_2^+$, this lack of data may be regarded as one of\nthe largest unknown aspects of this otherwise accurately known fundamental\nmolecular cation. We present measurements of the positions and widths of the\nlowest-lying quasi-bound rotational levels of H$_2^+$ and compare the\nexperimental results with the positions and widths we calculate using a\npotential model for the $X^+$ state of H$_2^+$ which includes adiabatic,\nnonadiabatic, relativistic and radiative corrections to the Born-Oppenheimer\napproximation.", "category": "physics_chem-ph" }, { "text": "Implicit Transfer Operator Learning: Multiple Time-Resolution Surrogates\n for Molecular Dynamics: Computing properties of molecular systems rely on estimating expectations of\nthe (unnormalized) Boltzmann distribution. Molecular dynamics (MD) is a broadly\nadopted technique to approximate such quantities. However, stable simulations\nrely on very small integration time-steps ($10^{-15}\\,\\mathrm{s}$), whereas\nconvergence of some moments, e.g. binding free energy or rates, might rely on\nsampling processes on time-scales as long as $10^{-1}\\, \\mathrm{s}$, and these\nsimulations must be repeated for every molecular system independently. Here, we\npresent Implict Transfer Operator (ITO) Learning, a framework to learn\nsurrogates of the simulation process with multiple time-resolutions. We\nimplement ITO with denoising diffusion probabilistic models with a new SE(3)\nequivariant architecture and show the resulting models can generate\nself-consistent stochastic dynamics across multiple time-scales, even when the\nsystem is only partially observed. Finally, we present a coarse-grained\nCG-SE3-ITO model which can quantitatively model all-atom molecular dynamics\nusing only coarse molecular representations. As such, ITO provides an important\nstep towards multiple time- and space-resolution acceleration of MD. Code is\navailable at\n\\href{https://github.com/olsson-group/ito}{https://github.com/olsson-group/ito}.", "category": "physics_chem-ph" }, { "text": "Applying Monte Carlo configuration interaction to transition metal\n dimers: exploring the balance between static and dynamic correlation: We calculate potential curves for transition metal dimers using Monte Carlo\nconfiguration interaction (MCCI). These results, and their associated\nspectroscopic values, are compared with experimental and computational studies.\nThe multireference nature of the MCCI wavefunction is quantified and we\nestimate the important orbitals. We initially consider the ground state of the\nchromium dimer. Next we calculate potential curves for Sc$_{2}$ where we\ncontrast the lowest triplet and quintet states. We look at the molybdenum dimer\nwhere we compare non-relativistic results with the partial inclusion of\nrelativistic effects via effective core potentials, and report results for\nscandium nickel.", "category": "physics_chem-ph" }, { "text": "Compound-tunable embedding potential method and its application to\n ytterbium fluoride crystals YbF$_2$ and YbF$_3$: Compound-tunable embedding potential (CTEP) method developed in previous\nworks to describe electronic structure of fragments in materials is applied to\ncrystals containing periodically arranged lanthanide atoms, which can have open\n$4f$ shell. We consider YbF$_2$ and YbF$_3$ as examples such that $4f$ shell is\nexcluded from both the crystal and cluster stages of generating the CTEP.\nInstead, 10 and 11 valence-electron pseudopotentials for Yb, correspondingly,\nare applied and the latter treats the $4f$-hole implicitly. At the next stage\nof the two-component embedded cluster studies of the YbF$_{2,3}$ crystals we\napply the 42 valence-electron relativistic pseudopotential for Yb and, thus,\n$4f$ shell is treated explicitly. A remarkable agreement of the electronic\ndensity and interatomic distances within the fragment with those of the\noriginal periodic crystal calculation is attained.", "category": "physics_chem-ph" }, { "text": "Time-Resolved Probing of the Nonequilibrium Structural Solvation\n Dynamics by the Time-Dependent Stokes Shift: The time-dependent fluorescence Stokes shifts monitors the relaxation of the\npolarization of a polar solvent in the surroundings of a photoexcited solute\nmolecule, but also the structural variation of the solute following\nphotoexcitation and the subsequent molecular charge redistribution. Here, we\nformulate a simple nonequilibrium quantum theory of solvation for an explicitly\ntime-dependent continuous solvent. The time-dependent solvent induces\nnonequilibrium fluctuations on the solvent dynamics which are directly\nreflected in different time components in the time-dependent Stokes shift. We\nillustrate the structural dynamics in the presence of an explicitly\ntime-dependent solvent by the example of a dynamically shrinking solute which\nleads to a bi-modal Stokes shift. Interestingly, both contributions are\nmutually coupled. Furthermore, we can explain a prominent long-tail decay of\nthe Stokes shift associated to slow structural dynamical variations.", "category": "physics_chem-ph" }, { "text": "Deep diving into the comparative study of Choline dynamics using\n molecular dynamics simulation and neutron scattering technique: We present here the comparative study between the dynamics Choline and\nTetra-methyl ammonium bromide. This is well known that deficiency in Choline\nwould cause many severe diseases. No wonder why Choline is crucial component\nfor our nutrients and dietary requirements. We present here a comprehensive\nstudy using all-atom molecular dynamics simulation combined with neutron\nscattering technique for solute behavior in aqueous solution. The solvent\nbehavior is discussed in the follow up work", "category": "physics_chem-ph" }, { "text": "Using CIPSI nodes in diffusion Monte Carlo: Several aspects of the recently proposed DMC-CIPSI approach consisting in\nusing selected Configuration Interaction (SCI) approaches such as CIPSI\n(Configuration Interaction using a Perturbative Selection done Iteratively) to\nbuild accurate nodes for diffusion Monte Carlo (DMC) calculations are presented\nand discussed. The main ideas are illustrated with a number of calculations for\ndiatomics molecules and for the benchmark G1 set.", "category": "physics_chem-ph" }, { "text": "Calculation of the Critical Temperature for 2- and 3-Dimensional Ising\n Models and for 2-Dimensional Potts Models Using the Transfer Matrix Method: A new graphical method is developed to calculate the critical temperature of\n2- and 3-dimensional Ising models as well as that of the 2-dimensional Potts\nmodels. This method is based on the transfer matrix method and using the\nlimited lattice for the calculation. The reduced internal energy per site has\nbeen accurately calculated for different 2-D Ising and Potts models using\ndifferent size-limited lattices. All calculated energies intersect at a single\npoint when plotted versus the reduced temperature. The reduced temperature at\nthe intersection is 0.4407, 0.2746, and 0.6585 for the square, triangular, and\nhoneycombs Ising lattices and 1.0050, 0.6309, and 1.4848 for the square,\ntriangular, and honeycombs Potts lattices, respectively. These values are\nexactly the same as the critical temperatures reported in the literature,\nexcept for the honeycomb Potts lattice. For the two-dimensional Ising model, we\nhave shown that the existence of such an intersection point is due to the\nduality relation. The method is then extended to the simple cubic Ising model,\nin which the intersection point is found to be dependent on the lattice sizes.\nWe have found a linear relation between the lattice size and the intersection\npoint. This relation is used to obtain the critical temperature of the\nunlimited simple cubic lattice. The obtained result, 0.221(2), is in a good\nagreement with the accurate value of 0.22165 reported by others.", "category": "physics_chem-ph" }, { "text": "NewtonNet: A Newtonian message passing network for deep learning of\n interatomic potentials and forces: We report a new deep learning message passing network that takes inspiration\nfrom Newton's equations of motion to learn interatomic potentials and forces.\nWith the advantage of directional information from trainable latent force\nvectors, and physics-infused operators that are inspired by the Newtonian\nphysics, the entire model remains rotationally equivariant, and many-body\ninteractions are inferred by more interpretable physical features. We test\nNewtonNet on the prediction of several reactive and non-reactive high quality\nab initio data sets including single small molecule dynamics, a large set of\nchemically diverse molecules, and methane and hydrogen combustion reactions,\nachieving state-of-the-art test performance on energies and forces with far\ngreater data and computational efficiency than other deep learning models.", "category": "physics_chem-ph" }, { "text": "Critical role of quantum dynamical effects in the Raman spectroscopy of\n liquid water: Understanding the Raman spectroscopy at the atomistic level is important for\nthe elucidation of dynamical processes in liquid water. Because the\npolarizability (or its time derivative) is often a highly nonlinear function of\ncoordinates or/and momenta, we employ the linearized semiclassical initial\nvalue representation for quantum dynamical simulations of liquid water (and\nheavy water) under ambient conditions based on an ab initio based, flexible,\npolarizable model (the POLI2VS force field). It is shown that quantum dynamical\neffects play a critical role in reproducing the peaks in the intermediate\nregion between the librational and bending bands, those between the bending and\nstretching bands, and the double-peak in the stretching band in the\nexperimental isotropic Raman spectrum. In contrast, quantum dynamical effects\nare important but less decisive in the anisotropic Raman spectrum. By\nselectively freezing either the intramolecular O-H stretching or H-O-H bending\nmode, we demonstrate that the peak in the intermediate region (2000-2400 cm-1)\nof the isotropic Raman spectrum arises from the interplay of the stretching and\nbending motions while a substantial part of the peak in the same intermediate\nregion of the anisotropic Raman spectrum may be attributed to the combined\nmotion of the bending and librational modes.", "category": "physics_chem-ph" }, { "text": "Towards numerically robust multireference theories: The driven\n similarity renormalization group truncated to one- and two-body operators: The first nonperturbative version of the multireference driven similarity\nrenormalization group (MR-DSRG) theory [C. Li and F. A. Evangelista, J. Chem.\nTheory Comput. $\\mathbf{11}$, 2097 (2015)] is introduced. The renormalization\ngroup structure of the MR-DSRG equations ensures numerical robustness and\navoidance of the intruder state problem, while the connected nature of the\namplitude and energy equations guarantees size consistency and extensivity. We\napproximate the MR-DSRG equations by keeping only one- and two-body operators\nand using a linearized recursive commutator approximation of the\nBaker--Campbell--Hausdorff expansion [T. Yanai and G. K.-L. Chan, J. Chem.\nPhys. $\\mathbf{124}$, 194106 (2006)]. The resulting MR-LDSRG(2) equations\ncontain only 39 terms and scales as ${\\cal O}(N^2 N_{\\rm P}^2 N_{\\rm H}^2)$\nwhere $N_{\\rm H}$, $N_{\\rm P}$, and $N$ correspond to the number of hole,\nparticle, and total orbitals, respectively. Benchmark MR-LDSRG(2) computations\non the hydrogen fluoride and molecular nitrogen binding curves and the\nsinglet-triplet splitting of $p$-benzyne yield results comparable in accuracy\nto those from multireference configuration interaction, Mukherjee\nmultireference coupled cluster theory, and internally-contracted multireference\ncoupled cluster theory.", "category": "physics_chem-ph" }, { "text": "Molecular librations in a liquid investigated by ultrafast optical Kerr\n effect spectroscopy: We propose a detail theoretical approach modeling molecular librations in\nliquid investigated by ultrafast optically heterodyne detected optical Kerr\neffect (OHD-OKE). The approach has been applied for fluoroform molecular liquid\nand new information about spectrum, relaxation time and time domain librations\nhas been obtained.", "category": "physics_chem-ph" }, { "text": "Small Open Chemical Systems Theory and Its Implications to Darwinian\n Evolutionary Dynamics, Complex Self-Organization and Beyond: The study of biological cells in terms of mesoscopic, nonequilibrium,\nnonlinear, stochastic dynamics of open chemical systems provides a paradigm for\nother complex, self-organizing systems with ultra-fast stochastic fluctuations,\nshort-time deterministic nonlinear dynamics, and long-time evolutionary\nbehavior with exponentially distributed rare events, discrete jumps among\npunctuated equilibria, and catastrophe.", "category": "physics_chem-ph" }, { "text": "Relaxation and fluctuation dynamics in coherent two-dimensional\n electronic spectra: Two-dimensional (2D) spectroscopy provides information about dissipative\nprocesses subsequent to electronic excitation, which play a functional role in\nenergy harvesting materials and devices. This technique is particularly\nsensitive to electronic and vibronic coherence dynamics. While the theoretical\ntreatment of relaxation in the context of 2D-spectroscopy is well-developed\nunder the assumption of different timescales of population transfer and\nfluctuation dynamics, the interplay between both kinds of processes lacks a\ncomprehensive description in terms of line shape functions. To bridge this gap,\nwe use the cumulant expansion approach to derive response functions, which\naccount for fluctuation dynamics and population transfer simultaneously. We\ncompare 2D-spectra from calculations with different model assumptions about\ncorrelations between fluctuations and point out under which conditions a\nsimplified treatment is justified. Our study shows that population transfer and\ndissipative fluctuation dynamics cannot be described independent of each other\nin general. Advantages and limitations of the proposed calculation method and\nits compatibility with the modified Redfield description are discussed.", "category": "physics_chem-ph" }, { "text": "Accurate transport cross sections for the Lennard-Jones potential: Physically motivated expressions for the transport cross sections describing\nclassical scattering in the Lennard-Jones potential are proposed. These\nexpressions, which agree with the numerical results better than to within $\\pm\n1%$, can be easy implemented in practical situations. Some relevant examples\nare provided.", "category": "physics_chem-ph" }, { "text": "Direct Base-to-Base Transitions in ssDNA Revealed by Tip-Enhanced Raman\n Scattering: In the present contribution, specifically designed single-stranded DNA\n(ssDNA) sequences composed of adenine and cytosine were used as nanometric\nrulers to target the maximum achievable spatial resolution of tip-enhanced\nRaman spectroscopy (TERS) under ambient conditions. By stepping along a strand\nwith a TERS tip, the obtained spectra allowed for a clear spectral\ndiscrimination including conformational information of the nucleobases, and\neven sharp adenine-cytosine transitions were detected repeatedly with a spatial\nresolution below 1 nm.", "category": "physics_chem-ph" }, { "text": "Improved CPS and CBS Extrapolation of PNO-CCSD(T) Energies: The MOBH35\n and ISOL24 Data Sets: Computation of heats of reaction of large molecules is now feasible using\ndomain-based PNO-CCSD(T) theory. However, to obtain agreement within 1~kcal/mol\nof experiment, it is necessary to eliminate basis set incompleteness error,\nwhich comprises of both the AO basis set error and the PNO truncation error.\nOur investigation into the convergence to the canonical limit of PNO-CCSD(T)\nenergies with PNO truncation threshold $T$ shows that errors follow the model\n$E(T) = E + A T^{1/2}$. Therefore, PNO truncation errors can be eliminated\nusing a simple two-point CPS extrapolation to the canonical limit, so that\nsubsequent CBS extrapolation is not limited by residual PNO truncation error.\nUsing the ISOL24 and MOBH35 data sets, we find that PNO truncation errors are\nlarger for molecules with significant static correlation, and that it is\nnecessary to use very tight thresholds of $T=10^{-8}$ to ensure errors do not\nexceed 1~kcal/mol. We present a lower-cost extrapolation scheme that uses\ninformation from small basis sets to estimate PNO truncation errors for larger\nbasis sets. In this way the canonical limit of CCSD(T) calculations on large\nmolecules with large basis sets can be reliably estimated in a practical way.\nUsing this approach, we report complete basis set limit CCSD(T) reaction\nenergies for the full ISOL24 and MOBH35 data sets.", "category": "physics_chem-ph" }, { "text": "Electronic Properties of Cyclacenes from TAO-DFT: Owing to the presence of strong static correlation effects, accurate\nprediction of the electronic properties (e.g., the singlet-triplet energy gaps,\nvertical ionization potentials, vertical electron affinities, fundamental gaps,\nsymmetrized von Neumann entropy, active orbital occupation numbers, and\nreal-space representation of active orbitals) of cyclacenes with n fused\nbenzene rings (n = 4-100) has posed a great challenge to traditional electronic\nstructure methods. To meet the challenge, we study these properties using our\nnewly developed thermally-assisted-occupation density functional theory\n(TAO-DFT), a very efficient method for the study of large systems with strong\nstatic correlation effects. Besides, to examine the role of cyclic topology,\nthe electronic properties of cyclacenes are also compared with those of acenes.\nSimilar to acenes, the ground states of cyclacenes are singlets for all the\ncases studied. In contrast to acenes, the electronic properties of cyclacenes,\nhowever, exhibit oscillatory behavior (for n <= 30) in the approach to the\ncorresponding properties of acenes with increasing number of benzene rings. On\nthe basis of the calculated orbitals and their occupation numbers, the larger\ncyclacenes are shown to exhibit increasing polyradical character in their\nground states, with the active orbitals being mainly localized at the\nperipheral carbon atoms.", "category": "physics_chem-ph" }, { "text": "Photon-blockade induced photon anti-bunching in photosynthetic Antennas\n with cyclic structures: One of the important nonclassical effects in quantum optics is the\nanti-bunching, which has been observed in a large class of physical systems -\nincluding light-harvesting antennas with cyclic structures. The units of the\nring couple with adjacent ones through dipole-dipole interactions. We show how\nthis strong dipole-dipole interaction leads to photon-blockade resulting in the\nsuppression of double excitation pathway and anti-bunching in photosynthesis\nsystems. The robustness of the photon blockade is demonstrated against the\ndisorder in the ring structures. We hypothesis that the effect may be utilized\nby light-harvesting systems to avoid damages from excess energy.", "category": "physics_chem-ph" }, { "text": "Electron transfer theory revisit: Quantum solvation effect: The effect of solvation on the electron transfer (ET) rate processes is\ninvestigated on the basis of the exact theory constructed in J. Phys. Chem. B\nVol. 110, (2006); quant-ph/0604071. The nature of solvation is studied in a\nclose relation with the mechanism of ET processes. The resulting Kramers'\nturnover and Marcus' inversion characteristics are analyzed accordingly. The\nclassical picture of solvation is found to be invalid when the solvent\nlongitudinal relaxation time is short compared with the inverse temperature.", "category": "physics_chem-ph" }, { "text": "Photoelectron and fragmentation dynamics of the H$^{+}$ + H$^{+}$\n dissociative channel in NH$_3$ following direct single-photon double\n ionization: We report measurements on the H$^{+}$ + H$^{+}$ fragmentation channel\nfollowing direct single-photon double ionization of neutral NH$_{3}$ at 61.5\neV, where the two photoelectrons and two protons are measured in coincidence\nusing 3-D momentum imaging. We identify four dication electronic states that\ncontribute to H$^{+}$ + H$^{+}$ dissociation, based on our multireference\nconfiguration-interaction calculations of the dication potential energy\nsurfaces. The extracted branching ratios between these four dication electronic\nstates are presented. Of the four dication electronic states, three dissociate\nin a concerted process, while the fourth undergoes a sequential fragmentation\nmechanism. We find evidence that the neutral NH fragment or intermediate NH$^+$\nion is markedly ro-vibrationally excited. We also identify differences in the\nrelative emission angle between the two photoelectrons as a function of their\nenergy sharing for the four different dication states, which bare some\nsimilarities to previous observations made on atomic targets.", "category": "physics_chem-ph" }, { "text": "Nanotechnology for biosensors: A Review: Biosensors are essential tools which have been traditionally used to monitor\nenvironmental pollution, detect the presence of toxic elements and biohazardous\nbacteria or virus in organic matter and biomolecules for clinical diagnostics.\nIn the last couple of decades, the scientific community has witnessed their\nwidespread application in the fields of military, health care, industrial\nprocess control, environmental monitoring, food-quality control, and\nmicrobiology. Biosensor technology has greatly evolved from the in vitro\nstudies based on the biosensing ability of organic beings to the highly\nsophisticated world of nanofabrication enabled miniaturized biosensors. The\nincorporation of nanotechnology in the vast field of biosensing has led to the\ndevelopment of novel sensors and sensing mechanisms, as well as an increase in\nthe sensitivity and performance of the existing biosensors. Additionally, the\nnanoscale dimension further assists the development of sensors for rapid and\nsimple detection in vivo as well as the ability to probe single-biomolecules\nand obtain critical information for their detection and analysis. However, the\nmajor drawbacks of this include, but are not limited to potential toxicities\nassociated with the unavoidable release of nanoparticles into the environment,\nminiaturization induced unreliability, lack of automation, and difficulty of\nintegrating the nanostructured-based biosensors as well as unreliable\ntransduction signals from these devices. Although the field of biosensors is\nvast, we intend to explore various nanotechnology enabled biosensors as part of\nthis review article and provide a brief description of their fundamental\nworking principles and potential applications.", "category": "physics_chem-ph" }, { "text": "Quantum Nuclei at Weakly Bonded Interfaces: The Case of Cyclohexane on\n Rh(111): The electronic properties of interfaces can depend on their isotopic\nconstitution. One known case is that of cyclohexane physisorbed on Rh(111), in\nwhich isotope effects have been measured on the work function change and\ndesorption energies. These effects can only be captured by calculations\nincluding nuclear quantum effects (NQE). In this paper, this interface is\naddressed employing dispersion-inclusive density-functional theory coupled to a\nquasi-harmonic (QH) approximation for NQE, as well as to fully anharmonic ab\ninitio path integral molecular dynamics (PIMD). The QH approximation is able to\ncapture that deuterated cyclohexane has a smaller adsorption energy and lies\nabout 0.01 A farther from the Rh(111) surface than its isotopologue, which can\nbe correlated to the isotope effect in the work function change. An\ninvestigation of the validity of the QH approximation relying on PIMD\nsimulations, leads to the conclusion that although this interface is highly\nimpacted by anharmonic quantum fluctuations in the molecular layer and at\nbonding sites, these anharmonic contributions play a minor role when analysing\nisotope effects at low temperatures. Nevertheless, anharmonic quantum\nfluctuations cause an increase in the distance between the molecular layer and\nRh(111), a consequent smaller overall work function change, and intricate\nchanges in orbital hybridization.", "category": "physics_chem-ph" }, { "text": "A perturbative solution to metadynamics ordinary differential equation: Metadynamics is a popular enhanced sampling scheme wherein by periodic\napplication of a repulsive bias, one can surmount high free energy barriers and\nexplore complex landscapes. Recently metadynamics was shown to be\nmathematically well founded, in the sense that the biasing procedure is\nguaranteed to converge to the true free energy surface in the long time limit\nirrespective of the precise choice of biasing parameters. A differential\nequation governing the post-transient convergence behavior of metadynamics was\nalso derived. In this short communication, we revisit this differential\nequation, expressing it in a convenient and elegant Riccati-like form. A\nperturbative solution scheme is then developed for solving this differential\nequation, which is valid for any generic biasing kernel. The solution clearly\ndemonstrates the robustness of metadynamics to choice of biasing parameters and\ngives further confidence in the widely used method.", "category": "physics_chem-ph" }, { "text": "Linear-response range-separated density-functional theory for atomic\n photoexcitation and photoionization spectra: We investigate the performance of the range-separated hybrid (RSH) scheme,\nwhich combines long-range Hartree-Fock (HF) and a short-range\ndensity-functional approximation (DFA), for calculating\nphotoexcitation/photoionization spectra of the H and He atoms, using a B-spline\nbasis set in order to correctly describe the continuum part of the spectra. The\nstudy of these simple systems allows us to quantify the influence on the\nspectra of the errors coming from the short-range exchange-correlation DFA and\nfrom the missing long-range correlation in the RSH scheme. We study the\ndifferences between using the long-range HF exchange (nonlocal) potential and\nthe long-range exact exchange (local) potential. Contrary to the former, the\nlatter supports a series of Rydberg states and gives reasonable\nphotoexcitation/photoionization spectra, even without applying linear-response\ntheory. The most accurate spectra are obtained with the linear-response\ntime-dependent range-separated hybrid (TDRSH) scheme. In particular, for the He\natom at the optimal value of the range-separation parameter, TDRSH gives\nslightly more accurate photoexcitation and photoioniza-tion spectra than\nstandard linear-response time-dependent HF. More generally, the present work\nshows the potential of range-separated density-functional theory for\ncalculating linear and nonlinear optical properties involving continuum states.", "category": "physics_chem-ph" }, { "text": "Extension of the Trotterized Unitary Coupled Cluster to Triple\n Excitations: The Trotterized Unitary Coupled Cluster Single and Double (UCCSD) ansatz has\nrecently attracted interest due to its use in Variation Quantum Eigensolver\n(VQE) molecular simulations on quantum computers. However, when the size of\nmolecules increases, UCCSD becomes less interesting as it cannot achieve\nsufficient accuracy. Including higher-order excitations is therefore mandatory\nto recover the UCC's missing correlation effects. In this Letter, we extend the\nTrotterized UCC approach via the addition of (true) Triple T excitations\nintroducing UCCSDT. We also include both spin and orbital symmetries. Indeed,\nin practice, these later help to reduce unnecessarily circuit excitations and\nthus accelerate the optimization process enabling to tackle larger molecules.\nOur initial numerical tests (12-14 qubits) show that UCCSDT improves the\noverall accuracy by at least two-orders of magnitudes with respect to standard\nUCCSD. Overall, the UCCSDT ansatz is shown to reach chemical accuracy and to be\ncompetitive with the CCSD(T) gold-standard classical method of quantum\nchemistry.", "category": "physics_chem-ph" }, { "text": "Doublet-triplet energy transfer dominated photon upconversion: Stable luminescent pi-radicals with doublet emission have aroused a growing\ninterest for functional molecular materials. We have demonstrated a neutral\npi-radical dye\n(4-N-carbazolyl-2,6-dichlorophenyl)bis(2,4,6-trichlorophenyl)-methyl (TTM-1Cz)\nwith remarkable doublet emission, which could be used as triplet sensitizer to\ninitiate the photophysical process of triplet-triplet annihilation photon\nupconversion (TTA-UC). Dexter-like excited doublet-triplet energy transfer\n(DTET) was confirmed by theoretical calculation. A mixed solution of TTM-1Cz\nand aromatic emitters could ambidextrous upconvert red light to cyan light or\ngreen light = 532 nm) to blue light. This finding of DTET phenomena provides a\nnew perspective in designing new triplet sensitizer for TTA-UC.", "category": "physics_chem-ph" }, { "text": "Machine Learning Approaches to Learn HyChem Models: The HyChem approach has recently been proposed for modeling high-temperature\ncombustion of real, multi-component fuels. The approach combines lumped\nreaction steps for fuel thermal and oxidative pyrolysis with detailed chemistry\nfor the oxidation of the resulting pyrolysis products. However, the approach\nusually shows substantial discrepancies with experimental data within the\nNegative Temperature Coefficient (NTC) regime, as the low-temperature chemistry\nis more fuel-specific than high-temperature chemistry. This paper proposes a\nmachine learning approach to learn the HyChem models that can cover both\nhigh-temperature and low-temperature regimes. Specifically, we develop a HyChem\nmodel using the experimental datasets of ignition delay times covering a wide\nrange of temperatures and equivalence ratios. The chemical kinetic model is\ntreated as a neural network model, and we then employ stochastic gradient\ndescent (SGD), a technique that was developed for deep learning, for the\ntraining. We demonstrate the approach in learning the HyChem model for F-24,\nwhich is a Jet-A derived fuel, and compare the results with previous work\nemploying genetic algorithms. The results show that the SGD approach can\nachieve comparable model performance with genetic algorithms but the\ncomputational cost is reduced by 1000 times. In addition, with regularization\nin SGD, the SGD approach changes the kinetic parameters from their original\nvalues much less than genetic algorithm and is thus more likely to retrain\nmechanistic meanings. Finally, our approach is built upon open-source packages\nand can be applied to the development and optimization of chemical kinetic\nmodels for internal combustion engine simulations.", "category": "physics_chem-ph" }, { "text": "Bridging the Physics and Chemistry of graphene. From Huckel aromaticity\n to Dirac cones and topological insulators: By bridging graphene and benzene through a well-defined sequence of\npolycyclic aromatic hydrocarbons and their inherent shell structure, J. Phys.\nChem. C, 2018, 122, 17526, it is shown that graphene is actually a coherent\narrangement of interwoven benzene molecules, which are coordinated by\naromaticity, shell structure and topology, all interrelated. The exotic\nproperties of graphene are in fact macroscopic manifestations of aromaticity.\nAt the molecular level this is revealed as a dynamical flipping of the atomic\npz-orbitals belonging to different sublattices, leading to a dynamical\ninterchange between aromatic and non-aromatic rings, associated with frontier\noccupied-unoccupied orbitals or valence-conduction bands interchange with\nopposite parities, in full agreement with many-body and topological insulators\ntheory. Such dynamical interchange or coupling is driven by inversion\nsymmetry-breaking, activated through geometrical frustration between sublattice\nand space group symmetry. This, for rectangular nanographenes, in contrast to\nhexagonal, leads to topological gapless edge states, which, contrary to\nopposite claims, are not spin polarized.", "category": "physics_chem-ph" }, { "text": "Accurate reduced models for the pH oscillations in the urea-urease\n reaction confined to giant lipid vesicles: This theoretical study concerns a pH oscillator based on the urea-urease\nreaction confined to giant lipid vesicles. Under suitable conditions,\ndifferential transport of urea and hydrogen ion across the unilamellar vesicle\nmembrane periodically resets the pH clock that switches the system from acid to\nbasic, resulting in self-sustained oscillations. We analyse the structure of\nthe phase flow and of the limit cycle, which controls the dynamics for giant\nvesicles and dominates the pronouncedly stochastic oscillations in small\nvesicles of submicrometer size. To this end, we derive reduced models, which\nare amenable to analytic treatments that are complemented by numerical\nsolutions, and obtain the period and amplitude of the oscillations as well as\nthe parameter domain, where oscillatory behavior persists. We show that the\naccuracy of these predictions is highly sensitive to the employed reduction\nscheme. In particular, we suggest an accurate two-variable model and show its\nequivalence to a three-variable model that admits an interpretation in terms of\na chemical reaction network. The faithful modeling of a single pH oscillator\nappears crucial for rationalizing experiments and understanding communication\nof vesicles and synchronization of rhythms.", "category": "physics_chem-ph" }, { "text": "Bayesian Design of Experiments: Implementation, Validation and\n Application to Chemical Kinetics: Bayesian experimental design (BED) is a tool for guiding experiments founded\non the principle of expected information gain. I.e., which experiment design\nwill inform the most about the model can be predicted before experiments in a\nlaboratory are conducted. BED is also useful when specific physical questions\narise from the model which are answered from certain experiments but not from\nother experiments. BED can take two forms, and these two forms are expressed in\nthree example models in this work. The first example takes the form of a\nBayesian linear regression, but also this example is a benchmark for checking\nnumerical and analytical solutions. One of two parameters is an estimator of\nthe synthetic experimental data, and the BED task is choosing among which of\nthe two parameters to inform (limited experimental observability). The second\nexample is a chemical reaction model with a parameter space of informed\nreaction free energy and temperature. The temperature is an independent\nexperimental design variable explored for information gain. The second and\nthird examples are of the form of adjusting an independent variable in the\nexperimental setup. The third example is a catalytic membrane reactor similar\nto a plug-flow reactor. For this example, a grid search over the independent\nvariables, temperature and volume, for the greatest information gain is\nconducted. Also, maximum information gain is conducted is optimized with two\nalgorithms: the differential evolution algorithm and steepest ascent, both of\nwhich benefitted in terms of initial guess from the grid search.", "category": "physics_chem-ph" }, { "text": "Exciton dynamics from the mapping approach to surface hopping:\n Comparison with F\u00f6rster and Redfield theories: We compare the recently introduced multi-state mapping approach to surface\nhopping (MASH) with the F\\\"orster and Redfield theories of excitation energy\ntransfer. Whereas F\\\"orster theory relies on weak coupling between\nchromophores, and Redfield theory assumes the electronic excitations to be\nweakly coupled to fast chromophore vibrations, MASH is free from any\nperturbative or Markovian approximations. We illustrate this with an example\napplication to the rate of energy transfer in a Frenkel-exciton dimer, showing\nthat MASH interpolates correctly between the opposing regimes in which the\nF\\\"orster and Redfield results are reliable. We then compare the three methods\nfor a realistic model of the Fenna-Matthews-Olson complex with a structured\nvibrational spectral density and static disorder in the excitation energies. In\nthis case there are no exact results for comparison so we use MASH to assess\nthe validity of F\\\"orster and Redfield theories. We find that F\\\"orster theory\nis the more accurate of the two on the picosecond timescale, as has been shown\npreviously for a simpler model of this particular light-harvesting complex. We\nalso explore various ways to sample the initial electronic state in MASH and\nfind that they all give very similar results for exciton dynamics.", "category": "physics_chem-ph" }, { "text": "Analytic gradients for spin multiplets in natural orbital functional\n theory: Analytic energy gradients with respect to nuclear motion are derived for\nnon-singlet compounds in the natural orbital functional theory. We exploit the\nformulation for multiplets in order to obtain a simple formula valid for any\nmany-electron system in its ground mixed state with a total spin S and all\npossible spin projection Sz values. We demonstrate that the analytic gradients\ncan be obtained without resorting to linear response theory or involving\niterative procedures. It is required a single evaluation, so integral\nderivatives can be computed on-the-fly along the calculation and thus improve\nthe effectiveness of screening by the Schwarz inequality. Results for small and\nmedium size molecules with many spin multiplicities are shown. Our results are\ncompared with experimental data and accurate theoretical equilibrium\ngeometries.", "category": "physics_chem-ph" }, { "text": "Generating stable molecules using imitation and reinforcement learning: Chemical space is routinely explored by machine learning methods to discover\ninteresting molecules, before time-consuming experimental synthesizing is\nattempted. However, these methods often rely on a graph representation,\nignoring 3D information necessary for determining the stability of the\nmolecules. We propose a reinforcement learning approach for generating\nmolecules in cartesian coordinates allowing for quantum chemical prediction of\nthe stability. To improve sample-efficiency we learn basic chemical rules from\nimitation learning on the GDB-11 database to create an initial model applicable\nfor all stoichiometries. We then deploy multiple copies of the model\nconditioned on a specific stoichiometry in a reinforcement learning setting.\nThe models correctly identify low energy molecules in the database and produce\nnovel isomers not found in the training set. Finally, we apply the model to\nlarger molecules to show how reinforcement learning further refines the\nimitation learning model in domains far from the training data.", "category": "physics_chem-ph" }, { "text": "Diblock copolymers at a homopolymer-homopolymer-interface: a Monte Carlo\n simulation: The properties of diluted symmetric A-B diblock copolymers at the interface\nbetween A and B homopolymer phases are studied by means of Monte Carlo (MC)\nsimulations of the bond fluctuation model. We calculate segment density\nprofiles as well as orientational properties of segments, of A and B blocks,\nand of the whole chain. Our data support the picture of oriented ``dumbbells'',\nwhich consist of mildly perturbed A and B Gaussian coils. The results are\ncompared to a self consistent field theory (SCFT) for single copolymer chains\nat a homopolymer interface. We also discuss the number of interaction contacts\nbetween monomers, which provide a measure for the ``active surface'' of\ncopolymers or homopolymers close to the interface.", "category": "physics_chem-ph" }, { "text": "The MC-QTAIM analysis reveals an exotic bond in the coherently quantum\n superposed Malonaldehyde: The proton between the two oxygen atoms of the malonaldehyde molecule\nexperiences an effective double-well potential in which the proton wavefunction\nis delocalized between the two wells. Herein we employed the state-of-the-art\nmulti-component quantum theory of atoms in molecules partitioning scheme to\nobtain the molecular structure, i.e. atoms in molecules and bonding network,\nfrom the superposed ab initio wavefunctions of malonaldehyde. In contrast to\nthe familiar clamped-proton portrayal of malonaldehyde, in which the proton\nforms a hydrogen basin, for the superposed states the hydrogen basin disappears\nand two novel hybrid oxygen-hydrogen basins appear instead, with an even\ndistribution of the proton population between the two basins. The interaction\nbetween the hybrid basins is stabilizing thanks to an unprecedented mechanism.\nThis involves the stabilizing classical Coulomb interaction of the one-proton\ndensity in one of the basins with the one-electron density in the other basin.\nThis stabilizing mechanism yields a bond foreign to the known bonding modes in\nchemistry.", "category": "physics_chem-ph" }, { "text": "Electronic Structure of Manganese Phthalocyanine Modified via Potassium\n Intercalation: a Comprehensive Experimental Study: Potassium (K) intercalated manganese phthalocyanine (MnPc) reveals vast\nchanges of its electronic states close to the Fermi level. However, theoretical\nstudies are controversial regarding the electronic configuration. Here, MnPc\ndoped with K was studied by ultraviolet, X-ray, and inverse photoemission, as\nwell as near edge X-ray absorption fine structure spectroscopy. Upon K\nintercalation the Fermi level shifts toward the lowest unoccupied molecular\norbital filling it up with donated electrons with the appearance of an\nadditional feature in the energy region of the occupied states. The electronic\nbands are pinned 0.5 eV above and 0.4 eV below the Fermi level. The branching\nratio of the Mn L3 and L2 edges indicate an increase of the spin state.\nMoreover, the evolution of the Mn L and N K edges reveals strong hybridization\nbetween Mn 3d and N 2p states of MnPc and sheds light on the electron\noccupation in the ground and n-doped configurations.", "category": "physics_chem-ph" }, { "text": "Modeling interstellar amorphous solid water grains by tight-binding\n based methods: comparison between GFN-XTB and CCSD(T) results for water\n clusters: One believed path to Interstellar Complexes Organic Molecules (iCOMs)\nformation inside the Interstellar Medium (ISM) is through chemical\nrecombination at the surface of amorphous solid water (ASW) mantle covering the\nsilicate-based core of the interstellar grains. The study of these iCOMs\nformation and their binding energy to the ASW, using computational chemistry,\ndepends strongly on the ASW models used, as different models may exhibit sites\nwith different adsorbing features. ASW extended models are rare in the\nliterature because large sizes require very large computational resources when\nquantum mechanical methods based on DFT are used. To circumvent this problem,\nwe propose to use the newly developed GFN-xTB Semi-empirical Quantum Mechanical\n(SQM) methods from the Grimme's group. These methods are, at least, two orders\nof magnitude faster than conventional DFT, only require modest central memory,\nand in this paper we aim to benchmark their accuracy against rigorous and\nresource hungry quantum mechanical methods. We focused on 38 water structures\nstudied by MP2 and CCSD(T) approaches comparing energetic and structures with\nthree levels of GFN-xTB parametrization (GFN0, GFN1, GFN2) methods. The\nextremely good results obtained at the very cheap GFN-xTB level for both water\ncluster structures and energetic paved the way towards the modeling of very\nlarge AWS models of astrochemical interest.", "category": "physics_chem-ph" }, { "text": "Gaussian Process Model for Collision Dynamics of Complex Molecules: We show that a Gaussian Process model can be combined with a small number (of\norder 100) of scattering calculations to provide a multi-dimensional dependence\nof scattering observables on the experimentally controllable parameters such as\nthe collision energy or temperature) as well as the potential energy surface\n(PES) parameters. For the case of Ar - C$_6$H$_6$ collisions, we show that 200\nclassical trajectory calculations are sufficient to provide a 10-dimensional\nhypersurface, giving the dependence of the collision lifetimes on the collision\nenergy, internal temperature and 8 PES parameters. This can be used for solving\nthe inverse scattering problem, the efficient calculation of thermally averaged\nobservables, for reducing the error of the molecular dynamics calculations by\naveraging over the PES variations, and the analysis of the sensitivity of the\nobservables to individual parameters determining the PES.Trained by a\ncombination of classical and quantum calculations, the model provides an\naccurate description of the quantum scattering cross sections, even near\nscattering resonances.", "category": "physics_chem-ph" }, { "text": "New opportunities for ultrafast and highly enantio-sensitive imaging and\n control of chiral nuclear dynamics: towards enantio-selective attochemistry: The recently introduced synthetic chiral light [D. Ayuso et al, Nat. Photon.\n13, 866-871 (2019)] has opened up new opportunities for ultrafast and highly\nefficient imaging and control of chiral matter. Here we show that the giant\nenantio-sensitivity enabled by such light could be exploited to probe chiral\nnuclear rearrangements during chemical reactions in an highly enantio-sensitive\nmanner. Using a state-of-the-art implementation of time-dependent density\nfunctional theory, we explore how the nonlinear response of the prototypical\nchiral molecule H2O2 changes as a function of its dihedral angle, which defines\nits handedness. The macroscopic intensity emitted from randomly oriented\nmolecules at even harmonic frequencies (of the fundamental) depends strongly on\nthis nuclear coordinate. Because of the ultrafast nature of such nonlinear\ninteractions, the direct mapping between chiral dichroism and nuclear geometry\nprovides a way to probe chiral nuclear dynamics at their natural time scales.\nOur work paves the way for ultrafast and highly efficient imaging of\nenantio-sensitive dynamics in more complex chiral systems, including\nbiologically relevant molecules.", "category": "physics_chem-ph" }, { "text": "Time Evolution of ML-MCTDH Wavefunctions I: Gauge Conditions, Basis\n Functions, and Singularities: We derive a family of equations of motion (EOMs) for evolving multi-layer\nmulticonfiguration time-dependent Hartree (ML-MCTDH) wavefunctions that, unlike\nthe standard ML-MCTDH EOMs, never require the evaluation of the inverse of\nsingular matrices. All members of this family of EOMs make use of alternative\nstatic gauge conditions than that used for standard ML-MCTDH. These alternative\nconditions result in an expansion of the wavefunction in terms of a set of\npotentially arbitrary orthonormal functions, rather than in terms of a set of\nnon-orthonormal and potentially linearly dependent functions, as is the case\nfor standard ML-MCTDH. We show that the EOMs used in the projector splitting\nintegrator (PSI) and the invariant EOMs approaches are two special cases of\nthis family obtained from different choices for the dynamic gauge condition,\nwith the invariant EOMs making use of a choice that introduces potentially\nunbounded operators into the EOMs. As a consequence, all arguments for the\nexistence of parallelizable integration schemes for the invariant EOMs can also\nbe applied to the PSI EOMs.", "category": "physics_chem-ph" }, { "text": "OH-Formation Following Vibrationally Induced Reaction Dynamics of\n H$_2$COO: The reaction dynamics of H$_2$COO to form linear HCOOH and dioxirane as first\nsteps for OH-elimination is quantitatively investigated. Using a machine\nlearned potential energy surface at the CASPT2/aug-cc-pVTZ level of theory\nvibrational excitation along the CH-normal mode $\\nu_{\\rm CH}$ with energies up\nto 40.0 kcal/mol ($\\sim 5 \\nu_{\\rm CH}$) leads almost exclusively to linear\nHCOOH which further decomposes into OH+HCO. Although the barrier to form\ndioxirane is only 21.4 kcal/mol the reaction probability to form dioxirane is\ntwo orders of magnitude lower if the CH-stretch mode is excited. Following the\ndioxirane-formation pathway is facile, however, if in addition the COO-bend\nvibration is excited with energies equivalent to $\\sim (2 \\nu_{\\rm CH} + 4\n\\nu_{\\rm COO})$ or $\\sim (3 \\nu_{\\rm CH} + \\nu_{\\rm COO})$. For OH-formation in\nthe atmosphere the pathway through linear HCOOH is probably most relevant\nbecause the alternative pathways (through dioxirane or formic acid) involve\nseveral intermediates that can de-excite through collisions, relax {\\it via}\nIntramolecular vibrational energy redistribution (IVR), or pass through very\nloose and vulnerable transition states (formic acid). This work demonstrates\nhow, by selectively exciting particular vibrational modes, it is possible to\ndial into desired reaction channels with a high degree of specificity for a\nprocess relevant to atmospheric chemistry.", "category": "physics_chem-ph" }, { "text": "Effect of Background Signal on Momentum Imaging: The velocity Slice Imaging technique has revolutionised electron molecule\ninteraction studies. Multiple electrostatic lens assemblies are often used in\nspectrometers for resolving low kinetic energy fragments. However, in a\ncrossed-beam experiment with an effusive molecular beam, the extended source of\nion generation due to the presence of the background gas creates artefacts on\nthe momentum images as we try to magnify them beyond a certain size. Here, we\npresent a systematic study of this effect on momentum imaging and the solutions\nto address this issue by background subtraction with suitable magnification.\nAdditionally, we demonstrated that a supersonic molecular beam target helps\nminimise these artefacts in the image magnification by reducing the background\nsignal. These systematic findings may bring valuable insight into the\ninvestigation of low kinetic energy release processes involving electron\nimpact, ion impact, and merge beam experiments with large interaction volumes\nwhere high magnification is needed.", "category": "physics_chem-ph" }, { "text": "Gas-phase spectroscopy of photostable PAH ions from the mid- to\n far-infrared: We present gas-phase InfraRed Multiple Photon Dissociation (IRMPD)\nspectroscopy of cationic phenanthrene, pyrene, and perylene over the 100$-$1700\ncm$^{-1}$ (6-95 $\\mu$m) spectral range. This range covers both local\nvibrational modes involving C$-$C and C$-$H bonds in the mid-IR, and\nlarge-amplitude skeletal modes in the far-IR. The experiments were done using\nthe 7T Fourier-Transform Ion Cyclotron Resonance (FTICR) mass spectrometer\nintegrated in the Free-Electron Laser for Intra-Cavity Experiments (FELICE),\nand findings were complemented with Density Functional Theory (DFT) calculated\nharmonic and anharmonic spectra, matching the experimental spectra well. The\nexperimental configuration that enables this sensitive spectroscopy of the\nstrongly-bound, photo-resistant Polycyclic Aromatic Hydrocarbons (PAHs) over a\nwide range can provide such high photon densities that even combination modes\nwith calculated intensities as low as 0.01 km$\\cdot$mol$^{-1}$ near 400\ncm$^{-1}$ (25 $\\mu$m) can be detected. Experimental frequencies from this work\nand all currently available IRMPD spectra for PAH cations were compared to\ntheoretical frequencies from the NASA Ames PAH IR Spectroscopic Database to\nverify predicted trends for far-IR vibrational modes depending on PAH shape and\nsize, and only a relatively small redshift (6$-$11 cm$^{-1}$) was found between\nexperiment and theory. The absence of spectral congestion and the drastic\nreduction in bandwidth with respect to the mid-IR make the far-IR fingerprints\nviable candidates for theoretical benchmarking, which can aid in the search for\nindividual large PAHs in the interstellar medium.", "category": "physics_chem-ph" }, { "text": "Scattering from Star Polymers including Excluded Volume Effects: In this work we present a new model for the form factor of a star polymer\nconsisting of self-avoiding branches. This new model incorporates excluded\nvolume effects and is derived from the two point correlation function for a\nstar polymer.. We compare this model to small angle neutron scattering (SANS)\nmeasurements from polystyrene (PS) stars immersed in a good solvent,\ntetrahydrofuran (THF). It is shown that this model provides a good description\nof the scattering signature originating from the excluded volume effect and it\nexplicitly elucidates the connection between the global conformation of a star\npolymer and the local stiffness of its constituent branch.", "category": "physics_chem-ph" }, { "text": "Electric dipole rovibrational transitions in HD molecule: The rovibrational electric dipole transitions in the ground electronic state\nof the HD molecule are studied. A simple, yet rigorous formula is derived for\nthe transition rates in terms of the electric dipole moment function $D(R)$,\nwhich is calculated in a wide range of $R$. Our numerical results for\ntransition rates are in moderate agreement with experiments and previous\ncalculations, but are at least an order of magnitude more accurate.", "category": "physics_chem-ph" }, { "text": "Quantum Optimal Control Theory for Solvated Systems: In this work, we extend the quantum optimal control theory of molecules\nsubject to ultrashort laser pulses to the case of solvated systems, explicitly\nincluding the solvent dielectric properties in the system Hamiltonian. A\nreliable description of the solvent polarization is accounted for within the\nPolarizable Continuum Model (PCM). The electronic dynamics for the molecule in\nsolution is coupled with the dynamics of the surrounding polarizable\nenvironment, that affects the features of the optimized light pulse. Examples\non test molecules are presented and discussed to illustrate such effects.", "category": "physics_chem-ph" }, { "text": "A quantum-mechanical investigation of O($^3P$) + CO scattering cross\n sections at superthermal collision energies: The kinetics and energetic relaxation associated with collisions between fast\nand thermal atoms are of fundamental interest for escape and therefore also for\nthe evolution of the Mars atmosphere. The total and differential cross-sections\nof fast O($^3P$) atom collisions with CO have been calculated from quantum\nmechanical calculations. The cross-sections are computed at collision energies\nfrom 0.4 to 5 eV in the center-of-mass frame relevant to the planetary science\nand astrophysics. All the three potential energy surfaces ($^3$A', $^3$A\" and 2\n$^3$A\" symmetry) of O($^3P$) + CO collisions separating to the atomic ground\nstate have been included in calculations of cross-sections. The cross-sections\nare computed for all three isotopes of energetic O($^3P$) atoms collisions with\nCO. The isotope dependence of the cross-sections are compared. Our newly\ncalculated data on the energy relaxation of O atoms and their isotopes with CO\nmolecules will be very useful to improve the modeling of escape and energy\ntransfer processes in the Mars' upper atmosphere.", "category": "physics_chem-ph" }, { "text": "Spin-orbit transitions in the N$^+$($^3P_{J_A}$) + H$_2$ $\\rightarrow$\n NH$^+$($X^2\u03a0$, $^4\u03a3^-$)+ H($^2S$) reaction, using adiabatic and mixed\n quantum-adiabatic statistical approaches: The cross section and rate constants for the title reaction are calculated\nfor all the spin-orbit states of N$^+$($^3P_{J_A}$) using two statistical\napproaches, one purely adiabatic and the other one mixing quantum capture for\nthe entrance channel and adiabatic treatment for the products channel. This is\nmade by using a symmetry adapted basis set combining electronic (spin and\norbital) and nuclear angular momenta in the reactants channel. To this aim,\naccurate {\\it ab initio} calculations are performed separately for reactants\nand products. In the reactants channel, the three lowest electronic states\n(without spin-orbit couplings) have been diabatized, and the spin-orbit\ncouplings have been introduced through a model localizing the spin-orbit\ninteractions in the N$^+$ atom, which yields accurate results as compared to\n{\\it ab initio} calculations including spin-orbit couplings. For the products,\neleven purely adiabatic spin-orbit states have been determined with {\\it ab\ninitio} calculations. The reactive rate constants thus obtained are in very\ngood agreement with the available experimental data for several ortho-H$_2$\nfractions, assuming a thermal initial distribution of spin-orbit states. The\nrate constants for selected spin-orbit $J_A$ states are obtained, to provide a\nproper validation of the spin-orbit effects to obtain the experimental rate\nconstants.", "category": "physics_chem-ph" }, { "text": "Topologically correct quantum nonadiabatic formalism for on-the-fly\n dynamics: On-the-fly quantum nonadiabatic dynamics for large systems greatly benefits\nfrom the adiabatic representation readily available from the electronic\nstructure programs. However, frequently occurring in this representation\nconical intersections introduce non-trivial geometric or Berry phases which\nrequire a special treatment for adequate modelling of the nuclear dynamics. We\nanalyze two approaches for nonadiabatic dynamics using the time-dependent\nvariational principle and the adiabatic representation. The first approach\nemploys adiabatic electronic functions with global parametric dependence on the\nnuclear coordinates. The second approach uses adiabatic electronic functions\nobtained only at the centres of moving localized nuclear basis functions (e.g.\nfrozen-width Gaussians). Unless a gauge transformation is used to enforce\nsingle-valued boundary conditions, the first approach fails to capture the\ngeometric phase. In contrast, the second approach accounts for the geometric\nphase naturally because of the absence of the global nuclear coordinate\ndependence in the electronic functions.", "category": "physics_chem-ph" }, { "text": "Electronic Structure of a Chemisorbed Layer at Electrochemical\n Interface: Copper Layer on Gold Electrode: An appropriate model Hamiltonian based formalism is proposed for a random\nadsorbate layer with arbitrary coverage and the ensuing two-dimensional band\nformation by metallic adsorbates in the monolayer regime. The coherent\npotential approximation is employed to handle the randomness. The adsorbate\nself-energy is evaluated explicitly using the density of states for the\nsubstrate band. This takes us beyond the conventional wide-band approximation\nand removes the logarithmic divergence associated with the binding energy\ncalculations. The formalism is applied to the electrosorption of copper ion on\ngold electrode, and the coverage dependence of adsorbate charge, binding\nenergy, and adsorbate density of states are determined. The analysis predicts a\nunique charge configuration of copper adsorbate, having a net positive charge,\nin the high-coverage regime, and multiple charge states when the coverage is\nlow. Though one of the charge configurations of copper is nearly neutral at\nsmall coverage, its positive charge state is the most stable in the entire\ncoverage range. The transition from the relative neutral state of copper at low\ncoverage to a positive charge configuration occurs sharply at the\nintermediate-coverage region. This transition is caused due to the progressive\ndesolvation of copper adion with increasing coverage. The energy calculations\nshow that copper s-orbital bonding contributes maximally toward the binding\nenergy at the metal-vacuum interface, whereas it is the copper d-orbital\nbonding which makes chemisorption feasible at the gold electrode. Finally, our\nnumerical results are compared with the relevant experimental studies.", "category": "physics_chem-ph" }, { "text": "iGVPT2 : an interface to computational chemistry packages for anharmonic\n corrections to vibrational frequencies: iGVPT2 is a program for computing anharmonic corrections to vibration\nfrequencies, based on force field expansion of the potential energy surface in\nnormal mode coordinates. It includes second order vibrational perturbation\ntheory (VPT2) algorithm and its derived methods (VPT2+K, DCPT2, HDCPT2). iGVPT2\nis interfaced with several computation chemistry packages to compute the\npotential energies and dipoles derivatives. The second, third and quartic\nderivatives can be computed at the same level of theory but they can be also\ncomputed using different methods via one or two computational packages. iGPVT2\nincludes also a very fast hybrid QM//MM approach for biomolecules. It is\nprovided free-of-charge for non-commercial research (see\n\\url{https://sites.google.com/site/allouchear/igvpt2}).", "category": "physics_chem-ph" }, { "text": "Descriptors for Electrolyte-Renormalized Oxidative Stability of Solvents\n in Lithium-ion Batteries: Electrolyte stability against oxidation is one of the important factors\nlimiting the development of high energy density batteries. HOMO level of\nsolvent molecules has been successfully used for understanding trends in their\noxidative stability but assumes a non-interacting environment. However, solvent\nHOMO levels are renormalized due to molecules in their solvation shells. In\nthis work, we first demonstrate an inexpensive and accurate method to determine\nthe HOMO level of solvent followed by simple descriptors for renormalization of\nHOMO level due to different electrolyte components. The descriptors are based\non Gutmann Donor and Acceptor numbers of solvent and other components. The\nmethod uses fast GGA-level DFT calculations compared to previously used\nexpensive, experimental data dependent methods. This method can be used to\nscreen for unexplored stable solvents among the large number of known organic\ncompounds to design novel high voltage stable electrolytes.", "category": "physics_chem-ph" }, { "text": "Additive polarizabilities in ionic liquids: An extended Designed regression analysis of experimental data on density and\nrefractive indices of several classes of ionic liquids yielded statistically\naveraged atomic volumes and polarizabilities of the constituting atoms. These\nvalues can be used to predict the molecular volume and polarizability of an\nunknown ionic liquid as well as its mass density and refractive index. Our\napproach does not need information on the molecular structure of the ionic\nliquid, but it turned out that the discrimination of the hybridization state of\nthe carbons improved the overall result. Our results are not only compared to\nexperimental data but also to quantum-chemical calculations. Furthermore,\nfractional charges of ionic liquid ions and their relation to polarizability\nare discussed.", "category": "physics_chem-ph" }, { "text": "Vibrational Polaritons with Broken In-Plane Translational Symmetry: For the calculation of polariton dispersion relations in planar Fabry-P\\'erot\nmicrocavities, the single-mode approximation is usually applied. This\napproximation becomes invalid when the molecular distribution along the cavity\nmirror plane breaks the in-plane translational symmetry. Herein, both\nperturbative theory and numerical calculations have been performed to study\npolariton dispersion relations with various in-plane molecular distribution\npatterns under vibrational strong coupling conditions. If a homogeneous\nin-plane molecular distribution is modulated by sinusoidal fluctuations, in\naddition to a pair of upper and lower polariton branches, a discrete number of\nside polariton branches may emerge in the polariton dispersion relation.\nMoreover, for a Gaussian molecular density distribution, only two, yet\nsignificantly broadened polariton branches exist in the spectra. This polariton\nlinewidth broadening is due to the breakdown of the single-mode approximation\nand the scattering between cavity modes at different in-plane frequencies,\nwhich is distinguished from known causes of polariton broadening such as the\nhomogeneous broadening of molecules and the cavity loss. Associated with the\nbroadened polariton branches, under the Gaussian in-plane inhomogeneity, a\nsignificant amount of the VSC eigenstates contain a non-zero contribution from\nthe cavity photon mode at zero in-plane frequency, blurring the distinction\nbetween the bright and the dark modes. Looking forward, our theoretical\ninvestigation should facilitate the experimental exploration of vibrational\npolaritons with patterned in-plane molecular density distributions.", "category": "physics_chem-ph" }, { "text": "Stochastic self-consistent second-order Green's function method for\n correlation energies of large electronic systems: The second-order Matsubara Green's function method (GF2) is a robust\ntemperature dependent quantum chemistry approach, extending beyond the\nrandom-phase approximation. However, till now the scope of GF2 applications was\nquite limited as they require computer resources which rise steeply with system\nsize. In each step of the self-consistent GF2 calculation there are two parts:\nthe estimation of the self-energy from the previous step's Green's function,\nand updating the Green's function from the self-energy. The first part formally\nscales as the fifth power of the system size while the second has a much\ngentler cubic scaling. Here, we develop a stochastic approach to GF2 (sGF2)\nwhich reduces the fifth power scaling of the first step to merely quadratic,\nleaving the overall sGF2 scaling as cubic. We apply the method to linear\nhydrogen chains containing up to 1000 electrons, showing that the approach is\nnumerically stable, efficient and accurate. The stochastic errors are very\nsmall, of the order of 0.1% or less of the correlation energy for large\nsystems, with only a moderate computational effort. The first iteration of GF2\nis an MP2 calculation that is done in linear scaling, hence we obtain an\nextremely fast stochastic MP2 (sMP2) method as a by-product. While here we\nconsider finite systems with large band gaps where at low temperatures effects\nare negligible, the sGF2 formalism is temperature dependent and general and can\nbe applied to finite or periodic systems with small gaps at finite\ntemperatures.", "category": "physics_chem-ph" }, { "text": "Field-free orientation of CO molecules by femtosecond two-color laser\n fields: We report the first experimental observation of non-adiabatic field-free\norientation of a heteronuclear diatomic molecule (CO) induced by an intense\ntwo-color (800 and 400 nm) femtosecond laser field. We monitor orientation by\nmeasuring fragment ion angular distributions after Coulomb explosion with an\n800 nm pulse. The orientation of the molecules is controlled by the relative\nphase of the two-color field. The results are compared to quantum mechanical\nrigid rotor calculations. The demonstrated method can be applied to study\nmolecular frame dynamics under field-free conditions in conjunction with a\nvariety of spectroscopy methods, such as high-harmonic generation, electron\ndiffraction and molecular frame photoemission.", "category": "physics_chem-ph" }, { "text": "On the application of Canonical Perturbation Theory up to the\n dissociation threshold: We investigate a model system consisting of a Morse oscillator strongly\ncoupled to a doubly-degenerate bending degree of freedom and show that\nCanonical Perturbation Theory is able to provide a fairly precise, though not\nexact, approximation of the Hamiltonian up to the dissociation threshold.\nQuantum mechanical results and classical ones are discussed in this Letter.", "category": "physics_chem-ph" }, { "text": "Width of reaction zones in A + B -> C type reaction-diffusion processes:\n Effects of an electric current: We investigate the effects of an electric current on the width of a\nstationary reaction zone in an irreversible A^- + B^+ -> C reaction-diffusion\nprocess. The ion dynamics of the electrolytes A = (A^+, A^-) and B = (B^+, B^-)\nis described by reaction-diffusion equations obeying local electroneutrality,\nand the stationary state is obtained by employing reservoirs of fixed\nelectrolyte concentrations at the opposite ends of a finite domain. We find\nthat the width of the reaction zone decreases when the current drives the\nreacting ions towards the reaction zone while it increases in the opposite\ncase. The linear response of the width to the current is estimated by\ndeveloping a phenomenological theory based on conservation laws, and on\nelectroneutrality. The theory is found to reproduce numerical solutions to a\ngood accuracy.", "category": "physics_chem-ph" }, { "text": "Thermal Density Functional Theory in Context: This chapter introduces thermal density functional theory, starting from the\nground-state theory and assuming a background in quantum mechanics and\nstatistical mechanics. We review the foundations of density functional theory\n(DFT) by illustrating some of its key reformulations. The basics of DFT for\nthermal ensembles are explained in this context, as are tools useful for\nanalysis and development of approximations. We close by discussing some key\nideas relating thermal DFT and the ground state. This review emphasizes thermal\nDFT's strengths as a consistent and general framework.", "category": "physics_chem-ph" }, { "text": "Local order of liquid water at the electrochemical interface: We study the structure and dynamics of liquid water in contact with Pd and Au\n(111) surfaces using \\emph{ab initio} molecular dynamics simulations with and\nwithout van der Waals interactions. Our results show that the structure of\nwater at the interface of these two metals is very different. For Pd, we\nobserve the formation of two different domains of preferred orientations, with\nopposite net interfacial dipoles. One of these two domains has a large degree\nof in-plane hexagonal order. For Au a single domain exists with no in-plane\norder. For both metals, the structure of liquid water at the interface is\nstrongly dependent on the use of dispersion forces. The origin of the\nstructural domains observed in Pd is associated to the interplay between\nwater/water and water/metal interactions. This effect is strongly dependent on\nthe charge transfer that occurs at the interface, and which is not modeled by\ncurrent state of the art semi-empirical force fields.", "category": "physics_chem-ph" }, { "text": "A novel crossed-molecular-beam experiment for investigating reactions of\n state- and conformationally selected strong-field-seeking molecules: The structure and quantum state of the reactants have a profound impact on\nthe kinetics and dynamics of chemical reactions. Over the past years,\nsignificant advances have been made in the control and manipulation of\nmolecules with external electric and magnetic fields in molecular-beam\nexperiments for investigations of their state-, structure- and energy-specific\nchemical reactivity. Whereas studies for neutrals have so far mainly focused on\nweak-field-seeking species, we report here progress towards investigating\nreactions of strong-field-seeking molecules by introducing a novel\ncrossed-molecular-beam experiment featuring an electrostatic deflector. The new\nsetup enables the characterisation of state- and geometry-specific effects in\nreactions under single-collision conditions. As a proof of principle, we\npresent results on the chemi-ionisation reaction of metastable neon atoms with\nrotationally state-selected carbonyl sulfide (OCS) molecules and show that the\nbranching ratio between the Penning and dissociative ionisation pathways\nstrongly depends on the initial rotational state of OCS.", "category": "physics_chem-ph" }, { "text": "On the time-dependent electrolyte Seebeck effect: Single-ion Soret coefficients $\\alpha_{i}$ characterize the tendency of ions\nin an electrolyte solution to move in a thermal gradient. When these\ncoefficients differ between cations and anions, an electric field can be\ngenerated. For this so-called electrolyte Seebeck effect to occur, the\ndifferent thermodiffusive fluxes need to be blocked by boundaries --\nelectrodes, for example. Local charge neutrality is then broken in the\nDebye-length vicinity of the electrodes. Confusingly, many authors point to\nthese regions as the source of the thermoelectric field yet ignore them in\nderivations of the time-dependent Seebeck coefficient $S(t)$, giving a false\nimpression that the electrolyte Seebeck effect is purely a bulk phenomenon.\nWithout enforcing local electroneutrality, we derive $S(t)$ generated by a\nbinary electrolyte with arbitrary ionic valencies subject to a time-dependent\nthermal gradient. Next, we experimentally measure $S(t)$ for five acids, bases,\nand salts near titanium electrodes. For the steady state we find\n$S\\approx2~\\mathrm{mV~K}^{-1}$ for many electrolytes, roughly one order of\nmagnitude larger than predictions based on literature $\\alpha_{i}$. We fit our\nexpression for $S(t)$ to the experimental data, treating the $\\alpha_{i}$ as\nfit parameters, and also find larger-than-literature values, accordingly.", "category": "physics_chem-ph" }, { "text": "Competing Ionization and Dissociation in the H$_2$ Gerade System: A numerically solvable two-dimensional (2D) model, employed by the authors to\nstudy the dissociative recombination of H$_2^+$ in the ungerade symmetry [Phys.\nRev. A $\\mathbf{98}$, 062706 (2018)], is extended to describe the collision\nprocess in the gerade symmetry of H$_2$. In this symmetry the ionization and\ndissociation processes are driven primarily by the direct, curve-crossing\nmechanism. The model is represented by a set of three coupled electronic\nchannels in 2D, in the space of $s,p,d$ partial waves of the colliding\nelectron. We demonstrate that the Born-Oppenheimer properties of the H$_2$\nmolecule in the relevant range of internuclear distances can be described by\nsuch a model. The molecular rotational degrees of freedom are accounted for by\nthe rotational frame transformation. The numerical solution of the model is\ndiscussed and the resulting rovibrationally inelastic and dissociative\nrecombination cross sections are compared with the available data.", "category": "physics_chem-ph" }, { "text": "Time-reversal symmetry adaptation in relativistic density matrix\n renormalization group algorithm: In the nonrelativistic Schr\\\"{o}dinger equation, the total spin $S$ and spin\nprojection $M$ are good quantum numbers. In contrast, spin symmetry is lost in\nthe presence of spin-dependent interactions such as spin-orbit couplings in\nrelativistic Hamiltonians. Previous implementations of relativistic density\nmatrix renormalization group algorithm (R-DMRG) only employing particle number\nsymmetry are much more expensive than nonrelativistic DMRG. Besides, artificial\nbreaking of Kramers degeneracy can happen in the treatment of systems with odd\nnumber of electrons. To overcome these issues, we introduce time-reversal\nsymmetry adaptation for R-DMRG. Since the time-reversal operator is\nantiunitary, this cannot be simply achieved in the usual way. We define a\ntime-reversal symmetry-adapted renormalized basis and present strategies to\nmaintain the structure of basis functions during the sweep optimization. With\ntime-reversal symmetry adaptation, only half of the renormalized operators are\nneeded and the computational costs of Hamiltonian-wavefunction multiplication\nand renormalization are reduced by half. The present construction of\ntime-reversal symmetry-adapted basis also directly applies to other tensor\nnetwork states without loops.", "category": "physics_chem-ph" }, { "text": "Acetylene weak bands at 2.5 $\u03bc$m from intracavity Cr2+:ZnSe laser\n absorption observed with time-resolved Fourier transform spectroscopy: The spectral dynamics of a mid-infrared multimode Cr^2+:ZnSe laser located in\na vacuum sealed chamber containing acetylene at low pressure is analyzed by a\nstepping-mode high-resolution time-resolved Fourier transform interferometer.\nDoppler-limited absorption spectra of C_2H_2 in natural isotopic abundance are\nrecorded around 4000 cm^-1 with kilometric absorption path lengths and\nsensitivities better than 3 10^-8 cm-1. Two cold bands are newly identified and\nassigned to the n_1+n_4^1 and n_3+n_5^1 transitions of ^12C^13CH_2. The\nn_1+n_5^1 band of ^12C_2HD and fourteen ^12C_2H_2 bands are observed, among\nwhich for the first time n_2+2n_4^2+n_5^-1.", "category": "physics_chem-ph" }, { "text": "Thermal Properties of Deng-Fan-Eckart Potential model using Poisson\n Summation Approach: The Deng-Fan-Eckart (DFE) potential is as good as the Morse potential in\nstudying atomic interaction in diatomic molecules. By using the improved\nPekeris-type approximation, to deal with the centrifugal term, we obtain the\nbound-state solutions of the radial Schr\\\"odinger equation with this adopted\nmolecular model via the Factorization Method. With the energy equation\nobtained, the thermodynamic properties of some selected diatomic molecules(H2 ,\nCO , and ScN ) were obtained using Poisson summation method.. The unnormalized\nwave function is also derived. The energy spectrum for a set of diatomic\nmolecules for different values of the vibrational n and rotational l are\nobtained. To show the accuracy of our results, we discuss some special cases by\nadjusting some potential parameters and also compute the numerical eigenvalue\nof the Deng-Fan potential for comparison sake. However, it was found out that\nour results agree excellently with the results obtained via other methods.", "category": "physics_chem-ph" }, { "text": "Low-Temperature Kinetic Isotope Effects in CH3OH+H -> CH2OH+H2 Shed\n Light on the Deuteration of Methanol in Space: We calculated reaction rate constants including atom tunneling for the\nhydrogen abstraction reaction CH3OH+H -> CH2OH+H2 with the instanton method.\nThe potential energy was fitted by a neural network, that was trained to\nUCCSD(T)-F12/VTZ-F12 data. Bimolecular gas-phase rate constants were calculated\nusing microcanonic instanton theory. All H/D isotope patterns on the CH3 group\nand the incoming H atom are studied. Unimolecular reaction rate constants,\nrepresenting the reaction on a surface, down to 30 K, are presented for all\nisotope patterns. At 30 K they range from 4100 for the replacement of the\nabstracted H by D to ~ 8 for the replacement of the abstracting H to about 2--6\nfor secondary KIEs. The $^\\text{12}$C/$^\\text{13}$C kinetic isotope effect is\n1.08 at 30 K, while the $^\\text{16}$O/$^\\text{18}$O kinetic isotope effect is\nvanishingly small. A simple kinetic surface model using these data predicts\nhigh abundances of the deuterated forms of methanol.", "category": "physics_chem-ph" }, { "text": "Robust Gaussian Process Regression method for efficient reaction pathway\n optimization: application to surface processes: Simulation of surface processes is a key part of computational chemistry that\noffers atomic-scale insights into mechanisms of heterogeneous catalysis,\ndiffusion dynamics, as well as quantum tunneling phenomena. The most common\ntheoretical approaches involve optimization of reaction pathways, including\nsemiclassical tunneling pathways (called instantons). However, the\ncomputational effort can be demanding, especially for instanton optimizations\nwith ab initio electronic structure. Recently, machine learning has been\napplied to accelerate reaction-pathway optimization, showing great potential\nfor a wide range of applications. However, previous methods suffer from\npractical issues such as unfavorable scaling with respect to the size of the\ndescriptor, and were mostly designed for reactions in the gas phase. We propose\nan improved framework based on Gaussian process regression for general\ntransformed coordinates, which can alleviate the size problem. The descriptor\ncombines internal and Cartesian coordinates, which improves the performance for\nmodeling surface processes. We demonstrate with eleven instanton optimizations\nin three example systems that the new approach makes ab initio instanton\noptimization significantly cheaper, such that it becomes not much more\nexpensive than a classical transition-state theory calculation.", "category": "physics_chem-ph" }, { "text": "Simulating Transient X-ray Photoelectron Spectra of Fe(CO)5 and Its\n Photodissociation Products With Multireference Algebraic Diagrammatic\n Construction Theory: Accurate simulations of transient X-ray photoelectron spectra (XPS) provide\nunique opportunities to bridge the gap between theory and experiment in\nunderstanding the photoactivated dynamics in molecules and materials. However,\nsimulating X-ray photoelectron spectra along a photochemical reaction pathway\nis challenging as it requires accurate description of electronic structure\nincorporating core-hole screening, orbital relaxation, electron correlation,\nand spin-orbit coupling in excited states or at nonequilibrium ground-state\ngeometries. In this work, we employ the recently developed multireference\nalgebraic diagrammatic construction theory (MR-ADC) to investigate the\ncore-ionized states and X-ray photoelectron spectra of Fe(CO)5 and its\nphotodissociation products (Fe(CO)4, Fe(CO)3) following excitation with 266 nm\nlight. The simulated transient Fe 3p and CO 3{\\sigma} XPS spectra incorporating\nspin-orbit coupling and high-order electron correlation effects are shown to be\nin a good agreement with the experimental measurements by Leitner et al. [J.\nChem. Phys. 149, 044307 (2018)]. Our calculations suggest that core-hole\nscreening, spin-orbit coupling, and ligand-field splitting effects are\nsimilarly important in reproducing the experimentally observed chemical shifts\nin transient Fe 3p XPS spectra of iron carbonyl complexes. Our results also\ndemonstrate that the MR-ADC methods can be very useful in interpreting the\ntransient XPS spectra of transition metal compounds.", "category": "physics_chem-ph" }, { "text": "OD + CO -> D + CO2 Branching Kinetics Probed with Time-Resolved\n Frequency Comb Spectroscopy: Time-resolved direct frequency comb spectroscopy (TRFCS) was used to study\nthe kinetics of the deuterated analogue of the OH+CO->H+CO2 reaction, which is\nimportant for atmospheric and combustion chemistry. Complementing our recent\nwork on quantifying the formation rate of the transient trans-DOCO radical, we\nreport measurements of the kinetics of the activated product channel, D+CO2, at\nroom temperature. Simultaneous measurements of the time-dependence of OD and\nCO2 concentrations allowed us to directly determine the formation rate,\nbranching yield, and dependence on pressure and bath gas of the activated\nproduct. Together with the trans-DOCO formation rate, these new measurements\nprovide absolute yields of branching channels for both products of OD+CO in the\nlow-pressure limit.", "category": "physics_chem-ph" }, { "text": "The \"sugar\" coarse-grained DNA model: More than twenty coarse-grained (CG) DNA models have been developed for\nsimulating the behavior of this molecule under various conditions, including\nthose required for nanotechnology. However, none of these models reproduces the\nDNA polymorphism associated with conformational changes in the ribose rings of\nthe DNA backbone. These changes make an essential contribution to the DNA local\ndeformability and provide the possibility of the transition of the DNA double\nhelix from the B-form to the A-form during interactions with biological\nmolecules. We propose a CG representation of the ribose conformational\nflexibility. We substantiate the choice of the CG sites (6 per nucleotide)\nneeded for the \"sugar\" GC DNA model, and obtain the potentials of the CG\ninteractions between the sites by the \"bottom-up\" approach using the all-atom\nAMBER force field. We show that the representation of the ribose flexibility\nrequires one non-harmonic and one three-particle potential, the forms of both\nthe potentials being different from the ones generally used. The model also\nincludes (i) explicit representation of ions (in an implicit solvent) and (ii)\nsequence dependence. With these features, the sugar CG DNA model reproduces\n(with the same parameters) both the B- and A- stable forms under corresponding\nconditions and demonstrates both the A to B and the B to A phase transitions.", "category": "physics_chem-ph" }, { "text": "Selectively pulsed spin order transfer increases parahydrogen-induced\n NMR amplification of insensitive nuclei and makes polarization transfer more\n robust: We describe a new method for pulsed spin order transfer (SOT) of parahydrogen\ninduced polarization (PHIP) that enables close to 100 % polarization in\nincompletely 2H-labeled molecules by exciting only the desired protons in a\nfrequency-selective manner. While a selective pulse (SP) on 1H at the beginning\nof pulsed SOT had been considered before, using SPs during the SOT suppresses\nundesired indirect spin-spin interactions. As a result, we achieved a more\nrobust SOT for the SP variants of the phINEPT+ sequence that we refer to as\nphSPINEPT+. Thereby, for the first time, we report a sequence that is effective\nfor all weakly coupled spin systems. Our simulations show that the method\nconverts close to 100 % of the parahydrogen-derived spin order into 13C\nhyperpolarization in weakly coupled three-spin systems and partially or fully\n2H-labeled molecules if relaxation is neglected. Experimentally we demonstrate\nhigh hyperpolarization of 13C with 15.8 % for 1-13C-hydroxyethyl propionate-d3\nand 12.6 % for 1-13C-ethyl acetate-d6, which corresponds to ~47 % and ~38 % if\nthe enrichment of parahydrogen had been 100 %. Even in non-2H-labeled\nmolecules, a remarkable 13C polarization is achieved, e.g. up to 20 % were\nsimulated for 100 % pH2, and 1.25 % were obtained experimentally for\n1-13C-ethyl pyruvate and 50 % pH2, which can be further improved by faster\nhydrogenation. As a result, full deuterium labeling may no longer be required\ne.g., when new PHIP agents are investigated, the synthesis of fully deuterated\nmolecules is too complex, or when a kinetic isotope effect regarding the\nmetabolic conversion rate of an agent is to be avoided. Using SPs during SOT\nseems very promising and may be extended to other sequences in the context of\nPHIP and be-yond to make them less prone to experimental imperfections or real\nmolecular environments.", "category": "physics_chem-ph" }, { "text": "Bulk viscosity of dilute monatomic gases: Extensive research has been carried out in the past to estimate the bulk\nviscosity of dense monatomic fluids; however, little attention has been paid to\nestimate the same in the dilute gas regime. In this work, we perform precise\nGreen-Kubo calculations in molecular dynamics simulations to estimate the bulk\nviscosity of dilute argon gas. The investigated temperature and pressure range\nis 300 to 750 K and 0.5 to 1.5 bar respectively. It is observed that the\nestimated bulk viscosity is $O(10^{-10})$ Pa s, which is several orders of\nmagnitude smaller than that of other diatomic and polyatomic gases, but\nnonetheless, not an absolute zero as typically assumed. It implies that Stokes'\nhypothesis is true for dilute monatomic gases only in an approximate rather\nthan absolute sense. The variation of bulk viscosity with pressures at constant\ntemperatures has also been studied and is found to be of quadratic nature. The\nobtained bulk viscosity values are also reported in the reduced Lennard-Jones\nunits to enable extension of the present results to other noble gases as well.\nIt has also been observed that the bulk viscosity of Lennard-Jones monatomic\ngases becomes temperature independent at very low densities.", "category": "physics_chem-ph" }, { "text": "Second-order Green's function perturbation theory for periodic systems: Despite recent advances, systematic quantitative treatment of the electron\ncorrelation problem in extended systems remains a formidable task.\nSystematically improvable Green's function methods capable of quantitatively\ndescribing weak and at least qualitatively strong correlations appear promising\ncandidates for computational treatment of periodic systems. We present a\nperiodic implementation of temperature-dependent self-consistent 2nd-order\nGreen's function method (GF2), where the self-energy is evaluated in the basis\nof atomic orbitals. Evaluating the real-space self-energy in atomic orbitals\nand solving the Dyson equation in $\\mathbf{k}$-space are the key components of\na computationally feasible algorithm. We apply this technique to the 1D\nhydrogen lattice - a prototypical crystalline system with a realistic\nHamiltonian. By analyzing the behavior of the spectral functions, natural\noccupations, and self-energies, we claim that GF2 is able to recover metallic,\nband insulating, and at least qualitatively Mott regimes. We observe that the\niterative nature of GF2 is essential to the emergence of the metallic and Mott\nphases.", "category": "physics_chem-ph" }, { "text": "Long-range coherent energy transport in Photosystem II: We simulate the long-range inter-complex electronic energy transfer in\nPhotosystem II -- from the antenna complex, via a core complex, to the reaction\ncenter -- using a non-Markovian (ZOFE) quantum master equation description that\nallows us to quantify the electronic coherence involved in the energy transfer.\nWe identify the pathways of the energy transfer in the network of coupled\nchromophores, using a description based on excitation probability currents. We\ninvestigate how the energy transfer depends on the initial excitation --\nlocalized, coherent initial excitation versus delocalized, incoherent initial\nexcitation -- and find that the energy transfer is remarkably robust with\nrespect to such strong variations of the initial condition. To explore the\nimportance of vibrationally enhanced transfer and to address the question of\noptimization in the system parameters, we vary the strength of the coupling\nbetween the electronic and the vibrational degrees of freedom. We find that the\noriginal parameters lie in a (broad) region that enables optimal transfer\nefficiency, and that the energy transfer appears to be very robust with respect\nto variations in the vibronic coupling. Nevertheless, vibrationally enhanced\ntransfer appears to be crucial to obtain a high transfer efficiency. We compare\nour quantum simulation to a \"classical\" rate equation based on a\nmodified-Redfield/generalized-F\\\"orster description that was previously used to\nsimulate energy transfer dynamics in the entire Photosystem II complex, and\nfind very good agreement between quantum and rate-equation simulation of the\noverall energy transfer dynamics.", "category": "physics_chem-ph" }, { "text": "Visible and Ultraviolet Laser Spectroscopy of ThF: The molecular ion ThF$^+$ is the species to be used in the next generation of\nsearch for the electron's Electric Dipole Moment (eEDM) at JILA. The\nmeasurement requires creating molecular ions in the eEDM sensitive state, the\nrovibronic ground state $^3\\Delta_1$, $v^+=0$, $J^+=1$. Survey spectroscopy of\nneutral ThF is required to identify an appropriate intermediate state for a\nResonance Enhanced Multi-Photon Ionization (REMPI) scheme that will create ions\nin the required state. We perform broadband survey spectroscopy (from 13000 to\n44000~cm$^{-1}$) of ThF using both Laser Induced Fluorescence (LIF) and $1+1'$\nREMPI spectroscopy. We observe and assign 345 previously unreported vibronic\nbands of ThF. We demonstrate 30\\% efficiency in the production of ThF$^+$ ions\nin the eEDM sensitive state using the $\\Omega = 3/2$ [32.85] intermediate\nstate. In addition, we propose a method to increase the aforementioned\nefficiency to $\\sim$100\\% by using vibrational autoionization via\ncore-nonpenetrating Rydberg states, and discuss theoretical and experimental\nchallenges. Finally, we also report 83 vibronic bands of an impurity species,\nThO.", "category": "physics_chem-ph" }, { "text": "Field-induced phases of an orientable charged particle in a dilute\n background of point charges: We study a dynamical model of a rod-like particle surrounded by a cloud of\nsmaller particles of the same charge and we show that, in the presence of a\nlow-frequency alternating electric field, the rod displays the same type of\nanomalous orientation (perpendicular to the field) that was recently observed\nin laboratory colloids. This indicates that the anomalous orientation is due to\nthe collective dynamics of the colloidal particles, and does not require\nelectro-osmotic effects. We also confirm the experimental observation that for\nhigher field frequencies the standard orientation (parallel to the field)\nprevails. In the simulations, these changes are abrupt enough to resemble a\nphase transition.", "category": "physics_chem-ph" }, { "text": "Water Density Fluctuations Relevant to Hydrophobic Hydration are\n Unaltered by Attractions: An understanding of density fluctuations in bulk water has made significant\ncontributions to our understanding of the hydration and interactions of\nidealized, purely repulsive hydrophobic solutes. To similarly inform the\nhydration of realistic hydrophobic solutes that have dispersive interactions\nwith water, here we characterize water density fluctuations in the presence of\nattractive fields that correspond to solute-water attractions. We find that\nwhen the attractive field acts only in the solute hydration shell, but not in\nthe solute core, it does not significantly alter water density fluctuations in\nthe solute core region. We further find that for a wide range of solute sizes\nand attraction strengths, the free energetics of turning on the attractive\nfields in bulk water are accurately captured by linear response theory. Our\nresults also suggest strategies for more efficiently estimating hydration free\nenergies of realistic solutes in bulk water and at interfaces.", "category": "physics_chem-ph" }, { "text": "High-precision gigahertz-to-terahertz spectroscopy of aqueous salt\n solutions as a probe of the femtosecond-to-picosecond dynamics of liquid\n water: Because it is sensitive to fluctuations occurring over femtoseconds to\npicoseconds, gigahertz-to-terahertz dielectric relaxation spectroscopy can\nprovide a valuable window into water's most rapid intermolecular motions. In\nresponse, we have built a vector network analyzer dielectric spectrometer\ncapable of measuring absorbance and index of refraction in this frequency\nregime with unprecedented precision. Using this to determine the complex\ndielectric response of water and aqueous salt solutions from 5.9 GHz to 1.12\nTHz (which we provide in the SI), we have obtained strong new constraints on\ntheories of water's collective dynamics. For example, while the\nsalt-dependencies we observe for water's two slower relaxations (8 and 1 ps)\nare easily reconciled with suggestions that they arise due to rotations of\nfully and partially hydrogen bonded molecules, respectively, the\nsalt-dependence of the fastest relaxation (180 fs) appears difficult to\nreconcile with its prior assignment to liberations of single hydrogen bonds.", "category": "physics_chem-ph" }, { "text": "Exact partition potential for model systems of interacting electrons in\n 1-D: We find the numerically exact partition potential for 1-D systems of\ninteracting electrons designed to model diatomic molecules. At integer fragment\noccupations, the kinetic contribution to the partition potential develops sharp\nfeatures in the internuclear region that nearly cancel corresponding features\nof exchange-correlation. They occur at locations that coincide with those of\nwell-known features of the underlying molecular Kohn-Sham potential. For\nnon-integer fragment occupations, we demonstrate that the fragment Kohn-Sham\ngaps determine the kinetic part of the partition potential. Our results\nhighlight the importance of non-additive noninteracting kinetic and\nexchange-correlation energy approximations in density-embedding methods at\nlarge internuclear separations and the importance of non-additive\nnoninteracting kinetic energy approximations at all separations.", "category": "physics_chem-ph" }, { "text": "Conformational isomerization dynamics in solvent violates both the\n Stokes-Einstein relation and Kramers' theory: Molecular isomerization kinetics in liquid solvents are determined by a\ncomplex interplay between the friction acting on a rotating dihedral due to\ninteractions with the solvent, internal dissipation effects (also known as\ninternal friction), the viscosity of the solvent, and the free energy profile\nover which a dihedral rotates. Currently, it is not understood how these\nquantities are related at the molecular scale. Here, we combine molecular\ndynamics simulations of isomerizing n-alkane chains and dipeptide molecules in\nmixed water-glycerol solvents with memory-kernel extraction techniques to\ndirectly evaluate the frequency-dependent friction acting on a rotating\ndihedral. We extract the friction and isomerization times over a range of\nglycerol concentrations and accurately evaluate the relationships between\nsolvent viscosity, isomerization kinetics, and dihedral friction. We show that\nthe total friction acting on a rotating dihedral does not scale linearly with\nsolvent viscosity, thus violating the Stokes-Einstein relation. Additionally,\nwe demonstrate that the kinetics of isomerization are significantly faster\ncompared to the Kramers prediction in the overdamped limit. We suggest that\nisomerization kinetics are determined by the multi-time-scale friction coupling\nbetween a rotating dihedral and its solvent environment, which results in\nnon-Markovian kinetic speed-up effects.", "category": "physics_chem-ph" }, { "text": "Learning neural network potentials from experimental data via\n Differentiable Trajectory Reweighting: In molecular dynamics (MD), neural network (NN) potentials trained bottom-up\non quantum mechanical data have seen tremendous success recently. Top-down\napproaches that learn NN potentials directly from experimental data have\nreceived less attention, typically facing numerical and computational\nchallenges when backpropagating through MD simulations. We present the\nDifferentiable Trajectory Reweighting (DiffTRe) method, which bypasses\ndifferentiation through the MD simulation for time-independent observables.\nLeveraging thermodynamic perturbation theory, we avoid exploding gradients and\nachieve around 2 orders of magnitude speed-up in gradient computation for\ntop-down learning. We show effectiveness of DiffTRe in learning NN potentials\nfor an atomistic model of diamond and a coarse-grained model of water based on\ndiverse experimental observables including thermodynamic, structural and\nmechanical properties. Importantly, DiffTRe also generalizes bottom-up\nstructural coarse-graining methods such as iterative Boltzmann inversion to\narbitrary potentials. The presented method constitutes an important milestone\ntowards enriching NN potentials with experimental data, particularly when\naccurate bottom-up data is unavailable.", "category": "physics_chem-ph" }, { "text": "Accurate potential energy curve for helium dimer retrieved from\n viscosity coefficient data at very low temperatures: The long range potential of helium-helium interaction, which requires\naccurate 'ab initio' calculation, due to the small value of the potential\ndepth, approximately 11 K (0.091 kJ/mol) at 2.96 angstrom, will be obtained in\nthis study by an alternative technique. This work presents a robust and\nconsistent procedure that provides the long range potential directly from\nexperimental data. However, it is difficult to obtain experimental data\ncontaining information regarding such a small potential depth. Thereby,\nsensitivity analysis will be used to circumvent this difficulty, from which\nviscosity data at lower temperatures (<5K) were chosen as appropriate data to\nbe used to retrieve the potential function between 3 and 4 angstrom. The linear\nrelationship between the potential energy function and the viscosity\ncoefficient will be established under quantum assumptions and the Bose-Einstein\nstatistic. The use of quantum theory is essential, since the temperatures are\nbelow 5K. The potential obtained in this study describes the viscosity with an\naverage error of 1.68% that is less than the experimental error (5%), with the\nresults being similar to those obtained for recent 'ab initio' potentials.", "category": "physics_chem-ph" }, { "text": "Machine Learning-Aided First-Principles Calculations of Redox Potentials: Redox potentials of electron transfer reactions are of fundamental importance\nfor the performance and description of electrochemical devices. Despite decades\nof research, accurate computational predictions for the redox potential of even\nsimple metals remain very challenging. Here we use a combination of first\nprinciples calculations and machine learning to predict the redox potentials of\nthree redox couples, $\\mathrm{Fe}^{2+}$/$\\mathrm{Fe}^{3+}$,\n$\\mathrm{Cu}^{+}$/$\\mathrm{Cu}^{2+}$ and $\\mathrm{Ag}^{+}$/$\\mathrm{Ag}^{2+}$.\nUsing a hybrid functional with a fraction of 25\\% exact exchange (PBE0) the\npredicted values are 0.92, 0.26 and 1.99 V in good agreement with the best\nexperimental estimates (0.77, 0.15, 1.98 V). We explain in detail, how we\ncombine machine learning, thermodynamic integration from machine learning to\nsemi-local functionals, as well as a combination of thermodynamic perturbation\ntheory and $\\Delta$-machine learning to determine the redox potentials for\ncomputationally expensive hybrid functionals. The combination of these\napproaches allows one to obtain statistically accurate results.", "category": "physics_chem-ph" }, { "text": "Unraveling Quantum Coherences Mediating Primary Charge Transfer\n Processes in Photosystem II Reaction Center: Photosystem II (PSII) reaction center is a unique protein-chromophore complex\nthat is capable of efficiently separating electronic charges across the\nmembrane after photoexcitation. In the PSII reaction center, the primary\nenergy- and charge-transfer (CT) processes occur on comparable ultrafast\ntimescales, which makes it extremely challenging to understand the fundamental\nmechanism responsible for the near-unity quantum efficiency of the transfer.\nHere, we elucidate the role of quantum coherences in the ultrafast energy and\nCT in the PSII reaction center by performing two-dimensional (2D) electronic\nspectroscopy at the cryogenic temperature of 20 K, which captures the distinct\nunderlying quantum coherences. Specifically, we uncover the electronic and\nvibrational coherences along with their lifetimes during the primary ultrafast\nprocesses of energy and CT. We also examine the functional role of the observed\nquantum coherences. To gather further insight, we construct a structure-based\nexcitonic model that provided evidence for coherent energy and CT at low\ntemperature in the 2D electronic spectra. The principles, uncovered by this\ncombination of experimental and theoretical analyses, could provide valuable\nguidelines for creating artificial photosystems with exploitation of\nsystem-bath coupling and control of coherences to optimize the photon\nconversion efficiency to specific functions.", "category": "physics_chem-ph" }, { "text": "A diabatic definition of geometric phase effects: Electronic wave-functions in the adiabatic representation acquire nontrivial\ngeometric phases (GPs) when corresponding potential energy surfaces undergo\nconical intersection (CI). These GPs have profound effects on the nuclear\nquantum dynamics and cannot be eliminated in the adiabatic representation\nwithout changing the physics of the system. To define dynamical effects arising\nfrom the GP presence the nuclear quantum dynamics of the CI containing system\nis compared with that of the system with artificially removed GP. We explore a\nnew construction of the system with removed GP via a modification of the\ndiabatic representation for the original CI containing system. Using an\nabsolute value function of diabatic couplings we remove the GP while preserving\nadiabatic potential energy surfaces and CI. We assess GP effects in dynamics of\na two-dimensional linear vibronic coupling model both for ground and excited\nstate dynamics. Results are compared with those obtained with a conventional\nremoval of the GP by ignoring double-valued boundary conditions of the real\nelectronic wave-functions. Interestingly, GP effects appear similar in two\napproaches only for the low energy dynamics. In contrast with the conventional\napproach, a new approach does not have substantial GP effects in the ultra-fast\nexcited state dynamics.", "category": "physics_chem-ph" }, { "text": "Direct measurements of quantum kinetic energy tensor in stable and\n metastable water near the triple point: an experimental benchmark: This study presents the first direct and quantitative measurements of the\nnuclear momentum distribution anisotropy and the quantum kinetic energy tensor\nin stable and metastable (supercooled) water near its triple point using Deep\nInelastic Neutron Scattering (DINS). From the experimental spectra accurate\nlineshapes of the hydrogen momentum distributions are derived using an\nanisotropic Gaussian and a model independent framework. The experimental\nresults, benchmarked with those obtained for the solid phase, provide the state\nof the art directional values of the hydrogen mean kinetic energy in metastable\nwater. The determinations of the direction kinetic energies in the supercooled\nphase, benchmarked with ice at the same temperature, provide accurate and\nquantitative measurements of these dynamical observables in metastable and\nstable phases, {i.e.} key insight in the physical mechanisms of the hydrogen\nquantum state in both disordered and polycrystalline systems. The remarkable\nfindings of this study establish novel insight to further expand the capacity\nand accuracy of DINS investigations of the nuclear quantum effects in water and\nrepresent reference experimental values for theoretical investigations.", "category": "physics_chem-ph" }, { "text": "Adsorption property of fatty acid on iron surface with $\u03a3$3(111)\n grain boundary: Reducing the coefficient of boundary friction on steel surfaces is one of key\ntechnologies to improve the efficiency of machines such as automotive engines.\nIt has been shown that the boundary friction on nanostructured steel surfaces\nin the sliding test using hydrocarbon lubricant molecules is smaller than the\nfriction of normal steel surfaces. The main difference between the\nnanostructured and a normal surfaces is the density of grain boundaries and\nother surface defects. The surface defect can attract lubricant molecules and\nenhance lubricating film formation on metal surfaces. This can be one of the\nmechanisms that induce the friction reduction on the nanosructured steel\nsurface. In this work, using first principles calculations, the adsorbability\nof a lubricant molecule, a fatty acid, on a defected iron surfaces has been\nstudied. Adsorbability of the Fe(110) surface with symmetrical tilt\n{\\Sigma}3(111) grain boundary was compared to that of the clean Fe(110)\nsurface. As a result, we found that the molecule is adsorbed on sites close to\nthe grain boundary more strongly (0.77 eV in average) than on the Fe surface\nwithout grain boundary.", "category": "physics_chem-ph" }, { "text": "Charge Transfer Database for Bio-molecule Tight Binding Model Derived\n from Thousands of Proteins: The anisotropic feature of charge transfer reactions in realistic proteins\ncannot be ignored, due to the highly complex chemical structure of\nbio-molecules. In this work, we have performed the first large-scale\nquantitative assessment of charge transfer preference in protein complexes by\ncalculating the charge transfer couplings in all 20*20 possible amino acid side\nchain combinations, which are extracted from available high-quality structures\nof thousands of protein complexes. The charge transfer database quantitatively\nshows distinct features of charge transfer couplings among millions of amino\nacid side-chains combinations. The knowledge graph of charge transfer couplings\nreveals that only one average or representative structure cannot be regarded as\nthe typical charge transfer preference in realistic proteins. This data driven\nmodel provides us an alternative route to comprehensively understand the\npairwise charge transfer coupling parameters based structural similarity,\nwithout any require of the knowledge of chemical intuition about the chemical\ninteractions.", "category": "physics_chem-ph" }, { "text": "A Hybrid Algebraic/Schr\u00f6dinger Approach to the 2D Franck-Condon\n Problem: We use recent results regarding the geometry of the U(3) bosonic algebraic\nmodel to motivate a hybrid algebraic-Schr\\\"odinger approach to the 2D\nFranck-Condon problem analogous to 1D approaches. This approach allows one to\nanalyze bent to linear Franck-Condon transitions of triatomic molecules as well\nas clarifies the angular momentum dependance of the Franck-Condon intensities.", "category": "physics_chem-ph" }, { "text": "Comparative Autoignition Trends in the Butanol Isomers at Elevated\n Pressure: Autoignition experiments of stoichiometric mixtures of s-, t-, and i-butanol\nin air have been performed using a heated rapid compression machine (RCM). At\ncompressed pressures of 15 and 30 bar and for compressed temperatures in the\nrange of 715-910 K, no evidence of a negative temperature coefficient region in\nterms of ignition delay response is found. The present experimental results are\nalso compared with previously reported RCM data of n-butanol in air. The order\nof reactivity of the butanols is\nn-butanol>s-butanol$\\approx$i-butanol>t-butanol at the lower pressure, but\nchanges to n-butanol>t-butanol>s-butanol>i-butanol at higher pressure. In\naddition, t-butanol shows pre-ignition heat release behavior, which is\nespecially evident at higher pressures. To help identify the controlling\nchemistry leading to this pre-ignition heat release, off-stoichiometric\nexperiments are further performed at 30 bar compressed pressure, for t-butanol\nat $\\phi$ = 0.5 and $\\phi$ = 2.0 in air. For these experiments, higher fuel\nloading (i.e. $\\phi$ = 2.0) causes greater pre-ignition heat release (as\nindicated by greater pressure rise) than the stoichiometric or $\\phi$ = 0.5\ncases. Comparison of the experimental ignition delays with the simulated\nresults using two literature kinetic mechanisms shows generally good agreement,\nand one mechanism is further used to explore and compare the fuel decomposition\npathways of the butanol isomers. Using this mechanism, the importance of peroxy\nchemistry in the autoignition of the butanol isomers is highlighted and\ndiscussed.", "category": "physics_chem-ph" }, { "text": "Bond type restricted radial distribution functions for accurate machine\n learning prediction of atomization energies: Understanding the performance of machine learning algorithms is essential for\ndesigning more accurate and efficient statistical models. It is not always\npossible to unravel the reasoning of neural networks. Here we propose a method\nfor calculating machine learning kernels in closed and analytic form by\ncombining atomic property weighted radial distribution function (AP-RDF)\ndescriptor with a Gaussian kernel. This allowed us to analyse and improve the\nperformance of the Bag-of-Bonds descriptor, when the bond type restriction is\nincluded in AP-RDF. The improvement is achieved for the prediction of molecular\natomization energies and is due to the incorporation of a tensor product into\nthe kernel which captures the multidimensional representation of the AP-RDF. On\nthe other hand, the numerical version of the AP-RDF is a constant size\ndescriptor, and it is more computationally efficient than Bag-of-Bonds. We have\nalso discussed a connection between molecular quantum similarity and machine\nlearning kernels with first principles kind of descriptors.", "category": "physics_chem-ph" }, { "text": "Efficient Estimation of Transition Rates as Functions of pH: Extracting the kinetic properties of a system whose dynamics depend on the pH\nof the environment with which it exchanges energy and atoms requires sampling\nthe Grand Canonical Ensemble. As an alternative, we present a novel strategy\nthat requires simulating only the most recurrent Canonical Ensembles that\ncompose the Grand Canonical Ensemble. The simulations are used to estimate the\nGran Canonical distribution for a specific pH value by reweighting and to\nconstruct the transition rate matrix by discretizing the Fokker-Planck equation\nby Square Root Approximation and robust Perron Cluster Cluster Analysis. As an\napplication, we have studied the tripeptide Ala-Asp-Ala.", "category": "physics_chem-ph" }, { "text": "Controlling the nonadiabatic electron-transfer reaction rate through\n molecular-vibration polaritons in the ultrastrong coupling regime: Recent experiments showed that the chemical reaction rate is modified, either\nincreased or decreased, by strongly coupling a nuclear vibration mode to the\nsingle mode of an optical cavity. Herein we investigate how the rate of an\nelectron-transfer reaction depends on the molecule-cavity coupling in the\nultrastrong coupling regime, where the coupling strength is comparable in\nmagnitude with both the vibrational and the cavity frequencies. We found two\nmain factors that determine the modification of the reaction rate: the relative\nshifts of the energy levels induced by the coupling and the mixing of the\nground and excited states of molecular vibration in the ground state of the\nhybrid molecule-plus-cavity system through which the Franck-Condon factor\nbetween the initial and final states of the transition is altered. The former\nis the dominant factor if the molecule-cavity coupling strengths for the\nreactant and product states differ significantly from each other and gives rise\nto an increase in the reaction rate over a wide range of system's parameters.\nThe latter dominates if the coupling strengths and energy levels of the\nreactant and product states are close to each other and it leads to a decrease\nin the reaction rate. The effect of the mixing of molecular vibrational states\non the reaction rate is, however, suppressed in a system containing a large\nnumber of molecules due to the collective nature of the resulting polariton,\nand thus should be observed in a system containing a small number of molecules.\nIn contrast, the effect of the relative shifts of the energy levels should be\nessentially independent of the number of molecules coupled to the cavity.", "category": "physics_chem-ph" }, { "text": "Constants of explosive limits: This work defines density factor as the ratio of before ignition density to\nafter ignition density of the ignition mixture. This work provides an\nestimation method for explosive limits of various fuels under room temperature\nand pressure by showing that for a large universe of fuels, constant adiabatic\nflame temperature and density factor are appropriate approximations at the\nlower explosive limit while only a constant density factor might be an\nappropriate approximation at the upper explosive limit.\n Thus the assumption of a constant adiabatic flame temperature can be used in\ncalculating lower explosive limit while the assumption of a constant density\nfactor can be used in approximating upper explosive limit.", "category": "physics_chem-ph" }, { "text": "Model for energy transfer by coherent Fermi pressure fluctuations in\n quantum soft matter: A 1-dimensional model for coherent quantum energy transfer through a complex\nof compressible boxes is investigated by numerical integration of the\ntime-dependent Schr\\\"odinger equation. Energy is communicated from one box to\nthe next by the resonant fluctuating Fermi pressure of the electrons in each\nbox pushing on the walls and doing work on adjacent boxes. Parameters are\nchosen similar to the chain molecules of typical light harvesting complexes.\nFor some parameter choices the system is found to have an instability leading\nto self-induced coherent energy transfer transparency.", "category": "physics_chem-ph" }, { "text": "Structure and Dynamics of [PF$_6$][P$_{1,2,2,4}$] from Molecular\n Dynamics Simulations: Diethyl(methyl)(isobutyl)phosphonium hexafluorophosphate,\n[PF$_6$][P$_{1,2,2,4}$], is an organic ionic plastic crystal with potential\nuses as a solid electrolyte in storage and light harvesting devices. In this\nwork we present a molecular dynamics simulation study for this material\ncovering an extended temperature range, from 175 K to 500 K. The simulations\npredicts a transition from the crystalline to a {\\em semi} plastic phase at 197\nK, the onset of cation jump-like rotations at 280 K, a third transition at 340\nK to a {\\em full} plastic phase and melting to 450 K. Overall, the simulations\nshow a good agreement with the experimental findings providing a wealth of\ndetail in the structural and dynamic properties of the system.", "category": "physics_chem-ph" }, { "text": "Overcharging by macroions: above all, an entropy effect: Model macroion solutions next to a charged wall show interface \\textit{true\novercharging}, charge reversal and inversion, and layering. Macroion layering\nis present, even if the wall or the macroparticle are \\textit{uncharged} or if\nthe wall and macroions are like-charged. An effective long-range attractive\nforce between the adsorbed macroions is implied. The results are obtained\nthrough an integral equation theory and a new extended Poisson-Boltzmann\ntheory, and are in accordance with experiments on confined macroions and\npolymer layering.", "category": "physics_chem-ph" }, { "text": "All l-state eigensolutions of the non-relativistic Schrodinger equation\n with the general molecular oscillator: In this study, we employ exact quantization rule (EQR) to derive the\nanalytical approximate l-wave solutions of the Schrodinger equation with the\ngeneral molecular oscillator (GMO). The energy eigenvalues equation and the\ncorresponding wave -functions have been obtained explicitly. Improved\nPekeris-type approximation Schemes have been used to deal with the orbital\ncentrifugal term. We have deduced expressions for the bound-state energy\neigenvalues of the Morse and shifted Deng-Fan oscillator as special cases of\nthe GMO, and computed their resulting bound-state energy eigenvalues for H2,\nCO, HCl and LiH diatomic molecules. Our results are in good agreement with\nother results in the literature.", "category": "physics_chem-ph" }, { "text": "Carbon Supported Polyaniline as Anode Catalyst: Pathway to Platinum-Free\n Fuel Cells: The effectiveness of carbon supported polyaniline as anode catalyst in a fuel\ncell (FC) with direct formic acid electrooxidation is experimentally\ndemonstrated. A prototype FC with such a platinum-free composite anode\nexhibited a maximum room-temperature specific power of about 5 mW/cm2", "category": "physics_chem-ph" }, { "text": "Electronic signature of the instantaneous asymmetry in the first\n coordination shell of liquid water: Interpretation of the X-ray spectra of water as evidence for its asymmetric\nstructure has challenged the conventional symmetric nearly-tetrahedral model\nand initiated an intense debate about the order and symmetry of the hydrogen\nbond network in water. Here, we present new insights into the nature of local\ninteractions in water obtained using a novel energy decomposition method. Our\nsimulations reveal that while a water molecule forms, on average, two strong\ndonor and two strong acceptor bonds, there is a significant asymmetry in the\nenergy of these contacts. We demonstrate that this asymmetry is a result of\nsmall instantaneous distortions of hydrogen bonds, which appear as fluctuations\non a timescale of hundreds of femtoseconds around the average symmetric\nstructure. Furthermore, we show that the distinct features of the X-ray\nabsorption spectra originate from molecules with high instantaneous asymmetry.\nOur findings have important implications as they help reconcile the symmetric\nand asymmetric views on the structure of water.", "category": "physics_chem-ph" }, { "text": "Deflection of Molecules by a Homogeneous Electric Field: A New Effect: In this work, we put forward a theoretical explanation of a peculiar effect\nfound very recently (A. Gonzalez Urena et al., Chem. Phys. Lett. 341 (2001)\n495). They have observed the deflection of a beam of molecules posessing a\npermanent electric dipole moment by a homogeneous electric field when a\nresonant oscillating field is superposed transverse to the static one.", "category": "physics_chem-ph" }, { "text": "Modelling the photochrome-TiO2 interface with Bethe-Salpeter and TD-DFT\n methods: Hybrid organic/inorganic-semiconductor systems have important applications in\nboth molecular electronics and in photo-responsive materials. The\ncharacterization of the interface and of the electronic excited-states of these\nhybrid systems remains a challenge for state-of-the-art computational methods,\nas the systems of interest are large. In the present investigation, we present\nfor the first time a many-body Green's function Bethe-Salpeter investigation of\na series of photochromic molecules adsorbed onto TiO2 nanoclusters. Based on\nthese studies, the performance of TD-DFT is assessed. Using a state-of-the-art\ncomputational protocol, the photochromic properties of different hybrid systems\nare assessed. This work shows that qualitatively different conclusions can be\nreached with TD-DFT relying on various exchange-correlation functionals for\nsuch organic/inorganic interfaces, and paves the way to more accurate\nsimulation of many materials.", "category": "physics_chem-ph" }, { "text": "A Transferable H2O Interaction Potential Based on a Single Center\n Multipole Expansion: SCME: A transferable potential energy function for describing the interaction\nbetween water molecules is presented. The electrostatic interaction is\ndescribed rigorously using a multipole expansion. Only one expansion center is\nused per molecule to avoid the introduction of monopoles. This single center\napproach turns out to converge and give close agreement with ab initio\ncalculations when carried out up to and including the hexadecapole. Both dipole\nand quadrupole polarizability is included. All parameters in the electrostatic\ninteraction as well as the dispersion interaction are taken from ab initio\ncalculations or experimental measurements of a single water molecule. The\nrepulsive part of the interaction is parametrized to fit ab initio calculations\nof small water clusters and experimental measurements of ice Ih. The\nparametrized potential function was then used to simulate liquid water and the\nresults agree well with experiment, even better than simulations using some of\nthe point charge potentials fitted to liquid water. The evaluation of the new\ninteraction potential for condensed phases is fast because point charges are\nnot present and the interaction can, to a good approximation, be truncated at a\nfinite range.", "category": "physics_chem-ph" }, { "text": "Negative Capacitance and Inverted Hysteresis: Matching Features in\n Perovskite Solar Cells: Negative capacitance at the low-frequency domain and inverted hysteresis are\nfamiliar features in perovskite solar cells, where the origin is still under\ndiscussion. Here we use Impedance Spectroscopy to analyse these responses in\nmethylammonium lead bromide cells treated with lithium cation at the electron\nselective layer/perovskite interface and in iodide devices exposed to different\nrelative humidity conditions. Employing the Surface Polarization Model, we\nobtain a time constant associated to the kinetics of the interaction of\nions/vacancies with the surface, {\\tau}kin, in the range of 10^0 - 10^2 s for\nall the cases exhibiting both features. These interactions lead to a decrease\nin the overall recombination resistance, modifying the low-frequency perovskite\nresponse and yielding to a flattening of the cyclic voltammetry. As consequence\nof these results we find that that negative capacitance and inverted hysteresis\nlead to a decrease in the fill factor and photovoltage values.", "category": "physics_chem-ph" }, { "text": "Nonequilibrium Entropy: We consider an isolated system in an arbitrary state and provide a general\nformulation using first principles for an additive and non-negative statistical\nquantity that is shown to reproduce the equilibrium thermodynamic entropy of\nthe isolated system. We further show that the statistical quantity represents\nthe nonequilibrium thermodynamic entropy when the latter is a state function of\nnonequilibrium state variables; see text. We consider an isolated 1-d ideal gas\nand determine its non-equilibrium statistical entropy as a function of the box\nsize as the gas expands freely isoenergetically, and compare it with the\nequilibrium thermodynamic entropy S_{0eq}. We find that the statistical entropy\nis less than S_{0eq} in accordance with the second law, as expected. To\nunderstand how the statistical entropy is different from thermodynamic entropy\nof classical continuum models that is known to become negative under certain\nconditions, we calculate it for a 1-d lattice model and discover that it can be\nrelated to the thermodynamic entropy of the continuum 1-d Tonks gas by taking\nthe lattice spacing {\\delta} go to zero, but only if the latter is\nstate-independent. We discuss the semi-classical approximation of our entropy\nand show that the standard quantity S_{f}(t) in the Boltzmann's H-theorem does\nnot directly correspond to the statistical entropy.", "category": "physics_chem-ph" }, { "text": "A straightforward a posteriori method for reduction of density-fitting\n error in coupled-cluster calculations: We present a simple method for \\emph{a posteriori} removal of a significant\nfraction of the density-fitting error from the calculated total coupled-cluster\nenergies. The method treats the difference between the exact and density-fitted\nintegrals as a perturbation, and simplified response-like equations allow to\ncalculate improved amplitudes and the corresponding energy correction. The\nproposed method is tested at the coupled-cluster singles and doubles level of\ntheory for a diverse set of moderately-sized molecules. On average, error\nreductions by a factor of approximately ten and twenty are observed in\ndouble-zeta and triple-zeta basis sets, respectively. Similar reductions are\nobserved in calculations of interaction energies of several model complexes.\nThe computational cost of the procedure is small in comparison with the\npreceding coupled-cluster iterations. The applicability of the method is not\nlimited to the density-fitting approximation; in principle, it can be used in\nconjunction with an arbitrary decomposition scheme of the electron repulsion\nintegrals.", "category": "physics_chem-ph" }, { "text": "Surface hopping molecular dynamics simulation of ultrafast methyl iodide\n photodissociation mapped by Coulomb explosion imaging: We present a highly efficient method to directly simulate the\nphotodissociation followed by Coulomb explosion of methyl iodide. In order to\nachieve statistical reliability, more than 40,000 trajectories are calculated\non accurate potential energy surfaces of both the neutral molecule and the\ndoubly charged cation. Non-adiabatic effects during photodissociation are\ntreated using a Landau-Zener surface hopping algorithm. The simulation is\nperformed analogous to a recent pump-probe experiment using coincident ion\nmomentum imaging [Ziaee \\textit{et al., Phys. Chem. Chem. Phys.} 2023,\n\\textbf{25}, 9999]. At large pump-probe delays, the simulated delay-dependent\nkinetic energy release signals show overall good agreement with the experiment,\nwith two major dissociation channels leading to $\\text{I}(^2\\text{P}_{3/2})$\nand $\\text{I}^*(^2\\text{P}_{1/2})$ products. At short pump-probe delays, the\nsimulated kinetic energy release shows a clear bifurcation near 12 fs, owing to\nnon-adiabatic transitions through a conical intersection. The developed method\nis particularly suitable and efficient in simulating processes that highly rely\non statistics or for identifying rare reaction channels.", "category": "physics_chem-ph" }, { "text": "A Deep Autoencoder Framework for Discovery of Metastable Ensembles in\n Biomacromolecules: Mini-proteins and peptides manifest dynamic conformational fluctuation and\ninvolve mutual interconversion among metastable states. A robust mapping of the\nconformational landscape underlying mini-proteins and peptides often requires\nlow-dimensional projection of the conformational ensemble along optimized\ncollective variables. However, the traditional choice for the collective\nvariable (CV) is often limited by user-intuition and prior knowledge about the\nsystem, which lacks a rigorous assessment of their optimality over other\ncandidate CVs. To address this issue, we propose a generic approach in which we\nfirst choose the possible combinations of inter-residue Calpha-distances within\na given macromolecule as a set of input CVs. Subsequently we derive a\nnon-linear combination of latent-space embedded collective variables via\nauto-encoding the unbiased MD simulation trajectories within the framework of\nfeed-forward neural network. We demonstrate the ability of the derived latent\nspace variables in elucidating the conformational landscape in three\nhierarchically complex systems. When the conformational dynamics is resolved\nalong the latent space CVs, it identifies key metastable states of a\nbead-in-a-spring polymer. The combination of the adopted dimensionally\nreduction technique with a Markov state model, built on the derived latent\nspace, efficiently projects the free energy landscape of GB1 beta-hairpin,\nrevealing multiple spatially well-resolved and kinetically well-separated\nmetastable conformations. A quantitative comparison based on variational\napproach to Markov Process of the auto encoder-derived latent-space CVs with\nthe ones obtained PCA or TICA confirms the optimality of the former. Finally,\nas a practical application, we demonstrate that the auto-encoder derived CVs\nsuccessfully predict the reinforced folding of Trp-cage mini-protein in an\naqueous osmolyte solution.", "category": "physics_chem-ph" }, { "text": "Adsorption behavior of conjugated {C}3-oligomers on Si(100) and HOPG\n surfaces: A pi-conjugated {C}3h-oligomer involving three dithienylethylene branches\nbridged at the meta positions of a central benzenic core has been synthesized\nand deposited either on the Si(100) surface or on the HOPG surface. On the\nsilicon surface, scanning tunneling microscopy allows the observation of\nisolated molecules. Conversely, by substituting the thiophene rings of the\noligomers with alkyl chains, a spontaneous ordered film is observed on the HOPG\nsurface. As the interaction of the oligomers is different with both surfaces,\nthe utility of the Si(100) surface to characterize individual oligomers prior\nto their use into a 2D layer is discussed.", "category": "physics_chem-ph" }, { "text": "Multi-scale Mechanical Characterization of Highly Swollen\n Photo-activated Collagen Hydrogels: Biological hydrogels have been increasingly sought after as e.g. wound\ndressings or scaffolds for regenerative medicine, due to their inherent\nbiofunctionality in biological environments. Especially in moist wound healing,\nthe ideal material should absorb large amounts of wound exudate whilst\nremaining mechanically competent in-situ. Despite their large hydration,\nhowever, current biological hydrogels still leave much to be desired in terms\nof mechanical properties in physiological conditions. To address this\nchallenge, a multi-scale approach is presented for the synthetic design of\ncyto-compatible collagen hydrogels with tunable mechanical properties (from\nnano- up to the macro-scale), uniquely high swelling ratios and retained (>70%)\ntriple-helical features. Type I collagen was covalently functionalized with\nthree different monomers, i.e. 4 vinylbenzyl chloride, glycidyl methacrylate\nand methacrylic anhydride, respectively. Backbone rigidity, hydrogen-bonding\ncapability and degree of functionalization (F: 16±12 &ndash\n91±7 mol.-%) of introduced moieties governed the structure-property\nrelationships in resulting collagen networks, so that the swelling ratio\n(SR: 707±51 &ndash 1996±182 wt.-%), bulk compressive modulus\n(Ec: 30±7 &ndash 168±40 kPa) and Atomic Force\nMicroscopy elastic modulus (EAFM: 16±2 &ndash\n387±66 kPa) were readily adjusted. In light of their remarkably high\nswelling and mechanical properties, these tunable collagen hydrogels may be\nfurther exploited for the design of advanced dressings for chronic wound care.", "category": "physics_chem-ph" }, { "text": "In Situ Electron Energy-Loss Spectroscopy in Liquids: In situ scanning transmission electron microscopy (STEM) through liquids is a\npromising approach for exploring biological and materials processes. However,\noptions for in situ chemical identification are limited: X-ray analysis is\nprecluded because the liquid cell holder shadows the detector, and electron\nenergy-loss spectroscopy (EELS) is degraded by multiple scattering events in\nthick layers. Here, we explore the limits of EELS for studying chemical\nreactions in their native environments in real time and on the nanometer scale.\nThe determination of the local electron density, optical gap and thickness of\nthe liquid layer by valence EELS is demonstrated. By comparing theoretical and\nexperimental plasmon energies, we find that liquids appear to follow the\nfree-electron model that has been previously established for solids. Signals at\nenergies below the optical gap and plasmon energy of the liquid provide a high\nsignal-to-background ratio regime as demonstrated for LiFePO4 in aqueous\nsolution. The potential for using valence EELS to understand in situ STEM\nreactions is demonstrated for beam-induced deposition of metallic copper: as\ncopper clusters grow, EELS develops low-loss peaks corresponding to metallic\ncopper. From these techniques, in situ imaging and valence EELS offer insight\ninto the local electronic structure of nanoparticles and chemical reactions.", "category": "physics_chem-ph" }, { "text": "Ground state of many-electron systems based on the action function: The Hilbert space for an interacting electron system increases exponentially\nwith electron number $N$. This limits the concept of wavefunctions $\\psi$ based\non solutions of the Schr\\\"odinger equation to $N \\leq N_0$ with $N_0 \\simeq\n10^3$ \\cite{Kohn1999}. It is argued that this exponential wall problem (EWP) is\nconnected with an increasing redundance of information contained, e.g., in the\nground-state of the system and it's wavefunction. The EWP as well as redundance\nof information are avoided when the characterization of the ground state is\nbased on the action function $R$ rather than on the solutions $\\psi$ of the\nSch\\\"odinger equation. Both are related through a logarithm, i.e., $R = -i\n\\hbar \\ ln \\psi$. Working with the logarithm is made possible by the use of\ncumulants. It is pointed out the way electronic structure calculations for\nperiodic solids may use this concept.", "category": "physics_chem-ph" }, { "text": "Photoelectrochemical water splitting with ITO/WO3/BiVO4/CoPi multishell\n nanotubes fabricated by soft-templating in vacuum: A well-established procedure for the photoelectrochemical (PEC) splitting of\nwater relies on using porous electrodes of WO3 sensitized with BiVO4 as a\nvisible scavenger photoanode semiconductor. In this work, we propose an evolved\nphotoelectrode fabricated by a soft-template approach consisting of supported\nmultishell nanotubes (NTs). These NTs are formed by a concentric layered\nstructure of indium tin oxide (ITO), WO3, and BiVO4, together with a final film\nof cobalt phosphate (CoPi) co-catalyst. Photoelectrode manufacturing is easily\nimplemented at large scale and combines thermal evaporation of single\ncrystalline organic nanowires (ONWs), magnetron sputtering (for ITO and WO3),\nsolution dripping, and electrochemical deposition processes (for BiVO4 and\nCoPi, respectively) plus annealing under mild conditions. The obtained NT\nelectrodes depict a large electrochemically active surface and outperform by\nmore than one order of magnitude the efficiency of equivalent planar-layered\nelectrodes. A thorough electrochemical analysis of the electrodes under blue\nand solar light illumination demonstrates the critical role of the WO3/BiVO4\nSchottky barrier heterojunction in the control of the NT electrode efficiency\nand its dependence on the BiVO4 outer layer thickness. Oxygen evolution\nreaction (OER) performance was maximized with the CoPi electrocatalyst,\nrendering high photocurrents under one sun illumination. The reported results\ndemonstrate the potential of the soft-template methodology for the large area\nfabrication of highly efficient multishell ITO/WO3/BiVO4/CoPi NT electrodes, or\nother alternative combinations, for the photoelectrochemical splitting of\nwater.", "category": "physics_chem-ph" }, { "text": "Assessing Parameters for Ring Polymer Molecular Dynamics Simulations at\n Low Temperatures: DH+H Chemical Reaction: Ring polymer molecular dynamics (RPMD) is an accurate method for calculating\nthermal chemical reaction rates. It has recently been discovered that\nlow-temperature calculations are strongly affected by the simulation\nparameters. Here, for the thermally activated reaction DH + H -> D + H2, we\ncalculate the RPMD rate constants at T = 50, 100, and 300 K and demonstrate\nthat for T >= 100 K the standard input parameters yield accurate results, but\nat low temperatures (e.g., 50 K) one must increase the asymptotic distance and\nforce constant, and decrease the umbrella integration step.", "category": "physics_chem-ph" }, { "text": "Benchmark of dynamic electron correlation models for seniority-zero\n wavefunctions and their application to thermochemistry: Wavefunctions restricted to electron-pair states are promising models to\ndescribe static/nondynamic electron correlation effects encountered, for\ninstance, in bond-dissociation processes and transition-metal and actinide\nchemistry. To reach spectroscopic accuracy, however, the missing dynamic\nelectron correlation effects that cannot be described by electron-pair states\nneed to be included \\textit{a posteriori}. In this article, we extend the\npreviously presented perturbation theory models with an Antisymmetric Product\nof 1-reference orbital Geminal (AP1roG) reference function that allow us to\ndescribe both static/nondynamic and dynamic electron correlation effects.\nSpecifically, our perturbation theory models combine a diagonal and\noff-diagonal zero-order Hamiltonian, a single-reference and multi-reference\ndual state, and different excitation operators used to construct the projection\nmanifold. We benchmark all proposed models as well as an \\textit{a posteriori}\nlinearized coupled cluster correction on top of AP1roG against CR-CCSD(T)\nreference data for reaction energies of several closed-shell molecules that are\nextrapolated to the basis set limit. Moreover, we test the performance of our\nnew methods for multiple bond breaking processes in the N$_2$, C$_2$, and BN\ndimers against MRCI-SD and MRCI-SD+Q reference data. Our numerical results\nindicate that the best performance is obtained from a linearized coupled\ncluster correction as well as second-order perturbation theory corrections\nemploying a diagonal and off-diagonal zero-order Hamiltonian and a\nsingle-determinant dual state. These dynamic corrections on top of AP1roG allow\nus to reliably model molecular systems dominated by static/nondynamic as well\nas dynamic electron correlation.", "category": "physics_chem-ph" }, { "text": "Simulated XUV Photoelectron Spectra of THz-pumped Liquid Water: Highly intense, sub-picosecond terahertz (THz) pulses can be used to induce\nultrafast temperature jumps (T-jumps) in liquid water. A supercritical state of\ngas-like water with liquid density is established, and the accompanying\nstructural changes are expected to give rise to time-dependent chemical shifts.\nWe investigate the possibility of using extreme ultraviolet (XUV) photoelectron\nspectroscopy as a probe for ultrafast dynamics induced by sub-picosecond THz\npulses of varying intensities and frequencies. To this end, we use ab initio\nmethods to calculate photoionization cross sections and photoelectron energies\nof (H2O)$_{20}$ clusters embedded in an aqueous environment represented by\npoint charges. The cluster geometries are sampled from ab initio molecular\ndynamics simulations modeling the THz-water interactions. We find that the\npeaks in the valence photoelectron spectrum are shifted by up to 0.4 eV after\nthe pump pulse, and that they are broadened with respect to unheated water. The\nshifts can be connected to structural changes caused by the heating, but due to\nsaturation effects they are not sensitive enough to serve as a thermometer for\nT-jumped water.", "category": "physics_chem-ph" }, { "text": "Stochastic Resetting for Enhanced Sampling: We present a method for enhanced sampling of molecular dynamics simulations\nusing stochastic resetting. Various phenomena, ranging from crystal nucleation\nto protein folding, occur on timescales that are unreachable in standard\nsimulations. This is often caused by broad transition time distributions in\nwhich extremely slow events have a non-negligible probability. Stochastic\nresetting, i.e., restarting simulations at random times, was recently shown to\nsignificantly expedite processes that follow such distributions. Here, we\nemploy resetting for enhanced sampling of molecular simulations for the first\ntime. We show that it accelerates long-timescale processes by up to an order of\nmagnitude in examples ranging from simple models to molecular systems. Most\nimportantly, we recover the mean transition time without resetting - typically\ntoo long to be sampled directly - from accelerated simulations at a single\nrestart rate. Stochastic resetting can be used as a standalone method or\ncombined with other sampling algorithms to further accelerate simulations.", "category": "physics_chem-ph" }, { "text": "Steric effects of CO2 binding to transition metal-benzene complexes: a\n first-principles study: Using density functional theory (DFT) calculations, we investigated the\nadsorption of CO2 molecules on 3d transition metal (TM)-benzene complexes. Our\ncalculations show that the maximum number of CO2 molecules adsorbable on Sc or\nTi atoms is three, but the 18-electron rule predicts it should be four. The\n18-electron rule is generally successful in predicting the maximum H2\nadsorption number for TM atoms including Sc or Ti atoms. We found that the\n18-electron rule fails to correctly predict CO2 binding on Sc- or Ti-benzene\ncomplexes because CO2 binding, in contrast to H2 binding, requires additional\nconsideration for steric hindrance due to the large bond length of CO2. We\ncalculated the occupation function for CO2 using the Tolman cone angle, which\nshows that three CO2 molecules fully occupy the available space around Sc- and\nTi-benzene complexes. This estimation is the same maximum CO2 adsorption number\npredicted by DFT calculations. Therefore, we propose that the occupation\nfunction for CO2 using the Tolman cone angle is an efficient model for\nevaluating steric hindrance of CO2 adsorption on a surface.", "category": "physics_chem-ph" }, { "text": "Polaritonic Coupled-Cluster Theory: We develop coupled-cluster theory for systems of electrons strongly coupled\nto photons, providing a promising theoretical tool in polaritonic chemistry\nwith a perspective of application to all types of fermion-boson coupled\nsystems. We show benchmark results for model molecular Hamiltonians coupled to\ncavity photons. By comparing to full configuration interaction results for\nvarious ground-state properties and optical spectra, we demonstrate that our\nmethod captures all key features present in the exact reference, including Rabi\nsplittings and multi-photon processes. Further, a path on how to incorporate\nour bosonic extension of coupled-cluster theory into existing quantum chemistry\nprograms is given.", "category": "physics_chem-ph" }, { "text": "Full- and reduced-dimensionality instanton calculations of the\n tunnelling splitting in the formic acid dimer: The ring-polymer instanton approach is applied to compute the ground-state\ntunnelling splitting of four isotopomers of the formic acid dimer using the\naccurate PES of Qu and Bowman [Phys. Chem. Chem. Phys., 2016, 18, 24835]. As\nwell as performing the calculations in full dimensionality, we apply a\nreduced-dimensionality approach to study how the results converge as\nsuccessively more degrees of freedom are included. The instanton approximation\ncompares well to exact quantum results where they are available but shows that\nnearly all the modes are required to quantitatively obtain the tunnelling\nsplitting. The full-dimensional instanton calculation reproduces the\nexperimental results, with an error of only about 20 percent.", "category": "physics_chem-ph" }, { "text": "Influence of chemical kinetics on detonation initiating by temperature\n gradients in methane/air: Different simplified and detailed chemical models and their impact on\nsimulations of combustion regimes initiating by the initial temperature\ngradient in methane/air mixtures are studied. The limits of the regimes of\nreaction wave propagation depend upon the spontaneous wave speed and the\ncharacteristic velocities of the problem. The present study mainly focus to\nidentify conditions required for the development a detonation and to compare\nthe difference between simplified chemical models and detailed chemistry. It is\nshown that a widely used simplified chemical schemes, such as one-step,\ntwo-step and other simplified models, do not reproduce correctly the ignition\nprocess in methane/air mixtures. The ignition delay times calculated using\nsimplified models are in orders of magnitude shorter than the ignition delay\ntimes calculated using detailed chemical models and measured experimentally.\nThis results in considerably different times when the exothermic reaction\naffects significantly the ignition, evolution, and coupling of the spontaneous\nreaction wave and pressure waves. We show that the temperature gradient capable\nto trigger detonation calculated using detailed chemical models is much\nshallower (the size of the hot spot is much larger) than that, predicted by\nsimulations with simplified chemical models. These findings suggest that the\nscenario leading to the deflagration to detonation transition (DDT) may depend\ngreatly on the chemical model used in simulations and that the Zeldovich\ngradient mechanism is not necessary a universal mechanism triggering DDT. The\nobtained results indicate that the conclusions derived from the simulations of\nDDT with simplified chemical models should be viewed with great caution.", "category": "physics_chem-ph" }, { "text": "Role of silicon and carbon on the structural and electrochemical\n properties of Si-Ni$_{3.4}$Sn$_4$-Al-C anodes for Li-ion batteries: Varying the amounts of silicon and carbon, different composites have been\nprepared by ball milling of Si, Ni$_{3.4}$Sn$_4$, Al and C. Silicon and carbon\ncontents are varied from 10 to 30 wt.% Si, and 0 to 20 wt.% C. The\nmicrostructural and electrochemical properties of the composites have been\ninvestigated by X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and\nelectrochemical galvanostatic cycling up to 1000 cycles. Impact of silicon and\ncarbon contents on the phase occurrence, electrochemical capacity and\ncycle-life are compared and discussed. For C-content comprised between 9 and 13\nwt.% and Si-content >= 20 wt.%, Si nanoparticles are embedded in a\nNi$_{3.4}$Sn$_4$-Al-C matrix which is chemically homogeneous at the micrometric\nscale. For other carbon contents and low Si-amount (10 wt.%), no homogeneous\nmatrix is formed around Si nanoparticles. When homogenous matrix is formed,\nboth Ni$_3$Sn$_4$ and Si participate to the reversible lithiation mechanism,\nwhereas no reaction between Ni$_3$Sn$_4$ and Li is observed for no homogenous\nmatrix. Moreover, best cycle-life performances are obtained when Si\nnanoparticles are embedded in a homogenous matrix and Si-content is moderate\n(<= 20 wt.%). Composites with carbon in the 9-13 wt.% range and 20 wt.% silicon\nlead to the best balance between capacity and life duration upon cycling. This\nwork experimentally demonstrates that embedding Si in an intermetallic/carbon\nmatrix allows to efficiently accommodate Si volume changes on cycling to ensure\nlong cycle-life.", "category": "physics_chem-ph" }, { "text": "Properties of Liquid Clusters in Large-scale Molecular Dynamics\n Nucleation Simulations: We have performed large-scale Lennard-Jones molecular dynamics simulations of\nhomogeneous vapor-to-liquid nucleation, with $10^9$ atoms. This large number\nallows us to resolve extremely low nucleation rates, and also provides\nexcellent statistics for cluster properties over a wide range of cluster sizes.\nThe nucleation rates, cluster growth rates, and size distributions are\npresented in Diemand et al. [J. Chem. Phys. {\\bf 139}, 74309 (2013)], while\nthis paper analyses the properties of the clusters. We explore the cluster\ntemperatures, density profiles, potential energies and shapes. A thorough\nunderstanding of the properties of the clusters is crucial to the formulation\nof nucleation models. Significant latent heat is retained by stable clusters,\nby as much as $\\Delta kT = 0.1 \\epsilon$ for clusters with size $i = 100$. We\nfind that the clusters deviate remarkably from spherical - with ellipsoidal\naxis ratios for critical cluster sizes typically within $b/c = 0.7\\pm 0.05$ and\n$a/c = 0.5 \\pm 0.05$. We examine cluster spin angular momentum, and find that\nit plays a negligible role in the cluster dynamics. The interfaces of large,\nstable clusters are thiner than planar equilibrium interfaces by $10-30\\%$. At\nthe critical cluster size, the cluster central densities are between $5-30\\%$\nlower than the bulk liquid expectations. These lower densities imply\nlarger-than-expected surface areas, which increase the energy cost to form a\nsurface, which lowers nucleation rates.", "category": "physics_chem-ph" }, { "text": "Spatial Separation of the Conformers of Methyl Vinyl Ketone: Methyl vinyl ketone (C$_4$H$_6$O) is a volatile, labile organic compound of\nimportance in atmospheric chemistry. We prepared a molecular beam of methyl\nvinyl ketone with a rotational temperature of 1.2(2)~K and demonstrated the\nspatial separation of the \\emph{s-cis} and \\emph{s-trans} conformers of methyl\nvinyl ketone using the electrostatic deflector. The resulting sample density\nwas $1.5(2)\\times10^{8}~\\text{cm}^{-3}$ for the direct beam in the laser\nionization region. These conformer-selected methyl vinyl ketone samples are\nwell suited for conformer-specific chemical reactivity studies such as in\nDiels-Alder cycloaddition reactions.", "category": "physics_chem-ph" }, { "text": "Converged Colored Noise Path Integral Molecular Dynamics Study of the\n Zundel Cation down to Ultra-low Temperatures at Coupled Cluster Accuracy: For a long time, performing converged path integral simulations at ultra-low,\nbut finite temperatures of a few Kelvin has been a nearly impossible task.\nHowever, recent developments in advanced colored noise thermostatting schemes\nfor path integral simulations, namely the Path Integral Generalized Langevin\nEquation Thermostat (PIGLET) and the Path Integral Quantum Thermal Bath\n(PIQTB), have been able to greatly reduce the computational cost of these\nsimulations, thus making the ultra-low temperature regime accessible in\npractice. In this work, we investigate the influence of these two\nthermostatting schemes on the description of hydrogen-bonded systems at\ntemperatures down to a few Kelvin as encountered, for example, in helium\nnanodroplet isolation or tagging photodissociation spectroscopy experiments.\nFor this purpose, we analyze the prototypical hydrogen bond in the Zundel\ncation (H$_5$O$_{2}^{+}$) as a function of both, oxygen-oxygen distance and\ntemperature in order to elucidate how the anisotropic quantum delocalization\nand, thus, the shape of the shared proton adapts depending on the\ndonor-acceptor distance. The underlying electronic structure of the Zundel\ncation is described in terms of Behler's Neural Network Potentials of\nessentially converged Coupled Cluster accuracy, CCSD(T*)-F12a/AVTZ. In\naddition, the performances of the PIQTB and PIGLET methods for energetic,\nstructural, and quantum delocalization properties are assessed and directly\ncompared. Overall, our results emphasize the validity and practical usefulness\nof these two modern thermostatting approaches for path integral simulations of\nhydrogen-bonded systems even at ultra-low temperatures.", "category": "physics_chem-ph" }, { "text": "Approaching exact hyperpolarizabilities via sum-over-states Monte Carlo\n configuration interaction: We propose using sum-over-states calculations with the compact wavefunctions\nof Monte Carlo configuration interaction to approach accurate values for\nhigher-order dipole properties up to second hyperpolarizabilities in a\ncontrolled way. We apply the approach to small systems that can generally be\ncompared with full configuration interaction (FCI) results. We consider\nhydrogen fluoride with a 6-31g basis and then look at results, including\nfrequency dependent properties, in an aug-cc-pVDZ basis. We extend one\ncalculation beyond FCI by using an aug-cc-pVTZ basis. The properties of an\nH$_{4}$ molecule with multireference character are calculated in an aug-cc-pVDZ\nbasis. We then investigate this method on a strongly multireference system with\na larger FCI space by modelling the properties of carbon monoxide with a\nstretched geometry. The behavior of the approach with increasing basis size is\nconsidered by calculating results for the neon atom using aug-cc-pVDZ to\naug-cc-pVQZ. We finally test if the unusual change in polarizability between\nthe first two states of molecular oxygen can be reproduced by this method in a\n6-31g basis.", "category": "physics_chem-ph" }, { "text": "Solvation-induced one-dimensional polarons and electron transfer: When a one-dimensional (1D) semiconductor nanostructure is immersed in a\nsluggish polar solvent, fluctuations of the medium may result in the appearance\nof localized electronic levels inside the band gap. An excess charge carrier\ncan occupy such a level and undergo self-localization into a large-radius\nadiabatic polaron surrounded by a self-consistent medium polarization pattern.\nWithin an appropriately adapted framework of the Marcus theory, we explore the\ndescription and qualitative picture of thermally activated electron transfer\ninvolving solvation-induced polaronic-like states by considering transfer\nbetween small and 1D species as well as between two 1D species. Illustrative\ncalculations are performed for tubular geometries with possible applications to\ncarbon nanotube systems.", "category": "physics_chem-ph" }, { "text": "Obtaining transferable chemical insight from solving machine-learning\n classification problems: Thermodynamical properties prediction, atomic\n composition as good as Coulomb matrix: Machine learning (ML) can be used to construct surrogate models for the fast\nprediction of a property of interest. ML can thus be applied to chemical\nprojects, where the usual experimentation or calculation techniques can take\nhours or days for just one sample. In this manner, the most promising candidate\nsamples could be extracted from an extensive database and subjected to further\nin-depth analysis.\n Despite their broad applicability, it can be challenging to apply ML methods\nto a given chemical problem since a multitude of design decisions must be made,\nsuch as the molecular descriptor to use or the optimizer to train the model.\n Here we present a methodology for the meaningful exploration of a given\nmolecular problem through classification experiments. This conceptually simple\nmethodology results in transferable insight on the selected problem and can be\nused as a platform from which prediction difficulty is estimated, molecular\nrepresentations are tested and refined, and more precise or ambitious projects\ncan be undertaken. Physicochemical insight can also be obtained.\n This methodology is illustrated through the use of multiple molecular\ndescriptors for the prediction of enthalpy, Gibbs' free energy, zero-point\nvibrational energy, and constant-volume calorific capacity of the molecules\nfrom the public database QM9 [Ramakrishnan2014] with 133,885 organic molecules.\nA noteworthy result is that for the classification problem we propose, the\nlow-resolution descriptor `atomic composition' [Tchagang2019] can reach a\nclassification rate almost on par with the high-resolution `sorted Coulomb\nmatrix' [Rupp2012,Montavon2012,Hansen2013] ($>90\\%$), provided that an\nappropriate optimizer is used during training.", "category": "physics_chem-ph" }, { "text": "TDSVD: A Way to Get The Single Solution From TR-Spectroscopy: This article reminds us the major contribution of orthogonality towards the\nESS assignment in TR-spectroscopy. In the field of particles, complete\northogonality is ubiquitous between any two different identical particles, and\nthe complete orthogonality (at the microscopic level) evolves into the partial\nspectral orthogonality between different ESSs at the mesoscopic level. As a\nresult, we developed SVD to TDSVD so as to reveal the relative amounts of\ndifferent ESSs in each time interval, and it is the first time that the single\nsolution can be drew from only the TA data set without any kinds of a priori\ninformation. In the previous articles, the mathematical underdetermination\nproblem has been addressed prominently, so it is no wonder that researchers are\nno longer keening to search the method for mathematically analyzing the data\nset in order to derive the single solution. However, TDSVD will offset this\ndeficiency and becomes an effectively autonomous method towards two-dimensional\ndata analysis. Mathematically, as long as there is enough orthogonality between\nany two 'ESSs' in any data set, the yield of the single solution is no longer a\nproblem. Therefore, TDSVD can be applied to lots of fields.", "category": "physics_chem-ph" }, { "text": "The Critical Effect of Hydration on the Resonant Signatures of THz\n Biospectroscopy: Here we present an original study of the effect of hydration on Terahertz\nabsorption signatures in biomolecular (lactose monohydrate and biotin) and\nbioparticles( Bacillus thuringiensis and Bacillus cereus spores). We observe\n\"read-shift\" in center frequency with increasing hydration in all samples,\nconsistent with Lorentzian-oscillator behavior. But the effect of hydration on\nlinewidth is ambiguous, sometimes increasing the linewdith (consistent with\nLorentzian behaviour) and sometimes decreasing the linewidth.", "category": "physics_chem-ph" }, { "text": "Sampling mobility profiles of confined fluids with equilibrium molecular\n dynamics simulations: We show how to evaluate mobility profiles, characterizing the transport of\nconfined fluids under a perturbation, from equilibrium molecular simulations.\nThe correlation functions derived with the Green-Kubo formalism are difficult\nto sample accurately and we consider two complementary strategies: improving\nthe spacial sampling thanks to a new estimator of the local fluxes involving\nthe forces acting on the particles in addition to their positions and\nvelocities, and improving temporal sampling thanks to the Einstein-Helfand\napproach instead of the Green-Kubo one. We illustrate this method on the case\nof a binary mixture confined between parallel walls, under a pressure or\nchemical potential gradient. All equilibrium methods are compared to standard\nnon-equilibrium molecular dynamics (NEMD) and provide the correct mobility\nprofiles. We recover quantitatively fluid viscosity and diffusio-osmostic\nmobility in the bulk part of the pore. Interestingly, the matrix of mobility\nprofiles for local fluxes is not symmetric, unlike the Onsager matrix for the\ntotal fluxes. Even the most computationally efficient equilibrium method\n(Einstein-Helfand combined with the force-based estimator) remains less\nefficient than NEMD to determine a single mobility profile. However, the\nequilibrium approach provides all responses to all perturbations\nsimultaneously, whereas NEMD requires the simulation of several types of\nperturbations to determine the various responses, each with different\nmagnitudes to check the validity of the linear regime. While NEMD seems more\ncompetitive for the present example, the balance should be different for more\ncomplex systems, in particular for electrolyte solutions for the responses to\npressure, salt concentration and electric potential gradients.", "category": "physics_chem-ph" }, { "text": "Introduction to Classical Density Functional Theory by a Computational\n Experiment: We propose an in-silico experiment to introduce classical density functional\ntheory (cDFT). Den- sity functional theories, whether quantum or classical,\nrely on abstract concepts that are non- intuitive. However, they are at the\nheart of powerful tools and active fields of research in both physics and\nchemistry. They led to the 1998 Nobel Prize in chemistry. DFT is illustrated\nhere in its most simple and yet physically relevant form: the classical density\nfunctional theory of an ideal fluid of classical particles. For illustration\npurpose, it is applied to the prediction of the molecular structure of liquid\nneon. The numerical experiment proposed therein is built around the writing of\na cDFT code by students in Mathematica. Students thus have to deal with (i) the\ncDFT theory, (ii) some basic concepts of statistical mechanics of simple\nfluids, (iii) functional minimization, and (iv) a useful functional programming\nlanguage. This computational experiment is proposed during a molecular\nsimulation class, but may also be of interest in a quantum chemistry class to\nillustrate electronic DFT, if one highlights the analogies between the quantum\nand classical DFTs.", "category": "physics_chem-ph" }, { "text": "Heavy atom quantum diffraction by scattering from surfaces: Typically one expects that when a heavy particle collides with a surface, the\nscattered angular distribution will follow classical mechanics. The heavy mass\nassures that the de Broglie wavelength of the incident particle in the\ndirection of the propagation of the particle (the parallel direction) will be\nmuch shorter than the characteristic lattice length of the surface, thus\nleading to a classical description. Recent work on molecular interferometry has\nshown that by increasing the perpendicular coherence length, one may observe\ninterference of very heavy species passing through a grating. Here we show,\nusing quantum mechanical simulations, that the same effect will lead to quantum\ndiffraction of heavy particles colliding with a surface. We find that the\neffect is robust with respect to the incident energy, the angle of incidence\nand the mass of the particle. It may also be used to verify the quantum nature\nof the surface and its fluctuations at very low temperatures.", "category": "physics_chem-ph" }, { "text": "New Insight into the Ground State of FePc: A Diffusion Monte Carlo Study: We have applied DMC to evaluate relative stability of the possible electronic\nconfigurations of an isolated FePc under $D_{4h}$ symmetry, considering some\nfixed nodes generated from different methods. They predict $A_{2g}$ ground\nstate consistently, supporting preceding DFT studies, with confidence\novercoming the ambiguity about exchange-correlation (XC) functionals. By\ncomparing DMC with several XC, we clarified the importance of the short range\nexchange to describe the relative stability. We examined why the predicted\n$A_{2g}$ is excluded from possible ground states in the recent ligand field\nbased model. Simplified assumptions made in the superposition model are\nidentified to give unreasonably less energy gain for $A_{2g}$ when compared\nwith the reality. The state is found to have possible reasons for the\nstabilization, reducing the occupations from an unstable anti-bonding orbital,\navoiding double occupation of a spatially localized orbital, and gaining\nexchange energy by putting a triplet spin pair in degenerate orbitals.", "category": "physics_chem-ph" }, { "text": "Mechanism of Cold-spot Autoignition in a Hydrogen/Air Mixture: When designing high-efficiency spark-ignition (SI) engines to operate at high\ncompression ratios, one of the main issues that have to be addressed is\ndetonation development from a pre-ignition front. In order to control this\nphenomenon, it is necessary to understand the mechanism by which the detonation\nis initiated. The development of a detonation from a pre-ignition front was\nanalyzed by considering a one-dimensional constant-volume stoichiometric\nhydrogen/air reactor with detailed chemistry. A spatially linear initial\ntemperature profile near the end-wall was employed, in order to account for the\nthermal stratification of the bulk mixture. A flame was initiated near the left\nwall and the effects of its propagation towards the cold end-wall were\nanalyzed. Attention was given on the autoignition that is manifested within the\ncold-spot ahead of the flame and far from the end-wall, which is followed by\ndetonation. Using CSP tools, the mechanism by which the generated pressure\nwaves influence the autoignition within the cold-spot was investigated. It is\nfound that the pressure oscillations induced by the reflected pressure waves\nand the pressure waves generated by the pre-ignition front tend to synchronize\nin the chamber, increasing the reactivity of the system in a periodic manner.\nThe average of the oscillating temperature is greater in the cold-spot,\ncompared to all other points ahead of the flame. As a result, the rate\nconstants of the most important reactions are larger there, leading to a more\nreactive state that accelerates the dynamics of the cold-spot and to its\nautoignition.", "category": "physics_chem-ph" }, { "text": "Molecular Parity Nonconservation in Nuclear Spin Couplings: The weak interaction does not conserve parity, which is apparent in many\nnuclear and atomic phenomena. However, thus far, parity nonconservation has not\nbeen observed in molecules. Here we consider nuclear-spin-dependent parity\nnonconserving contributions to the molecular Hamiltonian. These contributions\ngive rise to a parity nonconserving indirect nuclear spin-spin coupling which\ncan be distinguished from parity conserving interactions in molecules of\nappropriate symmetry, including diatomic molecules. We estimate the magnitude\nof the coupling, taking into account relativistic corrections. Finally, we\npropose and simulate an experiment to detect the parity nonconserving coupling\nusing liquid- or gas-state zero-field nuclear magnetic resonance of\nelectrically oriented molecules and show that $^{1}$H$^{19}$F should give\nsignals within the detection limits of current atomic vapor-cell magnetometers.", "category": "physics_chem-ph" }, { "text": "Analytical Potential Energy Function for the Ground State X^{1} Sigma^+\n of LaCl: The equilibrium geometry, harmonic frequency and dissociation energy of\nlanthanum monochloride have been calculated at B3LYP, MP2, QCISD(T) levels with\nenergy-consistent relativistic effective core potentials. The possible\nelectronic state and reasonable dissociation limit for the ground state are\ndetermined based on atomic and molecular reaction statics. Potential energy\ncurve scans for the ground state X^{1} Sigma^+ have been carried out with B3LYP\nand QCISD(T) methods due to their better performance in bond energy\ncalculations. We find the potential energy calculated with QCISD(T) method is\nabout 0.5 eV larger than dissociation energy when the diatomic distance is as\nlarge as 0.8 nm. The problem that single-reference ab initio methods don't meet\ndissociation limit during calculations of lanthanide heavy-metal elements is\nanalyzed. We propose the calculation scheme to derive analytical Murrell-Sorbie\npotential energy function and Dunham expansion at equilibrium position.\nSpectroscopic constants got by standard Dunham treatment are in good agreement\nwith results of rotational analyses on spectroscopic experiments. The\nanalytical function is of much realistic importance since it is possible to be\napplied to predict fine transitional structure and study reaction dynamic\nprocess.", "category": "physics_chem-ph" }, { "text": "Benchmark calculations for reduced density-matrix functional theory: Reduced density-matrix functional theory (RDMFT) is a promising alternative\napproach to the problem of electron correlation. Like standard density\nfunctional theory, it contains an unknown exchange-correlation functional, for\nwhich several approximations have been proposed in the last years. In this\narticle, we benchmark some of these functionals in an extended set of molecules\nwith respect to total and atomization energies. Our results show that the most\nrecent RDMFT functionals give very satisfactory results compared to more\ninvolved quantum chemistry and density functional approaches.", "category": "physics_chem-ph" }, { "text": "A simple strategy for enhanced production of nanoparticles by laser\n ablation in liquids: Upgrading the productivity of nanoparticles (NPs), generated by pulsed laser\nablation in liquid (PLAL), still remains challenging. Here a novel variant of\nPLAL was developed, where a doubled frequency Nd:YAG laser beam (532 nm, ~ 5\nns, 10 Hz) at different fluences and for different times was directed into a\nsealed vessel, toward the interface of the meniscus of ethanol with a tilted\nbulk metal target. Palladium, copper and silver NPs, synthesized in the\nperformed proof of concept experiments, were mass quantified, by an inductively\ncoupled plasma optical emission spectrometry, and characterized by\nultraviolet-visible extinction spectroscopy, transmission electron microscopy\nand X-ray diffraction. The NPs consist of crystalline metals of a few nm size\nand their ablation rates and agglomeration levels depend on the employed laser\nfluences. The ensuing laser power-specific productivity curves for each metal,\npeaked at specific laser fluences, were fitted to the results of a simple model\naccounting for plasma absorption and heat transfer. The resulting peaked yields\nand concentrations were more than an order of magnitude higher than those\nobtained for totally immersed targets. Besides, the measured productivities\nshowed nearly linear dependencies during time intervals up to 30 min of\nablation, but became saturated at 1 h, due to accumulation of a significant\nnumber of NPs along the laser beam path, reducing the laser intensity reaching\nthe target. This suggested approach could inspire future studies that will\ncontribute to further developments of efficient generation of NPs with\ncontrolled characteristics.", "category": "physics_chem-ph" }, { "text": "Pathfinder -- Navigating and Analyzing Chemical Reaction Networks with\n an Efficient Graph-based Approach: While the field of first-principles explorations into chemical reaction space\nhas been continuously growing, the development of strategies for analyzing\nresulting chemical reaction networks (CRNs) is lagging behind. A CRN consists\nof compounds linked by reactions. Analyzing how these compounds are transformed\ninto one another based on kinetic modeling is a nontrivial task. Here, we\npresent the graph-optimization-driven algorithm and program Pathfinder to allow\nfor such an analysis of a CRN. The CRN for this work has been obtained with our\nopen-source Chemoton reaction network exploration software. Chemoton probes\nreactive combinations of compounds for elementary steps and sorts them into\nreactions. By encoding these reactions of the CRN as a graph consisting of\ncompound and reaction vertices and adding information about activation barriers\nas well as required reagents to the edges of the graph yields a complete\ngraph-theoretical representation of the CRN. Since the probabilities of the\nformation of compounds depend on the starting conditions, the consumption of\nany compound during a reaction must be accounted for to reflect the\navailability of reagents. To account for this, we introduce compound costs to\nreflect compound availability. Simultaneously, the determined compound costs\nrank the compounds in the CRN in terms of their probability to be formed. This\nranking then allows us to probe easily accessible compounds in the CRN first\nfor further explorations into yet unexplored terrain. We first illustrate the\nworking principle on an abstract small CRN. Afterward, Pathfinder is\ndemonstrated in the example of the disproportionation of iodine with water and\nthe comproportionation of iodic acid and hydrogen iodide. Both processes are\nanalyzed within the same CRN which we construct with our autonomous\nfirst-principles CRN exploration software Chemoton guided by Pathfinder.", "category": "physics_chem-ph" }, { "text": "Many-body Hamiltonians in implicitly defined frames: We study the quantization of three-dimensional many-body systems in rotating\ncoordinate frames defined implicitly by frame conditions. We carry out the\nelimination of orientational degrees of freedom in general, giving the\nHamiltonian for the $N$-particle system in a broad class of body frames in\nterms of frame conditions and internal coordinates. We obtain several forms for\nthe kinetic energy operator and compare them to related expressions in the\nliterature.", "category": "physics_chem-ph" }, { "text": "The conceptual and mathematical foundations of the MC-QTAIM: The concept of atoms in molecules (AIM) is one of the cornerstones of the\nstructural theory of chemistry however, in contrast to the free atoms a\ncomprehensive quantum mechanical theory of AIM has never been proposed.\nCurrently the most satisfactory deduction of this concept is based on the\npartitioning methodologies that are trying to recover AIM from the ab initio\nwavefunctions (WF). One of these methodologies is the quantum theory of AIM\n(QTAIM), which retrieves AIM by an exhaustive partitioning of the one-electron\ndensity into atomic basins in real space. The molecular properties are then\npartitioned into the basin and inter-basin contributions as the incarnation of\nthe AIM properties and their interaction modes. The inputs of the QTAIM\npartitioning scheme are the electronic WF computed from the electronic\nSchrodinger equation (SE), which is basically a single-component equation\ntreating electrons as quantum particles and the nuclei as clamped point charges\n(CPC). A recently extended form of the QTAIM, called the multi-component QTAIM\n(MC-QTAIM), removes this restriction and enables AIM partitioning to be applied\nto the MC quantum systems. This is done using MC-WF as inputs that are derived\nfrom the MC-SE in which there are two or more types of quantum particles. This\nopens the possibility for the AIM partitioning of molecular systems where\ncertain nuclei, e.g. because of their non-adiabatic coupling to electrons, must\nbe treated as quantum particles instead of CPC. The same formalism allows the\npartitioning of exotic molecular systems in which there are other elementary\nparticles like muons or positrons, in addition to electrons and nuclei. The\napplication of the MC-QTAIM partitioning to such systems reveals that the\npositively charged muon may shape its own atomic basin, i.e. an example of\nexotic AIM, while positron may act as an agent of bonding, i.e. an example of\nexotic bonds.", "category": "physics_chem-ph" }, { "text": "Broadband 180 degree universal rotation pulses for NMR spectroscopy\n designed by optimal control: Broadband inversion pulses that rotate all magnetization components 180\ndegrees about a given fixed axis are necessary for refocusing and mixing in\nhigh-resolution NMR spectroscopy. The relative merits of various methodologies\nfor generating pulses suitable for broadband refocusing are considered. The de\nnovo design of 180 degree universal rotation pulses using optimal control can\nprovide improved performance compared to schemes which construct refocusing\npulses as composites of existing pulses. The advantages of broadband universal\nrotation by optimized pulses (BURBOP) are most evident for pulse design that\nincludes tolerance to RF inhomogeneity or miscalibration. We present new\nmodifications of the optimal control algorithm that incorporate symmetry\nprinciples and relax conservative limits on peak RF pulse amplitude for short\ntime periods that pose no threat to the probe. We apply them to generate a set\nof pulses suitable for widespread use in Carbon-13 spectroscopy on the majority\nof available probes.", "category": "physics_chem-ph" }, { "text": "Composite materials with uncured epoxy matrix exposed in stratosphere\n during NASA stratospheric balloon flight: A cassette of uncured composite materials with an epoxy resin matrix was\nexposed in the stratosphere (40 km altitude) over 3 days. Temperature\nvariations of -76...+32.50C and pressure up to 2.1 Torr were recorded during\nflight. An analysis of the chemical structure of the composites showed, that\nthe polymer matrix exposed in the stratosphere becomes crosslinked, while the\nground control materials react by way of polycondensation reaction of epoxy\ngroups. The space irradiations are considered to be responsible for\ncrosslinking of the uncured polymers exposed in the stratosphere. The\ncomposites were cured on Earth after landing. Analysis of the cured composites\nshowed, that the polymer matrix remains active under stratospheric conditions.\nThe results can be used for predicting curing processes of polymer composite in\na free space environment during an orbital space flight.", "category": "physics_chem-ph" }, { "text": "Collision-induced three-body polarizability of helium: We present first-principles theoretical determination of the three-body\npolarizability and the third dielectric virial coefficient of helium.\nCoupled-cluster theory and the full configuration interaction procedure were\nused to perform required electronic structure calculations. The mean absolute\nrelative uncertainty of the trace of the three-body polarizability tensor,\nresulting from the incompleteness of orbital basis set, was determined using\nextrapolation techniques. Additional uncertainty due to approximate treatment\nof triple and the neglect of higher excitations was estimated using full\nconfiguration interaction calculations. An analytic function was developed to\ndescribe the behavior of the polarizability and its asymptotic decay to\nthree-atomic and atom-diatom fragmentation channels. We also developed an\nanalytic function describing the local behavior of the total uncertainty of our\ncalculations. Using both fits we calculated the third dielectric virial\ncoefficient and its uncertainty using the classical and semiclassical\nFeynman-Hibbs approaches. The results of our calculations were compared with\navailable experimental data and with recent Path-Integral Monte Carlo (PIMC)\ncalculations employing the so-called superposition approximation of the\nthree-body polarizability. For temperatures above 200 K we observed significant\ndiscrepancy between the classical results obtained using either the\nsuperposition approximation or the ab initio computed polarizability. The\ntheoretical data reported in this work eliminate the main accuracy bottleneck\nof the development of optical pressure standard and are expected to facilitate\nfurther progress in the field of quantum thermal metrology", "category": "physics_chem-ph" }, { "text": "Simulation-based inference of single-molecule force spectroscopy: Single-molecule force spectroscopy (smFS) is a powerful approach to studying\nmolecular self-organization. However, the coupling of the molecule with the\never-present experimental device introduces artifacts, that complicates the\ninterpretation of these experiments. Performing statistical inference to learn\nhidden molecular properties is challenging because these measurements produce\nnon-Markovian time-series, and even minimal models lead to intractable\nlikelihoods. To overcome these challenges, we developed a computational\nframework built on novel statistical methods called simulation-based inference\n(SBI). SBI enabled us to directly estimate the Bayesian posterior, and extract\nreduced quantitative models from smFS, by encoding a mechanistic model into a\nsimulator in combination with probabilistic deep learning. Using synthetic\ndata, we could systematically disentangle the measurement of hidden molecular\nproperties from experimental artifacts. The integration of physical models with\nmachine learning density estimation is general, transparent, easy to use, and\nbroadly applicable to other types of biophysical experiments.", "category": "physics_chem-ph" }, { "text": "The Many Faces of Heterogeneous Ice Nucleation: Interplay Between\n Surface Morphology and Hydrophobicity: What makes a material a good ice nucleating agent? Despite the importance of\nheterogeneous ice nucleation to a variety of fields, from cloud science to\nmicrobiology, major gaps in our understanding of this ubiquitous process still\nprevent us from answering this question. In this work, we have examined the\nability of generic crystalline substrates to promote ice nucleation as a\nfunction of the hydrophobicity and the morphology of the surface. Nucleation\nrates have been obtained by brute-force molecular dynamics simulations of\ncoarse-grained water on top of different surfaces of a model fcc crystal,\nvarying the water-surface interaction and the surface lattice parameter. It\nturns out that the lattice mismatch of the surface with respect to ice,\ncustomarily regarded as the most important requirement for a good ice\nnucleating agent, is at most desirable but not a requirement. On the other\nhand, the balance between the morphology of the surface and its hydrophobicity\ncan significantly alter the ice nucleation rate and can also lead to the\nformation of up to three different faces of ice on the same substrate. We have\npinpointed three circumstances where heterogeneous ice nucleation can be\npromoted by the crystalline surface: (i) the formation of a water overlayer\nthat acts as an in-plane template; (ii) the emergence of a contact layer\nbuckled in an ice-like manner; and (iii) nucleation on compact surfaces with\nvery high interaction strength. We hope that this extensive systematic study\nwill foster future experimental work aimed at testing the physiochemical\nunderstanding presented herein.", "category": "physics_chem-ph" }, { "text": "Generalised single particle models for high-rate operation of graded\n lithium-ion electrodes: systematic derivation and validation: A derivation of the single particle model (SPM) is made from a porous\nelectrode theory model (or Newman model) of half-cell (dis)charge for an\nelectrode composed of uniformly sized spherical electrode particles of a single\nchemistry. The derivation uses a formal asymptotic method based on the\ndisparity between the size of the thermal voltage and that of the\ncharacteristic change in overpotential that occurs during (de)lithiation.\nComparison is made between solutions to the SPM and to the porous electrode\ntheory (PET) model for NMC, graphite and LFP. These are used to identify\nregimes where the SPM gives accurate predictions. For most chemistries, even at\nmoderate (dis)charge rates, there are appreciable discrepancies between the PET\nmodel and the SPM which can be attributed to spatial non-uniformities in the\nelectrolyte. This motivates us to calculate a correction term to the SPM. Once\nthis has been incorporated into the model its accuracy is significantly\nimproved. Generalised versions of the SPM, that can describe graded electrodes\ncontaining multiple electrode particle sizes (or chemistries), are also\nderived. The results of the generalised SPM, with the correction term, compare\nfavourably to the full PET model where the active electrode material is either\nNMC or graphite.", "category": "physics_chem-ph" }, { "text": "Effects of ultrafast molecular rotation on collisional decoherence: Using an optical centrifuge to control molecular rotation in an extremely\nbroad range of angular momenta, we study coherent rotational dynamics of\nnitrogen molecules in the presence of collisions. We cover the range of\nrotational quantum numbers between J=8 and J=66 at room temperature and study a\ncross-over between the adiabatic and non-adiabatic regimes of rotational\nrelaxation, which cannot be easily accessed by thermal means. We demonstrate\nthat the rate of rotational decoherence changes by more than an order of\nmagnitude in this range of J values, and show that its dependence on J can be\ndescribed by a simplified scaling law.", "category": "physics_chem-ph" }, { "text": "Lithium storage in titania films as a function of position: Unification\n of intercalation electrode and super-capacitor concepts: We carefully investigated the storage of lithium in titania films on various\nsubstrates as a function of thickness. The experiments enable us to precisely\nseparate contributions from bulk and boundary storage. The battery capacity\nmeasurements are complemented by bias dependent measurements of impedance,\nyielding interfacial resistance as well as interfacial capacitance. Independent\ninformation on electron and Li distribution is gained by scanning transmission\nelectron microscopy (STEM), electron energy loss spectroscopy (EELS),\naberration-corrected annular-bright-field (ABF) STEM. As a result, we obtain\nthe full picture in terms of equilibrium storage (lithium content) and charge\ncarrier concentrations as a function of spatial coordinates with cell voltage\nas a parameter. More importantly, both bulk storage which obeys\nelectroneutrality and boundary storage which follows the space charge picture\ncan be traced back to a common thermodynamic conception, and are obtained from\nit as special cases. This corresponds to no less than a unification of\nintercalation storage and super-capacitive storage, which are usually\nconsidered as independent phenomena, the reason for this lying in the hitherto\nlack of an adequate defect-chemical and nanoionic picture.", "category": "physics_chem-ph" }, { "text": "On the Origin of Ground-State Vacuum-Field Catalysis: Equilibrium\n Consideration: Recent experiments suggest that vibrational strong coupling (VSC) may\nsignificantly modify ground-state chemical reactions and their rates even\nwithout external pumping. The intrinsic mechanism of this \"vacuum-field\ncatalysis\" remains largely unclear. Generally, modifications of thermal\nreactions in the ground electronic states can be caused by equilibrium or\nnon-equilibrium effects. The former are associated with modifications of the\nreactant equilibrium distribution as expressed by the transition state theory\nof chemical reaction rates, while the latter stem from the dynamics of reaching\nand leaving transition configurations. Here, we examine the VSC effect in a\ncavity environment on chemical rates as calculated by transition state theory.\nOur approach is to examine the effect of coupling to cavity mode(s) on the\npotential of mean force (PMF) associated with the reaction coordinate. Within\nthe context of classical nuclei and classical photons, we find that while the\nPMF can be affected by the cavity environment, this effect is negligible for\nthe usual cavities used to examine VSC situations.", "category": "physics_chem-ph" }, { "text": "Concentration-Flux-Steered Mechanism Exploration with an Organocatalysis\n Application: Investigating a reactive chemical system with automated reaction network\nexploration algorithms provides a more detailed picture of its chemical\nmechanism than what would be accessible by manual investigation. In general,\nexploration algorithms cannot uncover reaction networks exhaustively for\nfeasibility reasons. They should therefore decide which part of a network is\nkinetically relevant under some external conditions given. Here, we propose an\nautomated algorithm that identifies and explores kinetically accessible regions\nof a reaction network on the fly by explicit modeling of concentration fluxes\nthrough an (incomplete) reaction network that is emerging during automated\nfirst-principles exploration. Key compounds are automatically identified and\nselected for the continuation of the exploration. As an example, we explore the\nreaction network of the multi-component proline-catalyzed Michael addition of\npropanal and nitropropene. Our algorithm provides a mechanistic picture of the\nMichael addition in unprecedented detail.", "category": "physics_chem-ph" }, { "text": "Boosting the accuracy and speed of quantum Monte Carlo: size-consistency\n and time-step: Diffusion Monte Carlo (DMC) simulations for fermions are becoming the\nstandard to provide high quality reference data in systems that are too large\nto be investigated via quantum chemical approaches. DMC with the fixed-node\napproximation relies on modifications of the Green function to avoid\nsingularities near the nodal surface of the trial wavefunction. We show that\nthese modifications affect the DMC energies in a way that is not\nsize-consistent, resulting in large time-step errors. Building on the\nmodifications of Umrigar {\\em et al.} and of DePasquale {\\em et al.} we propose\na simple Green function modification that restores size-consistency to large\nvalues of time-step; substantially reducing the time-step errors. The new\nalgorithm also yields remarkable speedups of up to two orders of magnitude in\nthe calculation of molecule-molecule binding energies and crystal cohesive\nenergies, thus extending the horizons of what is possible with DMC.", "category": "physics_chem-ph" }, { "text": "Machine Learning for Quantum Dynamics: Deep Learning of Excitation\n Energy Transfer Properties: Understanding the relationship between the structure of light-harvesting\nsystems and their excitation energy transfer properties is of fundamental\nimportance in many applications including the development of next generation\nphotovoltaics. Natural light harvesting in photosynthesis shows remarkable\nexcitation energy transfer properties, which suggests that pigment-protein\ncomplexes could serve as blueprints for the design of nature inspired devices.\nMechanistic insights into energy transport dynamics can be gained by leveraging\nnumerically involved propagation schemes such as the hierarchical equations of\nmotion (HEOM). Solving these equations, however, is computationally costly due\nto the adverse scaling with the number of pigments. Therefore virtual\nhigh-throughput screening, which has become a powerful tool in material\ndiscovery, is less readily applicable for the search of novel excitonic\ndevices. We propose the use of artificial neural networks to bypass the\ncomputational limitations of established techniques for exploring the\nstructure-dynamics relation in excitonic systems. Once trained, our neural\nnetworks reduce computational costs by several orders of magnitudes. Our\npredicted transfer times and transfer efficiencies exhibit similar or even\nhigher accuracies than frequently used approximate methods such as secular\nRedfield theory", "category": "physics_chem-ph" }, { "text": "On the Potential of Fourier-Encoded Saturation Transfers for Sensitizing\n Solid-State Magic-Angle Spinning NMR Experiments: Chemical exchange saturation transfer (CEST) is widely used for enhancing the\nsolution NMR signatures of magnetically-dilute spin pools; in particular\nspecies at low concentrations undergoing chemical exchanges with an abundant\nspin pool. CEST's main feature involves encoding and then detecting the weak\nNMR signals of the magnetically dilute spin pools on a magnetically abundant\nspin pool of much easier detection - for instance the protons of H2O. Inspired\nby this method, we propose and exemplify a methodology to enhance the\nsensitivity of magic-angle spinning (MAS) solid-state NMR spectra. Our proposal\nuses the abundant 1H reservoir arising in organic solids as the magnetically\nabundant spin pool, and relies on proton spin diffusion in lieu of chemical\nexchange to mediate polarization transfer between a magnetically dilute spin\npool and this magnetically abundant spin reporter. As an initial test of this\nidea we target the spectroscopy of naturally-abundant 13C, and rely on a\nFourier-encoded version of the CEST experiment for achieving broadbandness in\ncoordination with both MAS and heteronuclear decoupling - features normally\nabsent in CEST. Arbitrary evolutions of multiple 13C sites can thus be\nimprinted on the entire 1H reservoir, which is subsequently detected.\nTheoretical predictions suggest that orders-of-magnitude signal enhancements\nshould be achievable in this manner - on the order of the ratio between the 13C\nand the 1H reservoirs' abundances. Experiments carried out under magic-angle\nspinning conditions evidenced ca. 5-10x enhancements. Further opportunities and\nchallenges arising in this Fourier-Encoded Saturation Transfer (FEST) MAS NMR\napproach are briefly discussed.", "category": "physics_chem-ph" }, { "text": "Theory, Simulation and Nanotechnological Applications of Adsorption on a\n Surface with Defects: Theory of adsorption on a surface with nanolocal defects is proposed. Two\nefficacy parameters of surface modification for nanotechnological purposes are\nintroduced, where the modification is a creation of nanolocal artificial\ndefects. The first parameter corresponds to applications where it is necessary\nto increase the concentration of certain particles on the modified surface. And\nthe second one corresponds to the pattern transfer with the help of particle\nself-organization on the modified surface. The analytical expressions for both\nparameters are derived with the help of the thermodynamic and the kinetic\napproaches for two cases: jump diffusion and free motion of adsorbed particles\nover the surface. The possibility of selective adsorption of molecules is shown\nwith the help of simulation of the adsorption of acetylene and benzene\nmolecules in the pits on the graphite surface. The process of particle\nadsorption from the surface into the pit is theoretically studied by molecular\ndynamic technique. Some possible nanotechnological applications of adsorption\non the surface with artificial defects are considered: fabrication of sensors\nfor trace molecule detection, separation of isomers, and pattern transfer.", "category": "physics_chem-ph" }, { "text": "Mathematical Model of a pH-gradient Creation at Isoelectrofocusing. Part\n III: Numerical Solution of the Non-stationary Problem: The mathematical model describing the non-stationary natural pH-gradient\narising under the action of an electric field in an aqueous solution of\nampholytes (amino acids) is constructed and investigated. The model is part of\na more general model of the isoelectrofocusing (IEF) process. To numerical\nstudy of the model we use the finite elements method that allows to\nsignificantly reduce the computation time. We also examine the influence of the\ndifferent effects (taking into account the water ions, the various forms of\nOhm's law, the difference between isoelectric and isoionic points of the\nsubstances) on the process IEF.", "category": "physics_chem-ph" }, { "text": "The role of molecular structure on the microscopic thermodynamics:\n unveiling with Femtosecond Optical Tweezers: Microscopic thermodynamic studies can elucidate specific molecular\ninteractions. In this work, we report the microscopic thermodynamics in binary\nliquid mixtures, which elucidate the role of molecular structure in nonlinear\nsolvent response using femtosecond optical tweezers (FOT). We obtain the excess\nthermodynamics property of mixing in various Newtonian liquid mixtures by\nanalyzing Microrheology data from FOT. Using our noninvasive 780 nm pulse laser\nwe have trapped micron-sized particles to show how excess viscosity and\nresidual Gibbs free energy change due to mixing. Furthermore, we establish from\nthis study that hydrocarbon chain length and branching can modulate microscopic\nthermodynamics through intermolecular interaction. This work sheds light on the\nrelationship between thermodynamic properties and viscosity, which is of\nimmense importance for predicting transport properties, mixing, and chemical\nreactions.", "category": "physics_chem-ph" }, { "text": "Complexity reduction in self-interaction-free density functional\n calculations using the Fermi-L\u00f6wdin self-interaction correction method: Fermi-L\\\"owdin (FLO) self-interaction-correction (SIC) (FLOSIC) method uses\nsymmetric orthogonalized Fermi orbitals as localized orbitals in one-electron\nSIC schemes resulting in a formal reduction in the scaling of SIC methods (e.g.\nPerdew-Zunger SIC (PZSIC) method) but requires a set of Fermi orbital\ndescriptors used to define the FLOs which can be computationally taxing. Here,\nwe propose to simplify the SIC calculations using a selective orbital scaling\nself-interaction correction (SOSIC) by removing SIE from a select set of\norbitals that are of interest. We illustrate the approach by choosing a valence\nset of orbitals as active orbitals in the SOSIC approach. The results obtained\nusing the vSOSIC scheme are compared with those obtained with PZSIC which\ncorrects for SIE of all orbitals. The comparison is made for atomization\nenergies, barrier heights, ionization energies (absolute highest occupied\norbital [HOO] eigenvalues), exchange coupling constant and spin densities of\nCu-containing complexes, and vertical detachment energies (VDE) of water\ncluster anions. The agreement between the two methods is within a few percent\nfor the majority of the properties. The MAE in the VDE (absolute HOO\neigenvalue) of water cluster anions with vSOSIC-PBE with respect to benchmark\nCCSD(T) results is only 15 meV making vSOSIC-PBE an excellent alternative to\nthe CCSD(T) to obtain the VDE of water cluster anions. The vSOSIC calculation\non [Cu$_2$Cl$_6$]$^{2-}$ complex demonstrates that, in addition to the cost\nsavings from using fewer orbitals to account for SIC, the FOD optimization in\nvSOSIC is also substantially smoother and faster.", "category": "physics_chem-ph" }, { "text": "Theoretical development on the isosteric heat of adsorption and\n experimental confirmation: Theoretical framework for the isosteric heat of adsorption is developed\ntreating the effects of the non-ideal gas behavior and the adsorbed phase\nvolume. Rigorous thermodynamic treatment for the adsorbed phase volume is\npresented for multi-layer adsorption from low to high pressures. The proposed\nmodel for the isosteric heat of adsorption along with the adsorbed phase volume\nis validated and verified using experimental data for several, judiciously\nselected adsorbent + adsorbate (nonpolar molecules) systems. The predictions by\nthe model exhibit excellent agreement with the experimental data for both\nadsorption isotherms and the isosteric heat of adsorption.", "category": "physics_chem-ph" }, { "text": "The Exact Exchange-Correlation Potential in Time-Dependent Density\n Functional Theory: Choreographing Electrons with Steps and Peaks: The time-dependent exchange-correlation potential has an unusual task in\ndirecting fictitious non-interacting electrons to move with exactly the same\nprobability density as true interacting electrons. This has intriguing\nimplications for its structure, especially in the non-perturbative regime,\nleading to step and peak features that cannot be captured by bootstrapping any\nground-state functional approximations. We review what has been learned about\nthese features in the exact exchange-correlation potential in time-dependent\ndensity functional theory in the past decade or so, and implications for the\nperformance of simulations when electrons are driven far from any ground-state.", "category": "physics_chem-ph" }, { "text": "Tutorial on the chemical potential of ions in water and porous\n materials: electrical double layer theory and the influence of ion volume and\n ion-ion electrostatic interactions: In this tutorial we discuss the chemical potential of ions in water (i.e., in\na salt solution, in an electrolyte phase) and inside (charged) nanoporous\nmaterials such as porous membranes. In water treatment, such membranes are\noften used to selectively remove ions from water by applying pressure (which\npushes water through the membrane while most ions are rejected) or by current\n(which transports ions through the membrane). Chemical equilibrium across a\nboundary (such as the solution-membrane boundary) is described by an isotherm\nfor neutral molecules, and for ions by an electrical double layer (EDL) model.\nAn EDL model describes concentrations of ions inside a porous material as\nfunction of the charge and structure of the material. There are many\ncontributions to the chemical potential of an ion, and we address several of\nthese in this tutorial, including ion volume and the effect of ion-ion\nCoulombic interactions. We also describe transport and chemical reactions in\nsolution, and how they are affected by Coulombic interactions.", "category": "physics_chem-ph" }, { "text": "Machine learning of microscopic structure-dynamics relationships in\n complex molecular systems: In many complex molecular systems, the macroscopic ensemble's properties are\ncontrolled by microscopic dynamic events (or fluctuations) that are often\ndifficult to detect via pattern-recognition approaches. Discovering the\nrelationships between local structural environments and the dynamical events\noriginating from them would allow unveiling microscopic level\nstructure-dynamics relationships fundamental to understand the macroscopic\nbehavior of complex systems. Here we show that, by coupling advanced structural\n(e.g., Smooth Overlap of Atomic Positions, SOAP) with local dynamical\ndescriptors (e.g., Local Environment and Neighbor Shuffling, LENS) in a unique\ndataset, it is possible to improve both individual SOAP- and LENS-based\nanalyses, obtaining a more complete characterization of the system under study.\nAs representative examples, we use various molecular systems with diverse\ninternal structural dynamics. On the one hand, we demonstrate how the\ncombination of structural and dynamical descriptors facilitates decoupling\nrelevant dynamical fluctuations from noise, overcoming the intrinsic limits of\nthe individual analyses. Furthermore, machine learning approaches also allow\nextracting from such combined structural/dynamical dataset useful\nmicroscopic-level relationships, relating key local dynamical events (e.g.,\nLENS fluctuations) occurring in the systems to the local structural (SOAP)\nenvironments they originate from. Given its abstract nature, we believe that\nsuch an approach will be useful in revealing hidden microscopic\nstructure-dynamics relationships fundamental to rationalize the behavior of a\nvariety of complex systems, not necessarily limited to the atomistic and\nmolecular scales.", "category": "physics_chem-ph" }, { "text": "On the mass of atoms in molecules: Beyond the Born-Oppenheimer\n approximation: Describing the dynamics of nuclei in molecules requires a potential energy\nsurface, which is traditionally provided by the Born-Oppenheimer or adiabatic\napproximation. However, we also need to assign masses to the nuclei. There, the\nBorn-Oppenheimer picture does not account for the inertia of the electrons and\nonly bare nuclear masses are considered. Nowadays, experimental accuracy\nchallenges the theoretical predictions of rotational and vibrational spectra\nand requires to include the participation of electrons in the internal motion\nof the molecule. More than 80 years after the original work of Born and\nOppenheimer, this issue still is not solved in general. Here, we present a\ntheoretical and numerical framework to address this problem in a general and\nrigorous way. Starting from the exact factorization of the electron-nuclear\nwave function, we include electronic effects beyond the Born-Oppenheimer regime\nin a perturbative way via position-dependent corrections to the bare nuclear\nmasses. This maintains an adiabatic-like point of view: the nuclear degrees of\nfreedom feel the presence of the electrons via a single potential energy\nsurface, whereas the inertia of electrons is accounted for and the total mass\nof the system is recovered. This constitutes a general framework for describing\nthe mass acquired by slow degrees of freedom due to the inertia of light,\nbounded particles. We illustrate it with a model of proton transfer, where the\nlight particle is the proton, and with corrections to the vibrational spectra\nof molecules. Inclusion of the light particle inertia allows to gain orders of\nmagnitude in accuracy.", "category": "physics_chem-ph" }, { "text": "Experimental Autoignition of C4-C6 Saturated and Unsaturated Methyl and\n Ethyl Esters: Autoignition delay times, ?, of methyl crotonate, methyl acrylate, ethyl\nbutanoate, ethyl crotonate, and ethyl acrylate were studied in shock tube\nexperiments. A series of mixtures diluted with argon, of varying fuel/oxygen\nequivalence ratios (?=0.25, 0.4, 1.0, and 2.0), were measured behind reflected\nshock waves over the temperature range of 1280-1930 K, pressure range of 7-9.65\natm, during which the logarithm of ? varies linearly as a function of the\ninverse temperature for all equivalence ratios. The ignition delay time\ndecreases as temperature rises. The dependence of ? on temperature, and\nreactant concentrations is given in an empirical correlation. The results\nprovide a database for the validation of small saturated and unsaturated esters\nkinetic mechanisms at elevated temperatures and pressure combustion.", "category": "physics_chem-ph" }, { "text": "Construction of linearly independent non-orthogonal AGP states: We show how to construct a linearly independent set of antisymmetrized\ngeminal power (AGP) states, which allows us to rewrite our recently introduced\ngeminal replacement models as linear combinations of non-orthogonal AGPs. This\ngreatly simplifies the evaluation of matrix elements and permits us to\nintroduce an AGP-based selective configuration interaction method, which can\nreach arbitrary excitation levels relative to a reference AGP, balancing\naccuracy and cost as we see fit.", "category": "physics_chem-ph" }, { "text": "A setup for studies of photoelectron circular dichroism from chiral\n molecules in aqueous solution: We present a unique experimental design that enables the measurement of\nphotoelectron circular dichroism (PECD) from chiral molecules in aqueous\nsolution. The effect is revealed from the intensity difference of photoelectron\nemission into a backward-scattering angle relative to the photon propagation\ndirection when ionizing with circularly polarized light of different helicity.\nThis leads to asymmetries (normalized intensity differences) that depend on the\nhandedness of the chiral sample and exceed the ones in conventional dichroic\nmechanisms by orders of magnitude. The asymmetry is largest for photon energies\nwithin several electron volts above the ionization threshold. A primary aim is\nto explore the effect of hydration on PECD. The modular and flexible design of\nour experimental setup EASI (Electronic structure from Aqueous Solutions and\nInterfaces) also allows for detection of more common photoelectron angular\ndistributions (PADs), requiring distinctively different detection geometries,\nand typically using linearly polarized light. A microjet is used for\nliquid-sample delivery. We describe EASI's technical features and present two\nselected experimental results, one based on synchrotron-light measurements and\nthe other performed in the laboratory, using monochromatized He-II $\\alpha$\nradiation. The former demonstrates the principal effectiveness of PECD\ndetection, illustrated for prototypic gas-phase fenchone. We also discuss the\nfirst data from liquid fenchone. In the second example we present valence\nphotoelectron spectra from liquid water and NaI aqueous solution, here obtained\nfrom a planar-surface microjet (flatjet). This new development features a more\nfavorable symmetry for angle-dependent photoelectron measurements.", "category": "physics_chem-ph" }, { "text": "The structure of aqueous lithium chloride solutions at high\n concentrations as revealed by a comparison of classical interatomic potential\n models: Highly concentrated aqueous lithium chloride solutions were investigated by\nclassical molecular dynamics (MD) and reverse Monte Carlo (RMC) simulations. At\nfirst MD calculations were carried out applying twenty-nine combinations of\nion-water interaction models at four salt concentrations. The structural\npredictions of the different models were compared, the contributions of\ndifferent structural motifs to the partial pair correlation functions (PPCF)\nwere determined. Particle configurations obtained from MD simulations were\nfurther refined using the RMC method to get better agreement with experimental\nX-ray and neutron diffraction data. The PPCFs calculated from MD simulations\nwere fitted together with the experimental structure factors to construct\nstructural models that are as consistent as possible with both the experimental\nresults and the results of the MD simulations. The MD models were validated\naccording to the quality of the fits. Although none of the tested MD models can\ndescribe the structure perfectly at the highest investigated concentration,\ntheir comparison made it possible to determine the main structural properties\nof that solution as well. It was found that four nearest neighbors (oxygen\natoms and chloride ions together) are around a lithium ion at each\nconcentration, while in the surroundings of the chloride ion hydrogen atom\npairs are replaced by one lithium ion as the concentration increases. While in\npure liquid water four water molecules can be found around a central water\nmolecule, near the solubility limit nearly all water molecules are connected to\ntwo chloride ions (via their hydrogen atoms) and one lithium ion (by their\noxygen atoms).", "category": "physics_chem-ph" }, { "text": "Attosecond-recollision-controlled selective fragmentation of polyatomic\n molecules: Control over various fragmentation reactions of a series of polyatomic\nmolecules (acetylene, ethylene, 1,3-butadiene) by the optical waveform of\nintense few-cycle laser pulses is demonstrated experimentally. We show both\nexperimentally and theoretically that the responsible mechanism is inelastic\nionization from inner-valence molecular orbitals by recolliding electron\nwavepackets, whose recollision energy in few-cycle ionizing laser pulses\nstrongly depends on the optical waveform. Our work demonstrates an efficient\nand selective way of pre-determining fragmentation and isomerization reactions\nin polyatomic molecules on sub-femtosecond time-scales.", "category": "physics_chem-ph" }, { "text": "NMR chemical shift as analytical derivative of the Helmholtz free energy: We present a theory for the temperature-dependent nuclear magnetic shielding\ntensor of molecules with arbitrary electronic structure. The theory is a\ngeneralization of Ramsey's theory for closed-shell molecules. The shielding\ntensor is defined as a second derivative of the Helmholtz free energy of the\nelectron system in equilibrium with the applied magnetic field and the nuclear\nmagnetic moments. This derivative is analytically evaluated and expressed as a\nsum over states formula. Special consideration is given to a system with an\nisolated degenerate ground state for which the size of the degeneracy and the\ncomposition of the wave functions are arbitrary. In this case the paramagnetic\npart of the shielding tensor is expressed in terms of the $g$ and $A$ tensors\nof the EPR spin Hamiltonian of the degenerate state. As an illustration of the\nproposed theory, we provide an explicit formula for the paramagnetic shift of\nthe central lanthanide ion in endofullerenes Ln@C$_{60}$, with Ln=Ce$^{3+}$,\nNd$^{3+}$, Sm$^{3+}$, Dy$^{3+}$, Er$^{3+}$ and Yb$^{3+}$, where the ground\nstate can be a strongly spin-orbit coupled icosahedral sextet for which the\nparamagnetic shift cannot be described by previous theories.", "category": "physics_chem-ph" }, { "text": "Origin of Chirality in the Molecules of Life: Molecular chirality is inherent to biology and cellular chemistry. In this\nreport, the origin of enantiomeric selectivity is analyzed from the viewpoint\nof the \"RNA World\" model, based on the autocatalytic self-replication of\nglyceraldehyde as a precursor for simple sugars, and in particular ribose, as\npromoted by the formose reaction. Autocatalytic coupling of formaldehyde and\nglycolaldehyde produces glyceraldehyde, which contains a chiral carbon center\nthat is carried through in formation of the ribose ring. The parity\nnon-conserving weak interaction is the only inherently handed property in\nnature and is herein shown to be sufficient to differentiate between two\nenantiomeric forms in an autocatalytic reaction performed over geologically\nrelevant time scales, but only in the presence of a catalytic metal ion such as\ndivalent calcium or higher Z alkaline earth elements. This work details\ncalculations of the magnitude of the effect, the impact of various\ngeologically-available metal ions, and the influence on evolution and dominance\nof chirality in the molecules of life.", "category": "physics_chem-ph" }, { "text": "Electronic torsional sound in linear atomic chains: chemical energy\n transport at 1000 km/s: We investigate entirely electronic torsional vibrational modes in linear\ncumulene chains. The carbon nuclei of a cumulene are positioned along the\nprimary axis so they can participate only in transverse and longitudinal\nmotions. However, the interatomic electronic clouds behave as a torsion spring\nwith remarkable torsional stiffness. The collective dynamics of these clouds\ncan be described in terms of electronic vibrational quanta, which we name\ntorsitons. It is shown that the group velocity of the wavepacket of torsitons\nis much higher than the typical speed of sound, because of the small mass of\nparticipating electrons compared to the atomic mass. For the same reason the\nmaximum energy of the torsitons in cumulenes is as high as a few electronvolts,\nwhile the minimum possible energy is evaluated as a few hundred wavenumbers and\nthis minimum is associated with asymmetry of zero point atomic vibrations.\nMolecular systems for experimental evaluation of the predictions are proposed.", "category": "physics_chem-ph" }, { "text": "A general second order complete active space self-consistent-field\n solver for large-scale systems: We present a new second order complete active space self-consistent field\nimplementation to converge wavefunctions for both large active spaces and large\natomic orbital (AO) bases. Our algorithm decouples the active space\nwavefunction solver from the orbital optimization in the microiterations, and\nthus may be easily combined with various modern active space solvers. We also\nintroduce efficient approximate orbital gradient and Hessian updates, and step\nsize determination. We demonstrate its capabilities by calculating the\nlow-lying states of the Fe(\\Roman{2})-porphine complex with modest resources\nusing a density matrix renormalization group solver in a CAS(22,27) active\nspace and a 3000 AO basis.", "category": "physics_chem-ph" }, { "text": "Dissociative electron attachment to the H2O molecule. II. Nuclear\n dynamics on coupled electronic surfaces within the local complex potential\n model: We report the results of a first-principles study of dissociative electron\nattachment to H2O. The cross sections are obtained from nuclear dynamics\ncalculations carried out in full dimensionality within the local complex\npotential model by using the multi-configuration time-dependent Hartree method.\nThe calculations employ our previously obtained global, complex-valued,\npotential-energy surfaces for the three (doublet B1, doublet A1, and doublet\nB2) electronic Feshbach resonances involved in this process. These three\nmetastable states of H2O- undergo several degeneracies, and we incorporate both\nthe Renner-Teller coupling between the B1 and A1 states as well as the conical\nintersection between the A1 and B2 states into our treatment. The nuclear\ndynamics are inherently multidimensional and involve branching between\ndifferent final product arrangements as well as extensive excitation of the\ndiatomic fragment. Our results successfully mirror the qualitative features of\nthe major fragment channels observed, but are less successful in reproducing\nthe available results for some of the minor channels. We comment on the\napplicability of the local complex potential model to such a complicated\nresonant system.", "category": "physics_chem-ph" }, { "text": "Optical Imaging of Surface Chemistry and Dynamics in Confinement: The interfacial structure and dynamics of water in a microscopically confined\ngeometry is imaged in three dimensions and on millisecond time scales. We\ndeveloped a 3D wide-field second harmonic microscope that employs structured\nillumination. We image pH induced chemical changes on the curved and confined\ninner and outer surfaces of a cylindrical glass micro-capillary immersed in\naqueous solution. The image contrast reports on the orientational order of\ninterfacial water, induced by charge-dipole interactions between water\nmolecules and surface charges. The images constitute surface potential maps.\nSpatially resolved surface pKa,s values are determined for the silica\ndeprotonation reaction. Values range from 2.3