bluuebunny/crossref_metadata_2025 huggingface dataset:
Perturbation expansion theory corrected from basis set superposition error. I. Locally projected excited orbitals and single excitations
Authors: Nagata Takeshi , Iwata Suehiro
Published: February 2004

The locally projected self-consistent field molecular orbital method for molecular interaction (LP SCF MI) is reformulated for multifragment systems. For the perturbation expansion, two types of the local excited orbitals are defined; one is fully local in the basis set on a fragment, and the other has to be partially delocalized to the basis sets on the other fragments. The perturbation expansion calculations only within single excitations (LP SE MP2) are tested for water dimer, hydrogen fluoride dimer, and colinear symmetric ArM+Ar (M=Na and K). The calculated binding energies of LP SE MP2 are all close to the corresponding counterpoise corrected SCF binding energy. By adding the single excitations, the deficiency in LP SCF MI is thus removed. The results suggest that the exclusion of the charge-transfer effects in LP SCF MI might indeed be the cause of the underestimation for the binding energy.
Abstractive dissociation of oxygen over Al(111): A nonadiabatic quantum model
Authors: Katz Gil , Kosloff Ronnie , Zeiri Yehuda
Published: February 2004

The dissociation of oxygen on a clean aluminum surface is studied theoretically. A nonadiabatic quantum dynamical model is used, based on four electronically distinct potential energy surfaces characterized by the extent of charge transfer from the metal to the adsorbate. A flat surface approximation is used to reduce the computation complexity. The conservation of the helicopter angular momentum allows Boltzmann averaging of the outcome of the propagation of a three degrees of freedom wave function. The dissociation event is simulated by solving the time-dependent Schrödinger equation for a period of 30 femtoseconds. As a function of incident kinetic energy, the dissociation yield follows the experimental trend. An attempt at simulation employing only the lowest adiabatic surface failed, qualitatively disagreeing with both experiment and nonadiabatic calculations. The final products, adsorptive dissociation and abstractive dissociation, are obtained by carrying out a semiclassical molecular dynamics simulation with surface hopping which describes the back charge transfer from an oxygen atom negative ion to the surface. The final adsorbed oxygen pair distribution compares well with experiment. By running the dynamical events backward in time, a correlation is established between the products and the initial conditions which lead to their production. Qualitative agreement is thus obtained with recent experiments that show suppression of abstraction by rotational excitation.
Atomic oxygen reactions with semifluorinated and n-alkanethiolate self-assembled monolayers
Authors: Wagner A. J. , Wolfe G. M. , Fairbrother D. H.
Published: February 2004

The interaction of atomic oxygen (O(3P)) with semifluorinated self-assembled monolayers (CF-SAMs), two different n-alkanethiolate self-assembled monolayers, and a carbonaceous overlayer derived from an x-ray modified n-alkanethiolate SAM have been studied using in situ x-ray photoelectron spectroscopy. For short atomic oxygen exposures, CF-SAMs remain intact, an effect ascribed to the inertness of C–F and C–C bonds toward atomic oxygen and the well-ordered structure of the CF-SAMs. Following this initial induction period, atomic oxygen permeates through the CF3(CF2)7 overlayer and initiates reactions at the film/substrate interface, evidenced by the formation of sulfonate (RSO3) species and Au2O3. These reactions lead to the desorption of intact adsorbate chains, evidenced by the loss of carbon and fluorine from the film while the C(1s) spectral envelope and the C(1s)/F(1s) ratio remain virtually constant. In contrast, the reactivity of atomic oxygen with alkanethiolate SAMs is initiated at the vacuum/film interface, producing oxygen-containing carbon functional groups. Subsequent reactions of these new species with atomic oxygen lead to erosion of the hydrocarbon film. Experiments on the different hydrocarbon-based films reveal that the atomic oxygen-induced kinetics are influenced by the thickness as well as the structural and chemical characteristics of the hydrocarbon overlayer. Results from this investigation are also discussed in the context of material erosion by AO in low Earth orbit.
Growth dynamics of isotactic polypropylene single crystals during isothermal crystallization from a miscible polymeric solvent
Authors: Mehta Rujul , Keawwattana Wirunya , Kyu Thein
Published: February 2004

The present article presents a spatiotemporal growth of isotactic polypropylene (iPP) single crystals, melt crystallized from a polymeric solvent, i.e., poly (ethylene octene) copolymer that is known to be miscible with iPP. Optical and atomic force microscopic investigations reveal that the melt grown single crystals of iPP develop in the form of two parallel rows of crystal lamellae, but these crystals merge at the tips. To elucidate the mechanism of these emerging parallel rows of iPP crystals, a phase field model pertaining to solidification phenomena has been employed that involves a nonconserved crystal order parameter and a chain-tilting angle. This phase field model is based on the free energy of crystallization, having an asymmetric double well, and a tensorial surface free energy of the crystal interface coupled with a curvature elastic free energy that is possessed by the solid–liquid interface. The spatiotemporal simulation of iPP single crystal growth has been carried out on a square lattice based on the finite difference method for spatial steps and an explicit method for temporal steps with a periodic boundary condition. The appearance of the seemingly twin crystal is captured in the simulation, which may be attributed to the sector demarcation that is taking place in the anisotropically growing single crystal of iPP.
Adiabatic population transfer in a liquid: Taking advantage of a decaying target state
Authors: Gong Jiangbin , Rice Stuart A.
Published: February 2004

The feasibility of efficient population transfer between an initial state and a decaying target state of the same parity without populating an intermediate state, in the presence of large-amplitude stochastic energy level fluctuations that mimic the dephasing in a solute molecule due to the influence of a solvent, is demonstrated theoretically. In particular, it is shown that a decaying target state, whose decay rate constant is large compared with the band width of picosecond laser pulses but small compared with the associated peak Rabi frequencies, can dramatically suppress the dephasing-induced nonadiabaticity associated with the dynamics of population transfer, resulting in, irrespective of the correlation time of stochastic energy level fluctuations, negligible population in the intermediate state and complete population transfer to the decaying target state. These results should further motivate experimental studies of optical control of molecular dynamics in a liquid. An interesting connection between our results and the quantum Zeno and anti-Zeno effects is also discussed.
Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method
Authors: Nangia Shikha , Jasper Ahren W. , Miller Thomas F. , Truhlar Donald G.
Published: February 2004

The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom–diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mechanical calculations were performed, and the probabilities for nonadiabatic reaction and nonreactive deexcitation (quenching) were found to be on the order of 10−8. For such low-probability events the anteater sampling scheme requires a large number of trajectories (∼1010) to obtain good statistics and converged semiclassical results. In contrast by using the new army ants algorithm converged results were obtained by running 105 trajectories. Furthermore, the results were found to be in excellent agreement with the quantum mechanical results. Sampling errors were estimated using the bootstrap method, which is validated for use with the army ants algorithm.
Statisticodynamical approach of state distributions in the products of four-atom planar unimolecular reactions. I. Formal developments for conserved vibrations
Authors: Bonnet Laurent , Larrégaray Pascal , Rayez Jean-Claude
Published: February 2004

Traditional statistical approaches, entirely based on transition state theory (TST), do not allow the description of rotational state distributions in the products of indirect reactions governed by short-range forces. Owing to the interpretative power of TST, this limitation has long been acting as a brake upon a deep understanding of determining attributes of indirect reaction dynamics. Recently, however, we developed a statisticodynamical approach (SDA) of final state distributions for triatomic unimolecular reactions [P. Larrégaray, L. Bonnet, and J. C. Rayez, J. Chem. Phys. 114, 3349 (2001); Phys. Chem. Chem. Phys. 4, 1577 (2002); 4, 1781 (2002)]. The approach combines TST for the description of state distributions at the transition state (TS) and the linear transformation model for the description of their alteration on the way from the TS to the products. The whole description is mostly analytical, thus keeping the rationalizing spirit of TST. The goal of the present series is to extend SDA to the case of four-atom planar unimolecular reactions, assuming that internal vibrations of the nascent products are conserved from the TS on. This first part is concerned with formal developments while the remaining parts deal with their validation and application, in particular to the fragmentation of isocyanic acid.
Statisticodynamical approach of state distributions in the products of four-atom planar unimolecular reactions. II. Validation and distribution shape analysis in the barrier case
Authors: Bonnet Laurent , Larrégaray Pascal , Rayez Jean-Claude
Published: February 2004

In the first part of this series, we proposed a statisticodynamical approach of state distributions in the products of four-atom planar unimolecular reactions governed by short-range forces. In this second part, the approach is tested against quasiclassical trajectory calculations on an ab initio potential energy surface. The process considered is the fragmentation of isocyanic acid in the first excited singlet electronic state. The study leads to a very good agreement between both methods. In addition to that, we pinpoint in the barrier case the main mechanical parameters governing the shape of rotational state distributions. It appears that these parameters are related to two distinct physical effects. The first one is of the impulsive type. The second, already observed in triatomic processes, is the so-called bending effect.
Probe of bending motion following the 1s−1π* excitation of N2O
Authors: Machida M. , Lavollée M. , Randrianjafisoa J. , Laurent G. , Nagoshi M. , Okada K. , Koyano I. , Saito N.
Published: February 2004

The doubly degenerate core-excited Π state of N2O splits into two due to the static Renner–Teller effect. The lower state, A1, has a bent stable geometry and the molecule excited to this state starts to deform itself toward this bent geometry. To probe the effect of the potential energy surfaces of the core-excited A1 states on the nuclear motion, we measure the momenta of the three atomic ions in coincidence by means of the ion momentum imaging technique. We find that the potential energy surface affects the molecular deformation significantly. N2O in the terminal N 1s−13πA1 excited state is observed to be bent more than that in the central N 1s−13πA1 excited state. This means that N2O in the terminal N 1s−13πA1 excited state bends faster than that in the central N 1s−13πA1 excited state. When the excitation energy is decreased within the 1s−13π resonances, the nuclear motion in the A1 states becomes faster. This is interpreted by the notion that the excitation occurs onto the steeper slope part of the potential energy surface of the excited state for the lower excitation energy. The branching ratio of the A1 excitation increases with the decrease in the excitation energy.
“Spectral implementation” for creating a labeled pseudo-pure state and the Bernstein–Vazirani algorithm in a four-qubit nuclear magnetic resonance quantum processor
Authors: Peng Xinhua , Zhu Xiwen , Fang Ximing , Feng Mang , Liu Maili , Gao Kelin
Published: February 2004

A quantum circuit is introduced to describe the preparation of a labeled pseudo-pure state by multiplet-component excitation scheme which has been experimentally implemented on a 4-qubit nuclear magnetic resonance quantum processor. Meanwhile, we theoretically analyze and numerically investigate the low-power selective single-pulse implementation of a controlled-rotation gate, which manifests its validity in our experiment. Based on the labeled pseudo-pure state prepared, a 3-qubit Bernstein–Vazirani algorithm has been experimentally demonstrated by spectral implementation. The “answers” of the computations are identified from the split peak positions in the spectra of the observer spin, which are equivalent to projective measurements required by the algorithms.
Tunneling chemical reactions in solid parahydrogen: Direct measurement of the rate constants of R+H2→RH+H (R=CD3,CD2H,CDH2,CH3) at 5 K
Authors: Hoshina Hiromichi , Fushitani Mizuho , Momose Takamasa , Shida Tadamasa
Published: February 2004

Tunneling chemical reactions between deuterated methyl radicals and the hydrogen molecule in a parahydrogen crystal have been studied by Fourier transform infrared spectroscopy. The tunneling rates of the reactions R+H2→RH+H (R=CD3,CD2H,CDH2) in the vibrational ground state were determined directly from the temporal change in the intensity of the rovibrational absorption bands of the reactants and products in each reaction in solid parahydrogen observed at 5 K. The tunneling rate of each reaction was found to differ definitely depending upon the degree of deuteration in the methyl radicals. The tunneling rates were determined to be 3.3×10−6 s−1, 2.0×10−6 s−1, and 1.0×10−6 s−1 for the systems of CD3, CD2H, and CDH2, respectively. Conversely, the tunneling reaction between a CH3 radical and the hydrogen molecule did not proceed within a week’s time. The upper limit of the tunneling rate of the reaction of the CH3 radical was estimated to be 8×10−8 s−1.
Determination of the proton tunneling splitting of the vinyl radical in the ground state by millimeter-wave spectroscopy combined with supersonic jet expansion and ultraviolet photolysis
Authors: Tanaka Keiichi , Toshimitsu Masaaki , Harada Kensuke , Tanaka Takehiko
Published: February 2004

The vinyl radical in the ground vibronic state produced in a supersonic jet expansion by 193 nm excimer laser photolysis of vinyl bromide was investigated by millimeter-wave spectroscopy. Due to the proton tunneling, the ground state is split into two components, of which the lower and higher ones are denoted as 0+ and 0−, respectively. Eight pure rotational transitions with Ka=0 and 1 obeying a-type selection rules were observed for each of the 0+ and 0− states in the frequency region of 60–250 GHz. Tunneling–rotation transitions connecting the lower (0+) and upper (0−) components of the tunneling doublet, obeying b-type selection rules, were also observed in the frequency region of 190–310 GHz, including three R- and six Q-branch transitions. The observed frequencies of the pure rotational and tunneling–rotation transitions were analyzed by using an effective Hamiltonian in which the coupling between the 0+ and 0− states was taken into account. A set of precise molecular constants was obtained. Among others, the proton tunneling splitting in the ground state was determined to be ΔE0=16 272(2) MHz. The potential barrier height was estimated to be 1580 cm−1 from the proton tunneling splitting, by an analysis using a detailed one-dimensional model. The spin–rotation and hyperfine interaction constants were also determined for the 0+ and 0− states together with the off-diagonal interaction constants connecting the 0+ and 0− states, εab+εba for the spin–rotation interaction and Tab for the hyperfine interaction of the α (CH) proton. The hyperfine interaction constants, due to the α proton and the β (CH2) protons, are consistent with those derived from electron spin resonance studies.
Ultrafast nonadiabatic dynamics: Quasiclassical calculation of the transient photoelectron spectrum of I2−⋅(CO2)8
Authors: Yu N. , Margulis C. J. , Coker D. F.
Published: February 2004

In this paper we investigate the transient photoelectron spectrum of I2− in CO2 clusters recently measured by Neumark and co-workers. This work reveals a rich excited state dynamics with various competing electronic output channels. We find good agreement with experiments and we are able to relate the transient signal to different dynamical events that occur during the evolution of the cluster and its fragmentation products.
Performance of the τ-dependent functionals in predicting the magnetic coupling of ionic antiferromagnetic insulators
Authors: Ciofini Ilaria , Illas Francesc , Adamo Carlo
Published: February 2004

The performance of some kinetic energy density (τ) dependent functionals in predicting the effective Heisenberg exchange has been explored using the KNiF3 and K2NiF4 insulators as case examples. Our results show that this new generation of functionals represents an important improvement with respect to the current local and gradient corrected functionals yielding a semi-quantitative description of the antiferromagnetic coupling without the need of hybrid approaches thus avoiding the calculation of exact, Hartree–Fock exchange. This feature opens a wide field of application especially in solid state.
Second harmonic generation second hyperpolarizability of water calculated using the combined coupled cluster dielectric continuum or different molecular mechanics methods
Authors: Kongsted Jacob , Osted Anders , Mikkelsen Kurt V. , Christiansen Ove
Published: February 2004

In this article we report the first calculations of second harmonic generation second hyperpolarizability of liquid water using coupled cluster/molecular mechanics (CC/MM) methods or coupled cluster/dielectric continuum (CC/DC) methods. The latter approach treats the solvent as an isotropic homogeneous fluid while the former accounts for the discrete nature of the solvent molecules. The CC/MM approach may include or exclude polarization effects explicitly. Alternatively, polarization effects may be included using perturbation theory. The CC descriptions implemented are the coupled cluster second-order approximate singles and doubles (CC2) and coupled cluster singles and doubles models. The second harmonic generation second hyperpolarizabilities are, depending on the model, obtained using either an analytical implementation of the cubic response function or using an analytical implementation of the quadratic response function combined with the finite field technique. The CC/MM results for the second harmonic generation second hyperpolarizability compare excellently with experimental data while a significant overestimation is found when using the CC/DC model. Particular, the cavity radius in the CC/DC calculations have an enormous effects on this fourth-order property.
Modeling benzene with single-site potentials from ab initio calculations: A step toward hybrid models of complex molecules
Authors: Cacelli I. , Cinacchi G. , Prampolini G. , Tani A.
Published: February 2004

Extensive ab initio calculations at the MP2/6-31G* level have been carried out to sample the energy surface for the interactions of the benzene dimers. This database has been used to parameterize two anisotropic single-site models, meant to be used as building blocks in hybrid models of complex, liquid crystal forming molecules. A quadrupolar Gay–Berne (GBQIII) and an S-function (SF) Corner potentials have been obtained in this way. Their ability to reproduce, qualitatively at least, the phase diagram as well as energetic and structural properties of benzene has been tested with Monte Carlo simulations and compared with previous literature potentials, GBQI [S. Gupta et al., Mol. Phys. 65, 961 (1988)] and GBQII [T. R. Walsh, Mol. Phys. 100, 2867 (2002)]. It turned out that GBQI showed no melting transition in the temperature range explored (100–400 K), while GBQII underwent a phase transition from solid to gas, with no liquid phase. Conversely, both models parameterized on our database of ab initio interaction energies (GBQIII and SF) gave rise to a stable liquid phase. Melting has been observed between 100 and 150 K (GBQIII) and in the range 300–350 K (SF), i.e., substantially below and slightly above the experimental value at ambient pressure, 278 K. The description of the crystal structure of benzene at atmospheric pressure is also in better agreement with experimental data if the SF model is used, while positional correlations in the liquid are better described by the GBQIII potential. The S-function potential is also computationally more convenient. These results could be useful in the semirealistic modeling of more complex molecules.
Density functional calculations of the vibronic structure of electronic absorption spectra
Authors: Dierksen Marc , Grimme Stefan
Published: February 2004

Calculations of the vibronic structure in electronic spectra of large organic molecules based on density functional methods are presented. The geometries of the excited states are obtained from time-dependent density functional (TDDFT) calculations employing the B3LYP hybrid functional. The vibrational functions and transition dipole moment derivatives are calculated within the harmonic approximation by finite difference of analytical gradients and the transition dipole moment, respectively. Normal mode mixing is taken into account by the Duschinsky transformation. The vibronic structure of strongly dipole-allowed transitions is calculated within the Franck–Condon approximation. Weakly dipole-allowed and dipole-forbidden transitions are treated within the Franck–Condon–Herzberg–Teller and Herzberg–Teller approximation, respectively. The absorption spectra of several organic π systems (anthracene, pentacene, pyrene, octatetraene, styrene, azulene, phenoxyl) are calculated and compared with experimental data. For dipole-allowed transitions in general a very good agreement between theory and experiment is obtained. This indicates the good quality of the optimized geometries and harmonic force fields. Larger errors are found for the weakly dipole-allowed S0→S1 transition of pyrene which can tentatively be assigned to TDDFT errors for the relative energies of excited states close to the target state. The weak bands of azulene and phenoxyl are very well described within the Franck–Condon approximation which can be explained by the large energy gap (>1.2 eV) to higher-lying excited states leading to small vibronic couplings. Once corrections are made for the errors in the theoretical 0–0 transition energies, the TDDFT approach to calculate vibronic structure seems to outperform both widely used ab initio methods based on configuration interaction singles or complete active space self-consistent field wave functions and semiempirical treatments regarding accuracy, applicability, and computational effort. Together with the parallel computer implementations employed, the present approach appears to be a valuable tool for a quantitative description and detailed understanding of electronic excitation processes in large molecules.
Hybrid diatomics-in-molecules-based quantum mechanical/molecular mechanical approach applied to the modeling of structures and spectra of mixed molecular clusters Arn(HCl)m and Arn(HF)m
Authors: Bochenkova A. V. , Suhm M. A. , Granovsky A. A. , Nemukhin A. V.
Published: February 2004

A new hybrid QM/DIM approach aimed at describing equilibrium structures and spectroscopic properties of medium size mixed molecular clusters is developed. This methodology is applied to vibrational spectra of hydrogen chloride and hydrogen fluoride clusters with up to four monomer molecules embedded in argon shells Arn(H(Cl/F))m (n=1–62, m=1–4). The hydrogen halide complexes (QM part) are treated at the MP2/aug-cc-pVTZ level, while the interaction between HX molecules and Ar atoms (MM part) is described in terms of the semiempirical DIM methodology, based on the proper mixing between neutral and ionic states of the system [Grigorenko et al., J. Chem. Phys. 104, 5510 (1996)]. A detailed analysis of the resulting topology of the QM/DIM potential energy (hyper-)surface in the triatomic subsystem Ar–HX reveals more pronounced nonadditive atomic induction and dispersion contributions to the total interaction energy in the case of the Ar–HCl system. An extension of the original analytical DIM-based potential in the frame of the present model as well as the current limitations of the method are discussed. A modified algorithm for the gradient geometry optimization, along with partly analytical force constant matrix evaluation, is developed to treat large cages of argon atoms around molecular clusters. Calculated frequency redshifts of HX stretching vibrations in the mixed clusters relative to the isolated hydrogen-bonded complexes are in good agreement with experimental findings.
Direct determination of multipole moments of Cartesian Gaussian functions in spherical polar coordinates
Authors: Choi Cheol Ho
Published: February 2004

A new way of generating the multipole moments of Cartesian Gaussian functions in spherical polar coordinates has been established, bypassing the intermediary of Cartesian moment tensors. A new set of recurrence relations have also been derived for the resulting analytic integral values. The new method furnishes a conceptually simple and numerically efficient evaluation procedure for the multipole moments. The advantages over existing methods are documented. The results are relevant for the linear scaling quantum theories based on the fast multipole method.
Theoretical study of the hydrogen atom transfer in the heterodimer indole–ammonia and comparison with experimental results
Authors: Ritze H.-H. , Lippert H. , Stert V. , Radloff W. , Hertel I. V.
Published: February 2004

Ab initio calculations on the heterodimer C8H6NH⋯NH3 are carried out for its ground, the excited πσ*, and the ground cationic electronic states, enabling the description of hydrogen or proton transfer, respectively. Two-dimensional quantum-dynamical computations on the πσ* potential surface help one to understand the mechanism and the time scale of the hydrogen transfer. Subsequent decay processes are discussed depending on the vibrational excitation of the ammonium constituent. Finally, the theoretical results obtained are used for the interpretation of the time-dependent signals observed in femtosecond pump–probe experiments.
Connection between the observable and centroid structural properties of a quantum fluid: Application to liquid para-hydrogen
Authors: Blinov Nicholas , Roy Pierre-Nicholas
Published: February 2004

It is shown that the discrepancy between path integral Monte Carlo [M. Zoppi et al., Phys. Rev. B 65, 092204 (2002)] and path integral centroid molecular dynamics [F. J. Bermejo et al., Phys. Rev. Lett. 84, 5359 (2000)] calculations of the static structure factor of liquid para-hydrogen can be explained based on a deconvolution equation connecting centroid and physical radial distribution functions. An explicit expression for the kernel of the deconvolution equation has been obtained using functional derivative techniques. In the superposition approximation, this kernel is given by the functional derivative of the effective potential with respect to the pairwise classical potential. Results of path integral Monte Carlo calculations for the radial distribution function and the static structure factor of liquid para-hydrogen are presented.
Determination of solvation free energies by adaptive expanded ensemble molecular dynamics
Authors: Åberg K. Magnus , Lyubartsev Alexander P. , Jacobsson Sven P. , Laaksonen Aatto
Published: February 2004

A new method of calculating absolute free energies is presented. It was developed as an extension to the expanded ensemble molecular dynamics scheme and uses probability density estimation to continuously optimize the expanded ensemble parameters. The new method is much faster as it removes the time-consuming and expertise-requiring step of determining balancing factors. Its efficiency and accuracy are demonstrated for the dissolution of three qualitatively very different chemical species in water: methane, ionic salts, and benzylamine. A recently suggested optimization scheme by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)] was also implemented and found to be computationally less efficient than the proposed adaptive expanded ensemble method.
Morphology of microphase separated domains in rod–coil copolymer melts
Authors: Yamazaki N. , Motoyama M. , Nonomura M. , Ohta T.
Published: February 2004

We investigate the morphology of microphase separated domains in diblock copolymers where each chain consists of a stiff rod block and a flexible coil block. A simplified phenomenological model system is introduced, which is coarse-grained in terms of the local concentration difference between the two blocks and the local director field of the rod part. Computer simulations of this set of time-evolution equations in two dimensions show in the weak segregation regime that the elastic energy in the rod-block rich domains affects drastically the structures of microphase separated domains. A coil-to-rod transition is incorporated into the model system to examine the elastic and anisotropic effects. The effects of the external electric field are also investigated to control the domain morphology.
Computer simulation study of the global phase behavior of linear rigid Lennard-Jones chain molecules: Comparison with flexible models
Authors: Galindo A. , Vega C. , Sanz E. , MacDowell L. G. , de Miguel E. , Blas F. J.
Published: February 2004

The global phase behavior (i.e., vapor-liquid and fluid-solid equilibria) of rigid linear Lennard-Jones (LJ) chain molecules is studied. The phase diagrams for three-center and five-center rigid model molecules are obtained by computer simulation. The segment-segment bond lengths are L=σ, so that models of tangent monomers are considered in this study. The vapor-liquid equilibrium conditions are obtained using the Gibbs ensemble Monte Carlo method and by performing isobaric-isothermal NPT calculations at zero pressure. The phase envelopes and critical conditions are compared with those of flexible LJ molecules of tangent segments. An increase in the critical temperature of linear rigid chains with respect to their flexible counterparts is observed. In the limit of infinitely long chains the critical temperature of linear rigid LJ chains of tangent segments seems to be higher than that of flexible LJ chains. The solid-fluid equilibrium is obtained by Gibbs–Duhem integration, and by performing NPT simulations at zero pressure. A stabilization of the solid phase, an increase in the triple-point temperature, and a widening of the transition region are observed for linear rigid chains when compared to flexible chains with the same number of segments. The triple-point temperature of linear rigid LJ chains increases dramatically with chain length. The results of this work suggest that the fluid-vapor transition could be metastable with respect to the fluid-solid transition for chains with more than six LJ monomer units.
Diffusion-diffusion correlation and exchange as a signature for local order and dynamics
Authors: Callaghan P. T. , Furó I.
Published: February 2004

We demonstrate the use of new two-dimensional nuclear magnetic resonance experiments in the examination of local diffusional anisotropy under conditions of global isotropy. The methods, known as diffusion-diffusion correlation spectroscopy and diffusion exchange spectroscopy, employ successive pairs of magnetic field gradient pulses, with signal analysis using two-dimensional inverse Laplace transformation. Diffusional anisotropy is measured for water molecules in a polydomain lamellar phase lyotropic liquid crystal, 40 wt % nonionic surfactant C10E3 (C10H21O(CH2CH2O)6H) in H2O.
Analysis of the phase transitions in alkyl-mica by density and pressure profiles
Authors: Heinz Hendrik , Paul Wofgang , Suter Ulrich W. , Binder Kurt
Published: February 2004

In a previous work [Heinz, Castelijns, and Suter, J. Am. Chem. Soc. 115, 9500 (2003)], we developed an accurate force field and simulated the phase transitions in C18-mica (octadecyltrimethylammonium-mica) as well as the absence of such transitions in 2C18-mica (dioctadecyldimethylammonium-mica) between room temperature and 100 °C. Here we analyze (i) average z coordinates of the carbon atoms and interdigitation of the hydrocarbon bilayers, (ii) density profiles, and (iii) pressure profiles of the structures along all Cartesian axes. In C18-mica, the standard deviation in the z coordinate for the chain atoms is high and more than doubles in the disordered phase. The order–disorder transition is accompanied by a change in the orientation of the ammonium head group, as well as decreasing tensile and shear stress in the disordered phase. In 2C18-mica, the standard deviation in the z coordinate for the chain atoms is low and does not increase remarkably on heating. The backbones display a highly regular structure, which is slightly obscured by rotations in the C18 backbones and minor head group displacements at 100 °C. Close contacts between the bulky head groups with sidearms cause significant local pressure which is in part not relieved at 100 °C. An increase of the basal-plane spacing at higher temperature is found in both systems due to larger separation between the two hydrocarbon layers and an increased z spacing between adjacent chain atoms (=decreased tilt of the chains relative to the surface normal), and, in C18-mica only, a stronger upward orientation of the C18 chain at the ammonium head group. The likelihood for chain interdigitation between the two hydrocarbon layers is 24%–30% for C18-mica, and 65%–26% for 2C18-mica (for 20–100 °C).
Linear viscoelastic analysis of formation and relaxation of azobenzene polymer gratings
Authors: Saphiannikova Marina , Geue Thomas M. , Henneberg Oliver , Morawetz Knut , Pietsch Ullrich
Published: February 2004

Surface relief gratings on azobenzene containing polymer films were prepared under irradiation by actinic light. Finite element modeling of the inscription process was carried out using linear viscoelastic analysis. It was assumed that under illumination the polymer film undergoes considerable plastification, which reduces its original Young’s modulus by at least three orders of magnitude. Force densities of about 1011 N/m3 were necessary to reproduce the growth of the surface relief grating. It was shown that at large deformations the force of surface tension becomes comparable to the inscription force and therefore plays an essential role in the retardation of the inscription process. In addition to surface profiling the gradual development of an accompanying density grating was predicted for the regime of continuous exposure. Surface grating development under pulselike exposure cannot be explained in the frame of an incompressible fluid model. However, it was easily reproduced using the viscoelastic model with finite compressibility.
Assessing the efficiency of free energy calculation methods
Authors: Rodriguez-Gomez David , Darve Eric , Pohorille Andrew
Published: February 2004

The efficiencies of two recently developed methods for calculating free energy changes along a generalized coordinate in a system are discussed in the context of other, related approaches. One method is based on Jarzynski’s identity [Phys. Rev. Lett. 78, 2690 (1997)]. The second method relies on thermodynamic integration of the average force and is called the adaptive biasing force method [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)]. Both methods are designed such that the system evolves along the chosen coordinate(s) without experiencing free energy barriers and they require calculating the instantaneous, unconstrained force acting on this coordinate using the formula derived by Darve and Pohorille. Efficiencies are analyzed by comparing analytical estimates of statistical errors and by considering two numerical examples—internal rotation of hydrated 1,2-dichloroethane and transfer of fluoromethane across a water-hexane interface. The efficiencies of both methods are approximately equal in the first but not in the second case. During transfer of fluoromethane the system is easily driven away from equilibrium and, therefore, the performance of the method based on Jarzynski’s identity is poor.
A test of the method of images at the surface of molecular materials
Authors: Eilmes A. , Munn R. W.
Published: February 2004

The method of images is tested by comparing two ways of calculating the polarization energy in crystalline fullerene C60 and in bulk amorphous polyethylene (PE): (i) treating the whole molecular material microscopically, and (ii) replacing part of the material by a uniform dielectric continuum of the same relative permittivity. The method of images is accurate to within 5% once the distance of the charge from the surface of the dielectric continuum exceeds about twice the average spacing between the polarizable units in the molecular material. For C60 crystals the method of images always overestimates the magnitude of the polarization energy, partly because it ignores the reduction in the relative permittivity of the dielectric continuum near its surface. For amorphous PE the method of images can overestimate or underestimate the true result, depending on the local density around the charge.
Critical evaluation of approximate quantum decoherence rates for an electronic transition in methanol solution
Authors: Turi László , Rossky Peter J.
Published: February 2004

We present a quantum molecular dynamics calculation of a semiclassical decoherence function to evaluate the accuracy of alternative short-time approximations for coherence loss in the dynamics of condensed phase electronically nonadiabatic processes. The semiclassical function from mixed quantum-classical molecular dynamics simulations and frozen Gaussian wave packets is computed for the electronic transition of an excited state excess electron to the ground state in liquid methanol. The decoherence function decays on a 10 fs time scale that is qualitatively similar to the aqueous case. We demonstrate that it is the motion of the hydrogen atom, and, in particular, the hydrogen rotation around the oxygen-methyl bond which is predominantly responsible for destroying the quantum correlations between alternative states. Multiple time scales due to the slower diffusive nuclear modes, which dominate the solvation response of methanol, do not contribute to the coherence loss. The choice of the coordinate representation is investigated in detail and concluded to be irrelevant to the decay. Changes in both nuclear momenta and positions on the two alternative potential surfaces are found to contribute to decoherence, the former dominating at short times (t<5 fs), the latter controlling the decay at longer times. Various short-time approximations to the full dynamics for the decoherence function are tested for the first time. The present treatment rigorously develops the short-time description and establishes its range of validity. Whereas the lowest-order short-time approximation proves to be a very good approximation up to about 5 fs, we also find that it bounds the decay of the decoherence function. After 5 fs, the coherence decay in fact becomes faster than the single Gaussian predicted in the lowest-order short-time limit. This decay is well reflected by an enhanced low-order approximation, which is also easily computed from equilibrium classical forces.
Competition between compaction of single chains and bundling of multiple chains in giant DNA molecules
Authors: Iwataki Toshio , Kidoaki Satoru , Sakaue Takahiro , Yoshikawa Kenichi , Abramchuk Sergey S.
Published: February 2004

It has been established that in a dilute solution individual giant DNA molecules undergo a large discrete transition between an elongated coil state and a folded compact state. On the other hand, in concentrated solutions, DNA molecules assemble into various characteristic states, including multichain aggregate, liquid crystalline, ionic crystal, etc. In this study, we compared single-chain and multiple-chain events by observing individual chains using fluorescence microscopy. We used spermidine, SPD(3+), as a condensing agent for giant DNA. When the concentration of DNA is below 1 μM in base-pair units, individual DNA molecules exhibit a transition from an elongated state to a compact state. When the concentration of DNA is increased to 10 μM, a thick fiberlike assembly of multiple chains appears. AFM measurements of this thick fiber revealed that more than tens of DNA molecules form a bundle structure with parallel ordering of the chains. The transition between single-chain compaction and bundle formation with multiple-chain assemblies was reproduced by a theoretical calculation.
Thermal conductivity of solid argon from molecular dynamics simulations
Authors: Tretiakov Konstantin V. , Scandolo Sandro
Published: February 2004

The thermal conductivity of solid argon in the classical limit has been calculated by equilibrium molecular dynamic simulations using the Green–Kubo formalism and a Lennard-Jones interatomic potential. Contrary to previous theoretical reports, we find that the computed thermal conductivities are in good agreement with experimental data. The computed values are also in agreement with the high-temperature limit of the three-phonon scattering contribution to the thermal conductivity. We find that finite-size effects are negligible and that phonon lifetimes have two characteristic time scales, so that agreement with kinetic theory is obtained only after appropriate averaging of the calculated phonon lifetimes.
Relativistic hydrodynamics of magnetic and dielectric fluids in interaction with the electromagnetic field
Authors: Felderhof B. U.
Published: February 2004

The semirelativistic hydrodynamic equations of motion of de Groot and Mazur [Non-Equilibrium Thermodynamics (North-Holland, Amsterdam, 1962)] for a fluid with polarization and magnetization are derived from the relativistic energy–momentum conservation equation, mass conservation, and Maxwell’s equations on the basis of a systematic expansion in inverse powers of the velocity of light. A modification of the de Groot–Suttorp field energy–momentum tensor [de Groot and Suttorp, Foundations of Electrodynamics (North-Holland, Amsterdam, 1972)] based on a shift of terms to the internal energy density of the fluid yields relatively simple expressions for energy density, energy current density, momentum density, and stress tensor.
Thermal relaxation of glycerol and propylene glycol studied by photothermal spectroscopy
Authors: Bentefour E. H. , Glorieux C. , Chirtoc M. , Thoen J.
Published: February 2004

In this paper we report on experimental data for the frequency and temperature dependence of the thermal properties of supercooled glycerol and propylene glycol. By using a photopyroelectric method the specific heat capacity and thermal conductivity were separately determined in a bandwidth of several decades. We have recently shown that the thermal conductivity has no relaxation behavior, which simplifies the analysis of our results. The relaxation behavior of the specific heat capacity is compared with literature results for other physical quantities and a detailed analysis of the temperature dependence of the relaxation parameters is presented.
Searching for nanostructures of the cubic mesophase of liquid crystal molecules, BABH8
Authors: Yoneya Makoto , Nishikawa Etsushi , Yokoyama Hiroshi
Published: February 2004

Nanostructures of a thermotropic cubic phase forming liquid crystal compound, 1,2-bis-[4-n-octyloxy-benzoyl]-hydrazine was studied by molecular dynamics (MD) simulations. A model for its cubic phase structure was proposed, which was constructed from the building unit of a locally orientational ordered “bundle” consistent with the cell parameter and the space group (Ia3̄d) from the recent x-ray results. Stability of the model structure was studied by multinanosecond MD simulations. A periodic nanostructure with 2.6 nm periodicity [coincides with the Ia3̄d (211) reflection] was kept up to 60 ns in the reduced pressure simulation which realizes the experimental value of density. However, the calculated fourth-rank order parameter shows that the simulated final state above does not have cubic orientational symmetry but rather isotropic symmetry.
Static properties of end-tethered polymers in good solution: A comparison between different models
Authors: Kreer T. , Metzger S. , Müller M. , Binder K. , Baschnagel J.
Published: February 2004

We present a comparison between results, obtained from different simulation models, for the static properties of end-tethered polymer layers in good solvent. Our analysis includes data from two previous studies—the bond fluctuation model of Wittmer et al. [J. Chem. Phys. 101, 4379 (1994)] and the off-lattice bead–spring model of Grest and Murat [Macromolecules 26, 3108 (1993)]. Additionally, we explore the properties of a similar off-lattice model simulated close to the Θ temperature. We show that the data for the bond fluctuation and the Grest–Murat model can be analyzed in terms of scaling theory because chains are swollen inside the Pincus blob. In the vicinity of the Θ point the structure of the chains is essentially Gaussian in the Pincus blob. Therefore, the data for the second off-lattice model can be compared quantitatively to the self-consistent field theory. Different ways to determine the parameters of the self-consistent field theory are discussed.
Patch size effect on diffusion and incorporation in dilute suspension of partially active spheres
Authors: Lu Shih-Yuan
Published: February 2004

The normalized overall rate constant kp/kf for diffuse-and-incorporate processes in dilute suspension of spheres partially covered with randomly distributed nonoverlapping active patches is studied with a sped-up Brownian dynamic simulation scheme. The normalized overall rate constant is found to increase with decreasing characteristic size of the active patch under the condition of fixed fcover, the surface area fraction covered by the active patches. A scaling relation is proposed as (kp/kf)NDL/[(1+P)−(1+P/fcover)(kp/kf)NDL]∼Np1/2 with Np being the number of active patches on the sphere, P a parameter characterizing the relative dominance of surface incorporation over diffusion, and NDL signifying the nondiffusion-limited condition. This scaling relation is verified with rate constant data from the sped-up Brownian dynamic simulation. From this scaling relation, the maximum achievable kp/kf is derived to be (1+P)/(1+P/fcover). This result implies that kp/kf can approach unity under the diffusion-limited situation even for a partially active sphere by reducing the size of active patch, while it is not possible to achieve unit kp/kf for nondiffusion-limited systems.