American Institute of Physics: Journal of Chemical Physics

Journal of Chemical Physics: All Topics

Spectroscopic study of CHBrF up to 9500 cm: Vibrational analysis, integrated band intensities, and ab initio calculations
Andrea Pietropolli Charmet, Paolo Stoppa, Nicola Tasinato, Alessandro Baldan, Santi Giorgianni et al. The gas-phase infrared spectra of bromodifluoromethane, CHBrF, have been examined at medium resolution in the range of 2009500 cm. The assignment of the absorptions in terms of fundamental, overtone, combination, and hot bands, assisted by quantum chemical calculations is consistent all over the re ... [J. Chem. Phys. 133, 044310 (2010)] published Fri Jul 30, 2010.
Cross sections for rotational decoherence of perturbed nitrogen measured via decay of laser-induced alignment
N. Owschimikow, F. Konigsmann, J. Maurer, P. Giese, A. Ott et al. We quantitatively determine cross sections for rotational decoherence from the decay of nonadiabatic laser-induced alignment in nitrogen and nitrogen-foreign gas mixtures in a temperature range between 80 K and room temperature. The cross section for rotational decoherence in pure nitrogen decreases ... [J. Chem. Phys. 133, 044311 (2010)] published Fri Jul 30, 2010.
Finite temperature quantum statistics of H molecular ion
Ilkka Kylanpaa and Tapio T. Rantala Full quantum statistical NVT simulation of the five-particle system H has been carried out using the path integral Monte Carlo method. Structure and energetics are evaluated as a function of temperature up to the thermal dissociation limit. The weakly density dependent dissociation temperature is fo ... [J. Chem. Phys. 133, 044312 (2010)] published Fri Jul 30, 2010.
Comparisons of classical and Wigner sampling of transition state energy levels for quasiclassical trajectory chemical dynamics simulations
Lipeng Sun and William L. Hase Quasiclassical trajectory calculations are compared, with classical and Wigner sampling of transition state (TS) energy levels, for CHF-->HF+CH product energy partitioning and [Cl[centered ellipsis]CH[centered ellipsis]Cl] central barrier dynamics. The calculations with Wigner sampling are reported ... [J. Chem. Phys. 133, 044313 (2010)] published Fri Jul 30, 2010.
Multi-time density correlation functions in glass-forming liquids: Probing dynamical heterogeneity and its lifetime
Kang Kim and Shinji Saito A multi-time extension of a density correlation function is introduced to reveal temporal information about dynamical heterogeneity in glass-forming liquids. We utilize a multi-time correlation function that is analogous to the higher-order response function analyzed in multidimensional nonlinear sp ... [J. Chem. Phys. 133, 044511 (2010)] published Fri Jul 30, 2010.
Cubic gauche-CN: A superhard metallic compound predicted via first-principles calculations
Xiaoli Wang, Kuo Bao, Fubo Tian, Xing Meng, Changbo Chen et al. In this paper, we suggest a novel potential superhard material, a new carbon nitride phase consisted of sp hybridized bonds, possessing a cubic P23 symmetry (8 atoms/cell, labeled by cg-CN) which is similar to cubic gauche nitrogen (cg-N) by first-principles calculations. It is a metallic compound, ... [J. Chem. Phys. 133, 044512 (2010)] published Fri Jul 30, 2010.
Evolution of the isotropic to nematic phase transition in binary mixtures of octylcyanobiphenyl and n-hexane
K. P. Sigdel and G. S. Iannacchione High-resolution calorimetry has been performed to study the effect of dilution by a nonmesogenic, low-molecular weight solvent (linear n-hexane) on the isotropic-nematic (I-N) phase transition in the liquid crystal (LC) octylcyanobiphenyl (8CB) as a function of n-hexane concentration. Numerous tempe ... [J. Chem. Phys. 133, 044513 (2010)] published Fri Jul 30, 2010.
Erratum: Bimolecular reaction rates from ring polymer molecular dynamics [J. Chem. Phys. 130, 174713 (2009)]
Rosana Collepardo-Guevara, Yury V. Suleimanov, and David E. Manolopoulos Abstract not available. [J. Chem. Phys. 133, 049902 (2010)] published Fri Jul 30, 2010.
Defect mediated turbulence in a locally quasiperiodic chemical medium
Ghislain St-Yves and Jorn Davidsen Under a change of conditions, spiral waves in oscillatory reaction-diffusion media can become unstable and give rise to a multitude of emergent patterns. For example, in bounded domains spiral waves can undergo a resonant Hopf bifurcation leading to period-2 spirals which emit wave trains with doubl ... [J. Chem. Phys. 133, 044909 (2010)] published Fri Jul 30, 2010.
Reptation of a semiflexible polymer through porous media
Gimoon Nam, Albert Johner, and Nam-Kyung Lee We study the motion of a single stiff semiflexible filament of length S through an array of topological obstacles. By means of scaling arguments and two-dimensional computer simulations, we show that the stiff chain kinetics follows the reptation picture, albeit with kinetic exponents (for the centr ... [J. Chem. Phys. 133, 044908 (2010)] published Fri Jul 30, 2010.
Linear viscoelasticity of a single semiflexible polymer with internal friction
Tetsuya Hiraiwa and Takao Ohta The linear viscoelastic behaviors of single semiflexible chains with internal friction are studied based on the wormlike-chain model. It is shown that the frequency dependence of the complex compliance in the high frequency limit is the same as that of the Voigt model. This asymptotic behavior appea ... [J. Chem. Phys. 133, 044907 (2010)] published Fri Jul 30, 2010.
HartreeFock perturbative corrections for total and reaction energies
Jia Deng, Andrew T. B. Gilbert, and Peter M. W. Gill We have performed an assessment of the HartreeFock perturbative correction (HFPC) on a large and diverse set of molecules and reactions. Errors in both absolute and reaction energies with respect to converged secondary basis HartreeFock results are reported for a wide spectrum of primary/secondary b ... [J. Chem. Phys. 133, 044116 (2010)] published Fri Jul 30, 2010.
Transferability of anharmonic force fields in simulations of molecular vibrations
Vaclav Parchansky and Petr Bour Accurate simulations of vibrational molecular spectra require precise molecular force fields, at least with cubic and quartic anharmonic corrections beyond the harmonic limits. Generation of such force field terms becomes computationally prohibitive for larger molecules. In this work, an alternate p ... [J. Chem. Phys. 133, 044117 (2010)] published Fri Jul 30, 2010.
Ligand effect on uranium isotope fractionations caused by nuclear volume effects: An ab initio relativistic molecular orbital study
Minori Abe, Tatsuya Suzuki, Yasuhiko Fujii, Masahiko Hada, and Kimihiko Hirao We have calculated the nuclear volume term (ln K) of the isotope fractionation coefficient (epsilon) between UU isotope pairs by considering the effect of ligand coordination in a U(IV)U(VI) reaction system. The reactants were modeled as [UOCl] and [UOCl] for U(VI), and UCl for U(IV). We adopted the ... [J. Chem. Phys. 133, 044309 (2010)] published Fri Jul 30, 2010.
Effect of residual attractive interactions in size asymmetric colloidal mixtures: Theoretical analysis and predictions
Ph. Germain We analyze the influence of residual attractions on the static and some dynamic properties of size asymmetric mixtures of hard-sphere-like colloids. These attractions, usually neglected in the theoretical analysis, are characterized by a very short range and a moderate strength reflecting the underl ... [J. Chem. Phys. 133, 044905 (2010)] published Thu Jul 29, 2010.
Electrostatic origins of polyelectrolyte adsorption: Theory and Monte Carlo simulations
Lei Wang, Haojun Liang, and Jianzhong Wu Electrostatic interactions may promote or abate polyelectrolyte adsorption onto a charged surface depending on a number of interrelated factors including the surface and polymer charge densities, the salt concentration, and nonelectrostatic interactions such as van der Waals and hydrophobic forces. ... [J. Chem. Phys. 133, 044906 (2010)] published Thu Jul 29, 2010.
The boson peak of silicate glasses: The role of SiO, AlO, and SiN bonds
Nicolas F. Richet, Hitoshi Kawaji, and Tanguy Rouxel The role of SiO, AlO, and SiN bonds on the boson peak of silicate glasses has been investigated from a study of amorphous Si, SiO, and two calcium aluminosilicates with 0 (Ca28O) and 4.4 (Ca28N) mol % SiN. The low-frequency part of the vibrational density of states g(omega) has been calculated from ... [J. Chem. Phys. 133, 044510 (2010)] published Thu Jul 29, 2010.
Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations
Pietro Faccioli, Alice Lonardi, and Henri Orland The dominant reaction pathway (DRP) is an algorithm to microscopically compute the most probable reaction pathways in the overdamped Langevin dynamics without investing computational time in simulating the local thermal motion in the metastable configurations. In order to test the accuracy of such a ... [J. Chem. Phys. 133, 045104 (2010)] published Thu Jul 29, 2010.
Communication: Electric properties of the ThO(X Sigma) molecule
Alexei A. Buchachenko To assist the proposed search for the electric dipole moment of the electron with the thorium oxide, converged ab initio coupled cluster calculations are performed on the interaction energy, dipole moment, anisotropic static dipole polarizability, and quadrupole moment of the ThO(X Sigma) molecule a ... [J. Chem. Phys. 133, 041102 (2010)] published Thu Jul 29, 2010.
An efficient umbrella potential for the accurate calculation of free energies by molecular simulation
Di Wu Umbrella sampling has been widely used to calculate free energies in many chemical and biological applications because it can effectively bridge the systems of interest and sample in the united phase space that is essential to yield accurate results. Many algorithms have implemented the idea of umbr ... [J. Chem. Phys. 133, 044115 (2010)] published Thu Jul 29, 2010.
Cavity-enhanced resonant photoacoustic spectroscopy with optical feedback cw diode lasers: A novel technique for ultratrace gas analysis and high-resolution spectroscopy
Michael Hippler, Christian Mohr, Katherine A. Keen, and Edward D. McNaghten Cavity-enhanced resonant photoacoustic spectroscopy with optical feedback cw diode lasers (OF-CERPAS) is introduced as a novel technique for ultratrace gas analysis and high-resolution spectroscopy. In the scheme, a single-mode cw diode laser (3 mW, 635 nm) is coupled into a high-finesse linear cavi ... [J. Chem. Phys. 133, 044308 (2010)] published Thu Jul 29, 2010.
Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La
Cyril Terrier, Pierre Vitorge, Marie-Pierre Gaigeot, Riccardo Spezia, and Rodolphe Vuilleumier Structural and electronic properties of La immersed in bulk water have been assessed by means of density functional theory (DFT)-based CarParrinello molecular dynamics (CPMD) simulations. Correct structural properties, i.e., La(III)-water distances and La(III) coordination number, can be obtained wi ... [J. Chem. Phys. 133, 044509 (2010)] published Wed Jul 28, 2010.
Study of the sticking of a hydrogen atom on a graphite surface using a mixed classical-quantum dynamics method
S. Morisset, Y. Ferro, and A. Allouche The sticking of one hydrogen atom chemisorbed on the (0001) graphite surface is investigated using a mixed classical-quantum method. The phonon modes of the system in the collinear scattering approach are included in the dynamics calculations. The vibrational degrees of freedom of the surface (phono ... [J. Chem. Phys. 133, 044508 (2010)] published Wed Jul 28, 2010.
Free energy calculation using molecular dynamics simulation combined with the three dimensional reference interaction site model theory. I. Free energy perturbation and thermodynamic integration along a coupling parameter
Tatsuhiko Miyata, Yasuhiro Ikuta, and Fumio Hirata This article proposes a free energy calculation method based on the molecular dynamics simulation combined with the three dimensional reference interaction site model theory. This study employs the free energy perturbation (FEP) and the thermodynamic integration (TDI) along the coupling parameters t ... [J. Chem. Phys. 133, 044114 (2010)] published Wed Jul 28, 2010.
Structure and spectroscopy of ground and excited states of LiYb
P. Zhang, H. R. Sadeghpour, and A. Dalgarno Multireference configuration interaction and coupled cluster calculations have been carried out to determine the potential energy curves for the ground and low-lying excited states of the LiYb molecule. The scalar relativistic effects have been included by means of the DouglasKroll Hamiltonian and e ... [J. Chem. Phys. 133, 044306 (2010)] published Wed Jul 28, 2010.
IR spectra of protonated benzaldehyde clusters, CHOL (L=Ar,N;n<=2): Ion-ligand binding motifs of the cis and trans oxonium isomers
Shamik Chakraborty, Alexander Patzer, and Otto Dopfer Infrared photodissociation (IRPD) spectra of mass-selected protonated benzaldehyde (CHO,BZH) and its weakly bound clusters with Ar and N produced in an electron impact source are recorded in the CH and OH stretch ranges. The experimental results are supported by ab initio and density functional calc ... [J. Chem. Phys. 133, 044307 (2010)] published Wed Jul 28, 2010.
An analysis of the NEXAFS spectra of a molecular crystal: alpha-glycine
Craig P. Schwartz, Richard J. Saykally, and David Prendergast The nitrogen K-edge near edge x-ray absorption fine structure spectrum of alpha-crystalline glycine has been calculated for temperatures ranging from 0 to 450 K. Significant temperature dependent spectral changes are predicted. The calculated room temperature spectrum is in good agreement with the e ... [J. Chem. Phys. 133, 044507 (2010)] published Tue Jul 27, 2010.
Energy barrier of proton transfer at ice surfaces
Eui-Seong Moon, Jinha Yoon, and Heon Kang We estimated the energy barrier of proton transfer on ice film surfaces through the measurement of the H/D exchange kinetics of HO and DO molecules. The isotopomeric populations of water molecules and hydronium ions on the surface were monitored by using the techniques of reactive ion scattering and ... [J. Chem. Phys. 133, 044709 (2010)] published Tue Jul 27, 2010.
Kinetic Monte Carlo simulations of anisotropic Si(100) etching: Modeling the chemical origins of characteristic etch morphologies
Ankush Gupta, Brandon S. Aldinger, Marc F. Faggin, and Melissa A. Hines An atomistic, chemically realistic, kinetic Monte Carlo simulator of anisotropic Si(100) etching was developed. Surface silicon atoms were classified on the basis of their local structure, and all atoms of each class were etched with the same rate. A wide variety of morphologies, including rough, st ... [J. Chem. Phys. 133, 044710 (2010)] published Tue Jul 27, 2010.
Properties of knotted ring polymers. I. Equilibrium dimensions
Marc L. Mansfield and Jack F. Douglas We report calculations on three classes of knotted ring polymers: (1) simple-cubic lattice self-avoiding rings (SARs), (2) true theta-state rings, i.e., SARs generated on the simple-cubic lattice with an attractive nearest-neighbor contact potential (theta-SARs), and (3) ideal, Gaussian rings. Extra ... [J. Chem. Phys. 133, 044903 (2010)] published Tue Jul 27, 2010.
Properties of knotted ring polymers. II. Transport properties
Marc L. Mansfield and Jack F. Douglas We have calculated the hydrodynamic radius R and intrinsic viscosity [eta] of both lattice self-avoiding rings and lattice theta-state rings that are confined to specific knot states by our path-integration technique. We observe that naive scaling arguments based on the equilibrium polymer size fail ... [J. Chem. Phys. 133, 044904 (2010)] published Tue Jul 27, 2010.
Entropic potential field formed for a linear-motor protein near a filament: Statistical-mechanical analyses using simple models
Ken-ichi Amano, Takashi Yoshidome, Mitsuhiro Iwaki, Makoto Suzuki, and Masahiro Kinoshita We report a new progress in elucidating the mechanism of the unidirectional movement of a linear-motor protein (e.g., myosin) along a filament (e.g., F-actin). The basic concept emphasized here is that a potential field is entropically formed for the protein on the filament immersed in solvent due t ... [J. Chem. Phys. 133, 045103 (2010)] published Tue Jul 27, 2010.
Comment on Evaluation of surface tension and Tolman length as a function of droplet radius from experimental nucleation rate and supersaturation ratio: Metal vapor homogeneous nucleation [J. Chem. Phys. 124, 014506 (2006)]
J. Liu and S. C. Garrick Abstract not available. [J. Chem. Phys. 133, 047101 (2010)] published Tue Jul 27, 2010.
Response to Comment on `Ab initio molecular dynamics calculation of ion hydration free energies' [J. Chem. Phys. 133, 047103 (2010)]
Susan B. Rempe and Kevin Leung Abstract not available. [J. Chem. Phys. 133, 047104 (2010)] published Tue Jul 27, 2010.
Comment on Ab initio molecular dynamics calculation of ion hydration free energies [J. Chem. Phys. 130, 204507 (2009)]
Edward S. Chen and Edward C. M. Chen We suggest that the authors compare their theoretical Gibbs free energies DeltaG (kcal/mol) Li, 128(1), 135; Cl, 78(1), 70(2); and Ag, 120(1) to recent absolute experimental values Li, 128; Cl, 74; and Ag, 119 kcal/mol referenced to that for H, 266(2) kcal/mol. We present bulk Gibbs hydration free e ... [J. Chem. Phys. 133, 047103 (2010)] published Tue Jul 27, 2010.
Response to Comment on `Evaluation of surface tension and Tolman length as a function of droplet radius from experimental nucleation rate and supersaturation ratio: Metal vapor homogeneous nucleation' [J. Chem. Phys. 133, 047101 (2010)]
S. V. Vosel, A. A. Onischuk, and P. A. Purtov Abstract not available. [J. Chem. Phys. 133, 047102 (2010)] published Tue Jul 27, 2010.
Communication: High-frequency acoustic excitations and boson peak in glasses: A study of their temperature dependence
B. Ruta, G. Baldi, V. M. Giordano, L. Orsingher, S. Rols et al. The results of a combined experimental study of the high-frequency acoustic dynamics and of the vibrational density of states (VDOS) as a function of temperature in a glass of sorbitol are reported here. The excess in the VDOS at ~4.5 meV over the Debye, elastic continuum prediction (boson peak) is ... [J. Chem. Phys. 133, 041101 (2010)] published Tue Jul 27, 2010.
Fluctuating dynamics of nematic liquid crystals using the stochastic method of lines
A. K. Bhattacharjee, Gautam I. Menon, and R. Adhikari We construct Langevin equations describing the fluctuations of the tensor order parameter Q in nematic liquid crystals by adding noise terms to time-dependent variational equations that follow from the GinzburgLandaude Gennes free energy. The noise is required to preserve the symmetry and tracelessn ... [J. Chem. Phys. 133, 044112 (2010)] published Tue Jul 27, 2010.
Electronic excitation energy calculation by the fragment molecular orbital method with three-body effects
Mahito Chiba and Tetsuya Koido A scheme for full quantum electronic excited state calculation is proposed that is based on the fragment molecular orbital (FMO) method with three-body effects. The accuracy and efficiency of this scheme is checked by calculating the excitation energy of hydrated formaldehyde and hydrated phenol. In ... [J. Chem. Phys. 133, 044113 (2010)] published Tue Jul 27, 2010.
Use of complex configuration interaction calculations and the stationary principle for the description of metastable electronic states of HCl
Michael Honigmann, Heinz-Peter Liebermann, and Robert J. Buenker The complex multireference single- and double-excitation configuration interaction method has been employed to compute potential curves for the anion of the hydrogen chloride molecule. First, conventional CI calculations with real basis functions have been carried out to determine the potential curv ... [J. Chem. Phys. 133, 044305 (2010)] published Mon Jul 26, 2010.
Spatial averaging for small molecule diffusion in condensed phase environments
Nuria Plattner, J. D. Doll, and Markus Meuwly Spatial averaging is a new approach for sampling rare-event problems. The approach modifies the importance function which improves the sampling efficiency while keeping a defined relation to the original statistical distribution. In this work, spatial averaging is applied to multidimensional systems ... [J. Chem. Phys. 133, 044506 (2010)] published Mon Jul 26, 2010.
Edge versus interior in the chemical bonding and magnetism of zigzag edged triangular graphene molecules
Michael R. Philpott, Sinisa Vukovic, Yoshiyuki Kawazoe, and William A. Lester, Jr. Ab initio density functional theory calculations show that the CC bond lengths fall into three distinct groups: core, apex, and edge, irrespective of whether the molecular center is a single atom or a C-ring. The core, with a geometry that approximates infinite graphene, extends to the penultimate t ... [J. Chem. Phys. 133, 044708 (2010)] published Mon Jul 26, 2010.
Multi-Jastrow trial wavefunctions for electronic structure calculations with quantum Monte Carlo
Thomas Bouabca, Benoit Braida, and Michel Caffarel A new type of electronic trial wavefunction suitable for quantum Monte Carlo calculations of molecular systems is presented. In contrast with the standard JastrowSlater form built with a unique global Jastrow term, it is proposed to introduce individual Jastrow factors attached to molecular orbitals ... [J. Chem. Phys. 133, 044111 (2010)] published Fri Jul 23, 2010.
Vibrationally resolved photoelectron imaging of gold hydride cluster anions: AuH and AuH
Xia Wu, Zhengbo Qin, Hua Xie, Ran Cong, Xiaohu Wu et al. Photoelectron spectra and angular distributions in photodetachment of gold hydride anions AuH and AuH have been obtained using photoelectron velocity-map imaging. Both the images exhibit vibrationally resolved ground state transitions. The adiabatic electron affinities of AuH and AuH are measured to ... [J. Chem. Phys. 133, 044303 (2010)] published Fri Jul 23, 2010.
Sound-driven fluid dynamics in pressurized carbon dioxide
Maikel M. van Iersel, Robert Mettin, Nieck E. Benes, Dirk Schwarzer, and Jos T. F. Keurentjes Using high-speed visualization we demonstrate that ultrasound irradiation of pressurized carbon dioxide (CO) induces phenomena that do not occur in ordinary liquids at ambient conditions. For a near-critical mixture of CO and argon, sonication leads to extremely fast local phase separation, in which ... [J. Chem. Phys. 133, 044304 (2010)] published Fri Jul 23, 2010.
Stability of critical bubble in stretched fluid of square-gradient density-functional model with triple-parabolic free energy
Masao Iwamatsu and Yutaka Okabe The square-gradient density-functional model with triple-parabolic free energy, which was used previously to study the homogeneous bubble nucleation [M. Iwamatsu, J. Chem. Phys. 129, 104508 (2008)], is used to study the stability of the critical bubble nucleated within the bulk undersaturated stretc ... [J. Chem. Phys. 133, 044706 (2010)] published Fri Jul 23, 2010.
Adsorption and switching properties of a N-benzylideneaniline based molecular switch on a Au(111) surface
Laszlo Ovari, Ying Luo, Felix Leyssner, Rainer Haag, Martin Wolf et al. High resolution electron energy loss spectroscopy has been employed to analyze the adsorption geometry and the photoisomerization ability of the molecular switch carboxy-benzylideneaniline (CBA) adsorbed on Au(111). CBA on Au(111) adopts a planar (trans) configuration in the first monolayer (ML) as ... [J. Chem. Phys. 133, 044707 (2010)] published Fri Jul 23, 2010.
Isomerization-induced surface relief gratings formation: A comparison between the probe and the matrix dynamics
M. Saiddine, V. Teboul, and J. M. Nunzi We report molecular dynamics simulations of the effect of the photoisomerization of probe molecules on the nonequilibrium dynamics of a bulk amorphous matrix. Is it the matrix or the probe that drives the dynamics in SRG formation? In the first picture, the probe isomerization induces the motion of ... [J. Chem. Phys. 133, 044902 (2010)] published Fri Jul 23, 2010.
Polymer translocation through alpha-hemolysin pore with tunable polymer-pore electrostatic interaction
Chiu Tai Andrew Wong and M. Muthukumar We have measured the ionic current blockages produced by single molecules of sodium poly(styrene sulfonate) passing through an alpha-hemolysin protein pore under an electric field. Most of the blockage events were composed of one or two blockage levels of ionic current. By analyzing the statistics o ... [J. Chem. Phys. 133, 045101 (2010)] published Fri Jul 23, 2010.
Publisher's Note: Molecular anion formation in 9,10-anthraquinone: Dependence of the electron detachment rate on temperature and incident electron energy [J. Chem. Phys. 132, 244313 (2010)]
Stanislav A. Pshenichnyuk, Alexander S. Vorob'ev, Nail L. Asfandiarov, and Alberto Modelli Abstract not available. [J. Chem. Phys. 133, 049901 (2010)] published Fri Jul 23, 2010.