AndreaBozzo/ceres-open-data-index huggingface dataset:
In silico discovery of covalent organic frameworks for carbon capture

We screen a database of more than 69,000 hypothetical covalent organic frameworks (COFs) for carbon capture, using parasitic energy as a metric. In order to compute CO2-framework interactions in molecular simulations, we develop a genetic algorithm to tune the charge equilibration method and derive accurate framework partial charges. Nearly 400 COFs are identified with parasitic energy lower than that of an amine scrubbing process using monoethanolamine; over 70 are better performers than the best experimental COFs; and several perform similarly to Mg-MOF-74. We analyze the effect of pore topology on carbon capture performance in order to guide development of improved carbon capture materials.

Tags: cofs, computational-screening, covalent-organic-frameworks, erc, gas-adsorption, marveldd4
Structure database of glass-ceramic lithium thiophosphate electrolytes

This database contains computationally generated atomic structures of glass-ceramics lithium thiophosphates (gc-LPS) with the general composition (Li2S)x(P2S5)1-x in the XCrySDen structure format (XSF). Total energies and interatomic forces from density-functional theory (DFT) calculations are included as additional meta information. The extended XSF format is compatible with the atomic energy network (ænet) package for artificial neural network (ANN) potential construction and application. The DFT calculations used projector-augmented-wave (PAW) pseudopotentials and the Perdew−Burke−Ernzerhof (PBE) exchange-correlation functional as implemented in the Vienna Ab Initio Simulation Package (VASP) and a kinetic energy cutoff of 520 eV. The first Brillouin zone was sampled using VASP's fully automatic k-point scheme with a length parameter Rk = 25Å. The gc-LPS structures were generated using a combination of different sampling methods. Initial amorphous structure models were generated with ab initio molecular dynamics (AIMD) simulations of supercells at 1200 K using a Nose-Hoover thermostat with a time step of 1 fs. To obtain near-ground-state structures as reference for the machine-learning potential, 150 evenly spaced snapshots were extracted from the AIMD trajectories that were reoptimized with DFT geometry optimizations at zero Kelvin. Additional structures were generated by scaling the lattice parameters of the crystalline LPS structures (see below) by ±15% and perturbing atomic positions in AIMD simulations as described above.
The resulting database was used to train a specialized ANN potential for the sampling of structures along the Li2S–P2S5 composition line with a genetic-algorithm (GA) as implemented in the atomistic evolution (ævo) package, following a previously reported protocol. Starting from supercells of the ideal crystal structures, either Li and S atoms were removed with a ratio of 2:1, or P and S atoms were removed with a ratio of 2:5, and low-energy configurations were determined with GA sampling. A population size of 32 trials and a mutation rate of 10% were employed. The ANN potential was iteratively refined by including additional sampled structures in the training. For each composition, at least 10 lowest energy structure models identified with the ANN-GA approach were selected and fully relaxed with DFT.
Also included in the present database are the XSF files of the previously reported crystalline phases LiPS3, Li2PS3, Li4P2S7, Li7P3S11, α-Li3PS4, β-Li3PS4, γ-Li3PS4, and Li48P16S61. The crystal structures were obtained from the Inorganic Crystal Structure Database (ICSD), the Materials Project (MP) database, the Open Quantum Materials Database (OQMD), and the AFLOW database. The directory names indicate the journal reference and the database.
Further details can be found in the associated research article.

Tags: aenet, dft, lithium-thiophosphates, solid-electrolytes, vasp
Origin of high strength in the CoCrFeNiPd high-entropy alloy

Recent experiments show that the CoCrFeNiPd high-entropy alloy (HEA) is significantly stronger than CoCrFeNi and with nanoscale composition fluctuations beyond those expected for random alloys. These fluctuations were suggested to be responsible for strengthening. Here, a recent parameter-free theory for initial yield strength in fcc random alloys is shown to predict the strength of CoCrFeNiPd in good agreement with experiments. The strengthening is due mainly to the large misfit volume of Pd in CoCrFeNi, indicating that the effects of the non-random composition fluctuations are secondary. Analyses of strength variations and strengthening-associated length scales help rationalize why dislocation motion is insensitive to such fluctuations. These findings point to the value of theory for understanding the mechanical behavior of HEAs.

Tags: epfl, high-entropy-alloys, marveldd2, palladium, solute-strengthening-theory, yield-strength
On-surface light-induced generation of higher acenes and elucidation of their open-shell character

In this work we demonstrate the on surface synthesis of  nonacene and heptacene and we discuss their open shell character comparing experimental evidence to theoretical predictions. The record contains input files to reproduce the calculations discussed in the manuscript and the raw data of the experimental images discussed.

Tags: ab-initio, gw, marveldd3, on-surface-synthesis, scanning-probe-microscopy
Property map collective variable as a useful tool for force field correction

Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the difference between the accurate and inaccurate potential for i-th landmark structure x_i, lambda is a chosen prefactor, D is a distance (e.g. RMSD or MSD) and x are atomic coordinates. The concept was tested on alanine dipeptide (all combinations of 7 force fields, one used as a model of accurate and one as inaccurate). Next it was applied on an anticancer drug Imatinib (General AMBER Force Field corrected to DFT).
Simulations were carried out in Gromacs 2016.4. DFTB/MM simulation was carried out in CP2K 7.1. Correction was Implemented using Plumed 2.4. DFT energies were calculated by ORCA 4.0 at the BP86/def2-TZVP level of theory.

Tags: dft, free-energy, molecular-dynamics-simulation, molecular-mechanics
Crystal field, ligand field, and interorbital effects in two-dimensional transition metal dichalcogenides across the periodic table

Two-dimensional (2D) transition metal dichalcogenides (TMDs) exist in two polymorphs, referred to as 1T and 1H, depending on the coordination sphere of the transition metal atom. The broken octahedral and trigonal prismatic symmetries lead to different crystal and ligand field splittings of the d electron states, resulting in distinct electronic properties. In this work, we quantify the crystal and ligand field parameters of 2D TMDs using a Wannier-function approach. We adopt the methodology proposed by Scaramucci et al (2015 J. Phys.: Condens. Matter 27 175503) that allows to separate various contributions to the ligand field by choosing different manifolds in the construction of the Wannier functions. We discuss the relevance of the crystal and ligand fields in determining the relative stability of the two polymorphs as a function of the filling of the d-shell. Based on the calculated parameters, we conclude that the ligand field, while leading to a small stabilizing factor for the 1H polymorph in the d1 and d2 TMDs, plays mostly an indirect role and that hybridization between different d orbitals is the dominant feature. We investigate trends across the periodic table and interpret the variations of the calculated crystal and ligand fields in terms of the change of charge-transfer energy, which allows developing simple chemical intuition

Tags: crystal-field, epfl, hybridization, ligand-field, transition-metal-dichalcogenides, wannier-functions
Iterative unbiasing of quasi-equilibrium sampling

This repository contains the PLUMED-2 input files required to generate the data used in the ITRE publications. ITRE is a method to reweight Molecular Dynamics trajectory biased with a history-dependent potential (such as Metadynamics), and calculate unbiased thermodynamic observables. Since it uses the trajectory itself as a proxy of a grid, its scaling does not depend on the dimensionality of the space explored. In addition, thanks to its formulation, it is less affected by out-of-equilibrium points that characterize the early stages of a biased calculation and are usually discarded. Thanks to this feature, it can be used to increase the statistics when evaluating a thermodynamic observable from biased calculation.

Tags: enhanced-sampling, epfl, erc, molecular-dynamics, snsf, statistical-mechanics
Stable structures of exohedrally decorated C60-fullerenes

A good hydrogen storage material should adsorb hydrogen in high concentrations and with optimal binding energies. Exohedrally metal decorated carbon fullerene structures were proposed as a promising material in this context. We present a fully ab-initio, unbiased structure search of the configurational space of decorated C60 fullerenes and find that many of the hitherto postulated ground state structures are not ground states. We determine the energetically lowest configurations for decorations with a varying number of decorating atoms (2 ≤ n ≤ 32) for alkali metals, alkaline-earth metals as well as some other important elements and find that the dense uniform distribution of the decorating atoms over the surface of the C60 , desired for hydrogen storage, can be obtained only for a few elements. An understanding of the behavior of the decorating atoms can be obtained by analyzing their bonding characteristics via the electron localization function.

Tags: c60, elements, exohedral, marveldd1, snsf
Molecular Dynamics Simulations of Crystal Nucleation from Solution at Constant Chemical Potential

A widespread method of crystal preparation is to precipitate it from a supersaturated solution. In such a process, control of solution concentration is of paramount importance. The nucleation process, polymorph selection, and crystal habits depend crucially on this thermodynamic parameter. When performing molecular dynamics simulations with a fixed number of molecules in the canonical ensemble, crystal growth is accompanied by a decrease in the solution concentration. This modification of the thermodynamic condition leads to significant artifacts. Inspired by the recent development of the constant chemical potential molecular dynamics simulation method by Perego et al. [J. Chem. Phys. 2015, 142, 144113], we develop a spherical variant of it to study nucleation from solution. Our method allows determining the crystal nucleus size and nucleation rates at constant supersaturation. As an example, we study the homogeneous nucleation of sodium chloride from its supersaturated aqueous solution.

Tags: constant-chemical-potential-molecular-dynamics-simulations, erc, marveldd1, nucleation, nucleation-kinetics, solution-crystallization
Oxygen evolution reaction: Bifunctional mechanism breaking the linear scaling relationship

The bifunctional mechanism for the oxygen evolution reaction (OER) involving two distinct reaction sites is studied through the computational hydrogen electrode method for a set of catalyst materials including rutile TiO2(110), anatase TiO2(101), SnO2(110), RuO2(110), IrO2(110), Ni2P(0001), and BiVO4(001). The calculations are performed both at the semilocal level and at the hybrid functional level. Moreover, anodic conditions are modeled and their effect on the OER free energy steps is evaluated. The free energies of the reaction steps indicate that for specific combinations of catalysts, the limitations due to the linear scaling relationship can be overcome, leading to smaller overpotentials for the overall OER. At the same time, a detailed analysis of the results reveals a strong dependence on the adopted functional. For both functionals, it is shown that the energy level of the highest occupied electronic state can serve as a descriptor to guide the search for the optimal catalyst acting as a hydrogen acceptor. These results support the bifunctional mechanism as a means to break the linear scaling relationship and to further reduce the overpotential of the OER.

Tags: bifunctional, epfl, free-energy, interface, linear-scaling, marveldd3, oer, overpotential, oxygen-evolution-reaction
Ni Nanoparticles on CeO2(111): Energetics, Electron Transfer and Structure by Ni Adsorption Calorimetry, Spectroscopies and DFT

The morphology, interfacial bonding energetics and charge transfer of Ni clusters and nanoparticles on slightly-reduced CeO2-x(111) surfaces at 100 to 300 K have been studied using single crystal adsorption calorimetry (SCAC), low-energy ion scattering spectroscopy (LEIS), X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED) and density functional theory (DFT).  The initial heat of adsorption of Ni vapor decreased with the extent of pre-reduction (x) of the CeO2-x(111), showing that stoichiometric ceria adsorbs Ni more strongly than oxygen vacancies.  On CeO1.95(111) at 300 K, the heat dropped quickly with coverage in the first 0.1 ML, attributed to nucleation of Ni clusters on stoichiometric steps, followed by the Ni particles spreading onto less favorable terrace sites. At 100 K, the clusters nucleate on terraces due to slower diffusion. Adsorbed Ni monomers are in the +2 oxidation state, and they bind by ~45 kJ/mol more strongly to step sites than terraces. The measured heat of adsorption versus average particle size on terraces is favorably compared to DFT calculations.  The Ce 3d XPS lineshape showed an increase in Ce3+/Ce4+ ratio with Ni coverage, providing the number of electrons donated to the ceria per Ni atom. The charge transferred per Ni is initially large but strongly decreases with increasing cluster size for both experiments and DFT, and shows large differences between clusters at steps versus terraces. This charge is localized on the interfacial Ni and Ce atoms in their atomic layers closest to the interface. This knowledge is crucial to understanding the nature of the active sites on the surface of Ni-CeO2 catalysts for which metal-oxide interactions play a very important role in the activation of O-H and C-H bonds.  The changes in these interactions with Ni particle size (metal loading) and the extent of reduction of the ceria help to explain how previously reported catalytic activity and selectivity change with these same structural details.

Tags: ni-charge-transfer, ni-heat-of-adsorption, ni-on-ceo2-terrace-and-steps
Electron and Hole Polarons at the BiVO4–Water Interface

We determine the transition levels of electron and hole polarons at the BiVO4–water interface through thermodynamic integration within a hybrid functional scheme, thereby accounting for the liquid nature of the water component. The electron polaron is found to be less stable at the interface than in the bulk by 0.18 eV, while for the hole polaron the binding energy increases by 0.20 eV when the charge localizes in the surface layer of BiVO4. These results indicate that interfacial effects on the polaron binding energy and charge distribution are sizeable and cannot trivially be inferred from bulk calculations.

Tags: bivo4, marvel, molecular-dynamics, polarons, water-splitting
Free-Energy Surface Prediction by Flying Gaussian Method

Molecular simulations are computationally expensive, especially in systems with multiple free energy minima. To address this problem many enhanced sampling techniques have been developed. Metadynamics uses a bias potential defined as a sum of Gaussian hills in space of few (one or two) collective variables. This bias potential disfavors states that have been visited since the beginning of the simulation. Multiple walker metadynamics simulates the system in multiple parallel replicas. The bias potential disfavors states that have been visited since the beginning of the simulation in any replica. Flying Gaussian method presented here also simulates the system in multiple parallel replicas. It disfavors states that are, at certain moment, similar in two or more replicas. It was demonstrated on Alanine Dipeptide in vacuum and water, cis/trans-isomerisation of Proline-containing peptides and Met-enkephalin.

Tags: enhanced-sampling, free-energy, metadynamics, molecular-dynamics-simulation
On-surface synthesis of antiaromatic and open-shell indeno[2,1-b]fluorene polymers and their lateral fusion into porous ribbons

This record contains the experimental and computational data needed to support the work done on on-surface synthesis of conjugated polymers consisting of indeno[2,1-b]fluorene units, which are antiaromatic and open-shell biradicaloids. The observed reaction products have been characterized via low-temperature scanning tunneling microscopy/spectroscopy and noncontact atomic force microscopy, complemented by density-functional theory calculations. These polymers present a low band gap when adsorbed on Au(111). Moreover, their pronounced antiaromaticity and radical character, elucidated by ab initio calculations, make them promising candidates for applications in electronics and spintronics. Further, they provide a rich playground to explore magnetism in low-dimensional organic nanomaterials.

Tags: antiaromatic, density-functional-theory, marveldd3, nics, on-surface-reactions, polymers
Yttrium tantalum oxynitride multiphases as photoanodes for water oxidation

Perovskite yttrium tantalum oxynitride is theoretically proposed as a promising semiconductor for solar water splitting because of the predicted bandgap and energy positions of band edges. In experiment, however, we show here that depending on processing parameters, yttrium tantalum oxynitrides exist in multiphases, including the desired perovskite YTaON2, defect fluorite YTa(O,N,o)4, and N-doped YTaO4. These multiphases have bandgaps ranging between 2.13 and 2.31 eV, all responsive to visible light. The N-doped YTaO4, perovskite main phase, and fluorite main phase derived from crystalline fergusonite oxide precursors exhibit interesting photoelectrochemical performances for water oxidation, while the defect fluorite derived from low crystallized scheelite-type oxide precursors show negligible activity. Preliminarily measurements show that loading IrOx cocatalyst on N-doped YTaO4 significantly improves its photoelectrochemical performance encouraging further studies to optimize this new material for solar fuel production.

Tags: computational-screening, marvel, oxynitride-perovskite, solar-water-splitting
Hidden spontaneous polarisation in the chalcohalide photovoltaic Sn2SbS2I3

Enormous research efforts are currently devoted to the discovery of 'perovskite-inspired materials', aiming to replicate the astonishing optoelectronic performance of lead-halide perovskites (LHPs). Recently, chalco halides of group IV/V elements have attracted attention due to the stability provided by stronger metal-chalcogen bonds, alongside compositional flexibility and ns2 cations — a performance-defining feature of LHPs. Following the experimental report of stable, solution-grown tin-antimony sulfoiodide (Sn2SbS2I3) solar cells, with power conversion efficiencies above 4%, we comprehensively characterise the structural and electronic properties of this emerging material. We find that the experimentally-reported centrosymmetric Cmcm crystal structure represents an average over multiple polar Cmc2_1 configurations. This dynamic crystal structure and ferroelectric behaviour could benefit photovoltaic performance. Using state-of-the-art ab initio methods, we assess the efficiency limits of this material, finding maximal solar-conversion efficiencies η_max > 30 % with film thicknesses t > 0.5μm, at the radiative limit.

Open-access Materials Horizons paper: https://doi.org/10.1039/D1MH00764E
Talks on this and other works at: https://www.youtube.com/channel/UCoVGnBeZeWmKzv8_-PzCKCw

Tags: chalcohalide, defect-tolerance, density-functional-theory, earth-abundant, epsrc, erc, ferroelectric, lone-pair, perovskite-inspired, photovoltaic, polarisation, sn2sbs2i3, symmetry-breaking, thin-film-photovoltaic, vasp
Effects of perturbation order and basis set on alchemical predictions within 14 electron diatomic molecules series, detailed analysis of the various sources of errors

This Dataset contains Supplementary information to the article "Effects of perturbation order and basis set on alchemical predictions" by Giorgio Domenichini, Guido Falk von Rudorff and O. Anatole von Lilienfeld.
Our numerical analysis of potential energy estimates, and resulting binding curves, is based on CCSD reference results, and is limited to all neutral diatomics with 14 electrons (AlH ...  N2).  
From those data can be predicted binding energy, equilibrium distance, and vibrational frequencies of neighboring out-of-sample diatomics with near CCSD quality using perturbations up to 5th order.

The data stored as Comma Separated Value files (.csv) contain all the predictions within the 14 electron diatomics series, those are referred to the sections IIIA-IIIE of the article.
To every file corresponds one of the eight basis sets used.
The data are stored using consistently atomic units: Bohrs for length, electrons for charge and Hartrees for energy.
For a better visualization using Jupyter notebooks and Pandas library the notebook "Display_data.ipynb" already contains the code to open the data as pandas' data frames.

Tags: apdft, erc, error-estimation, marvel, quantum-alchemy, snsf
Temperature dependence of the electronic structure of semiconductors and insulators

The renormalization of electronic eigenenergies due to electron-phonon coupling (temperature dependence and zero-point motion effect) is sizable in many materials with light atoms. This effect, often neglected in ab initio calculations, can be computed using the perturbation-based Allen-Heine-Cardona theory in the adiabatic or non-adiabatic harmonic approximation. After a short description of the recent progresses in this field and a brief overview of the theory, we focus on the issue of phonon wavevector sampling convergence, until now poorly understood. Indeed, the renormalization is obtained numerically through a slowly converging q-point integration. For non-zero Born effective charges, we show that a divergence appears in the electron-phonon matrix elements at q → Γ, leading to a divergence of the adiabatic renormalization at band extrema. This problem is exacerbated by the slow convergence of Born effective charges with electronic wavevector sampling, which leaves residual Born effective charges in ab initio calculations on materials that are physically devoid of such charges. Here, we propose a solution that improves this convergence. However, for materials where Born effective charges are physically non-zero, the divergence of the renormalization indicates a breakdown of the adiabatic harmonic approximation, which we assess here by switching to the non-adiabatic harmonic approximation. Also, we study the convergence behavior of the renormalization and develop reliable extrapolation schemes to obtain the converged results. Finally, the adiabatic and non-adiabatic theories, with corrections for the slow Born effective charge convergence problem (and the associated divergence) are applied to the study of five semiconductors and insulators: α-AlN, β-AlN, BN, diamond, and silicon. For these five materials, we present the zero-point  renormalization, temperature dependence, phonon-induced lifetime broadening, and the renormalized electronic band structure.

Tags: ab-initio, allen-heine-cardona, electron-phonon-coupling, first-principles, temperature-dependence, zero-point-renormalization