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28 Oct 2009

Volume 131, Issue 16, Articles (16xxxx)

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J. Chem. Phys. 131, 164901 (2009); http://dx.doi.org/10.1063/1.3247191 (12 pages)

Tu C. Le, B. D. Todd, P. J. Daivis, and A. Uhlherr
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Composition and concentration anomalies for structure and dynamics of Gaussian-core mixtures

Mark J. Pond, William P. Krekelberg, Vincent K. Shen, Jeffrey R. Errington, and Thomas M. Truskett

J. Chem. Phys. 131, 161101 (2009); http://dx.doi.org/10.1063/1.3256235 (4 pages) | Cited 16 times

Online Publication Date: 22 October 2009

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We report molecular dynamics simulation results for two-component fluid mixtures of Gaussian-core particles, focusing on how tracer diffusivities and static pair correlations depend on temperature, particle concentration, and composition. At low particle concentrations, these systems behave like simple atomic mixtures. However, for intermediate concentrations, the single-particle dynamics of the two species largely decouple, giving rise to the following anomalous trends. Increasing either the concentration of the fluid (at fixed composition) or the mole fraction of the larger particles (at fixed particle concentration) enhances the tracer diffusivity of the larger particles but decreases that of the smaller particles. In fact, at sufficiently high particle concentrations, the larger particles exhibit higher mobility than the smaller particles. Each of these dynamic behaviors is accompanied by a corresponding structural trend that characterizes how either concentration or composition affects the strength of the static pair correlations. Specifically, the dynamic trends observed here are consistent with a single empirical scaling law that relates an appropriately normalized tracer diffusivity to its pair-correlation contribution to the excess entropy.
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61.20.Ja Computer simulation of liquid structure
65.20.-w Thermal properties of liquids
61.25.-f Studies of specific liquid structures
66.10.C- Diffusion and thermal diffusion
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Laboratory observation of the valence anion of cyanoacetylene, a possible precursor for negative ions in space

Daniel J. Goebbert, Dmitry Khuseynov, and Andrei Sanov

J. Chem. Phys. 131, 161102 (2009); http://dx.doi.org/10.1063/1.3257174 (3 pages) | Cited 2 times

Online Publication Date: 23 October 2009

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Valence anions of cyanoacetylene, HCCCN−, are synthesized by the 1,2-H2+ abstraction reaction of O− with acrylonitrile, H2C = CHCN, while the competing 1,1-H2+ channel of the same reaction yields the cyanovinylidene anions, CCHCN−. The key to the formation of the elusive, adiabatically weakly bound HCCCN− is the bent −math = math–C ≡ skeleton of the reactant. The photoelectron spectrum of HCCCN−, measured by means of photoelectron imaging at 532 nm, consists of a broad structureless band with a vertical detachment energy of 1.04±0.05 eV. The observed anions are stable counterparts of the low-lying anionic resonances of cyanoacetylene, which may contribute (by way of dissociative attachment) to the formation of carbon-rich and CN-containing negative ions in extraterrestrial environments.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
95.30.Ft Molecular and chemical processes and interactions
34.80.Ht Dissociation and dissociative attachment
33.60.+q Photoelectron spectra
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Hydrophobic effects on multivalent-salt-induced self-condensation of DNA

Tomonari Sumi, Chiaki Suzuki, and Hideo Sekino

J. Chem. Phys. 131, 161103 (2009); http://dx.doi.org/10.1063/1.3256982 (4 pages) | Cited 2 times

Online Publication Date: 26 October 2009

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Hydrophobic effects on multivalent-salt-induced self-condensation of a single polyelectrolyte chain such as DNA are investigated through a multiscale coarse-grained simulation based on density functional theory. We show that the water-mediated hydrophobic effect that was enhanced by hydration of multivalent salts plays an essential role in self-condensation of DNA. The self-condensation is interpreted as an entropy-driven compaction due to the hydration entropy gain.
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87.14.gk DNA
87.15.B- Structure of biomolecules
87.15.R- Reactions and kinetics
36.20.Fz Constitution (chains and sequences)
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Grand potential in thermodynamics of solid bodies and surfaces

A. I. Rusanov, A. K. Shchekin, and D. V. Tatyanenko

J. Chem. Phys. 131, 161104 (2009); http://dx.doi.org/10.1063/1.3254324 (4 pages) | Cited 5 times

Online Publication Date: 26 October 2009

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Using the chemical potential of a solid in a dissolved state or the corresponding component of the chemical potential tensor at equilibrium with the solution, a new concept of grand thermodynamic potential for solids has been suggested. This allows generalizing the definition of Gibbs’ quantity σ (surface work often called the solid-fluid interfacial free energy) at a planar surface as an excess grand thermodynamic potential per unit surface area that (1) does not depend on the dividing surface location and (2) is common for fluids and solids.
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65.40.G- Other thermodynamical quantities
65.60.+a Thermal properties of amorphous solids and glasses: heat capacity, thermal expansion, etc.
05.70.Ce Thermodynamic functions and equations of state
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Ubiquitous T-shaped isomers of OCS-hydrocarbon van der Waals complexes

J. Norooz Oliaee, M. Dehghany, Mahin Afshari, N. Moazzen-Ahmadi, and A. R. W. McKellar

J. Chem. Phys. 131, 161105 (2009); http://dx.doi.org/10.1063/1.3257934 (4 pages) | Cited 4 times

Online Publication Date: 27 October 2009

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Many weakly bound OCS-hydrocarbon complexes exhibit a relatively simple rotation-vibration band, characteristic of a T-shaped structure, which is redshifted (by 5–12 cm−1) from the OCS monomer ν1 frequency. Spectra of OCS with seven chain and ring hydrocarbons are described here. They allow a straightforward comparison of intermolecular force effects (vibrational shift and intermolecular separation) over a range of molecules, which could be extended to other hydrocarbons and other probes such as CO2 and N2O.
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34.50.Ez Rotational and vibrational energy transfer
34.20.Gj Intermolecular and atom-molecule potentials and forces
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
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Spatial updating in the great grand canonical ensemble

G. Orkoulas and Daniel P. Noon

J. Chem. Phys. 131, 161106 (2009); http://dx.doi.org/10.1063/1.3257111 (4 pages) | Cited 4 times

Online Publication Date: 27 October 2009

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In spatial updating grand canonical Monte Carlo, particle transfers are implemented by examining the local environment around a point in space. In the present work, these algorithms are extended to very high densities by allowing the volume to fluctuate, thus forming a great grand canonical ensemble. Since fluctuations are unbounded, a constraint must be imposed. The constrained ensemble may be viewed as a superposition of either constant-pressure or grand canonical ensembles. Each simulation of the constrained ensemble requires a set of weights that must be determined iteratively. The outcome of a single simulation is the density of states in terms of all its independent variables. Since all extensive variables fluctuate, it is also possible to estimate absolute free energies and entropies from a single simulation. The method is tested on a system of hard spheres and the transition from the fluid to a face-centered cubic crystal is located with high precision.
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64.70.dg Crystallization of specific substances
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Observation of buried water molecules in phospholipid membranes by surface sum-frequency generation spectroscopy

Maria Sovago, Erik Vartiainen, and Mischa Bonn

J. Chem. Phys. 131, 161107 (2009); http://dx.doi.org/10.1063/1.3257600 (4 pages) | Cited 13 times

Online Publication Date: 29 October 2009

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We investigate the structure and orientation of water molecules at the water-lipid interface, using vibrational sum-frequency generation in conjunction with a maximum entropy phase retrieval method. We find that interfacial water molecules have an orientation opposite to that predicted by electrostatics and thus are likely localized between the lipid headgroup and its apolar alkyl chain. This type of water molecule is observed for phospholipids but not for structurally simpler surfactants.
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87.64.K- Spectroscopy
87.16.D- Membranes, bilayers, and vesicles
42.65.Ky Frequency conversion; harmonic generation, including higher-order harmonic generation
87.15.B- Structure of biomolecules
87.15.M- Spectra of biomolecules
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The stiffness of a fully stretched polyethylene chain: A Raman jet spectroscopy extrapolation

Tobias N. Wassermann, Jonas Thelemann, Philipp Zielke, and Martin A. Suhm

J. Chem. Phys. 131, 161108 (2009); http://dx.doi.org/10.1063/1.3256221 (4 pages) | Cited 5 times

Online Publication Date: 29 October 2009

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Linear alkanes with n = 5–16 C-atoms are partially relaxed into their stretched all-trans conformation by supersonic jet expansion. Their longitudinal acoustic modes are identified by spontaneous Raman scattering and deperturbed from transverse bending mode components and Fermi resonance with combination states of the same symmetry. Comparison with quantum chemical predictions of the longitudinal modes in hydrocarbon chains with up to 54 C-atoms allows for a reliable extrapolation to the limiting product n⋅mathn = 2310±30 cm−1 for large n, from which the elastic modulus of an ideal polyethylene chain in vacuum may be estimated at 309±8 GPa. Differences to solid state determinations of this quantity are discussed.
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62.20.dq Other elastic constants
62.20.F- Deformation and plasticity
62.65.+k Acoustical properties of solids
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Theory of coherent resonance energy transfer for coherent initial condition

Seogjoo Jang

J. Chem. Phys. 131, 164101 (2009); http://dx.doi.org/10.1063/1.3247899 (12 pages) | Cited 24 times

Online Publication Date: 22 October 2009

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A theory of coherent resonance energy transfer [ Jang et al., J. Chem. Phys. 129, 101104 (2008) ] is extended for coherent initial condition. For the situation where the initial excitation is an arbitrary linear combination of donor and acceptor excitations, a second order time local quantum master equation combined with polaron transformation is derived. Inhomogeneous terms in the resulting equation have contributions not only from initial donor and acceptor populations but also from their coherence terms. Numerical tests are performed for general super Ohmic spectral density where the bath degrees of freedom coupled to donor and acceptor can be correlated with each other. Calculation results demonstrate sensitivity of early nonstationary population dynamics on the relative sign of initial donor and acceptor excitation states. It is shown that contribution of inhomogeneous terms is more significant for coherent initial condition than for localized one. The overall model calculations provide details of the interplay between quantum coherence and nonequilibrium/non-Markovian effects in the time dependent donor population dynamics.
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71.38.-k Polarons and electron-phonon interactions
71.10.Li Excited states and pairing interactions in model systems
71.15.Qe Excited states: methodology

Accurate ab initio energy gradients in chemical compound space

O. Anatole von Lilienfeld

J. Chem. Phys. 131, 164102 (2009); http://dx.doi.org/10.1063/1.3249969 (6 pages) | Cited 5 times

Online Publication Date: 22 October 2009

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Analytical potential energy derivatives, based on the Hellmann–Feynman theorem, are presented for any pair of isoelectronic compounds. Since energies are not necessarily monotonic functions between compounds, these derivatives can fail to predict the right trends of the effect of alchemical mutation. However, quantitative estimates without additional self-consistency calculations can be made when the Hellmann–Feynman derivative is multiplied with a linearization coefficient that is obtained from a reference pair of compounds. These results suggest that accurate predictions can be made regarding any molecule’s energetic properties as long as energies and gradients of three other molecules have been provided. The linearization coefficent can be interpreted as a quantitative measure of chemical similarity. Presented numerical evidence includes predictions of electronic eigenvalues of saturated and aromatic molecular hydrocarbons.
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31.15.A- Ab initio calculations
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions

Correct virial formulation in the isotropic periodic sum method

Iordan H. Hristov, Reginald Paul, and Stephen J. Paddison

J. Chem. Phys. 131, 164103 (2009); http://dx.doi.org/10.1063/1.3247876 (5 pages)

Online Publication Date: 22 October 2009

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The original formulation of the virial in the isotropic periodic sum (IPS) method assumes that the sphere defining the local region has a constant radius (the cutoff) independent of the system size. This assumption neglects a virial term originating from the separation between the local sphere and its periodic images. When comparing the IPS virial with that calculated from the cutoff plus long range correction method, the difference observed can be erroneously attributed to the representation of the infinite region. We show that when the two virials are calculated consistently the observed difference is significantly reduced. Additionally, the correct virial that includes the previously missing term is much simpler to calculate. We prove that in the IPS method the virial can be obtained as n/3 times the potential energy for the case of 1/rn type potentials.
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31.50.-x Potential energy surfaces
31.10.+z Theory of electronic structure, electronic transitions, and chemical binding

Quantum cluster theory for the polarizable continuum model. I. The CCSD level with analytical first and second derivatives

R. Cammi

J. Chem. Phys. 131, 164104 (2009); http://dx.doi.org/10.1063/1.3245400 (14 pages) | Cited 12 times

Online Publication Date: 23 October 2009

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We present a general formulation of the coupled-cluster (CC) theory for a molecular solute described within the framework of the polarizable continuum model (PCM). The PCM-CC theory is derived in its complete form, called PTDE scheme, in which the correlated electronic density is used to have a self-consistent reaction field, and in an approximate form, called PTE scheme, in which the PCM-CC equations are solved assuming the fixed Hartree–Fock solvent reaction field. Explicit forms for the PCM-CC-PTDE equations are derived at the single and double (CCSD) excitation level of the cluster operator. At the same level, explicit equations for the analytical first derivatives of the PCM basic energy functional are presented, and analytical second derivatives are also discussed. The corresponding PCM-CCSD-PTE equations are given as a special case of the full theory.
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31.15.bw Coupled-cluster theory
31.15.xr Self-consistent-field methods

First-principles methodology for quantum transport in multiterminal junctions

Kamal K. Saha, Wenchang Lu, J. Bernholc, and Vincent Meunier

J. Chem. Phys. 131, 164105 (2009); http://dx.doi.org/10.1063/1.3247880 (9 pages) | Cited 3 times

Online Publication Date: 23 October 2009

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We present a generalized approach for computing electron conductance and I-V characteristics in multiterminal junctions from first-principles. Within the framework of Keldysh theory, electron transmission is evaluated employing an O(N) method for electronic-structure calculations. The nonequilibrium Green function for the nonequilibrium electron density of the multiterminal junction is computed self-consistently by solving Poisson equation after applying a realistic bias. We illustrate the suitability of the method on two examples of four-terminal systems, a radialene molecule connected to carbon chains and two crossed-carbon chains brought together closer and closer. We describe charge density, potential profile, and transmission of electrons between any two terminals. Finally, we discuss the applicability of this technique to study complex electronic devices.
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73.40.-c Electronic transport in interface structures

On the definition of discrete hydrodynamic variables

Pep Español and Ignacio Zúñiga

J. Chem. Phys. 131, 164106 (2009); http://dx.doi.org/10.1063/1.3247586 (13 pages) | Cited 4 times

Online Publication Date: 23 October 2009

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The Green–Kubo formula for discrete hydrodynamic variables involves information about not only the fluid transport coefficients but also about discrete versions of the differential operators that govern the evolution of the discrete variables. This gives an intimate connection between discretization procedures in fluid dynamics and coarse-graining procedures used to obtain hydrodynamic behavior of molecular fluids. We observed that a natural definition of discrete hydrodynamic variables in terms of Voronoi cells leads to a Green–Kubo formula which is divergent, rendering the full coarse-graining strategy useless. In order to understand this subtle issue, in the present paper we consider the coarse graining of noninteracting Brownian particles. The discrete hydrodynamic variable for this problem is the number of particles within Voronoi cells. Thanks to the simplicity of the model we spot the origin of the singular behavior of the correlation functions. We offer an alternative definition, based on the concept of a Delaunay cell that behaves properly, suggesting the use of the Delaunay construction for the coarse graining of molecular fluids at the discrete hydrodynamic level.
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47.11.-j Computational methods in fluid dynamics

Molecular acidity: A quantitative conceptual density functional theory description

Shubin Liu, Cynthia K. Schauer, and Lee G. Pedersen

J. Chem. Phys. 131, 164107 (2009); http://dx.doi.org/10.1063/1.3251124 (7 pages) | Cited 9 times

Online Publication Date: 23 October 2009

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Accurate predictions of molecular acidity using ab initio and density functional approaches are still a daunting task. Using electronic and reactivity properties, one can quantitatively estimate pKa values of acids. In a recent paper [ S. B. Liu and L. G. Pedersen, J. Phys. Chem. A 113, 3648 (2009) ], we employed the molecular electrostatic potential (MEP) on the nucleus and the sum of valence natural atomic orbital (NAO) energies for the purpose. In this work, we reformulate these relationships on the basis of conceptual density functional theory and compare the results with those from the thermodynamic cycle method. We show that MEP and NAO properties of the dissociating proton of an acid should satisfy the same relationships with experimental pKa data. We employ 27 main groups and first to third row transition metal-water complexes as illustrative examples to numerically verify the validity of these strong linear correlations. Results also show that the accuracy of our approach and that of the conventional method through the thermodynamic cycle are statistically similar.
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82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.20.Ej Quantum theory of reaction cross section
82.60.Hc Chemical equilibria and equilibrium constants

Wavepacket approach to the cumulative reaction probability within the flux operator formalism

Sophya Garashchuk and Tijo Vazhappilly

J. Chem. Phys. 131, 164108 (2009); http://dx.doi.org/10.1063/1.3251333 (7 pages) | Cited 2 times

Online Publication Date: 26 October 2009

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Expressions for the singular flux operator eigenfunctions and eigenvalues are given in terms of the Dirac δ-function representable as a localized Gaussian wavepacket. This functional form enables computation of the cumulative reaction probability N(E) from the wavepacket time-correlation functions. The Gaussian based form of the flux eigenfunctions, which is not tied to a finite basis of a quantum-mechanical calculation, is particularly useful for approximate calculation of N(E) with the trajectory based wavepacket propagation techniques. Numerical illustration is given for the Eckart barrier using the conventional quantum-mechanical propagation and the quantum trajectory dynamics with the approximate quantum potential. N(E) converges with respect to the Gaussian width parameter, and the convergence is faster at low energy. The approximate trajectory calculation overestimates tunneling in the low energy regime, but gives a significant improvement over the parabolic estimate of the tunneling probability.
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82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Xr Quantum effects in rate constants (tunneling, resonances, etc.)
82.20.Fd Collision theories; trajectory models

A diffusional bimolecular propensity function

Daniel T. Gillespie

J. Chem. Phys. 131, 164109 (2009); http://dx.doi.org/10.1063/1.3253798 (13 pages) | Cited 4 times

Online Publication Date: 27 October 2009

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We derive an explicit formula for the propensity function (stochastic reaction rate) of a generic bimolecular chemical reaction in which the reactant molecules move about by diffusion, as solute molecules in a bath of much smaller and more numerous solvent molecules. Our derivation assumes that the solution is macroscopically well stirred and dilute in the solute molecules. It effectively extends the physical rationale for the chemical master equation and the stochastic simulation algorithm from well-stirred dilute gases to well-stirred dilute solutions, with the former becoming a limiting case of the latter. This extension is important for cellular systems, where the solvent molecules are typically water and the solute (reactant) molecules are much larger organic structures, whose relatively low populations often require a discrete-stochastic formalism. In the course of our derivation, we illuminate some limitations on the ability of the classical diffusion equation to accurately describe how a diffusing molecule moves on spatial and temporal scales that are relevant to collision-induced chemical reactions.
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82.20.Yn Solvent effects on reactivity
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

A pseudospectral method for optimal control of open quantum systems

Jr-Shin Li, Justin Ruths, and Dionisis Stefanatos

J. Chem. Phys. 131, 164110 (2009); http://dx.doi.org/10.1063/1.3253796 (9 pages) | Cited 3 times

Online Publication Date: 28 October 2009

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In this paper, we present a unified computational method based on pseudospectral approximations for the design of optimal pulse sequences in open quantum systems. The proposed method transforms the problem of optimal pulse design, which is formulated as a continuous-time optimal control problem, to a finite-dimensional constrained nonlinear programming problem. This resulting optimization problem can then be solved using existing numerical optimization suites. We apply the Legendre pseudospectral method to a series of optimal control problems on open quantum systems that arise in nuclear magnetic resonance spectroscopy in liquids. These problems have been well studied in previous literature and analytical optimal controls have been found. We find an excellent agreement between the maximum transfer efficiency produced by our computational method and the analytical expressions. Moreover, our method permits us to extend the analysis and address practical concerns, including smoothing discontinuous controls as well as deriving minimum-energy and time-optimal controls. The method is not restricted to the systems studied in this article and is applicable to optimal manipulation of both closed and open quantum systems.
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61.20.Ja Computer simulation of liquid structure
76.60.-k Nuclear magnetic resonance and relaxation

Effective interaction between large colloidal particles immersed in a bidisperse suspension of short-ranged attractive colloids

A. Jamnik

J. Chem. Phys. 131, 164111 (2009); http://dx.doi.org/10.1063/1.3253694 (8 pages) | Cited 1 time

Online Publication Date: 28 October 2009

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The effective force between two large hard spheres mimicking lyophobic colloids (solute) immersed in an asymmetric two-component mixture of smaller particles (solvents), interacting via Baxter’s sticky hard sphere (SHS) potential, was studied using integral equation theory and Monte Carlo simulation. The theoretical predictions were calculated from the analytic solution of the Percus–Yevick/Ornstein–Zernike integral equation for spatial correlations in a three-component mixture at vanishing solute concentration, while the simulation results were obtained by applying a special simulation technique developed for sampling the hard-sphere collision force. Due to layering of the solvent molecules, the effective force between the particles of the solute oscillates with periods equal to the molecular diameters of both solvent components. The attractive force between the solute particles in the SHS mixture comprising strongly attractive molecules of either component decays slower than that in the mixture with weaker interparticle attraction. Similar features are also observed when inspecting the separate contributions of individual components to the total solute-solute force. At sufficient strength of the interparticle stickiness, these oscillations disappear, the force becoming long ranged and attractive at all separations.
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82.70.Dd Colloids
82.70.Kj Emulsions and suspensions
61.20.Ja Computer simulation of liquid structure

Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies

Qin Wu, Paul W. Ayers, and Yingkai Zhang

J. Chem. Phys. 131, 164112 (2009); http://dx.doi.org/10.1063/1.3253797 (8 pages) | Cited 12 times

Online Publication Date: 28 October 2009

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The first purely density-based energy decomposition analysis (EDA) for intermolecular binding is developed within the density functional theory. The most important feature of this scheme is to variationally determine the frozen density energy, based on a constrained search formalism and implemented with the Wu–Yang algorithm [ Q. Wu and W. Yang, J. Chem. Phys. 118, 2498 (2003) ]. This variational process dispenses with the Heitler–London antisymmetrization of wave functions used in most previous methods and calculates the electrostatic and Pauli repulsion energies together without any distortion of the frozen density, an important fact that enables a clean separation of these two terms from the relaxation (i.e., polarization and charge transfer) terms. The new EDA also employs the constrained density functional theory approach [ Q. Wu and T. Van Voorhis, Phys. Rev. A 72, 24502 (2005) ] to separate out charge transfer effects. Because the charge transfer energy is based on the density flow in real space, it has a small basis set dependence. Applications of this decomposition to hydrogen bonding in the water dimer and the formamide dimer show that the frozen density energy dominates the binding in these systems, consistent with the noncovalent nature of the interactions. A more detailed examination reveals how the interplay of electrostatics and the Pauli repulsion determines the distance and angular dependence of these hydrogen bonds.
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31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)
34.20.Gj Intermolecular and atom-molecule potentials and forces
36.20.Hb Configuration (bonds, dimensions)
34.70.+e Charge transfer

Analytic second derivatives in closed-shell coupled-cluster theory with spin-orbit coupling

Fan Wang and Jürgen Gauss

J. Chem. Phys. 131, 164113 (2009); http://dx.doi.org/10.1063/1.3245954 (9 pages) | Cited 4 times

Online Publication Date: 28 October 2009

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The theory for geometrical second derivatives of the energy is outlined for the recently suggested two-component coupled-cluster approach using relativistic effective core potentials with spin-orbit coupling included in the post-Hartree–Fock treatment [ F. Wang, J. Gauss, and C. van Wüllen, J. Chem. Phys. 129, 064113 (2008) ], and an implementation is reported at the coupled-cluster singles and doubles (CCSD) level as well as at the CCSD level augmented by a perturbative treatment of triple excitations [CCSD(T)]. The applicability of the developed analytic second-derivative techniques is demonstrated by computing harmonic and fundamental frequencies for PtH2, PbH2, and HgH2 with the required cubic and semidiagonal quartic force fields obtained by numerical differentiation of the analytically evaluated quadratic force constants. Spin-orbit coupling effects are shown to be non-negligible for the three considered molecules and thus need to be considered in the case of high-accuracy predictions.
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31.15.bw Coupled-cluster theory
31.15.xr Self-consistent-field methods
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.xp Perturbation theory
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.20.Tp Vibrational analysis
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions

Implicit and explicit solvent models for the simulation of a single polymer chain in solution: Lattice Boltzmann versus Brownian dynamics

Tri T. Pham, Ulf D. Schiller, J. Ravi Prakash, and Burkhard Dünweg

J. Chem. Phys. 131, 164114 (2009); http://dx.doi.org/10.1063/1.3251771 (11 pages) | Cited 5 times

Online Publication Date: 29 October 2009

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We present a comparative study of two computer simulation methods to obtain static and dynamic properties of dilute polymer solutions. The first approach is a recently established hybrid algorithm based on dissipative coupling between molecular dynamics and lattice Boltzmann (LB), while the second is standard Brownian dynamics (BD) with fluctuating hydrodynamic interactions. Applying these methods to the same physical system (a single polymer chain in a good solvent in thermal equilibrium) allows us to draw a detailed and quantitative comparison in terms of both accuracy and efficiency. It is found that the static conformations of the LB model are distorted when the box length L is too small compared to the chain size. Furthermore, some dynamic properties of the LB model are subject to an L−1 finite-size effect, while the BD model directly reproduces the asymptotic L→∞ behavior. Apart from these finite-size effects, it is also found that in order to obtain the correct dynamic properties for the LB simulations, it is crucial to properly thermalize all the kinetic modes. Only in this case, the results are in excellent agreement with each other, as expected. Moreover, Brownian dynamics is found to be much more efficient than lattice Boltzmann as long as the degree of polymerization is not excessively large.
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61.25.he Polymer solutions
61.20.Ja Computer simulation of liquid structure

Transformations of the distribution of nuclei formed in a nucleation pulse: Interface-limited growth

Vitaly A. Shneidman

J. Chem. Phys. 131, 164115 (2009); http://dx.doi.org/10.1063/1.3254322 (13 pages) | Cited 2 times

Online Publication Date: 29 October 2009

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A typical nucleation-growth process is considered: a system is quenched into a supersaturated state with a small critical radius r∗− and is allowed to nucleate during a finite time interval tn, after which the supersaturation is abruptly reduced to a fixed value with a larger critical radius r∗+. The size-distribution of nucleated particles f(r,t) further evolves due to their deterministic growth and decay for r larger or smaller than r∗+, respectively. A general analytic expressions for f(r,t) is obtained, and it is shown that after a large growth time t this distribution approaches an asymptotic shape determined by two dimensionless parameters, λ related to tn, and Λ = r∗+/r∗−. This shape is strongly asymmetric with an exponential and double-exponential cutoffs at small and large sizes, respectively, and with a broad near-flat top in case of a long pulse. Conversely, for a short pulse the distribution acquires a distinct maximum at r = rmax(t) and approaches a universal shape exp[ζ−eζ], with ζ∝r−rmax, independent of the pulse duration. General asymptotic predictions are examined in terms of Zeldovich–Frenkel nucleation model where the entire transient behavior can be described in terms of the Lambert W function. Modifications for the Turnbull–Fisher model are also considered, and analytics is compared with exact numerics. Results are expected to have direct implementations in analysis of two-step annealing crystallization experiments, although other applications might be anticipated due to universality of the nucleation pulse technique.
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64.60.qj Studies of nucleation in specific substances
64.70.-p Specific phase transitions
81.40.Gh Other heat and thermomechanical treatments

Transition state analysis of solid-solid transformations in nanocrystals

Michael Grünwald and Christoph Dellago

J. Chem. Phys. 131, 164116 (2009); http://dx.doi.org/10.1063/1.3253700 (10 pages) | Cited 5 times

Online Publication Date: 30 October 2009

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A systematic simulation methodology is introduced for the accurate determination of experimentally measurable quantities characterizing solid-solid phase transformations under pressure. The atomistic mechanisms of nucleation and growth in a structural transformation of pressurized CdSe nanocrystals are identified using transition path sampling computer simulation. A committor-based transition state analysis is applied to extract activation enthalpies and activation volumes from transformation pathways at experimental conditions. The qualitative dependence of activation enthalpies on nanocrystal size is in good agreement with experimental data and supports the observed nucleation mechanism, which is characterized by a critical nucleus of elongated shape located on the crystal surface. Based on committor distributions along typical transformation pathways, the coordination number is identified as a suitable reaction coordinate for the process.
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64.70.kg Semiconductors
61.46.Df Structure of nanocrystals and nanoparticles ("colloidal" quantum dots but not gate-isolated embedded quantum dots)
81.05.Dz II-VI semiconductors
61.66.Fn Inorganic compounds
65.80.-g Thermal properties of small particles, nanocrystals, nanotubes, and other related systems

Local behavior of the first-order gradient correction to the Thomas–Fermi kinetic energy functional

David García-Aldea, T. Martín-Blas, and J. E. Alvarellos

J. Chem. Phys. 131, 164117 (2009); http://dx.doi.org/10.1063/1.3246863 (7 pages) | Cited 1 time

Online Publication Date: 30 October 2009

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The first-order gradient correction to the Thomas–Fermi functional proposed by Haq et al. [ Chem. Phys. Lett. 111, 79 (1984) ] has been tested by evaluating both the total kinetic energy and the local kinetic energy density. For the kinetic energy density, we have evaluated its deviation from the exact orbital-based result through a quality factor that reflects the quality of the functionals in a better way than their relative errors. The study is performed on two different systems: Light atoms (up to Z = 18) and a noninteracting model of fermions confined in a Coulombic-type potential, a system that provides useful insights about the performance of the functionals when the ground state is degenerate. It is found that this approximation gives very low relative errors and a better local behavior than any other kinetic energy density functional.
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31.15.bt Statistical model calculations (including Thomas-Fermi and Thomas-Fermi-Dirac models)
31.15.E- Density-functional theory
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