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21 Dec 2011

Volume 135, Issue 23, Articles (23xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 135, 235101 (2011); http://dx.doi.org/10.1063/1.3660197 (6 pages)

Prem P. Chapagain, Chola K. Regmi, and William Castillo
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Communication: Quantum polarized fluctuating charge model: A practical method to include ligand polarizability in biomolecular simulations

S. Roy Kimura, Ramkumar Rajamani, and David R. Langley

J. Chem. Phys. 135, 231101 (2011); http://dx.doi.org/10.1063/1.3671638 (4 pages) | Cited 1 time

Online Publication Date: 21 December 2011

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We present a simple and practical method to include ligand electronic polarization in molecular dynamics (MD) simulation of biomolecular systems. The method involves periodically spawning quantum mechanical (QM) electrostatic potential (ESP) calculations on an extra set of computer processors using molecular coordinate snapshots from a running parallel MD simulation. The QM ESPs are evaluated for the small-molecule ligand in the presence of the electric field induced by the protein, solvent, and ion charges within the MD snapshot. Partial charges on ligand atom centers are fit through the multi-conformer restrained electrostatic potential (RESP) fit method on several successive ESPs. The RESP method was selected since it produces charges consistent with the AMBER/GAFF force-field used in the simulations. The updated charges are introduced back into the running simulation when the next snapshot is saved. The result is a simulation whose ligand partial charges continuously respond in real-time to the short-term mean electrostatic field of the evolving environment without incurring additional wall-clock time. We show that (1) by incorporating the cost of polarization back into the potential energy of the MD simulation, the algorithm conserves energy when run in the microcanonical ensemble and (2) the mean solvation free energies for 15 neutral amino acid side chains calculated with the quantum polarized fluctuating charge method and thermodynamic integration agree better with experiment relative to the Amber fixed charge force-field.
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87.15.Pc Electronic and electrical properties
36.20.Ey Conformation (statistics and dynamics)
36.20.Kd Electronic structure and spectra
87.19.Pp Biothermics and thermal processes in biology
87.15.ak Monte Carlo simulations
87.15.B- Structure of biomolecules
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back to top Theoretical Methods and Algorithms

Molecular binding energies from partition density functional theory

Jonathan Nafziger, Qin Wu, and Adam Wasserman

J. Chem. Phys. 135, 234101 (2011); http://dx.doi.org/10.1063/1.3667198 (6 pages) | Cited 2 times

Online Publication Date: 16 December 2011

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Approximate molecular calculations via standard Kohn-Sham density functional theory are exactly reproduced by performing self-consistent calculations on isolated fragments via partition density functional theory [P. Elliott, K. Burke, M. H. Cohen, and A. Wasserman, Phys. Rev. A 82, 024501 (2010)]. We illustrate this with the binding curves of small diatomic molecules. We find that partition energies are in all cases qualitatively similar and numerically close to actual binding energies. We discuss qualitative features of the associated partition potentials.
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33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.15.xr Self-consistent-field methods
31.15.E- Density-functional theory

Monte Carlo simulation methods for computing the wetting and drying properties of model systems

Kaustubh S. Rane, Vaibhaw Kumar, and Jeffrey R. Errington

J. Chem. Phys. 135, 234102 (2011); http://dx.doi.org/10.1063/1.3668137 (13 pages)

Online Publication Date: 16 December 2011

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We introduce general Monte Carlo simulation methods for determining the wetting and drying properties of model systems. We employ an interface-potential-based approach in which the interfacial properties of a system are related to the surface excess free energy of a thin fluid film in contact with a surface. Two versions of this approach are explored: a “spreading” method focused on the growth of a thin liquid film from a surface in a mother vapor and a “drying” method focused on the growth of a thin vapor film from a surface in a mother liquid. The former provides a direct measure of the spreading coefficient while the latter provides an analogous drying coefficient. When coupled with an independent measure of the liquid–vapor surface tension, these coefficients enable one to compute the contact angle. We also show how one can combine information gathered from application of the spreading and drying methods at a common state point to obtain direct measures of the contact angle and liquid–vapor surface tension. The computational strategies introduced here are applied to two model systems. One includes a monatomic Lennard-Jones fluid that interacts with a structureless substrate via a long-ranged substrate potential. The second model contains a monatomic Lennard-Jones fluid that interacts with an atomistically detailed substrate via a short-ranged potential. Expanded ensemble techniques are coupled with the interface potential approach to compile the temperature- and substrate strength-dependence of various interfacial properties for these systems. Overall, we find that the approach pursued here provides an efficient and precise means to calculate the wetting and drying properties of model systems.
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61.20.Ja Computer simulation of liquid structure
68.03.Cd Surface tension and related phenomena
68.08.Bc Wetting
68.15.+e Liquid thin films
65.20.De General theory of thermodynamic properties of liquids, including computer simulation

Modelling charge transfer reactions with the frozen density embedding formalism

Michele Pavanello and Johannes Neugebauer

J. Chem. Phys. 135, 234103 (2011); http://dx.doi.org/10.1063/1.3666005 (13 pages) | Cited 1 time

Online Publication Date: 16 December 2011

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The frozen density embedding (FDE) subsystem formulation of density–functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two π-stacked nucleobase dimers of B-DNA: 5′-GG-3′ and 5′-GT-3′. The calculations rely on two assumptions: the two–state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionals are used the electronic couplings are grossly overestimated.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Wt Computational modeling; simulation
82.20.Fd Collision theories; trajectory models

Towards a more accurate reference interaction site model integral equation theory for molecular liquids

Bernarda Kežić and Aurélien Perera

J. Chem. Phys. 135, 234104 (2011); http://dx.doi.org/10.1063/1.3666006 (11 pages)

Online Publication Date: 16 December 2011

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A systematic approach for increasing the accuracy of the reference interaction site model (RISM) theory is introduced that uses input from simulation results to produce very accurate site-site pair correlation functions for single component molecular liquids. The methodology allows the computation of the “RISM bridge function.” Realistic molecular liquids such as water, alcohols, amides, and others are investigated, and the merits and limitations of the method for each of these liquids are examined in relation to the known deficiencies of the RISM theory.
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61.20.Ja Computer simulation of liquid structure

Analytic derivative couplings between configuration-interaction-singles states with built-in electron-translation factors for translational invariance

Shervin Fatehi, Ethan Alguire, Yihan Shao, and Joseph E. Subotnik

J. Chem. Phys. 135, 234105 (2011); http://dx.doi.org/10.1063/1.3665031 (21 pages) | Cited 1 time

Online Publication Date: 19 December 2011

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We present a method for analytically calculating the derivative couplings between a pair of configuration-interaction-singles (CIS) excited states obtained in an atom-centered basis. Our theory is exact and has been derived using two completely independent approaches: one inspired by the Hellmann-Feynman theorem and the other following from direct differentiation. (The former is new, while the latter is in the spirit of existing approaches in the literature.) Our expression for the derivative couplings incorporates all Pulay effects associated with the use of an atom-centered basis, and the computational cost is minimal, roughly comparable to that of a single CIS energy gradient. We have validated our method against CIS finite-difference results and have applied it to the lowest lying excited states of naphthalene; we find that naphthalene derivative couplings include Pulay contributions sufficient to have a qualitative effect. Going beyond standard problems in analytic gradient theory, we have also constructed a correction, based on perturbative electron-translation factors, for including electronic momentum and eliminating spurious components of the derivative couplings that break translational symmetry. This correction is general and can be applied to any level of electronic structure theory.
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31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.xf Finite-difference schemes
31.15.xp Perturbation theory

Nonequilibrium Fermi golden rule for electronic transitions through conical intersections

Artur F. Izmaylov, David Mendive–Tapia, Michael J. Bearpark, Michael A. Robb, John C. Tully, and Michael J. Frisch

J. Chem. Phys. 135, 234106 (2011); http://dx.doi.org/10.1063/1.3667203 (14 pages)

Online Publication Date: 19 December 2011

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We consider photoinduced electronic transitions through conical intersections in large molecules. Starting from the linear vibronic model Hamiltonian and treating linear diabatic couplings within the second order cumulant expansion, we have developed a simple analytical expression for the time evolution of electronic populations at finite temperature. The derived expression can be seen as a nonequilibrium generalization of the Fermi golden rule due to a nonequilibrium character of the initial photoinduced nuclear distribution. All parameters in our model are obtained from electronic structure calculations followed by a diabatization procedure. The results of our model are found to agree well with those of quantum dynamics for a test set of systems: fulvene molecule, 2,6-bis(methylene) adamantyl cation, and its dimethyl derivative.
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33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.bt Statistical model calculations (including Thomas-Fermi and Thomas-Fermi-Dirac models)

Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. II. Canonical and isokinetic ensembles

Igor P. Omelyan and Andriy Kovalenko

J. Chem. Phys. 135, 234107 (2011); http://dx.doi.org/10.1063/1.3669385 (12 pages)

Online Publication Date: 19 December 2011

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We have developed several multiple time stepping techniques to overcome the limitations on efficiency of molecular dynamics simulations of complex fluids. They include the modified canonical and isokinetic schemes, as well as the extended isokinetic Nosé-Hoover chain approach. The latter generalizes the method of Minary, Tuckerman, and Martyna for translational motion [Phys. Rev. Lett. 93, 150201 (2004)]10.1103/PhysRevLett.93.150201 to systems with both translational and orientational degrees of freedom. Although the microcanonical integrators are restricted to relatively small outer time steps of order of 16 fs, we show on the basis of molecular dynamics simulations of ambient water that in the canonical and isokinetic thermostats the size of these steps can be increased to 50 and 75 fs, respectively (at the same inner time step of 4 fs). Within the generalized isokinetic Nosé-Hoover chain algorithm we have derived, huge outer time steps of order of 500 fs can be used without losing numerical stability and affecting equilibrium properties
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61.20.Ja Computer simulation of liquid structure
02.60.Nm Integral and integrodifferential equations

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events

Min K. Roh, Bernie J. Daigle, Jr., Dan T. Gillespie, and Linda R. Petzold

J. Chem. Phys. 135, 234108 (2011); http://dx.doi.org/10.1063/1.3668100 (11 pages)

Online Publication Date: 20 December 2011

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In recent years there has been substantial growth in the development of algorithms for characterizing rare events in stochastic biochemical systems. Two such algorithms, the state-dependent weighted stochastic simulation algorithm (swSSA) and the doubly weighted SSA (dwSSA) are extensions of the weighted SSA (wSSA) by H. Kuwahara and I. Mura [J. Chem. Phys. 129, 165101 (2008)]10.1063/1.2987701. The swSSA substantially reduces estimator variance by implementing system state-dependent importance sampling (IS) parameters, but lacks an automatic parameter identification strategy. In contrast, the dwSSA provides for the automatic determination of state-independent IS parameters, thus it is inefficient for systems whose states vary widely in time. We present a novel modification of the dwSSA—the state-dependent doubly weighted SSA (sdwSSA)—that combines the strengths of the swSSA and the dwSSA without inheriting their weaknesses. The sdwSSA automatically computes state-dependent IS parameters via the multilevel cross-entropy method. We apply the method to three examples: a reversible isomerization process, a yeast polarization model, and a lac operon model. Our results demonstrate that the sdwSSA offers substantial improvements over previous methods in terms of both accuracy and efficiency.
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82.39.-k Chemical kinetics in biological systems
87.15.R- Reactions and kinetics
82.30.Qt Isomerization and rearrangement

Dependence of dispersion coefficients on atomic environment

Erin R. Johnson

J. Chem. Phys. 135, 234109 (2011); http://dx.doi.org/10.1063/1.3670015 (6 pages) | Cited 1 time

Online Publication Date: 21 December 2011

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Addition of a dispersion-energy correction to density-functional theory significantly improves potential-energy curves for dispersion-bound complexes. The exchange-hole dipole moment (XDM) model allows non-empirical calculation of atomic and molecular dispersion coefficients using only occupied orbitals and polarizabilities. In this work, the XDM model is applied to examine the dependence of dispersion coefficients on changes in atomic environment, such as charge, oxidation state, and hybridization. The variations in dispersion coefficients, and resulting energy contributions, are assessed for selected chemical examples.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
32.30.-r Atomic spectra
31.50.Bc Potential energy surfaces for ground electronic states

Polarizable model of water with field-dependent polarization

András Baranyai and Péter T. Kiss

J. Chem. Phys. 135, 234110 (2011); http://dx.doi.org/10.1063/1.3670962 (7 pages) | Cited 1 time

Online Publication Date: 21 December 2011

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The polarizable charge-on-spring model of water with three Gaussian charges developed by the present authors [A. Baranyai and P. T. Kiss, J. Chem. Phys. 133, 144109 (2010)10.1063/1.3490660] was studied. We introduced an analytic function for the polarizability in terms of the local electric field. Following theoretical suggestions, the polarizability decreases from its experimental gas-phase value, in our approach, toward a high-field threshold. Using this modified polarizability, we reparameterized the model by calculating its dielectric constant and obtained good estimates of density and internal energy for ambient water, hexagonal ice, and water cluster properties. Mimicked by the new model, we studied liquid water under the impact of homogeneous static electric field in the rage of 0–2.5 V/Å. Both the density and the average dipole moment increase with the strength of the electric field. However, the internal energy shows a minimum at ∼0.35 V/Å. At this field strength, the model starts ordering into a crystal structure. At higher fields the liquid forms a crystalline structure which is a special version of cubic ice.
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77.22.Ej Polarization and depolarization
77.84.Nh Liquids, emulsions, and suspensions; liquid crystals
61.25.Em Molecular liquids
77.22.Ch Permittivity (dielectric function)

A comparison of Coulombic interaction methods in non-equilibrium studies of heat transfer in water

Jordan Muscatello and Fernando Bresme

J. Chem. Phys. 135, 234111 (2011); http://dx.doi.org/10.1063/1.3670965 (8 pages)

Online Publication Date: 21 December 2011

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We investigate the impact of the treatment of electrostatic interactions on the heat conduction of liquid water. With this purpose, we report a series of non-equilibrium molecular dynamics computer simulations of the Modified Central Force Model of water. We consider both the Ewald summation approach, which includes the full range of the electrostatic interactions, and the Wolf method, which uses a cutoff to truncate the long range contributions. It is shown that the relaxation of the temperature profiles towards the stationary state solution and the equation of state of the liquid are not affected by the treatment of the electrostatic interactions. However, the truncation of the interactions results in lower internal energy fluxes as well as lower thermal conductivities. We also find that the anomalous increase of the thermal conductivity of water with temperature is reproduced by the different methods considered in this work, showing that this physical behavior is independent of the treatment of the long range electrostatic interactions.
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66.25.+g Thermal conduction in nonmetallic liquids
61.20.Ja Computer simulation of liquid structure
64.30.Jk Equations of state of nonmetals
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Adiabatic and non-adiabatic quantum dynamics calculation of O(1D) + D2 → OD + D reaction

Zhaopeng Sun, Shi Ying Lin, and Yujun Zheng

J. Chem. Phys. 135, 234301 (2011); http://dx.doi.org/10.1063/1.3668084 (7 pages)

Online Publication Date: 15 December 2011

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Adiabatic (1A′ or 1A′′ state) and non-adiabatic (2A′/1A′ states) quantum dynamics calculations have been carried out for the title reaction (O(1D) + D2 → OD + D) to obtain the initial state-specified (vi = 0, ji = 0) integral cross section and rate constant using the potential energy surfaces of Dobbyn and Knowles. A total of 50 partial wave contributions have been calculated using the Chebyshev wave packet method with full Coriolis coupling to achieve convergence up to the collision energy of 0.28 eV. The total integral cross section and rate constant are in excellent agreement with experimental as well as quasi-classical trajectory results. Contributions from the adiabatic pathway of the 1A′′ state and the non-adiabatic pathway of the 2A′/1A′ states, increase significantly with the collision energy. Compared to the O(1D) + H2 system, the kinetic isotope effect (k(D)/k(H)) is found to be nearly temperature independent above 100 K and its value of 0.77 ± 0.01 shows excellent agreement with the experimental result of 0.81.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Tr Kinetic isotope effects including muonium

Guided ion beam and theoretical study of the reactions of Os+ with H2, D2, and HD

Christopher S. Hinton, Murat Citir, and P. B. Armentrout

J. Chem. Phys. 135, 234302 (2011); http://dx.doi.org/10.1063/1.3669425 (11 pages)

Online Publication Date: 16 December 2011

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Reactions of the third-row transition metal cation Os+ with H2, D2, and HD to form OsH+ (OsD+) were studied using a guided ion beam tandem mass spectrometer. A flow tube ion source produces Os+ in its 6D (6s15d6) electronic ground state level. Corresponding state-specific reaction cross sections are obtained. The kinetic energy dependences of the cross sections for the endothermic formation of OsH+ and OsD+ are analyzed to give a 0 K bond dissociation energy of D0(Os+–H) = 2.45 ± 0.10 eV. Quantum chemical calculations are performed here at several levels of theory, with B3LYP approaches generally overestimating the experimental bond energy whereas results obtained using BHLYP and CCSD(T), coupled-cluster with single, double, and perturbative triple excitations, levels show good agreement. Theory also provides the electronic structures of these species and the potential energy surfaces for reaction. Results from the reactions with HD provide insight into the reaction mechanism and indicate that Os+ reacts via a direct reaction. We also compare this third-row transition metal system with the first-row and second-row congeners, Fe+ and Ru+, and find that Os+ reacts more efficiently with dihydrogen, forming a stronger M+–H bond. These differences can be attributed to the lanthanide contraction and relativistic effects.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
33.15.Fm Bond strengths, dissociation energies
33.15.Ta Mass spectra

Cooperative effects in the oxidation of CO by palladium oxide cations

Arthur C. Reber, Shiv N. Khanna, Eric C. Tyo, Christopher L. Harmon, and A. W. Castleman, Jr.

J. Chem. Phys. 135, 234303 (2011); http://dx.doi.org/10.1063/1.3669428 (7 pages)

Online Publication Date: 19 December 2011

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Cooperative reactivity plays an important role in the oxidation of CO to CO2 by palladium oxide cations and offers insight into factors which influence catalysis. Comprehensive studies including guided-ion-beam mass spectrometry and theoretical investigations reveal the reaction products and profiles of PdO2+ and PdO3+ with CO through oxygen radical centers and dioxygen complexes bound to the Pd atom. O radical centers are more reactive than the dioxygen complexes, and experimental evidence of both direct and cooperative CO oxidation with the adsorption of two CO molecules are observed. The binding of multiple electron withdrawing CO molecules is found to increase the barrier heights for reactivity due to decreased binding of the secondary CO molecule, however, reactivity is enhanced by the increase in kinetic energy available to hurdle the barrier. We examine the effect of oxygen sites, cooperative ligands, and spin including two-state reactivity.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
33.15.Ta Mass spectra
68.43.Mn Adsorption kinetics

Rotationally elastic and inelastic dynamics of NO(X2Π, v = 0) in collisions with Ar

G. Paterson, A. Relf, M. L. Costen, K. G. McKendrick, M. H. Alexander, and P. J. Dagdigian

J. Chem. Phys. 135, 234304 (2011); http://dx.doi.org/10.1063/1.3665135 (11 pages) | Cited 1 time

Online Publication Date: 19 December 2011

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A combined theoretical and experimental study of the depolarization of selected NO(X2Π, v = 0, j, F, ɛ) levels in collisions with a thermal bath of Ar has been carried out. Rate constants for elastic depolarization of rank K = 1 (orientation) and K = 2 (alignment) were extracted from collision-energy-dependent quantum scattering calculations, along with those for inelastic population transfer to discrete product levels. The rate constants for total loss of polarization of selected initial levels, which are the sum of elastic depolarization and population transfer contributions, were measured using a two-color polarization spectroscopy technique. Theory and experiment agree qualitatively that the rate constants for total loss of polarization decline modestly with j, but the absolute values differ by significantly more than the statistical uncertainties in the measurements. The reasons for this discrepancy are as yet unclear. The lack of a significant K dependence in the experimental data is, however, consistent with the theoretical prediction that elastic depolarization makes only a modest contribution to the total loss of polarization. This supports a previous conclusion that elastic depolarization for NO(X2Π) + Ar is significantly less efficient than for the electronically closely related system OH(X2Π) + Ar [P. J. Dagdigian and M. H. Alexander, J. Chem. Phys. 130, 204304 (2009)].
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34.50.Ez Rotational and vibrational energy transfer
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Sn Rotational analysis
34.50.Bw Energy loss and stopping power

Accurate partition function for acetylene, 12C2H2, and related thermodynamical quantities

B. Amyay, A. Fayt, and M. Herman

J. Chem. Phys. 135, 234305 (2011); http://dx.doi.org/10.1063/1.3664626 (9 pages)

Online Publication Date: 19 December 2011

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The internal partition function (Qint) of ethyne (acetylene), 12C2H2, is calculated by explicit summation of the contribution of all individual vibration-rotation energy levels up to 15 000 cm−1. The corresponding energies are predicted from a global model and constants reproducing within 3σ all 18 415 published vibration-rotation lines in the literature involving vibrational states up to 8900 cm−1, as produced by Amyay et al. [J. Mol. Spectrosc. 267, 80 (2011)]. Values of Qint, with distinct calculations for para and ortho species are provided from 1 to 2000 K, in step of 1 K. The total internal partition function at 298.15 K is 104.224387(47) or 416.89755(19), with the nuclear degeneracy spin factors taken as 1/4: 3/4 (astronomer convention) or 1:3 (atmospheric convention), respectively, for para:ortho species. The Helmholtz function, Gibbs enthalpy function, entropy, and specific heat at constant pressure are also calculated over the same temperature range. Accuracies as well as the missing contribution of the vinylidene isomer of acetylene in the calculations are discussed.
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33.20.Vq Vibration-rotation analysis
05.70.Ce Thermodynamic functions and equations of state
33.20.Tp Vibrational analysis

First principles potential for the acetylene dimer and refinement by fitting to experiments

Claude Leforestier, Adem Tekin, Georg Jansen, and Michel Herman

J. Chem. Phys. 135, 234306 (2011); http://dx.doi.org/10.1063/1.3668283 (9 pages) | Cited 1 time

Online Publication Date: 19 December 2011

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We report the definition and refinement of a new first principles potential for the acetylene dimer. The ab initio calculations were performed with the DFT-SAPT combination of symmetry-adapted intermolecular perturbation method and density functional theory, and fitted to a model site-site functional form. Comparison of the calculated microwave spectrum with experimental data revealed that the barriers to isomerization were too low. This potential was refined by fitting the model parameters in order to reproduce the observed transitions, an excellent agreement within ∼1 MHz being achieved.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
31.15.A- Ab initio calculations
31.15.E- Density-functional theory
33.20.Bx Radio-frequency and microwave spectra

An ab initio quasi-diabatic potential energy matrix for OH(2Σ) + H2

Michael A. Collins, Oded Godsi, Shu Liu, and Dong H. Zhang

J. Chem. Phys. 135, 234307 (2011); http://dx.doi.org/10.1063/1.3664759 (14 pages)

Online Publication Date: 19 December 2011

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A diabatic potential energy matrix for three electronic states of OH3 has been constructed by interpolation of multi-reference configuration interaction electronic structure data. The reactive, exchange and non-reactive quenching dynamics are investigated using surface hopping classical trajectories. Classical trajectory simulations show good agreement with cross molecular beam data for the OH(2Σ) + D2 → HOD + D reaction.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Wt Computational modeling; simulation
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Fd Collision theories; trajectory models

Br2 molecular elimination in photolysis of (COBr)2 at 248 nm by using cavity ring-down absorption spectroscopy: A photodissociation channel being ignored

Chia-Ching Wu, Hsiang-Chin Lin, Yuan-Bin Chang, Po-Yu Tsai, Yu-Ying Yeh, He Fan, King-Chuen Lin, and J. S. Francisco

J. Chem. Phys. 135, 234308 (2011); http://dx.doi.org/10.1063/1.3664782 (9 pages)

Online Publication Date: 20 December 2011

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A primary dissociation channel of Br2 elimination is detected following a single-photon absorption of (COBr)2 at 248 nm by using cavity ring-down absorption spectroscopy. The technique contains two laser beams propagating in a perpendicular configuration. The tunable laser beam along the axis of the ring-down cell probes the Br2 fragment in the B3Πou+–X1Σg+ transition. The measurements of laser energy- and pressure-dependence and addition of a Br scavenger are further carried out to rule out the probability of Br2 contribution from a secondary reaction. By means of spectral simulation, the ratio of nascent vibrational population for v = 0, 1, and 2 levels is evaluated to be 1:(0.65 ± 0.09):(0.34 ± 0.07), corresponding to a Boltzmann vibrational temperature of 893 ± 31 K. The quantum yield of the ground state Br2 elimination reaction is determined to be 0.11 ± 0.06. With the aid of ab initio potential energy calculations, the pathway of molecular elimination is proposed on the energetic ground state (COBr)2 via internal conversion. A four-center dissociation mechanism is followed synchronously or sequentially yielding three fragments of Br2 + 2CO. The resulting Br2 is anticipated to be vibrationally hot. The measurement of a positive temperature effect supports the proposed mechanism.
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82.50.-m Photochemistry
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.20.Wt Computational modeling; simulation
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Hf Product distribution
82.20.Fd Collision theories; trajectory models

Differential elastic electron scattering cross sections for CCl4 by 1.5–100 eV energy electron impact

P. Limão-Vieira, M. Horie, H. Kato, M. Hoshino, F. Blanco, G. García, S. J. Buckman, and H. Tanaka

J. Chem. Phys. 135, 234309 (2011); http://dx.doi.org/10.1063/1.3669429 (6 pages) | Cited 1 time

Online Publication Date: 20 December 2011

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We report absolute elastic differential, integral and momentum transfer cross sections for electron interactions with CCl4. The incident electron energy range is 1.5–100 eV, and the scattered electron angular range for the differential measurements varies from 15°–130°. The absolute scale of the differential cross section was set using the relative flow technique with helium as the reference species. Comparison with previous total cross sections shows good agreement. Atomic-like behaviour in this scattering system is shown here for the first time, and is further investigated by comparing the CCl4 elastic cross sections to recent results on the halomethanes and atomic chlorine at higher impact energies [H. Kato, T. Asahina, H. Masui, M. Hoshino, H. Tanaka, H. Cho, O. Ingólfsson, F. Blanco, G. Garcia, S. J. Buckman, and M. J. Brunger, J. Chem. Phys. 132, 074309 (2010)]10.1063/1.3319761.
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34.80.Bm Elastic scattering

High-resolution infrared spectrum of jet-cooled methyl acetate in the C=O stretching region: Internal rotations of two inequivalent methyl tops

Fumie X. Sunahori, Nicole Borho, Xunchen Liu, and Yunjie Xu

J. Chem. Phys. 135, 234310 (2011); http://dx.doi.org/10.1063/1.3668140 (8 pages)

Online Publication Date: 20 December 2011

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The jet-cooled high resolution infrared (IR) spectrum of methyl acetate (MA), CH3–C(=O)–O–CH3, in the C=O fundamental band region was recorded by using a rapid scan IR laser spectrometer equipped with an astigmatic multipass cell. No high resolution IR analyses of the ro-vibrational transitions between the ground and non-torsionally excited vibrational states have hitherto been reported for molecules with two inequivalent methyl rotors. Because of the two chemically different methyl tops in MA, i.e., the acetyl –CH3 and methoxy –CH3, each rotational energy level is split into more than two torsional sublevels by internal rotations of these methyl groups. We were able to assign ro-vibrational transitions of four torsional species by using the ground state combination differences calculated from the molecular constants of the vibrational ground state recently determined by a global fit of the microwave and millimeter wave lines [M. Tudorie, I. Kleiner, J. T. Hougen, S. Melandri, L. W. Sutikdja, and W. Stahl, J. Mol. Spectrosc. 269, 211 (2011)]. The assigned lines were successfully fitted using the BELGI-Cs-IR program to an overall standard deviation which is comparable to the measurement accuracy. This study is also of interest in understanding the role of methyl rotors in the intramolecular vibrational-energy redistribution processes in mid-size organic molecules.
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33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Ea Infrared spectra
31.15.vj Electron correlation calculations for atoms and ions: excited states
37.10.Mn Slowing and cooling of molecules

Orbital alignment in photodissociation probed using strong field ionization

Yun Fei Lin, Lu Yan, Suk Kyoung Lee, Thushani Herath, and Wen Li

J. Chem. Phys. 135, 234311 (2011); http://dx.doi.org/10.1063/1.3671456 (4 pages)

Online Publication Date: 20 December 2011

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The photodissociation of molecules often produces atomic fragments with polarized electronic angular momentum, and the atomic alignment, for example, can provide valuable information on the dynamical pathways of chemical reactions unavailable by other means. In this work, we demonstrate for the first time that orbital polarization in chemical reactions can be measured with great sensitivity using strong field ionization by exploiting its extreme nonlinearity.
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82.50.Hp Processes caused by visible and UV light
32.30.-r Atomic spectra
32.80.Fb Photoionization of atoms and ions
33.80.Gj Diffuse spectra; predissociation, photodissociation
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Crystal structures of ethylene glycol and ethylene glycol monohydrate

A. Dominic Fortes and Emmanuelle Suard

J. Chem. Phys. 135, 234501 (2011); http://dx.doi.org/10.1063/1.3668311 (7 pages)

Online Publication Date: 15 December 2011

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We have carried out a neutron powder diffraction study of deuterated ethylene glycol (1,2-ethanediol), and deuterated ethylene glycol monohydrate with the D2B high-resolution diffractometer at the Institut Laue-Langevin. Using these data, we have refined the complete structure, including all hydrogen atoms, of the anhydrous phase at 220 K. In addition, we have determined the structure of ethylene glycol monohydrate at 210 K using direct space methods. Anhydrous ethylene glycol crystallizes in space-group P212121 with four formula units in a unit-cell of dimensions a = 5.0553(1) Å, b = 6.9627(1) Å, c = 9.2709(2) Å, and V = 326.319(8) Å3 [ρ calc deuterated = 1386.26(3) kg m−3] at 220 K. Ethylene glycol monohydrate crystallizes in space-group P21/c with four formula units in a unit-cell of dimensions a = 7.6858(3) Å, b = 7.2201(3) Å, c = 7.7356(4) Å, β = 92.868(3)°, and V = 428.73(2) Å3 [ρ calc deuterated = 1365.40(7) kg m−3] at 210 K. Both the structures are characterized by the gauche conformation of the ethylene glycol molecule; however, the anhydrous phase contains the tGg′ rotamer (or its mirror, g′Gt), whereas the monohydrate contains the gGg′ rotamer. In the monohydrate, each water molecule is tetrahedrally coordinated, donating two hydrogen bonds to, and accepting two hydrogen bonds from the hydroxyl groups of neighboring ethylene glycol molecules. There are substantial differences in the degree of weak C−D···O hydrogen bonding between the two crystals, which calls into question the role of these interactions in determining the conformation of the ethylene glycol molecule.
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61.66.Hq Organic compounds

Inversion of sequence of diffusion and density anomalies in core-softened systems

Yu. D. Fomin, E. N. Tsiok, and V. N. Ryzhov

J. Chem. Phys. 135, 234502 (2011); http://dx.doi.org/10.1063/1.3668313 (8 pages)

Online Publication Date: 15 December 2011

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In this paper we present a simulation study of water-like anomalies in core-softened system introduced in our previous papers. We investigate the anomalous regions for a system with the same functional form of the potential but with different parameters and show that the order of the region of anomalous diffusion and the region of density anomaly is inverted with increasing the width of the repulsive shoulder.
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66.10.cd Thermal diffusion and diffusive energy transport
61.20.Ja Computer simulation of liquid structure
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