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7 Dec 2009

Volume 131, Issue 21, Articles (21xxxx)

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J. Chem. Phys. 131, 214501 (2009); http://dx.doi.org/10.1063/1.3244981 (8 pages)

James J. Haycraft
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Charge transfer by electronic excitation: Direct measurement by high resolution spectroscopy in the gas phase

A. J. Fleisher, P. J. Morgan, and D. W. Pratt

J. Chem. Phys. 131, 211101 (2009); http://dx.doi.org/10.1063/1.3259690 (4 pages) | Cited 4 times

Online Publication Date: 2 December 2009

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We report a quantitative measurement of the amount of charge that is transferred when the single ammonia complex of the photoacid β-naphthol (2HNA) is excited by light. The measurement was made by comparing the permanent electric dipole moments of cis-2HNA in its ground (S0) and excited (S1) states, determined by Stark-effect studies of its fully resolved S1←S0 electronic spectrum. While the increase in electron transfer from the donor (NH3) to the acceptor (2HN) upon excitation is small ( ∼ 0.05e), it is sufficient to redshift the electronic spectrum of the complex by ∼ 600 cm−1 ( ∼ 0.1 eV). Thereby explored is the incipient motion of the acid-base complex along the excited state (electron-coupled) proton transfer coordinate.
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34.70.+e Charge transfer
31.50.Df Potential energy surfaces for excited electronic states
33.70.Jg Line and band widths, shapes, and shifts
33.57.+c Magneto-optical and electro-optical spectra and effects
33.50.Dq Fluorescence and phosphorescence spectra
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
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Continuum remover-complex absorbing potential: Efficient removal of the nonphysical stabilization points

Y. Sajeev, V. Vysotskiy, L. S. Cederbaum, and N. Moiseyev

J. Chem. Phys. 131, 211102 (2009); http://dx.doi.org/10.1063/1.3271350 (4 pages) | Cited 8 times

Online Publication Date: 4 December 2009

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By adding a negative imaginary potential of variable strength η to the Hamiltonian, the resonance state of a system can be found as complex energy stabilized points in the η-trajectories of the eigenvalues. One problem that arises in practical calculations is the appearance of nonphysical complex energy stabilized points. A new method for separating the physical from the nonphysical complex energy stabilized points is proposed. The method is best illustrated with strongly correlated two-electron systems.
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33.80.Eh Autoionization, photoionization, and photodetachment
31.15.aq Strongly correlated electron systems: generalized tight-binding method
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
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back to top Theoretical Methods and Algorithms

Resolution of identity approximation for the Coulomb term in molecular and periodic systems

Asbjörn M. Burow, Marek Sierka, and Fawzi Mohamed

J. Chem. Phys. 131, 214101 (2009); http://dx.doi.org/10.1063/1.3267858 (6 pages) | Cited 8 times

Online Publication Date: 1 December 2009

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A new formulation of resolution of identity approximation for the Coulomb term is presented, which uses atom-centered basis and auxiliary basis functions and treats molecular and periodic systems of any dimensionality on an equal footing. It relies on the decomposition of an auxiliary charge density into charged and chargeless components. Applying the Coulomb metric under periodic boundary conditions constrains the explicit form of the charged part. The chargeless component is determined variationally and converged Coulomb lattice sums needed for its determination are obtained using chargeless linear combinations of auxiliary basis functions. The lattice sums are partitioned in near- and far-field portions which are treated through an analytical integration scheme employing two- and three-center electron repulsion integrals and multipole expansions, respectively, operating exclusively in real space. Our preliminary implementation within the TURBOMOLE program package demonstrates consistent accuracy of the method across molecular and periodic systems. Using common auxiliary basis sets the errors of the approximation are small, in average about 20 μhartree per atom, for both molecular and periodic systems.
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31.15.E- Density-functional theory
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions

Effective medium approach for heterogeneous reaction-diffusion media

Sergio Alonso, Markus Bär, and Raymond Kapral

J. Chem. Phys. 131, 214102 (2009); http://dx.doi.org/10.1063/1.3265987 (9 pages) | Cited 3 times

Online Publication Date: 1 December 2009

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An effective medium theory that can be used to calculate effective diffusion and reaction rate coefficients in random heterogeneous reaction-diffusion systems is described. The predictions of the theory are compared with simulations of spatially distributed media with different types of heterogeneity. The magnitude of the front velocity in bistable media is used to gauge the accuracy of the theoretical predictions. Quantitative agreement is found if the diffusion length in the heterogeneities is large compared to the characteristic width of the front. However, for small diffusion lengths the agreement depends on the type of heterogeneity. The effective medium predictions are also compared with simulations on systems with regular or temporal disorder.
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82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Db Transition state theory and statistical theories of rate constants

Accurate dipole polarizabilities for water clusters n = 2–12 at the coupled-cluster level of theory and benchmarking of various density functionals

Jeff R. Hammond, Niranjan Govind, Karol Kowalski, Jochen Autschbach, and Sotiris S. Xantheas

J. Chem. Phys. 131, 214103 (2009); http://dx.doi.org/10.1063/1.3263604 (9 pages) | Cited 11 times

Online Publication Date: 2 December 2009

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The static dipole polarizabilities of water clusters (2 ≤ N ≤ 12) are determined at the coupled-cluster level of theory (CCSD). For the dipole polarizability of the water monomer it was determined that the role of the basis set is more important than that of electron correlation and that the basis set augmentation converges with two sets of diffuse functions. The CCSD results are used to benchmark a variety of density functionals while the performance of several families of basis sets (Dunning, Pople, and Sadlej) in producing accurate values for the polarizabilities was also examined. The Sadlej family of basis sets was found to produce accurate results when compared to the ones obtained with the much larger Dunning basis sets. It was furthermore determined that the PBE0 density functional with the aug-cc-pVDZ basis set produces overall remarkably accurate polarizabilities at a moderate computational cost.
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33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
36.40.Cg Electronic and magnetic properties of clusters
31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
31.15.V- Electron correlation calculations for atoms, ions and molecules

An accurate model potential for alkali neon systems

D. Zanuttini, E. Jacquet, E. Giglio, J. Douady, and B. Gervais

J. Chem. Phys. 131, 214104 (2009); http://dx.doi.org/10.1063/1.3269801 (10 pages) | Cited 3 times

Online Publication Date: 2 December 2009

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We present a detailed investigation of the ground and lowest excited states of M-Ne dimers, for M = Li, Na, and K. We show that the potential energy curves of these Van der Waals dimers can be obtained accurately by considering the alkali neon systems as one-electron systems. Following previous authors, the model describes the evolution of the alkali valence electron in the combined potentials of the alkali and neon cores by means of core polarization pseudopotentials. The key parameter for an accurate model is the M+-Ne potential energy curve, which was obtained by means of ab initio CCSD(T) calculation using a large basis set. For each MNe dimer, a systematic comparison with ab initio computation of the potential energy curve for the X, A, and B states shows the remarkable accuracy of the model. The vibrational analysis and the comparison with existing experimental data strengthens this conclusion and allows for a precise assignment of the vibrational levels.
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31.50.Df Potential energy surfaces for excited electronic states
31.15.A- Ab initio calculations
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.bw Coupled-cluster theory

Introducing sampling entropy in repository based adaptive umbrella sampling

Han Zheng and Yingkai Zhang

J. Chem. Phys. 131, 214105 (2009); http://dx.doi.org/10.1063/1.3267549 (8 pages)

Online Publication Date: 2 December 2009

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Determining free energy surfaces along chosen reaction coordinates is a common and important task in simulating complex systems. Due to the complexity of energy landscapes and the existence of high barriers, one widely pursued objective to develop efficient simulation methods is to achieve uniform sampling among thermodynamic states of interest. In this work, we have demonstrated sampling entropy (SE) as an excellent indicator for uniform sampling as well as for the convergence of free energy simulations. By introducing SE and the concentration theorem into the biasing-potential-updating scheme, we have further improved the adaptivity, robustness, and applicability of our recently developed repository based adaptive umbrella sampling (RBAUS) approach [ H. Zheng and Y. Zhang, J. Chem. Phys. 128, 204106 (2008) ]. Besides simulations of one dimensional free energy profiles for various systems, the generality and efficiency of this new RBAUS-SE approach have been further demonstrated by determining two dimensional free energy surfaces for the alanine dipeptide in gas phase as well as in water.
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05.70.Ce Thermodynamic functions and equations of state
02.50.-r Probability theory, stochastic processes, and statistics
02.60.Cb Numerical simulation; solution of equations

Ring-polymer molecular dynamics rate-theory in the deep-tunneling regime: Connection with semiclassical instanton theory

Jeremy O. Richardson and Stuart C. Althorpe

J. Chem. Phys. 131, 214106 (2009); http://dx.doi.org/10.1063/1.3267318 (12 pages) | Cited 19 times

Online Publication Date: 3 December 2009

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We demonstrate that the ring-polymer molecular dynamics (RPMD) method is equivalent to an automated and approximate implementation of the “Im F” version of semiclassical instanton theory when used to calculate reaction rates in the deep-tunneling regime. This explains why the RPMD method is often reliable in this regime and also shows how it can be systematically improved. The geometry of the beads at the transition state on the ring-polymer potential surface describes a finite-difference approximation to the “instanton” trajectory (a periodic orbit in imaginary time βℏ on the inverted potential surface). The deep-tunneling RPMD rate is an approximation to the rate obtained by applying classical transition-state theory (TST) in ring-polymer phase-space using the optimal dividing surface; this TST rate is in turn an approximation to a free-energy version of the Im F instanton rate. The optimal dividing surface is in general a function of several modes of the ring polymer, which explains why centroid-based quantum-TSTs break down at low temperatures for asymmetric reaction barriers. Numerical tests on one-dimensional models show that the RPMD rate tends to overestimate deep-tunneling rates for asymmetric barriers and underestimate them for symmetric barriers, and we explain that this is likely to be a general trend. The ability of the RPMD method to give a dividing-surface-independent rate in the deep-tunneling regime is shown to be a consequence of setting the bead-masses equal to the physical mass.
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61.41.+e Polymers, elastomers, and plastics
82.35.-x Polymers: properties; reactions; polymerization
65.40.G- Other thermodynamical quantities

Single-molecule photon emission statistics for systems with explicit time dependence: Generating function approach

Yonggang Peng, Shijie Xie, Yujun Zheng, and Frank L. H. Brown

J. Chem. Phys. 131, 214107 (2009); http://dx.doi.org/10.1063/1.3265855 (11 pages) | Cited 4 times

Online Publication Date: 3 December 2009

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Generating function calculations are extended to allow for laser pulse envelopes of arbitrary shape in numerical applications. We investigate photon emission statistics for two-level and V- and Λ-type three-level systems under time-dependent excitation. Applications relevant to electromagnetically induced transparency and photon emission from single quantum dots are presented.
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81.07.Ta Quantum dots
73.21.La Quantum dots
78.67.Hc Quantum dots
42.50.Md Optical transient phenomena: quantum beats, photon echo, free-induction decay, dephasings and revivals, optical nutation, and self-induced transparency

A singularity free surface hopping expansion for the multistate wave function

Michael F. Herman

J. Chem. Phys. 131, 214108 (2009); http://dx.doi.org/10.1063/1.3268923 (13 pages)

Online Publication Date: 4 December 2009

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A version of a surface hopping wave function for nonadiabatic multistate problems, which is free of turning point singularities, is derived and tested. The primitive semiclassical form of the particular surface hopping method considered has been shown to be highly accurate, even for classically forbidden processes. However, this semiclassical wave function displays the usual singular behavior at turning points and caustics in the classical motion. Numerical data has shown that this somewhat reduces its accuracy when the energy is near the crossing energy of the diabatic electronic surfaces. The singularity free version of this surface hopping wave function is derived by partitioning the x-axis into a large number of small steps for one dimensional problems. The adiabatic electronic energy surfaces are approximated to be linear functions within each step. The matching conditions required by the continuity of the wave function and its derivative at each step boundary provide the needed conditions to obtain the amplitudes for changes in electronic state and/or reflection of the trajectory for the motion of the nuclei. This leads to a form of the surface hopping wave function that is free of turning point singularities. The method is tested for a one dimensional model problem, and it is found to be highly accurate at all energies considered, even when the energy is near the crossing energy.
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73.20.At Surface states, band structure, electron density of states
73.25.+i Surface conductivity and carrier phenomena

A selective integrated tempering method

Lijiang Yang and Yi Qin Gao

J. Chem. Phys. 131, 214109 (2009); http://dx.doi.org/10.1063/1.3266563 (8 pages)

Online Publication Date: 4 December 2009

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In this paper, based on the integrated tempering sampling we introduce a selective integrated tempering sampling (SITS) method for the efficient conformation sampling and thermodynamics calculations for a subsystem in a large one, such as biomolecules solvated in aqueous solutions. By introducing a potential surface scaled with temperature, the sampling over the configuration space of interest (e.g., the solvated biomolecule) is selectively enhanced but the rest of the system (e.g., the solvent) stays largely unperturbed. The applications of this method to biomolecular systems allow highly efficient sampling over both energy and configuration spaces of interest. Comparing to the popular and powerful replica exchange molecular dynamics (REMD), the method presented in this paper is significantly more efficient in yielding relevant thermodynamics quantities (such as the potential of mean force for biomolecular conformational changes in aqueous solutions). It is more important that SITS but not REMD yielded results that are consistent with the traditional umbrella sampling free energy calculations when explicit solvent model is used since SITS avoids the sampling of the irrelevant phase space (such as the boiling water at high temperatures).
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87.15.N- Properties of solutions of macromolecules
87.15.hp Conformational changes
82.60.Lf Thermodynamics of solutions

Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method

Divesh Bhatt and Daniel M. Zuckerman

J. Chem. Phys. 131, 214110 (2009); http://dx.doi.org/10.1063/1.3269674 (10 pages) | Cited 2 times

Online Publication Date: 4 December 2009

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We demonstrate a nondynamical Monte Carlo method to compute free energies and generate equilibrium ensembles of dense fluids. In this method, based on step-by-step polymer growth algorithms, an ensemble of n+1 particles is obtained from an ensemble of n particles by generating configurations of the n+1st particle. A statistically rigorous resampling scheme is utilized to remove configurations with low weights and to avoid a combinatorial explosion; the free energy is obtained from the sum of the weights. In addition to the free energy, the method generates an equilibrium ensemble of the full system. We consider two different system sizes for a Lennard-Jones fluid and compare the results with conventional Monte Carlo methods.
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65.20.Jk Studies of thermodynamic properties of specific liquids
61.25.he Polymer solutions
61.20.Ja Computer simulation of liquid structure

Hierarchical quantum master equation with semiclassical Drude dissipation

Rui-Xue Xu, Bao-Ling Tian, Jian Xu, Qiang Shi, and YiJing Yan

J. Chem. Phys. 131, 214111 (2009); http://dx.doi.org/10.1063/1.3268922 (8 pages) | Cited 8 times

Online Publication Date: 4 December 2009

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We propose a nonperturbative quantum dissipation theory, in term of hierarchical quantum master equation, which may be used with a great degree of confidence to various dynamics systems in condensed phases. The theoretical development is rooted in an improved semiclassical treatment of Drude bath, beyond the conventional high temperature approximations. It leads to the new theory a simple but important improvement over the conventional stochastic Liouville equation theory, without extra numerical cost. Its broad range of validity and applicability is extensively demonstrated with two-level electron transfer model systems, where the new theory can be considered as the modified Zusman equation. Criterion is also proposed to estimate the performance of the hierarchical quantum master equation.
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03.65.Sq Semiclassical theories and applications
02.30.Rz Integral equations
02.50.Ey Stochastic processes
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Backward stimulated Bragg scattering in multiphoton active CdTexSe1−x quantum dots system

Guang S. He, Jing Zhu, Ken-Tye Yong, Rui Hu, Yiping Cui, and P. N. Prasad

J. Chem. Phys. 131, 214301 (2009); http://dx.doi.org/10.1063/1.3266938 (8 pages)

Online Publication Date: 1 December 2009

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The backward stimulated Bragg scattering (SBgS) of CdTexSe1−x quantum dots in chloroform is investigated at three pump laser wavelengths (532, 816, and 1064 nm) in nanosecond regime. The spectral and temporal structures of the backward stimulated scattering and pump threshold dependence on the concentration are presented in this paper. The energy conversion efficiency from input pump pulse to SBgS pulse was measured to be ≥ 14%. In addition, the samples exhibit multi- (two-, three-)photon absorption capability over the spectral range we investigated. More importantly, both mechanisms of SBgS and multiphoton absorption provided an enhanced optical limiting performance. The measured nonlinear transmissivity was changed from ∼ 0.73 to ∼ 0.17 for 532 nm laser pulses and from ∼ 0.9 to ∼ 0.35 for 816 nm laser pulses when the input pulse energy was changed from 10 to ∼ 1500 μJ.
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78.67.Hc Quantum dots
42.65.Es Stimulated Brillouin and Rayleigh scattering
42.50.Hz Strong-field excitation of optical transitions in quantum systems; multiphoton processes; dynamic Stark shift

Photoabsorption spectra of small cationic xenon clusters from time-dependent density functional theory

Micael J. T. Oliveira, Fernando Nogueira, Miguel A. L. Marques, and Angel Rubio

J. Chem. Phys. 131, 214302 (2009); http://dx.doi.org/10.1063/1.3265767 (6 pages)

Online Publication Date: 1 December 2009

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Upon ionization, rare-gas (like Ar and Xe) clusters shift their absorption spectrum from the ultraviolet to the visible. This happens as bonding becomes much stronger due to the removal of an electron from a strongly antibonding orbital. In this article, we study the absorption spectrum of small cationic xenon clusters (Xen+, with n = 3,…,35) by means of time-dependent density functional theory. These calculations include relativistic effects through the use of relativistic j-dependent pseudopotentials in a two-spinor formulation of the Kohn–Sham equations. The peak positions in our calculated spectra are in fairly good agreement with experiment and confirm that absorption is mainly due to a charged linear core composed of 3, 4, or 5 Xe atoms where the positive charge is localized. However, we find large deviations concerning the oscillator strengths, which can be partially explained by the unsatisfactory treatment of exchange in common density functionals. Furthermore, we find that adequate ground-state geometries are necessary for the correct prediction of the qualitative features of the spectra.
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36.40.Mr Spectroscopy and geometrical structure of clusters
32.80.Fb Photoionization of atoms and ions
31.30.jc Relativistic corrections to atomic structure and properties
31.15.ee Time-dependent density functional theory
32.70.Cs Oscillator strengths, lifetimes, transition moments

A conformational and vibrational study of CF3COSCH2CH3

María Eliana Defonsi Lestard, María Eugenia Tuttolomondo, Derek A. Wann, Heather E. Robertson, David W. H. Rankin, and Aida Ben Altabef

J. Chem. Phys. 131, 214303 (2009); http://dx.doi.org/10.1063/1.3267633 (12 pages) | Cited 2 times

Online Publication Date: 3 December 2009

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The molecular structure and conformational properties of S-ethyl trifluorothioacetate, CF3COSCH2CH3, were determined in the gas phase by electron diffraction and vibrational spectroscopy (IR and Raman). The experimental investigations were supplemented by ab initio (Møller Plesset of second order) and density functional theory quantum chemical calculations at different levels of theory. Both experimental and theoretical methods reveal two structures with Cs (anti, anti) and C1 (anti, gauche) symmetries, although there are disagreements about which is more stable. The electron diffraction intensities are best interpreted with a mixture of 51(3)% anti, anti and 49(3)% anti, gauche conformers. This conformational preference was studied using the total energy scheme and the natural bond orbital scheme. In addition, the infrared spectra of CF3COSCH2CH3 are reported for the gas, liquid and solid phases as well as the Raman spectrum of the liquid. Using calculated frequencies as a guide, evidence for both Cs and C1 structures is obtained in the IR spectra. Harmonic vibrational frequencies and scaled force fields have been calculated for both conformers.
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33.20.Fb Raman and Rayleigh spectra (including optical scattering)
33.20.Ea Infrared spectra
78.30.Jw Organic compounds, polymers
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

The elastic constants and related properties of the epsilon polymorph of the energetic material CL-20 determined by Brillouin scattering

James J. Haycraft

J. Chem. Phys. 131, 214501 (2009); http://dx.doi.org/10.1063/1.3244981 (8 pages)

Online Publication Date: 1 December 2009

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The acoustic phonons of the epsilon polymorph of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazatetracyclo [5.5.0.05,9.03,11] dodecane (ε-CL-20) have been studied using Brillouin scattering spectroscopy. Analysis of the acoustic phonon velocities allowed determination of the complete stiffness tensor for this energetic material. The results are compared to a theoretical determination of the ε-CL-20 elastic constants, bulk moduli, and shear moduli. The observed ordering of elastic constants, C22>C33>C11, is noted to be different from other nitramine energetic materials. Finally, the elasticity of ε-CL-20 is compared to recently published reports on cyclotrimethylene trinitramine’s (RDX) elasticity and the beta polymorph of cyclotetramethylene tetranitramine’s (β-HMX) elasticity.
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81.40.Jj Elasticity and anelasticity, stress-strain relations
62.20.de Elastic moduli
63.20.D- Phonon states and bands, normal modes, and phonon dispersion
78.35.+c Brillouin and Rayleigh scattering; other light scattering
61.66.Hq Organic compounds
62.65.+k Acoustical properties of solids

Two-dimensional femtosecond stimulated Raman spectroscopy: Observation of cascading Raman signals in acetonitrile

Kristina C. Wilson, Brendon Lyons, Randy Mehlenbacher, Randy Sabatini, and David W. McCamant

J. Chem. Phys. 131, 214502 (2009); http://dx.doi.org/10.1063/1.3263909 (15 pages) | Cited 6 times

Online Publication Date: 1 December 2009

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A new methodology for two-dimensional Raman spectroscopy—termed two-dimensional femtosecond stimulated Raman spectroscopy (2D-FSRS)—is presented and experimental results for acetonitrile are discussed. 2D-FSRS can potentially observe molecular anharmonicity by measuring the modulation of the frequency of a probed Raman mode, at frequency ωhi, by the coherent motion of an impulsively driven mode, at frequency ωlow. In acetonitrile, the signal is generated by driving the CCN bend (379 cm−1) and CC stretch (920 cm−1) into coherence via impulsive stimulated Raman scattering and subsequently probing the stimulated Raman spectrum of the CC stretch, the CN stretch (2250 cm−1) and the CH stretch (2942 cm−1). The resultant signal can be generated by two alternative mechanisms: a fifth-order Raman process that would directly probe anharmonic coupling between the two modes, or a third-order cascade in which a third-order coherent Raman process produces a field that goes on to participate in a third-order stimulated Raman transition. The third-order cascade is shown to dominate the 2D-FSRS spectrum as determined by comparison with the predicted magnitude of the two signals, the 2D spectrum of a mixed isotope experiment, and the concentration dependence of the signal. In acetonitrile, theoretical calculations of the vibrational anharmonicity indicate that the third-order cascade signal should be 104 times larger than the fifth-order Raman signal. 2D-FSRS signals are observed between acetonitrile’s CCN bend, of E symmetry, and several different A1 modes but are forbidden by symmetry in the fifth-order pathway. A 2D-FSRS spectrum of a 50:50 mixture of acetonitrile and d3-acetonitrile shows equivalent intensity for intramolecular coupling peaks and intermolecular coupling peaks, indicating that the observed signal cannot be probing molecular anharmonicity. Finally, the magnitudes of the 2D-FSRS peaks are observed to be proportional to the square of the number density, supporting the cascade mechanism.
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33.20.Fb Raman and Rayleigh spectra (including optical scattering)
42.65.Dr Stimulated Raman scattering; CARS
42.65.Es Stimulated Brillouin and Rayleigh scattering
33.70.Fd Absolute and relative line and band intensities
31.30.Gs Hyperfine interactions and isotope effects
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis

On violations of Le Chatelier’s principle for a temperature change in small systems observed for short times

Pouria Dasmeh, Debra J. Searles, Davood Ajloo, Denis J. Evans, and Stephen R. Williams

J. Chem. Phys. 131, 214503 (2009); http://dx.doi.org/10.1063/1.3261849 (7 pages)

Online Publication Date: 2 December 2009

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Le Chatelier’s principle states that when a system is disturbed, it will shift its equilibrium to counteract the disturbance. However for a chemical reaction in a small, confined system, the probability of observing it proceed in the opposite direction to that predicted by Le Chatelier's principle, can be significant. This work gives a molecular level proof of Le Chatelier’s principle for the case of a temperature change. Moreover, a new, exact mathematical expression is derived that is valid for arbitrary system sizes and gives the relative probability that a single experiment will proceed in the endothermic or exothermic direction, in terms of a microscopic phase function. We show that the average of the time integral of this function is the maximum possible value of the purely irreversible entropy production for the thermal relaxation process. Our result is tested against computer simulations of the unfolding of a polypeptide. We prove that any equilibrium reaction mixture on average responds to a temperature increase by shifting its point of equilibrium in the endothermic direction.
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87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
82.60.-s Chemical thermodynamics
82.30.Qt Isomerization and rearrangement
87.14.ef Peptides

Analytical energy gradient for reference interaction site model self-consistent field explicitly including spatial electron density distribution

Daisuke Yokogawa, Hirofumi Sato, and Shigeyoshi Sakaki

J. Chem. Phys. 131, 214504 (2009); http://dx.doi.org/10.1063/1.3265856 (6 pages) | Cited 5 times

Online Publication Date: 3 December 2009

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Analytical energy gradient formula was derived for reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD). RISM-SCF-SEDD is a combination method of ab initio electronic structure theory and statistical mechanics for molecular liquids [ D. Yokogawa et al., J. Chem. Phys. 126, 244504 (2007) ]. As shown previously, RISM-SCF-SEDD is numerically stable and has expanded the applicability of the solvation theory. The energy gradient is an indispensable tool to compute molecular geometry and its implementation further extends the capability of RISM-SCF-SEDD. The present method was applied to chemical systems in aqueous solution; hydration structure and geometry of phosphate anion PO43− and tautomerization between 2-pyridone and 2-hydroxypyridine. Compared to available experimental data, the present method correctly reproduced the geometries and relative energies of solvated molecules with microscopic solvent distribution. It is clearly shown that highly sophisticated quantum chemical calculation such as coupled cluster with single and double and perturbative triple excitations coupled with solvation effect is a powerful tool to accurately evaluate molecular properties.
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61.20.Gy Theory and models of liquid structure
61.25.Em Molecular liquids
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
82.30.Nr Association, addition, insertion, cluster formation
82.30.Qt Isomerization and rearrangement

Hydrogen storage capacity of C60(OM)12 (M = Li and Na) clusters

Qi Peng, Gang Chen, Hiroshi Mizuseki, and Yoshiyuki Kawazoe

J. Chem. Phys. 131, 214505 (2009); http://dx.doi.org/10.1063/1.3268919 (8 pages) | Cited 9 times

Online Publication Date: 3 December 2009

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By using density functional theory, the hydrogen storage capacity of C60(OM)12 (M = Li and Na) clusters has been studied. The atomic charge transfer process has been analyzed to explain the reason why H2 molecules can be attracted. Through our calculation, we found that C60(OM)12 (M = Li and Na) possesses an adequate hydrogen binding energy which is suitable for practical storage usage at ambient temperature. When these clusters reach their maximum H2 uptake capacity, the mean hydrogen binding energy is 0.115 eV/H2 for C60(OLi)12⋅54H2 and 0.122 eV/H2 for C60(ONa)12⋅54H2 with the gravimetric hydrogen percentage of 9.78 and 8.33 wt %, respectively.
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88.30.rd Inorganic metal hydrides
68.43.Nr Desorption kinetics

Augmented stability of hydrogen clathrate hydrates by weakly polar molecules

Takato Nakayama, Kenichiro Koga, and Hideki Tanaka

J. Chem. Phys. 131, 214506 (2009); http://dx.doi.org/10.1063/1.3271341 (10 pages) | Cited 4 times

Online Publication Date: 4 December 2009

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Thermodynamic stability of hydrogen clathrate hydrates has been examined in a wide range of pressure based solely on the intermolecular interactions involved. We show that the stability is indeed augmented by a second guest species (here acetone) called a promoter, a consequence of which is notable reduction in the dissociation pressure of the hydrates encaging hydrogen alone. This evaluation is made by extension of the van der Waals–Platteeuw theory combined with semi-grand-canonical Monte Carlo (GCMC) simulations where the number of hydrogen molecules is allowed to vary while those of host water and promoter acetone molecules are fixed. The GCMC simulations then provide various types of cage occupancies of hydrogen from single to quadruple, from which the chemical potential of water in the clathrate hydrate is obtained as a function of the cage occupancy by acetone and the pressure. These occupancies are used to calculate the chemical potential of water in the clathrate hydrate. The stability is estimated by comparison of the chemical potential of water in the clathrate hydrate with that in hexagonal ice. We show the extent to which the dissociation pressure is reduced with increasing the occupancy of the larger cages by acetone.
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65.20.Jk Studies of thermodynamic properties of specific liquids
31.15.bt Statistical model calculations (including Thomas-Fermi and Thomas-Fermi-Dirac models)
33.15.Bh General molecular conformation and symmetry; stereochemistry
34.20.Gj Intermolecular and atom-molecule potentials and forces
61.20.Ja Computer simulation of liquid structure
61.25.Em Molecular liquids

The dynamic formation of low-dimensional inorganic nanotubes by filling carbon nanotubes

Mark Wilson

J. Chem. Phys. 131, 214507 (2009); http://dx.doi.org/10.1063/1.3268781 (10 pages) | Cited 3 times

Online Publication Date: 4 December 2009

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The filling of groups of carbon nanotubes (CNTs) by a generic molten salt of stoichiometry MX is observed using molecular dynamics computer simulation. The CNTs are grouped in terms of their diameters. The salt fills the CNTs to yield low-dimensional inorganic NT (INT) structures whose morphologies can be understood with reference to the folding of a sheet of percolating hexagons. The use of a relatively simple model to describe the interatomic interactions allows multiple filling events to be observed from the same pressure-temperature state point and so permits a rudimentary statistical analysis (often lacking in experimental investigation) of the formed INT morphologies in terms of fundamental CNT properties. The filling events are characterized in terms of the obtained INT morphologies. The thermodynamic and kinetic factors controlling the INT formation, including potential control over their morphology, are discussed. Kinetics (mechanistic) control is found to be significant compared with entropic effects. The role of the CNTs is discussed in terms of behavior as energy landscape filters. The results indicate that a complete morphological control over INTs formed in this fashion may be problematic even if the encasing CNT morphology can be strongly controlled.
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61.46.Fg Nanotubes
61.66.Bi Elemental solids
61.66.Dk Alloys
65.40.gd Entropy

Mechanism of alkane dehydrogenation catalyzed by acidic zeolites: Ab initio transition path sampling

Tomáš Bučko, Lubomir Benco, Orest Dubay, Christoph Dellago, and Jürgen Hafner

J. Chem. Phys. 131, 214508 (2009); http://dx.doi.org/10.1063/1.3265715 (11 pages) | Cited 9 times

Online Publication Date: 4 December 2009

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The dehydrogenation of propane over acidic chabazite has been studied using ab initio density-functional simulations in combination with static transition-state searches and dynamic transition path sampling (TPS) methods at elevated temperatures. The acidic zeolite has been modeled both using a small cluster and a large periodic model consisting of two unit cells, the TPS simulations allow to account for the effect of temperature and entropy. In agreement with experimental observations we find propene as the dominant reaction product and that the barrier for the dehydrogenation of a methyl group is higher than that for a methylene group. However, whereas all studies based on small cluster models (including the present one) conclude that the reaction proceeds via the formation of an alkoxy intermediate, our TPS studies based on a large periodic model lead to the conclusion that propene formation occurs via the formation of various forms of propyl cations stabilized by entropy, while the formation of an alkoxy species is a relatively rare event. It was observed only in 15% of the reactive trajectories for methyl dehydrogenation and even in only 8% of the methylene dehydrogenation reactions. Our studies demonstrate the importance of entropic effects and the need to account for the structure and flexibility of the zeolitic framework by using large periodic models.
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82.75.Qt Mechanism and kinetics of catalysis in zeolites (measurements or simulations)
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.15.Pd Molecular dynamics calculations (Car-Parrinello) and other numerical simulations
65.40.gd Entropy
82.33.Jx Reactions in zeolites

Rounded stretched exponential for time relaxation functions

J. G. Powles, D. M. Heyes, G. Rickayzen, and W. A. B. Evans

J. Chem. Phys. 131, 214509 (2009); http://dx.doi.org/10.1063/1.3268702 (8 pages) | Cited 2 times

Online Publication Date: 7 December 2009

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A rounded stretched exponential function is introduced, C(t) = exp{(τ0/τE)β[1−(1+(t/τ0)2)β/2]}, where t is time, and τ0 and τE are two relaxation times. This expression can be used to represent the relaxation function of many real dynamical processes, as at long times, t⪢τ0, the function converges to a stretched exponential with normalizing relaxation time, τE, yet its expansion is even or symmetric in time, which is a statistical mechanical requirement. This expression fits well the shear stress relaxation function for model soft soft-sphere fluids near coexistence, with τE⪡τ0. The function gives the correct limits at low and high frequency in Cole–Cole plots for dielectric and shear stress relaxation (both the modulus and viscosity forms). It is shown that both the dielectric spectra and dynamic shear modulus imaginary parts approach the real axis with a slope equal to 0 at high frequency, whereas the dynamic viscosity has an infinite slope in the same limit. This indicates that inertial effects at high frequency are best discerned in the modulus rather than the viscosity Cole–Cole plot. As a consequence of the even expansion in time of the shear stress relaxation function, the value of the storage modulus derived from it at very high frequency exceeds that in the infinite frequency limit (i.e., G∞).
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61.20.Gy Theory and models of liquid structure
77.22.Gm Dielectric loss and relaxation
62.10.+s Mechanical properties of liquids
66.20.-d Viscosity of liquids; diffusive momentum transport
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