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7 Oct 2011

Volume 135, Issue 13, Articles (13xxxx)

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J. Chem. Phys. 135, 135101 (2011); http://dx.doi.org/10.1063/1.3634004 (15 pages)

Sudipta Kumar Sinha and Sanjoy Bandyopadhyay
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Communication: Rigorous calculation of dissociation energies (D0) of the water trimer, (H2O)3 and (D2O)3

Yimin Wang and Joel M. Bowman

J. Chem. Phys. 135, 131101 (2011); http://dx.doi.org/10.1063/1.3647584 (3 pages)

Online Publication Date: 3 October 2011

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Using a recent, full-dimensional, ab initio potential energy surface [Y. Wang, X. Huang, B. C. Shepler, B. J. Braams, and J. M. Bowman, J. Chem. Phys. 134, 094509 (2011)]10.1063/1.3554905 together with rigorous diffusion Monte Carlo calculations of the zero-point energy of the water trimer, we report dissociation energies, D0, to form one monomer plus the water dimer and three monomers. The calculations make use of essentially exact zero-point energies for the water trimer, dimer, and monomer, and benchmark values of the electronic dissociation energies, De, of the water trimer [J. A. Anderson, K. Crager, L. Fedoroff, and G. S. Tschumper, J. Chem. Phys. 121, 11023 (2004)]10.1063/1.1799931. The D0 results are 3855 and 2726 cm−1 for the 3H2O and H2O + (H2O)2 dissociation channels, respectively, and 4206 and 2947 cm−1 for 3D2O and D2O + (D2O)2 dissociation channels, respectively. The results have estimated uncertainties of 20 and 30 cm−1 for the monomer plus dimer and three monomer of dissociation channels, respectively.
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36.40.Jn Reactivity of clusters
31.15.A- Ab initio calculations
31.50.-x Potential energy surfaces
33.15.Fm Bond strengths, dissociation energies
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
34.50.-s Scattering of atoms and molecules
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Communication: Broken-ergodicity and the emergence of solid behaviour in amorphous materials

Stephen R. Williams

J. Chem. Phys. 135, 131102 (2011); http://dx.doi.org/10.1063/1.3650323 (4 pages) | Cited 1 time

Online Publication Date: 4 October 2011

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Using a combination of theory and molecular dynamics simulations, we show how solid behaviour emerges in amorphous materials from microscopic considerations. The effect on the systems response to a sudden change in strain, upon entering the history dependent glass state, is focused on. An important symmetry that is always present in a fluid state, is shown to be broken for a simulated history dependent amorphous solid. Details of how this applies to a single sample and an ensemble of independent samples are discussed, along with the dependence on the time scale the system is monitored on.
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61.43.Bn Structural modeling: serial-addition models, computer simulation
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Communication: Convergence of anharmonic infrared intensities of hydrogen fluoride in traditional and explicitly correlated coupled cluster calculations

Kalju Kahn, Bernard Kirtman, Alexander Hagen, and Jozef Noga

J. Chem. Phys. 135, 131103 (2011); http://dx.doi.org/10.1063/1.3647566 (4 pages)

Online Publication Date: 6 October 2011

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It is shown that the convergence of anharmonic infrared spectral intensities with respect to the basis set size is much enhanced in explicitly correlated calculations as compared to traditional configuration interaction type wave function expansion. Explicitly correlated coupled cluster (CC) calculations using Slater-type geminal correlation factor (CC-F12) yield well-converged dipole derivatives and vibrational intensities for hydrogen fluoride with basis set involving f functions on the heavy atom. Combination of CC-F12 with singles, doubles, and non-iterative triples (CCSD(T)-F12) with small corrections due to quadruple excitations, core-electron correlation, and relativistic effects yields vibrational line positions, dipole moments, and transition dipole matrix elements in good agreement with the best experimental values.
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33.70.Fd Absolute and relative line and band intensities
33.20.Tp Vibrational analysis
33.20.Ea Infrared spectra
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
31.15.vn Electron correlation calculations for diatomic molecules
31.15.bw Coupled-cluster theory
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Communication: Effects of stress on the tube confinement potential and dynamics of topologically entangled rod fluids

Daniel M. Sussman and Kenneth S. Schweizer

J. Chem. Phys. 135, 131104 (2011); http://dx.doi.org/10.1063/1.3651143 (4 pages)

Online Publication Date: 7 October 2011

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A microscopic theory for the effect of applied stress on the transverse topological confinement potential and slow dynamics of heavily entangled rigid rods is presented. The confining entanglement force localizing a polymer in a tube is predicted to have a finite strength. As a consequence, three regimes of terminal relaxation behavior are predicted with increasing stress: accelerated reptation due to tube widening (dilation), relaxation via deformation-assisted activated transverse barrier hopping, and complete destruction of the lateral tube constraints corresponding to microscopic yielding or a disentanglement transition.
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62.10.+s Mechanical properties of liquids
61.25.hk Polymer melts and blends
47.57.Ng Polymers and polymer solutions
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Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β-, and γ-glycine

Nathan Duff and Baron Peters

J. Chem. Phys. 135, 134101 (2011); http://dx.doi.org/10.1063/1.3638268 (10 pages)

Online Publication Date: 3 October 2011

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Crystal nucleation is important for many processes including pharmaceutical crystallization, biomineralization, and material synthesis. The progression of structural changes which occur during crystal nucleation are often described using order parameters. Polymorph specific order parameters have been developed for crystallization of spherically symmetric particles; however, polymorph specific order parameters for molecular crystals remain a challenge. We introduce template based polymorph specific order parameters for molecular crystals. For each molecule in a simulation, we compute the root mean squared deviation (RMSD) between the local environment around the molecule and a template of the perfect crystal structure for each polymorph. The RMSD order parameters can clearly distinguish the α-, β-, and γ-glycine polymorph crystal structures in the bulk crystal and also in solvated crystallites. Surface melting of glycine crystallites in supersaturated aqueous solution is explored using the newly developed order parameters. The solvated α-glycine crystallite has a thinner surface melted layer than the γ-glycine crystallite. α-glycine forms first out of aqueous solution, so surface melted layer thickness may provide insight into interfacial energy and polymorph selection.
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87.15.nt Crystallization
87.15.R- Reactions and kinetics
87.15.B- Structure of biomolecules

Van der Waals interactions: Evaluations by use of a statistical mechanical method

Johan S. Høye

J. Chem. Phys. 135, 134102 (2011); http://dx.doi.org/10.1063/1.3643339 (10 pages)

Online Publication Date: 3 October 2011

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In this work the induced van der Waals interaction between a pair of neutral atoms or molecules is considered by use of a statistical mechanical method. With use of the Schrödinger equation this interaction can be obtained by standard quantum mechanical perturbation theory to second order. However, the latter is restricted to electrostatic interactions between dipole moments. So with radiating dipole-dipole interaction where retardation effects are important for large separations of the particles, other methods are needed, and the resulting induced interaction is the Casimir-Polder interaction usually obtained by field theory. It can also be evaluated, however, by a statistical mechanical method that utilizes the path integral representation. We here show explicitly by use of this method the equivalence of the Casimir-Polder interaction and the van der Waals interaction based upon the Schrödinger equation. The equivalence is to leading order for short separations where retardation effects can be neglected. In recent works [J. S. Høye, Physica A 389, 1380 (2010)10.1016/j.physa.2009.12.003; Phys. Rev. E 81, 061114 (2010)]10.1103/PhysRevE.81.061114, the Casimir-Polder or Casimir energy was added as a correction to calculations of systems like the electron clouds of molecules. The equivalence to van der Waals interactions indicates that the added Casimir energy will improve the accuracy of calculated molecular energies. Thus, we give numerical estimates of this energy including analysis and estimates for the uniform electron gas.
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34.20.Cf Interatomic potentials and forces
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
02.50.Fz Stochastic analysis
31.15.xp Perturbation theory
31.15.bt Statistical model calculations (including Thomas-Fermi and Thomas-Fermi-Dirac models)
31.15.xk Path-integral methods

A discrete interaction model/quantum mechanical method to describe the interaction of metal nanoparticles and molecular absorption

Seth Michael Morton and Lasse Jensen

J. Chem. Phys. 135, 134103 (2011); http://dx.doi.org/10.1063/1.3643381 (12 pages)

Online Publication Date: 3 October 2011

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A frequency-dependent quantum mechanics/molecular mechanics method for the calculation of response properties of molecules adsorbed on metal nanoparticles is presented. This discrete interaction model/quantum mechanics (DIM/QM) method represents the nanoparticle atomistically, thus accounting for the local environment of the nanoparticle surface on the optical properties of the adsorbed molecule. Using the DIM/QM method, we investigate the coupling between the absorption of a silver nanoparticle and of a substituted naphthoquinone. This system is chosen since it shows strong coupling due to a molecular absorption peak that overlaps with the plasmon excitation in the metal nanoparticle. We show that there is a strong dependence not only on the distance of the molecule from the metal nanoparticle but also on its orientation relative to the nanoparticle. We find that when the transition dipole moment of an excitation is oriented towards the nanoparticle there is a significant increase in the molecular absorption as a result of coupling to the metal nanoparticle. In contrast, we find that the molecular absorption is decreased when the transition dipole moment is oriented parallel to the metal nanoparticle. The coupling between the molecule and the metal nanoparticle is found to be surprisingly long range and important on a length scale comparable to the size of the metal nanoparticle. A simple analytical model that describes the molecule and the metal nanoparticle as two interacting point objects is found to be in excellent agreement with the full DIM/QM calculations over the entire range studied. The results presented here are important for understanding plasmon–exciton hybridization, plasmon enhanced photochemistry, and single-molecule surface-enhanced Raman scattering.
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68.43.Mn Adsorption kinetics
61.46.Df Structure of nanocrystals and nanoparticles ("colloidal" quantum dots but not gate-isolated embedded quantum dots)
71.35.-y Excitons and related phenomena
82.37.Vb Single molecule photochemistry
78.30.Hv Other nonmetallic inorganics

Density functional theory calculations of dynamic first hyperpolarizabilities for organic molecules in organic solvent: Comparison to experiment

Shih-I Lu, Cheng-Chang Chiu, and Ying-Fung Wang

J. Chem. Phys. 135, 134104 (2011); http://dx.doi.org/10.1063/1.3644336 (7 pages)

Online Publication Date: 3 October 2011

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Against experimental values obtained from solution-phase dc electric field induced second-harmonic generation measurements at a fundamental wavelength of 1910 nm, the performance of 20 exchange-correlation functionals in density functional theory in evaluation of solvent modulated dynamic first hyperpolarizabilities of 82 organic molecules in chloroform, 1,4-dioxane, and/or dichloromethane was evaluated. The used exchange-correlation functionals consisted of generalized gradient approximation (GGA), meta-GGA, global hybrids, and range-separated hybrids. The PCM-X/6-311+G(2d,p)//PCM-B3LYP/6-31G(2df,p) level of theory was employed. The calculated results showed functionals with the exact asymptote of the exchange potential gave satisfying linear correlation with R2 of 0.95 between experimental data and theoretical values. With a linear correction, these functionals also provided a better accuracy with mean absolute error of 5 × 10−30 esu than other functionals. The solvent effect and solvation scheme on the calculated property were also studied.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
42.65.Ky Frequency conversion; harmonic generation, including higher-order harmonic generation

Polarizability and alignment of dielectric nanoparticles in an external electric field: Bowls, dumbbells, and cuboids

Bas W. Kwaadgras, Maarten Verdult, Marjolein Dijkstra, and René van Roij

J. Chem. Phys. 135, 134105 (2011); http://dx.doi.org/10.1063/1.3637046 (15 pages) | Cited 2 times

Online Publication Date: 3 October 2011

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We employ the coupled dipole method to calculate the polarizability tensor of various anisotropic dielectric clusters of polarizable atoms, such as cuboid-, bowl-, and dumbbell-shaped nanoparticles. Starting from a Hamiltonian of a many-atom system, we investigate how this tensor depends on the size and shape of the cluster. We use the polarizability tensor to calculate the energy difference associated with turning a nanocluster from its least to its most favorable orientation in a homogeneous static electric field, and we determine the cluster dimension for which this energy difference exceeds the thermal energy such that particle alignment by the field is possible. Finally, we study in detail the (local) polarizability of a cubic-shaped cluster and present results indicating that, when retardation is ignored, a bulk polarizability cannot be reached by scaling up the system.
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61.46.Df Structure of nanocrystals and nanoparticles ("colloidal" quantum dots but not gate-isolated embedded quantum dots)
82.70.Dd Colloids

Monte Carlo simulation of osmotic equilibria

Sebastian Schreiber and Reinhard Hentschke

J. Chem. Phys. 135, 134106 (2011); http://dx.doi.org/10.1063/1.3644766 (4 pages)

Online Publication Date: 3 October 2011

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We present a Metropolis Monte Carlo simulation algorithm for the Tpπ-ensemble, where T is the temperature, p is the overall external pressure, and π is the osmotic pressure across the membrane. The algorithm, which can be applied to small molecules or sorption of small molecules in polymer networks, is tested for the case of Lennard-Jones interactions.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.bt Statistical model calculations (including Thomas-Fermi and Thomas-Fermi-Dirac models)

An efficient linear scaling procedure for constructing localized orbitals of large molecules based on the one-particle density matrix

Yang Guo, Wei Li, and Shuhua Li

J. Chem. Phys. 135, 134107 (2011); http://dx.doi.org/10.1063/1.3644893 (7 pages)

Online Publication Date: 3 October 2011

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We have developed a linear-scaling algorithm for obtaining the Boys localized molecular orbitals from the one-particle density matrix. The algorithm is made up of two steps: the Cholesky decomposition of the density matrix to obtain Cholesky molecular orbitals and the subsequent Boys localization process. Linear-scaling algorithms have been proposed to achieve linear-scaling calculations of these two steps, based on the sparse matrix technique and the locality of the Cholesky molecular orbitals. The present algorithm has been applied to compute the Boys localized orbitals in a number of systems including α-helix peptides, water clusters, and protein molecules. Illustrative calculations demonstrate that the computational time of obtaining Boys localized orbitals with the present algorithm is asymptotically linear with increasing the system size.
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31.15.-p Calculations and mathematical techniques in atomic and molecular physics

Size-extensive vibrational self-consistent field method

Murat Keçeli and So Hirata

J. Chem. Phys. 135, 134108 (2011); http://dx.doi.org/10.1063/1.3644895 (11 pages)

Online Publication Date: 3 October 2011

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The vibrational self-consistent field (VSCF) method is a mean-field approach to solve the vibrational Schrödinger equation and serves as a basis of vibrational perturbation and coupled-cluster methods. Together they account for anharmonic effects on vibrational transition frequencies and vibrationally averaged properties. This article reports the definition, programmable equations, and corresponding initial implementation of a diagrammatically size-extensive modification of VSCF, from which numerous terms with nonphysical size dependence in the original VSCF equations have been eliminated. When combined with a quartic force field (QFF), this compact and strictly size-extensive VSCF (XVSCF) method requires only quartic force constants of the ∂4V/∂Qi2∂Qj2 type, where V is the electronic energy and Qi is the ith normal coordinate. Consequently, the cost of a XVSCF calculation with a QFF increases only quadratically with the number of modes, while that of a VSCF calculation grows quartically. The effective (mean-field) potential of XVSCF felt by each mode is shown to be harmonic, making the XVSCF equations subject to a self-consistent analytical solution without matrix diagonalization or a basis-set expansion, which are necessary in VSCF. Even when the same set of force constants is used, XVSCF is nearly three orders of magnitude faster than VSCF implemented similarly. Yet, the results of XVSCF and VSCF are shown to approach each other as the molecular size is increased, implicating the inclusion of unnecessary, nonphysical terms in VSCF. The diagrams of the XVSCF energy expression and their evaluation rules are also proposed, underscoring their connected structures.
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31.15.xr Self-consistent-field methods
33.20.Tp Vibrational analysis
31.15.xp Perturbation theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.bw Coupled-cluster theory
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Correction factors for boundary diffusion in reaction-diffusion master equations

Andre Leier and Tatiana T. Marquez-Lago

J. Chem. Phys. 135, 134109 (2011); http://dx.doi.org/10.1063/1.3634003 (11 pages)

Online Publication Date: 3 October 2011

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The reaction-diffusion master equation (RDME) has been widely used to model stochastic chemical kinetics in space and time. In recent years, RDME-based trajectorial approaches have become increasingly popular. They have been shown to capture spatial detail at moderate computational costs, as compared to fully resolved particle-based methods. However, finding an appropriate choice for the discretization length scale is essential for building a reasonable RDME model. Moreover, it has been recently shown [R. Erban and S. J. Chapman, Phys. Biol. 4, 16 (2007)10.1088/1478-3975/4/1/003 ; R. Erban and S. J. Chapman, Phys. Biol. 6, 46001 (2009)10.1088/1478-3975/6/4/046001 ; D. Fange, O. G. Berg, P. Sjöberg, and J. Elf, Proc. Natl. Acad. Sci. U.S.A. 107, 46 (2010)] that the reaction rates commonly used in RDMEs have to be carefully reassessed when considering reactive boundary conditions or binary reactions, in order to avoid inaccurate – and possibly unphysical – results. In this paper, we present an alternative approach for deriving correction factors in RDME models with reactive or semi-permeable boundaries. Such a correction factor is obtained by solving a closed set of equations based on the moments at steady state, as opposed to modifying probabilities for absorption or reflection. Lastly, we briefly discuss existing correction mechanisms for bimolecular reaction rates both in the limit of fast and slow diffusion, and argue why our method could also be applied for such purpose.
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82.20.Uv Stochastic theories of rate constants
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Fd Collision theories; trajectory models

Charge carrier dynamics in phonon-induced fluctuation systems from time-dependent wavepacket diffusion approach

Xinxin Zhong and Yi Zhao

J. Chem. Phys. 135, 134110 (2011); http://dx.doi.org/10.1063/1.3644965 (10 pages)

Online Publication Date: 4 October 2011

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A time-dependent wavepacket diffusion method is proposed to deal with charge transport in organic crystals. The electron-phonon interactions in both site energies and electronic couplings are incorporated by the time-dependent fluctuations which are generated from the corresponding spectral density functions. The numerical demonstrations reveal that the present approach predicts the consistent charge carrier dynamics with the rigorous quantum approaches. In addition, the diffusion coefficients obtained from the Marcus formula are well reproduced at the weak electronic coupling and high temperature limits. It is also found that the charge mobility feature of the crossover from the band-like to the hopping-type cannot be predicted from the fluctuations induced by the linear electron-phonon interactions with an Ohmic spectral density; however, it indeed appears as the electronic coupling fluctuation exponentially depends on the nuclear coordinates. Finally, it should be noted that although the present approach neglects the imaginary fluctuation, it essentially incorporates the coherent motion of the charge carrier and quantum effect of the phonon motion with a broad regime of the fluctuations for symmetric systems. Besides, the approach can easily be applied to systems having thousands of sites, which allows one to investigate charge transport in nanoscale organic crystals.
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66.30.-h Diffusion in solids
05.60.-k Transport processes
63.22.-m Phonons or vibrational states in low-dimensional structures and nanoscale materials
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion

An infinite swapping approach to the rare-event sampling problem

Nuria Plattner, J. D. Doll, Paul Dupuis, Hui Wang, Yufei Liu, and J. E. Gubernatis

J. Chem. Phys. 135, 134111 (2011); http://dx.doi.org/10.1063/1.3643325 (14 pages) | Cited 1 time

Online Publication Date: 5 October 2011

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We describe a new approach to the rare-event Monte Carlo sampling problem. This technique utilizes a symmetrization strategy to create probability distributions that are more highly connected and, thus, more easily sampled than their original, potentially sparse counterparts. After discussing the formal outline of the approach and devising techniques for its practical implementation, we illustrate the utility of the technique with a series of numerical applications to Lennard-Jones clusters of varying complexity and rare-event character.
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34.20.Cf Interatomic potentials and forces
02.50.Cw Probability theory
02.50.Ng Distribution theory and Monte Carlo studies

Zero-variance zero-bias quantum Monte Carlo estimators for the electron density at a nucleus

Manolo C. Per, Ian K. Snook, and Salvy P. Russo

J. Chem. Phys. 135, 134112 (2011); http://dx.doi.org/10.1063/1.3644964 (7 pages)

Online Publication Date: 6 October 2011

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We derive new quantum Monte Carlo (QMC) estimators for the electronic density at the position of a point nucleus using the zero-variance and zero-bias principles. The resulting estimators are highly efficient, and are significantly simpler to implement and use than alternative methods, as they contain no adjustable parameters. In addition, they can be used in both variational and diffusion QMC calculations. Our best estimator is used to calculate the most accurate available estimates of the total electron density at the nucleus for the first-row atoms Li-Ne, the Ar atom, and the diatomic molecules B2, N2, and F2.
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31.15.xt Variational techniques
02.70.Uu Applications of Monte Carlo methods

Linking the historical and chemical definitions of diabatic states for charge and excitation energy transfer reactions in condensed phase

Michele Pavanello and Johannes Neugebauer

J. Chem. Phys. 135, 134113 (2011); http://dx.doi.org/10.1063/1.3645181 (6 pages)

Online Publication Date: 6 October 2011

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Marcus theory of electron transfer (ET) and Förster theory of excitation energy transfer (EET) rely on the Condon approximation and the theoretical availability of initial and final states of ET and EET reactions, often called diabatic states. Recently [Subotnik et al., J. Chem. Phys. 130, 234102 (2009)10.1063/1.3148777], diabatic states for practical calculations of ET and EET reactions were defined in terms of their interactions with the surrounding environment. However, from a purely theoretical standpoint, the definition of diabatic states must arise from the minimization of the dynamic couplings between the trial diabatic states. In this work, we show that if the Condon approximation is valid, then a minimization of the derived dynamic couplings leads to corresponding diabatic states for ET reactions taking place in solution by diagonalization of the dipole moment matrix, which is equivalent to a Boys localization algorithm; while for EET reactions in solution, diabatic states are found through the Edmiston–Ruedenberg localization algorithm. In the derivation, we find interesting expressions for the environmental contribution to the dynamic coupling of the adiabatic states in condensed-phase processes. In one of the cases considered, we find that such a contribution is trivially evaluable as a scalar product of the transition dipole moment with a quantity directly derivable from the geometry arrangement of the nuclei in the molecular environment. Possibly, this has applications in the evaluation of dynamic couplings for large scale simulations.
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82.20.Db Transition state theory and statistical theories of rate constants
71.23.An Theories and models; localized states

Gauge-origin independent calculations of Jones birefringence

Dmitry Shcherbin, Andreas J. Thorvaldsen, Dan Jonsson, and Kenneth Ruud

J. Chem. Phys. 135, 134114 (2011); http://dx.doi.org/10.1063/1.3645182 (10 pages)

Online Publication Date: 6 October 2011

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We present the first gauge-origin independent formulation of Jones birefringence at the Hartree–Fock level of theory. Gauge-origin independence is achieved through the use of London atomic orbitals. The implementation is based on a recently proposed atomic orbital-based response theory formulation that allows for the use of both time- and perturbation-dependent basis sets [Thorvaldsen, Ruud, Kristensen, Jørgensen, and Coriani, J. Chem. Phys. 129, 214108 (2008)]. We present the detailed expressions for the response functions entering the Jones birefringence when London atomic orbitals are used. The implementation is tested on a set of polar and dipolar molecules at the Hartree–Fock level of theory. It is demonstrated that London orbitals lead to much improved basis-set convergence, and that the use of small, conventional basis sets may lead to the wrong sign for the calculated birefringence. For large basis sets, London orbitals and conventional basis sets converge to the same results.
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31.15.xr Self-consistent-field methods
31.15.xp Perturbation theory
32.30.-r Atomic spectra

Doubled heterogeneous crystal nucleation in sediments of hard sphere binary-mass mixtures

Hartmut Löwen and Elshad Allahyarov

J. Chem. Phys. 135, 134115 (2011); http://dx.doi.org/10.1063/1.3646212 (9 pages)

Online Publication Date: 6 October 2011

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Crystallization during the sedimentation process of a binary colloidal hard spheres mixture is explored by Brownian dynamics computer simulations. The two species are different in buoyant mass but have the same interaction diameter. Starting from a completely mixed system in a finite container, gravity is suddenly turned on, and the crystallization process in the sample is monitored. If the Peclet numbers of the two species are both not too large, crystalline layers are formed at the bottom of the cell. The composition of lighter particles in the sedimented crystal is non-monotonic in the altitude: it is first increasing, then decreasing, and then increasing again. If one Peclet number is large and the other is small, we observe the occurrence of a doubled heterogeneous crystal nucleation process. First, crystalline layers are formed at the bottom container wall which are separated from an amorphous sediment. At the amorphous-fluid interface, a secondary crystal nucleation of layers is identified. This doubled heterogeneous nucleation can be verified in real-space experiments on colloidal mixtures.
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64.60.qe General theory and computer simulations of nucleation
64.75.Cd Phase equilibria of fluid mixtures, including gases, hydrates, etc.
82.70.Dd Colloids

Mesoscale hydrodynamic modeling of a colloid in shear-thinning viscoelastic fluids under shear flow

Shichen Ji, Run Jiang, Roland G. Winkler, and Gerhard Gompper

J. Chem. Phys. 135, 134116 (2011); http://dx.doi.org/10.1063/1.3646307 (11 pages)

Online Publication Date: 6 October 2011

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In order to study the dynamics of colloidal suspensions with viscoelastic solvents, a simple mesoscopic model of the solvent is required. We propose to extend the multiparticle collision dynamics (MPC) technique—a particle-based simulation method, which has been successfully applied to study the hydrodynamic behavior of many complex fluids with Newtonian solvent—to shear-thinning viscoelastic solvents. Here, the normal MPC particles are replaced by dumbbells with finite-extensible nonlinear elastic (FENE) springs. We have studied the properties of FENE-dumbbell fluids under simple shear flow with shear rate math. The stress tensor is calculated, and the viscosity η and the first normal-stress coefficient Ψ1 are obtained. Shear-thinning behavior is found for reduced shear rates Γ = mathτ>1, where τ is a characteristic dumbbell relaxation time. Here, both η and Ψ1 display power-law behavior in the shear-thinning regime. Thus, the FENE-dumbbell fluid with MPC collisions provides a good description of viscoelastic fluids. As a first application, we study the flow behavior of a colloid in a shear-thinning viscoelastic fluid in two dimensions. A slowing down of the colloid rotation in a viscoelastic fluid compared to a Newtonian fluid is obtained, in agreement with recent numerical calculations and experimental results.
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47.50.Cd Modeling
46.35.+z Viscoelasticity, plasticity, viscoplasticity
82.70.Kj Emulsions and suspensions
02.60.-x Numerical approximation and analysis
82.70.Dd Colloids

Electronic structures of low-lying Bu excited states in trans-oligoenes: Pariser-Parr-Pople and ab initio calculations

Dawei Zhang and Chungen Liu

J. Chem. Phys. 135, 134117 (2011); http://dx.doi.org/10.1063/1.3643838 (9 pages) | Cited 2 times

Online Publication Date: 6 October 2011

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Two lowest-lying excited singlets with Bu symmetry of all-trans-oligoenes, the well-known ionic 11Bu+ state as well as the “hidden” ionic-covalent-mixed 11Bu− state, are calculated within both the Pariser-Parr-Pople (PPP) model at full configuration interaction (FCI) level and ab initio methods. The vertical excitation energies as well as wavefunctions from PPP-FCI calculations are found to be in good agreement with those from high-level multi-reference methods, such as multi-reference complete active space self-consistent field (CASSCF) with second order perturbative corrections (CASPT2), multi-reference Møller-Plesset perturbation theory (MRMP), and complete active space valence bond theory (CASVB). The oscillator strengths from PPP calculation are in good agreement with spectroscopy experiments. The relatively small oscillator strength of 11Bu− is due to the approximate electron-hole symmetry of this state. In addition, the bond lengths in both states are found to show remarkable relativity with the bond orders calculated with ground state geometries, which suggests a possible strategy for initial guess in geometry optimization of excited states.
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31.15.ae Electronic structure and bonding characteristics
31.15.bu Semi-empirical and empirical calculations (differential overlap, Hückel, PPP methods, etc.)
31.15.vq Electron correlation calculations for polyatomic molecules
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Dj Interatomic distances and angles
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors

On basis set superposition error corrected stabilization energies for large n-body clusters

Katarzyna Walczak, Joachim Friedrich, and Michael Dolg

J. Chem. Phys. 135, 134118 (2011); http://dx.doi.org/10.1063/1.3644961 (11 pages)

Online Publication Date: 7 October 2011

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In this contribution, we propose an approximate basis set superposition error (BSSE) correction scheme for the site-site function counterpoise and for the Valiron-Mayer function counterpoise correction of second order to account for the basis set superposition error in clusters with a large number of subunits. The accuracy of the proposed scheme has been investigated for a water cluster series at the CCSD(T), CCSD, MP2, and self-consistent field levels of theory using Dunning's correlation consistent basis sets. The BSSE corrected stabilization energies for a series of water clusters are presented. A study regarding the possible savings with respect to computational resources has been carried out as well as a monitoring of the basis set dependence of the approximate BSSE corrections.
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36.40.Mr Spectroscopy and geometrical structure of clusters
31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory
31.15.xr Self-consistent-field methods

Phase diagram of the uniaxial and biaxial soft–core Gay–Berne model

Roberto Berardi, Juho S. Lintuvuori, Mark R. Wilson, and Claudio Zannoni

J. Chem. Phys. 135, 134119 (2011); http://dx.doi.org/10.1063/1.3646310 (10 pages) | Cited 1 time

Online Publication Date: 7 October 2011

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Classical molecular dynamics simulations have been used to explore the phase diagrams for a family of attractive–repulsive soft–core Gay–Berne models [R. Berardi, C. Zannoni, J. S. Lintuvuori, and M. R. Wilson, J. Chem. Phys. 131, 174107 (2009)] and determine the effect of particle softness, i.e., of a moderately repulsive short–range interaction, on the order parameters and phase behaviour of model systems of uniaxial and biaxial ellipsoidal particles. We have found that isotropic, uniaxial, and biaxial nematic and smectic phases are obtained for the model. Extensive calculations of the nematic region of the phase diagram show that endowing mesogenic particles with such soft repulsive interactions affect the stability range of the nematic phases, and in the case of phase biaxiality it also shifts it to lower temperatures. For colloidal particles, stabilised by surface functionalisation, (e.g., with polymer chains), we suggest that it should be possible to tune liquid crystal behaviour to increase the range of stability of uniaxial and biaxial phases (by varying solvent quality). We calculate second virial coefficients and show that they are a useful means of characterising the change in effective softness for such systems. For thermotropic liquid crystals, the introduction of softness in the interactions between mesogens with overall biaxial shape (e.g., through appropriate conformational flexibility) could provide a pathway for the actual chemical synthesis of stable room–temperature biaxial nematics.
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81.30.Dz Phase diagrams of other materials
61.30.Vx Polymer liquid crystals
64.30.Jk Equations of state of nonmetals
61.20.Ja Computer simulation of liquid structure
82.70.Dd Colloids

A new parametrizable model of molecular electronic structure

Dimitri N. Laikov

J. Chem. Phys. 135, 134120 (2011); http://dx.doi.org/10.1063/1.3646498 (10 pages)

Online Publication Date: 7 October 2011

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A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the parametrization procedure – making a direct link to the correlated wavefunction theory. The model has been trained for 15 elements (H, Li–F, Na–Cl, 720 parameters) on a set of 5581 molecules (including ions, transition states, and weakly bound complexes) whose first- and second-order properties were computed by the coupled-cluster theory as a reference, and a good agreement is seen. The model looks promising for the study of large molecular systems, it is believed to be an important step forward from the traditional semiempirical models towards higher accuracy at nearly as low a computational cost.
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31.15.bw Coupled-cluster theory
31.15.xr Self-consistent-field methods
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
31.15.xt Variational techniques
34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.xp Perturbation theory

A general and efficient Monte Carlo method for sampling intramolecular degrees of freedom of branched and cyclic molecules

Jindal K. Shah and Edward J. Maginn

J. Chem. Phys. 135, 134121 (2011); http://dx.doi.org/10.1063/1.3644939 (11 pages)

Online Publication Date: 7 October 2011

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A simple and easily implemented Monte Carlo algorithm is described which enables configurational-bias sampling of molecules containing branch points and rings with endocyclic and exocyclic atoms. The method overcomes well-known problems associated with sequential configurational-bias sampling methods. A “reservoir” or “library” of fragments are generated with known probability distributions dependent on stiff intramolecular degrees of freedom. Configurational-bias moves assemble the fragments into whole molecules using the energy associated with the remaining degrees of freedom. The methods for generating the fragments are validated on models of propane, isobutane, neopentane, cyclohexane, and methylcyclohexane. It is shown how the sampling method is implemented in the Gibbs ensemble, and validation studies are performed in which the liquid coexistence curves of propane, isobutane, and 2,2-dimethylhexane are computed and shown to agree with accepted values. The method is general and can be used to sample conformational space for molecules of arbitrary complexity in both open and closed statistical mechanical ensembles.
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33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.15.Bh General molecular conformation and symmetry; stereochemistry
61.20.Ja Computer simulation of liquid structure
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