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28 Feb 2013

Volume 138, Issue 8, Articles (08xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 138, 084701 (2013); http://dx.doi.org/10.1063/1.4792142 (5 pages)

Jinying Wang, Ruiqi Zhao, Mingmei Yang, Zhongfan Liu, and Zhirong Liu
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Communication: Influence of graphene interlayers on the interaction between cobalt phthalocyanine and Ni(111)

Johannes Uihlein, Heiko Peisert, Mathias Glaser, Małgorzata Polek, Hilmar Adler, Fotini Petraki, Ruslan Ovsyannikov, Maximilian Bauer, and Thomas Chassé

J. Chem. Phys. 138, 081101 (2013); http://dx.doi.org/10.1063/1.4793523 (4 pages)

Online Publication Date: 25 February 2013

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The influence of graphene interlayers on electronic interface properties of cobalt phthalocyanine on Ni(111) is studied using both photoemission and X-ray absorption spectroscopy. A charge transfer associated with a redistribution of the d-electrons at the Co-atom of the phthalocyanine occurs at the interface to Ni(111). Even a graphene buffer layer cannot prevent the charge transfer at the interface to Ni(111); however, the detailed electronic situation is different.
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73.20.At Surface states, band structure, electron density of states
78.70.Dm X-ray absorption spectra
79.60.-i Photoemission and photoelectron spectra
82.80.Pv Electron spectroscopy (X-ray photoelectron (XPS), Auger electron spectroscopy (AES), etc.)
71.70.-d Level splitting and interactions
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Communication: Simplified two-beam rotational CARS signal generation demonstrated in 1D

Alexis Bohlin, Brian D. Patterson, and Christopher J. Kliewer

J. Chem. Phys. 138, 081102 (2013); http://dx.doi.org/10.1063/1.4793556 (4 pages)

Online Publication Date: 26 February 2013

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We explore a novel phase matching scheme for gas-phase rotational coherent anti-Stokes Raman spectroscopy (CARS). The scheme significantly simplifies the employment of the technique in general. Two laser beams, one broadband and one narrowband, are crossed at arbitrary angle and the generated rotational CARS signal, copropagating with the probe beam, is isolated using a polarization gating technique. The effect of phase-vector mismatch for various experimental implementations was measured experimentally and compared to calculations. The spatial resolution of the current technique is improved by more than an order of magnitude over standard gas-phase CARS experimental arrangements, providing an interaction length of less than 50 μm when desired. Both the pump and Stokes photons originate from the broadband pulse, and are therefore automatically overlapped temporally and spatially. Significantly improved signal levels are achieved because of both the ease of alignment and the higher pulse energy available to the pump and Stokes fields. We demonstrate the technique for single-laser-shot 1D rotational CARS signal generation over approximately a 1 cm field in a flame.
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33.20.Fb Raman and Rayleigh spectra (including optical scattering)
33.15.Mt Rotation, vibration, and vibration-rotation constants
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back to top Theoretical Methods and Algorithms

Multi-configuration time-dependent density-functional theory based on range separation

Emmanuel Fromager, Stefan Knecht, and Hans Jørgen Aa. Jensen

J. Chem. Phys. 138, 084101 (2013); http://dx.doi.org/10.1063/1.4792199 (14 pages) | Cited 2 times

Online Publication Date: 22 February 2013

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Multi-configuration range-separated density-functional theory is extended to the time-dependent regime. An exact variational formulation is derived. The approximation, which consists in combining a long-range Multi-Configuration-Self-Consistent Field (MCSCF) treatment with an adiabatic short-range density-functional (DFT) description, is then considered. The resulting time-dependent multi-configuration short-range DFT (TD-MC-srDFT) model is applied to the calculation of singlet excitation energies in H2, Be, and ferrocene, considering both short-range local density (srLDA) and generalized gradient (srGGA) approximations. As expected, when modeling long-range interactions with the MCSCF model instead of the adiabatic Buijse-Baerends density-matrix functional as recently proposed by Pernal [J. Chem. Phys. 136, 184105 (2012)10.1063/1.4712019], the description of both the 11D doubly-excited state in Be and the 11Σu+ state in the stretched H2 molecule are improved, although the latter is still significantly underestimated. Exploratory TD-MC-srDFT/GGA calculations for ferrocene yield in general excitation energies at least as good as TD-DFT using the Coulomb attenuated method based on the three-parameter Becke-Lee-Yang-Parr functional (TD-DFT/CAM-B3LYP), and superior to wave-function (TD-MCSCF, symmetry adapted cluster-configuration interaction) and TD-DFT results based on LDA, GGA, and hybrid functionals.
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31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.ee Time-dependent density functional theory
31.15.xr Self-consistent-field methods
31.15.xt Variational techniques
31.50.Df Potential energy surfaces for excited electronic states

Useful lower limits to polarization contributions to intermolecular interactions using a minimal basis of localized orthogonal orbitals: Theory and analysis of the water dimer

R. Julian Azar, Paul Richard Horn, Eric Jon Sundstrom, and Martin Head-Gordon

J. Chem. Phys. 138, 084102 (2013); http://dx.doi.org/10.1063/1.4792434 (14 pages) | Cited 1 time

Online Publication Date: 22 February 2013

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The problem of describing the energy-lowering associated with polarization of interacting molecules is considered in the overlapping regime for self-consistent field wavefunctions. The existing approach of solving for absolutely localized molecular orbital (ALMO) coefficients that are block-diagonal in the fragments is shown based on formal grounds and practical calculations to often overestimate the strength of polarization effects. A new approach using a minimal basis of polarized orthogonal local MOs (polMOs) is developed as an alternative. The polMO basis is minimal in the sense that one polarization function is provided for each unpolarized orbital that is occupied; such an approach is exact in second-order perturbation theory. Based on formal grounds and practical calculations, the polMO approach is shown to underestimate the strength of polarization effects. In contrast to the ALMO method, however, the polMO approach yields results that are very stable to improvements in the underlying AO basis expansion. Combining the ALMO and polMO approaches allows an estimate of the range of energy-lowering due to polarization. Extensive numerical calculations on the water dimer using a large range of basis sets with Hartree-Fock theory and a variety of different density functionals illustrate the key considerations. Results are also presented for the polarization-dominated Na+CH4 complex. Implications for energy decomposition analysis of intermolecular interactions are discussed.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.E- Density-functional theory
31.15.xp Perturbation theory
31.15.xr Self-consistent-field methods
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

Accuracy of a Markov state model generated by searching for basin escape pathways

Vijesh J. Bhute and Abhijit Chatterjee

J. Chem. Phys. 138, 084103 (2013); http://dx.doi.org/10.1063/1.4792439 (9 pages) | Cited 1 time

Online Publication Date: 22 February 2013

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Markov state models (MSMs) are employed extensively in literature with the kinetic Monte Carlo (KMC) method for studying state-to-state dynamics in a wide range of material systems. A MSM contains a list of atomic processes and their rate constants for different states of the system. In many situations, only few of the possible atomic processes are included in the MSM. The use of an incomplete MSM with the KMC method can lead to an error in the dynamics. In this work, we develop an error measure to assess the accuracy of a MSM generated using dynamical basin escape pathway searches. We show that the error associated with an incomplete MSM depends on the rate constants missing from the MSM. A procedure to estimate the missing rate constants is developed. We demonstrate our approach using some examples.
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82.20.Uv Stochastic theories of rate constants
82.20.Wt Computational modeling; simulation
02.50.Ga Markov processes

Multidimensional master equation and its Monte-Carlo simulation

Juan Pang, Zhan-Wu Bai, and Jing-Dong Bao

J. Chem. Phys. 138, 084104 (2013); http://dx.doi.org/10.1063/1.4792300 (5 pages)

Online Publication Date: 26 February 2013

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We derive an integral form of multidimensional master equation for a Markovian process, in which the transition function is obtained in terms of a set of discrete Langevin equations. The solution of master equation, namely, the probability density function is calculated by using the Monte-Carlo composite sampling method. In comparison with the usual Langevin-trajectory simulation, the present approach decreases effectively coarse-grained error. We apply the master equation to investigate time-dependent barrier escape rate of a particle from a two-dimensional metastable potential and show the advantage of this approach in the calculations of quantities that depend on the probability density function.
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02.50.Ga Markov processes
02.30.-f Function theory, analysis
02.50.Cw Probability theory

Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials

Jianfeng Lu and Eric Vanden-Eijnden

J. Chem. Phys. 138, 084105 (2013); http://dx.doi.org/10.1063/1.4790706 (9 pages)

Online Publication Date: 26 February 2013

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Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently Plattner et al. [J. Chem. Phys. 135, 134111 (2011)10.1063/1.3643325] proposed a method to implement infinite swapping REMD in practice. Here we introduce a natural modification of this method that involves molecular dynamics simulations over a mixture potential. This modification is both simple to implement in practice and provides a better, energy based understanding of how to choose the temperatures in REMD to optimize efficiency. It also has implications for generalizations of REMD in which the swaps involve other parameters than the temperature.
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31.15.xv Molecular dynamics and other numerical methods

An effective method for computing the noise in biochemical networks

Jiajun Zhang, Qing Nie, Miao He, and Tianshou Zhou

J. Chem. Phys. 138, 084106 (2013); http://dx.doi.org/10.1063/1.4792444 (16 pages)

Online Publication Date: 26 February 2013

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We present a simple yet effective method, which is based on power series expansion, for computing exact binomial moments that can be in turn used to compute steady-state probability distributions as well as the noise in linear or nonlinear biochemical reaction networks. When the method is applied to representative reaction networks such as the ON-OFF models of gene expression, gene models of promoter progression, gene auto-regulatory models, and common signaling motifs, the exact formulae for computing the intensities of noise in the species of interest or steady-state distributions are analytically given. Interestingly, we find that positive (negative) feedback does not enlarge (reduce) noise as claimed in previous works but has a counter-intuitive effect and that the multi-OFF (or ON) mechanism always attenuates the noise in contrast to the common ON-OFF mechanism and can modulate the noise to the lowest level independently of the mRNA mean. Except for its power in deriving analytical expressions for distributions and noise, our method is programmable and has apparent advantages in reducing computational cost.
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87.15.R- Reactions and kinetics
02.50.Cw Probability theory
87.16.-b Subcellular structure and processes
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On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

Benoît Roux and Jonathan Weare

J. Chem. Phys. 138, 084107 (2013); http://dx.doi.org/10.1063/1.4792208 (8 pages)

Online Publication Date: 27 February 2013

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An issue of general interest in computer simulations is to incorporate information from experiments into a structural model. An important caveat in pursuing this goal is to avoid corrupting the resulting model with spurious and arbitrary biases. While the problem of biasing thermodynamic ensembles can be formulated rigorously using the maximum entropy method introduced by Jaynes, the approach can be cumbersome in practical applications with the need to determine multiple unknown coefficients iteratively. A popular alternative strategy to incorporate the information from experiments is to rely on restrained-ensemble molecular dynamics simulations. However, the fundamental validity of this computational strategy remains in question. Here, it is demonstrated that the statistical distribution produced by restrained-ensemble simulations is formally consistent with the maximum entropy method of Jaynes. This clarifies the underlying conditions under which restrained-ensemble simulations will yield results that are consistent with the maximum entropy method.
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05.70.Ce Thermodynamic functions and equations of state
31.15.xv Molecular dynamics and other numerical methods
02.50.Ng Distribution theory and Monte Carlo studies

Derivation of a true (t → 0+) quantum transition-state theory. I. Uniqueness and equivalence to ring-polymer molecular dynamics transition-state-theory

Timothy J. H. Hele and Stuart C. Althorpe

J. Chem. Phys. 138, 084108 (2013); http://dx.doi.org/10.1063/1.4792697 (13 pages)

Online Publication Date: 28 February 2013

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Surprisingly, there exists a quantum flux-side time-correlation function which has a non-zero t → 0+ limit and thus yields a rigorous quantum generalization of classical transition-state theory (TST). In this Part I of two articles, we introduce the new time-correlation function and derive its t → 0+ limit. The new ingredient is a generalized Kubo transform which allows the flux and side dividing surfaces to be the same function of path-integral space. Choosing this function to be a single point gives a t → 0+ limit which is identical to an expression introduced on heuristic grounds by Wigner in 1932; however, this expression does not give positive-definite quantum statistics, causing it to fail while still in the shallow-tunnelling regime. Positive-definite quantum statistics is obtained only if the dividing surface is invariant to imaginary-time translation, in which case the t → 0+ limit is identical to ring-polymer molecular dynamics (RPMD) TST. The RPMD-TST rate is not a strict upper bound to the exact quantum rate, but is a good approximation to one if real-time coherence effects are small. Part II will show that the RPMD-TST rate is equal to the exact quantum rate in the absence of recrossing.
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82.20.Db Transition state theory and statistical theories of rate constants
82.20.Xr Quantum effects in rate constants (tunneling, resonances, etc.)
82.20.Pm Rate constants, reaction cross sections, and activation energies

Minimum energy pathways via quantum Monte Carlo

S. Saccani, C. Filippi, and S. Moroni

J. Chem. Phys. 138, 084109 (2013); http://dx.doi.org/10.1063/1.4792717 (5 pages)

Online Publication Date: 28 February 2013

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We perform quantum Monte Carlo (QMC) calculations to determine minimum energy pathways of simple chemical reactions, and compare the computed geometries and reaction barriers with those obtained with density functional theory (DFT) and quantum chemistry methods. We find that QMC performs in general significantly better than DFT, being also able to treat cases in which DFT is inaccurate or even unable to locate the transition state. Since the wave function form employed here is particularly simple and can be transferred to larger systems, we suggest that a QMC approach is both viable and useful for reactions difficult to address by DFT and system sizes too large for high level quantum chemistry methods.
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82.20.Db Transition state theory and statistical theories of rate constants
82.20.Kh Potential energy surfaces for chemical reactions
02.70.Ss Quantum Monte Carlo methods
31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods

All-time dynamics of continuous-time random walks on complex networks

Hamid Teimouri and Anatoly B. Kolomeisky

J. Chem. Phys. 138, 084110 (2013); http://dx.doi.org/10.1063/1.4792726 (7 pages)

Online Publication Date: 28 February 2013

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The concept of continuous-time random walks (CTRW) is a generalization of ordinary random walk models, and it is a powerful tool for investigating a broad spectrum of phenomena in natural, engineering, social, and economic sciences. Recently, several theoretical approaches have been developed that allowed to analyze explicitly dynamics of CTRW at all times, which is critically important for understanding mechanisms of underlying phenomena. However, theoretical analysis has been done mostly for systems with a simple geometry. Here we extend the original method based on generalized master equations to analyze all-time dynamics of CTRW models on complex networks. Specific calculations are performed for models on lattices with branches and for models on coupled parallel-chain lattices. Exact expressions for velocities and dispersions are obtained. Generalized fluctuations theorems for CTRW models on complex networks are discussed.
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05.40.Fb Random walks and Levy flights
02.50.-r Probability theory, stochastic processes, and statistics
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
05.90.+m Other topics in statistical physics, thermodynamics, and nonlinear dynamical systems (restricted to new topics in section 05)
02.30.-f Function theory, analysis
02.40.-k Geometry, differential geometry, and topology

Dynamics of the sub-Ohmic spin-boson model: A time-dependent variational study

Ning Wu, Liwei Duan, Xin Li, and Yang Zhao

J. Chem. Phys. 138, 084111 (2013); http://dx.doi.org/10.1063/1.4792502 (7 pages) | Cited 1 time

Online Publication Date: 28 February 2013

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The Dirac-Frenkel time-dependent variation is employed to probe the dynamics of the zero temperature sub-Ohmic spin-boson model with strong friction utilizing the Davydov D1 ansatz. It is shown that initial conditions of the phonon bath have considerable influence on the dynamics. Counterintuitively, even in the very strong coupling regime, quantum coherence features still manage to survive under the polarized bath initial condition, while such features are absent under the factorized bath initial condition. In addition, a coherent-incoherent transition is found at a critical coupling strength α ≈ 0.1 for s = 0.25 under the factorized bath initial condition. We quantify how faithfully our ansatz follows the Schrödinger equation, finding that the time-dependent variational approach is robust for strong dissipation and deep sub-Ohmic baths (s ≪ 1).
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05.30.Jp Boson systems
02.30.Xx Calculus of variations
03.65.Ge Solutions of wave equations: bound states
03.65.Ta Foundations of quantum mechanics; measurement theory
back to top Atoms, Molecules, and Clusters

Potential energy curves for the interaction of Ag(5s) and Ag(5p) with noble gas atoms

J. Loreau, H. R. Sadeghpour, and A. Dalgarno

J. Chem. Phys. 138, 084301 (2013); http://dx.doi.org/10.1063/1.4790586 (8 pages)

Online Publication Date: 22 February 2013

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We investigate the interaction of ground and excited states of a silver atom with noble gases (NG), including helium. Born-Oppenheimer potential energy curves are calculated with quantum chemistry methods and spin-orbit effects in the excited states are included by assuming a spin-orbit splitting independent of the internuclear distance. We compare our results with experimentally available spectroscopic data, as well as with previous calculations. Because of strong spin-orbit interactions, excited Ag-NG potential energy curves cannot be fitted to Morse-like potentials. We find that the labeling of the observed vibrational levels has to be shifted by one unit.
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31.15.bw Coupled-cluster theory
31.50.Bc Potential energy surfaces for ground electronic states
31.50.Df Potential energy surfaces for excited electronic states
32.70.Jz Line shapes, widths, and shifts
33.20.Tp Vibrational analysis
34.50.-s Scattering of atoms and molecules

Relaxation of rotational-vibrational energy and volume viscosity in H–H2 mixtures

Domenico Bruno, Fabrizio Esposito, and Vincent Giovangigli

J. Chem. Phys. 138, 084302 (2013); http://dx.doi.org/10.1063/1.4792148 (17 pages)

Online Publication Date: 22 February 2013

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We investigate a kinetic model for H–H2 mixtures in a regime where translational/rotational and vibrational-resonant energy exchanges are fast whereas vibrational energy variations are slow. In a relaxation regime, the effective volume viscosity is found to involve contributions from the rotational volume viscosity, the vibrational volume viscosity, the relaxation pressure, and the perturbed source term. In the thermodynamic equilibrium limit, the sum of these four terms converges toward the one-temperature two-mode volume viscosity. The theoretical results are applied to the calculation of the volume viscosities of molecular hydrogen in the trace limit on the basis of a complete set of state-selected cross sections for the H + H2(v, j) system.
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34.50.Ez Rotational and vibrational energy transfer
33.15.Mt Rotation, vibration, and vibration-rotation constants

EXAFS Debye-Waller factors issued from Car-Parrinello molecular dynamics: Application to the fit of oxaliplatin and derivatives

K. Provost, E. C. Beret, D. Bouvet Muller, A. Michalowicz, and E. Sánchez Marcos

J. Chem. Phys. 138, 084303 (2013); http://dx.doi.org/10.1063/1.4790516 (10 pages)

Online Publication Date: 25 February 2013

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One of the main pitfalls in EXAFS fitting is correlation among parameters, which can lead to unreliable fits. The use of theoretical Debye-Waller factors (DWs) is a promising way to reduce the number of fitted parameters. When working with molecular dynamics, it is not only possible to evaluate DWs from the statistical distributions issued from the trajectory but also to estimate the distribution anharmonicity, and to compute simulated average EXAFS spectra that can be fitted as experimental ones, in order to assess the ability of EXAFS fitting to recover information on DWs, as well as other structural and spectroscopical parameters. The case studied is oxaliplatin, a third generation anticancer drug. The structural information and the simulated average spectra were derived from a Car-Parrinello molecular dynamics (CP-MD) trajectory of a compound closely related to oxaliplatin. We present the DWs issued from this simulation and their use, by taking their theoretical absolute values (no DW fitted) or their ratios (one DW fitted). In this second approach, the fit of oxaliplatin experimental spectra leads to DWs values very close to the theoretical ones. This shows that the CP-MD trajectory provides a good representation of the distance distributions for oxaliplatin. Transferability of oxaliplatin DWs, for all relevant single and multiple scattering paths, to closely related compounds is proven for the case of bis(oxalato)platinum(II) and bis(ethylene diamine)platinum(II).
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78.70.Dm X-ray absorption spectra

The toluene-Ar complex: S0 and S1 van der Waals modes, changes to methyl rotation, and torsion-van der Waals vibration coupling

Jason R. Gascooke and Warren D. Lawrance

J. Chem. Phys. 138, 084304 (2013); http://dx.doi.org/10.1063/1.4792642 (11 pages) | Cited 1 time

Online Publication Date: 25 February 2013

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The methyl rotor and van der Waals vibrational levels in the S1 and S0 states of toluene-Ar have been investigated by the technique of two-dimensional laser induced fluorescence (2D-LIF). The S0 van der Waals and methyl rotor levels are reported for the first time, while improved S1 values are presented. The correlations seen in the 2D-LIF images between the S0 and S1 states lead to a reassignment of key features in the S1 ← S0 excitation spectrum. This reassignment reveals that there are significant changes in the methyl rotor levels in the complex compared with those in bare toluene, particularly at low m. The observed rotor energies are explained by the introduction of a three-fold, V3, term in the torsion potential (this term is zero in toluene) and a reduction in the height of the six-fold, V6, barriers in S0 and S1 from their values in bare toluene. The V3 term is larger in magnitude than the V6 term in both S0 and S1. The constants determined are |V3(S1)| = 33.4 ± 1.0 cm−1, |V3(S0)| = 20.0 ± 1.0 cm−1, V6(S1) = −10.7 ± 1.0 cm−1, and V6(S0) = −1.7 ± 1.0 cm−1. The methyl rotor is also found to couple with van der Waals vibration; specifically, the m″ = 2 rotor state couples with the combination level involving one quantum of the long axis bend and m″ = 1. The coupling constant is determined to be 1.9 cm−1, which is small compared with the values typically reported for torsion-vibration coupling involving ring modes.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.80.-b Photon interactions with molecules
33.50.Dq Fluorescence and phosphorescence spectra
33.15.Bh General molecular conformation and symmetry; stereochemistry

Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction

M. Monge-Palacios, C. Rangel, and J. Espinosa-Garcia

J. Chem. Phys. 138, 084305 (2013); http://dx.doi.org/10.1063/1.4792719 (14 pages)

Online Publication Date: 25 February 2013

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A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200–2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Tr Kinetic isotope effects including muonium
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

On the structures and bonding in boron-gold alloy clusters: B6Aun− and B6Aun (n = 1−3)

Qiang Chen, Hua-Jin Zhai, Si-Dian Li, and Lai-Sheng Wang

J. Chem. Phys. 138, 084306 (2013); http://dx.doi.org/10.1063/1.4792501 (8 pages)

Online Publication Date: 26 February 2013

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Photoelectron spectroscopy and density-functional theory are combined to investigate the electronic and structural properties of a series of B−Au alloy clusters: B6Aun− and B6Aun (n = 1−3). Rich spectral features are observed for each species, and vibrational structures are resolved for numerous detachment transitions of B6Au− and B6Au2−. Electron affinities of B6Aun (n = 1−3) are evaluated to be 2.70 ± 0.03, 2.91 ± 0.02, and 3.21 ± 0.05 eV, respectively. Global structural searches are performed for both the anions and their neutrals. The calculated electronic binding energies are compared with experimental measurements to establish the anion global-minimum structures and their corresponding neutral states. The ground-state structures of these clusters are shown to be planar or quasi-planar with an elongated B6 core, to which the first and second Au atoms are bonded terminally and the third Au in a bridging position. All three anion clusters are π antiaromatic. Natural bond orbital analyses show that the B−Au bonding is highly covalent, providing new examples for the Au/H analogy in Au alloy clusters.
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36.40.Mr Spectroscopy and geometrical structure of clusters
31.15.ee Time-dependent density functional theory
33.60.+q Photoelectron spectra
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
36.40.Cg Electronic and magnetic properties of clusters

A comprehensive experimental and theoretical study of H2−CO spectra

Piotr Jankowski, L. A. Surin, A. Potapov, S. Schlemmer, A. R. W. McKellar, and Krzysztof Szalewicz

J. Chem. Phys. 138, 084307 (2013); http://dx.doi.org/10.1063/1.4791712 (23 pages)

Online Publication Date: 27 February 2013

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A detailed description of a new ab initio interaction potential energy surfaces for the H2−CO complex computed on a six-dimensional grid (i.e., including the dependence on the H−H and C−O separations) is presented. The interaction energies were first calculated using the coupled-cluster method with single, double, and noniterative triple excitations and large basis sets, followed by an extrapolation procedure. Next, a contribution from iterative triple and noniterative quadruple excitations was added from calculations in smaller basis sets. The resulting interaction energies were then averaged over the ground-state and both ground- and first-excited-states vibrational wave functions of H2 and CO, respectively. The two resulting four-dimensional potential energy surfaces were fitted by analytic expressions. Theoretical infrared spectra calculated from these surfaces have already been shown [P. Jankowski, A. R. W. McKellar, and K. Szalewicz, Science 336, 1147 (2012)] to agree extremely well, to within a few hundredth of wavenumber, with the experimental spectra of the para and orthoH2−CO complex. In the latter case, this agreement enabled an assignment of the experimental spectrum, ten years after it had been measured. In the present paper, we provide details concerning the development of the surfaces and the process of spectral line assignment. Furthermore, we assign some transitions for paraH2−CO that have not been assigned earlier. A completely new element of the present work are experimental investigations of the orthoH2−CO complex using microwave spectroscopy. Vast parts of the measured spectrum have been interpreted by comparisons with the infrared experiments, including new low-temperature ones, and theoretical spectrum. Better understanding of the spectra of both para and orthoH2−CO complexes provides a solid foundation for a new search of the bound H2−CO complex in space.
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31.50.Df Potential energy surfaces for excited electronic states
33.20.Bx Radio-frequency and microwave spectra
33.20.Ea Infrared spectra
33.20.Tp Vibrational analysis
31.15.ag Excitation energies and lifetimes; oscillator strengths
31.15.bw Coupled-cluster theory

Dielectric controlled excited state relaxation pathways of a representative push-pull stilbene: A mechanistic study using femtosecond fluorescence up-conversion technique

Shahnawaz Rafiq and Pratik Sen

J. Chem. Phys. 138, 084308 (2013); http://dx.doi.org/10.1063/1.4792933 (10 pages)

Online Publication Date: 28 February 2013

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Femtosecond fluorescence up-conversion technique was employed to reinvestigate the intriguing dependence of fluorescence quantum yield of trans-4-dimethylamino-4′-nitrostilbene (DNS) on dielectric properties of the media. In polar solvents, such as methanol and acetonitrile, the two time components of the fluorescence transients were assigned to intramolecular charge transfer (ICT) dynamics and to the depletion of the ICT state to the ground state via internal conversion along the torsional coordinate of nitro moiety. The viscosity independence of the first time component indicates the absence of any torsional coordinate in the charge transfer process. In slightly polar solvent (carbon tetrachloride) the fluorescence transients show a triple exponential behavior. The first time component was assigned to the formation of the ICT state on a 2 ps time scale. Second time component was assigned to the relaxation of the ICT state via two torsion controlled channels. First channel involves the torsional motion about the central double bond leading to the trans-cis isomerization via a conical intersection or avoided crossing. The other channel contributing to the depopulation of ICT state involves the torsional coordinates of dimethylanilino and/or nitrophenyl moieties and leads to the formation of a conformationally relaxed state, which subsequently relaxes back to the ground state radiatively, and is responsible for the high fluorescence quantum yield of DNS in slightly polar solvents such as carbon tetrachloride, toluene, etc. The excited singlet state which is having a dominant π-π* character may also decay via intersystem crossing to the n-π* triplet manifold and thus accounts for the observed triplet yield of the molecule in slightly polar solvents.
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33.50.Dq Fluorescence and phosphorescence spectra
33.50.Hv Radiationless transitions, quenching
33.80.Be Level crossing and optical pumping
34.70.+e Charge transfer
31.70.Dk Environmental and solvent effects
33.15.Mt Rotation, vibration, and vibration-rotation constants

Calculation of the transport properties of a dilute gas consisting of Lennard-Jones chains

Robert Hellmann, Nicolas Riesco, and Velisa Vesovic

J. Chem. Phys. 138, 084309 (2013); http://dx.doi.org/10.1063/1.4793221 (11 pages) | Cited 1 time

Online Publication Date: 28 February 2013

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The transport properties in the dilute gas limit have been calculated by the classical-trajectory method for a gas consisting of chain-like molecules. The molecules were modelled as rigid chains consisting of spherical segments that interact through a combination of site-site Lennard-Jones 12-6 potentials. Results are reported for shear viscosity, self-diffusion, and thermal conductivity for chains consisting of 1, 2, 3, 4, 5, 6, 7, 8, 10, 13, and 16 segments in the reduced temperature range of 0.3 − 50. The results indicate that the transport properties increase with temperature and decrease with chain length. At high temperatures the dependence of the transport properties is governed effectively by the repulsive part of the potential. No simple scaling with chain length has been observed. The higher order correction factors are larger than observed for real molecules so far, reaching asymptotic values of 1.019 − 1.033 and 1.060 − 1.072 for viscosity and thermal conductivity, respectively. The dominant contribution comes from the angular momentum coupling. The agreement with molecular dynamics calculations for viscosity is within the estimated accuracy of the two methods for shorter chains. However, for longer chains differences of up to 7% are observed.
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51.20.+d Viscosity, diffusion, and thermal conductivity
back to top Liquids, Glasses, and Crystals
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Fast scanning calorimetry studies of the glass transition in doped amorphous solid water: Evidence for the existence of a unique vicinal phase

Stephanie A. McCartney and Vlad Sadtchenko

J. Chem. Phys. 138, 084501 (2013); http://dx.doi.org/10.1063/1.4789629 (10 pages) | Cited 1 time

Online Publication Date: 22 February 2013

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The fast scanning calorimetry (FSC) was employed to investigate glass transition phenomena in vapor deposited amorphous solid water (ASW) films doped with acetic acid, pentanol, and carbon tetrachloride. In all three cases, FSC thermograms of doped ASW films show well pronounced glass transitions at temperatures near 180 K. Systematic FSC studies of the glass transition temperature and the excess heat capacity dependence on the concentration of impurities indicate the possible existence of two distinct non-crystalline phases of H2O in binary aqueous solutions. According to our conjecture, bulk pure ASW is a glass at temperatures up to its crystallization near 205 K. However, guest molecules in the ASW matrix may be enveloped in an H2O phase which undergoes a glass transition prior to crystallization. In the case of CH3COOH, we estimate that such a viscous liquid shell contains approximately 25 H2O molecules. We discuss the implications of these findings for past studies of molecular kinetics in pure vitreous water and in binary aqueous solutions.
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64.70.P- Glass transitions of specific systems
65.60.+a Thermal properties of amorphous solids and glasses: heat capacity, thermal expansion, etc.
64.70.dg Crystallization of specific substances
68.55.at Other materials
61.43.Er Other amorphous solids

Phase transitions in four-dimensional binary hard hypersphere mixtures

Marvin Bishop and Paula A. Whitlock

J. Chem. Phys. 138, 084502 (2013); http://dx.doi.org/10.1063/1.4789953 (8 pages)

Online Publication Date: 22 February 2013

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Previous Monte Carlo investigations of binary hard hyperspheres in four-dimensional mixtures are extended to higher densities where the systems may solidify. The ratios of the diameters of the hyperspheres examined were 0.4, 0.5, and 0.6. Only the 0.4 system shows a clear two phase, solid-liquid transition and the larger component solidifies into a D4 crystal state. Its pair correlation function agrees with that of a one component fluid at an appropriately scaled density. The 0.5 systems exhibit states that are a mix of D4 and A4 regions. The 0.6 systems behave similarly to a jammed state rather than solidifying into a crystal. No demixing into two distinct fluid phases was observed for any of the simulations.
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64.70.D- Solid-liquid transitions
64.75.Cd Phase equilibria of fluid mixtures, including gases, hydrates, etc.
81.30.Fb Solidification
64.60.De Statistical mechanics of model systems (Ising model, Potts model, field-theory models, Monte Carlo techniques, etc.)

Thermostats and thermostat strategies for molecular dynamics simulations of nanofluidics

Xin Yong and Lucy T. Zhang

J. Chem. Phys. 138, 084503 (2013); http://dx.doi.org/10.1063/1.4792202 (10 pages)

Online Publication Date: 22 February 2013

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The thermostats in molecular dynamics (MD) simulations of highly confined channel flow may have significant influences on the fidelity of transport phenomena. In this study, we exploit non-equilibrium MD simulations to generate Couette flows with different combinations of thermostat algorithms and strategies. We provide a comprehensive analysis on the effectiveness of three thermostat algorithms Nosé-Hoover chain (NHC), Langevin (LGV) and dissipative particle dynamics (DPD) when applied in three thermostat strategies, thermostating either walls (TW) or fluid (TF), and thermostating both the wall and fluid (TWTF). Our results of thermal and mechanical properties show that the TW strategy more closely resembles experimental conditions. The TF and TWTF systems also produce considerably similar behaviors in weakly sheared systems, but deviate the dynamics in strongly sheared systems due to the isothermal condition. The LGV and DPD thermostats used in the TF and TWTF systems provide vital ways to yield correct dynamics in coarse-grained systems by tuning the fluid transport coefficients. Using conventional NHC thermostat to thermostat fluid only produces correct thermal behaviors in weakly sheared systems, and breaks down due to significant thermal inhomogeneity in strongly sheared systems.
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47.15.Rq Laminar flows in cavities, channels, ducts, and conduits
47.60.Dx Flows in ducts and channels
02.70.Ns Molecular dynamics and particle methods
47.11.Mn Molecular dynamics methods
02.30.Hq Ordinary differential equations
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