JCP Nameplate
  • Volume/Page
  • Keyword
  • DOI
  • Citation
  • Advanced
   
 
 
 

You Tube Flickr Twitter UniPHY Group iResearch App Facebook

BROWSE VOLUMES

Year Range: 
Search Issue | RSS Feeds RSS
Previous Issue Next Issue

21 Jul 2008

Volume 129, Issue 3, Articles (03xxxx)

Page 1 of 2 Pages Next Page | Jump to Page
back to top
RSS Feeds
back to top Theoretical Methods and Algorithms

Why are time-dependent density functional theory excitations in solids equal to band structure energy gaps for semilocal functionals, and how does nonlocal Hartree–Fock-type exchange introduce excitonic effects?

Artur F. Izmaylov and Gustavo E. Scuseria

J. Chem. Phys. 129, 034101 (2008); http://dx.doi.org/10.1063/1.2953701 (10 pages) | Cited 16 times

Online Publication Date: 16 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We examine the time-dependent density functional theory (TD-DFT) equations for calculating excitation energies in solids with Gaussian orbitals and analytically show that for semilocal functionals, their lowest eigenvalue collapses to the minimum band orbital energy difference. With the introduction of nonlocal Hartree–Fock-type exchange (as in hybrid functionals), this result is no longer valid, and the lowest TD-DFT eigenvalue reflects the appearance of excitonic effects. Previously reported “charge-transfer” problems with semilocal TD-DFT excitations in molecules can be deduced from our analysis by taking the limit to infinite lattice constant.
Show PACS
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
71.35.-y Excitons and related phenomena

Nonadiabatic corrections to the wave function and energy

Krzysztof Pachucki and Jacek Komasa

J. Chem. Phys. 129, 034102 (2008); http://dx.doi.org/10.1063/1.2952517 (7 pages) | Cited 13 times

Online Publication Date: 16 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Nonadiabatic corrections in molecules composed of a few atoms are considered. It is demonstrated that a systematic perturbative expansion around the adiabatic solution is possible, with the expansion parameter being the electron-nucleus mass ratio to the 3/4 power. Closed form formulas for the leading corrections to the wave function and to the energy are derived. Their applicability is demonstrated by a comparison of numerical results for the hydrogen molecule with the former nonadiabatic calculations and the experimental values. Good agreement with the recent experiment is achieved for the ground state dissociation energy of both H2 and D2.
Show PACS

A statistical analysis of the precision of reweighting-based simulations

Tongye Shen and Donald Hamelberg

J. Chem. Phys. 129, 034103 (2008); http://dx.doi.org/10.1063/1.2944250 (9 pages) | Cited 12 times

Online Publication Date: 17 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Various advanced simulation techniques, which are used to sample the statistical ensemble of systems with complex Hamiltonians, such as those displayed in condensed matters and biomolecular systems, rely heavily on successfully reweighting the sampled configurations. The sampled points of a system from an elevated thermal environment or on a modified Hamiltonian are reused with different statistical weights to evaluate its properties at the initial desired temperature or of the original Hamiltonian. Often, the decrease of accuracy induced by this procedure is ignored and the final results can be far from what is expected. We have addressed the reasons behind such a phenomenon and have provided a quantitative method to estimate the number of sampled points required in the crucial step of reweighting of these advanced simulation methods. We also provided examples from temperature histogram reweighting and accelerated molecular dynamics reweighting to illustrate this idea, which can be generalized to the dynamic reweighting as well. The study shows that this analysis may provide a priori guidance for the strategy of setting up the parameters of advanced simulations before a lengthy one is carried out. The method can therefore provide insights for optimizing the parameters for high accuracy simulations with finite amount of computational resources.
Show PACS
02.50.-r Probability theory, stochastic processes, and statistics
02.70.Ns Molecular dynamics and particle methods

Quantum mechanical methods applied to excitation energy transfer: A comparative analysis on excitation energies and electronic couplings

A. Muñoz-Losa, C. Curutchet, I. Fdez. Galván, and B. Mennucci

J. Chem. Phys. 129, 034104 (2008); http://dx.doi.org/10.1063/1.2953716 (16 pages) | Cited 18 times

Online Publication Date: 17 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We present a comparative study on the influence of the quantum mechanical (QM) method (including basis set) on the evaluation of transition energies, transition densities and dipoles, and excitation energy transfer (EET) electronic couplings for a series of chromophores (and the corresponding pairs) typically found in organic electro-optical devices and photosynthetic systems. On these systems we have applied five different QM levels of description of increasing accuracy (ZINDO, CIS, TD-DFT, CASSCF, and SAC-CI). In addition, we have tested the effects of a surrounding environment (either mimicking a solvent or a protein matrix) on excitation energies, transition dipoles, and electronic couplings through the polarizable continuum model (PCM) description. Overall, the results obtained suggest that the choice of the QM level of theory affects the electronic couplings much less than it affects excitation energies. We conclude that reasonable estimates can be obtained using moderate basis sets and inexpensive methods such as configuration interaction of single excitations or time-dependent density functional theory when appropriately coupled to realistic solvation models such as PCM.
Show PACS
87.15.ag Quantum calculations
87.15.kr Protein-solvent interactions
82.50.-m Photochemistry
87.15.R- Reactions and kinetics
87.14.E- Proteins

A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations

Lianqing Zheng, Irina O. Carbone, Alexey Lugovskoy, Bernd A. Berg, and Wei Yang

J. Chem. Phys. 129, 034105 (2008); http://dx.doi.org/10.1063/1.2953321 (7 pages) | Cited 7 times

Online Publication Date: 18 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Recently, we developed an efficient free energy simulation technique, the simulated scaling (SS) method [ H. Li et al., J. Chem. Phys. 126, 024106 (2007) ], in the framework of generalized ensemble simulations. In the SS simulations, random walks in the scaling parameter space are realized so that both phase space overlap sampling and conformational space sampling can be simultaneously enhanced. To flatten the distribution in the scaling parameter space, in the original SS implementation, the Wang–Landau recursion was employed due to its well-known recursion capability. In the Wang–Landau recursion based SS free energy simulation scheme, at the early stage, recursion efficiencies are high and free energy regions are quickly located, although at this stage, the errors of estimated free energy values are large; at the later stage, the errors of estimated free energy values become smaller, however, recursions become increasingly slow and free energy refinements require very long simulation time. In order to robustly resolve this efficiency problem during free energy refinements, a hybrid recursion strategy is presented in this paper. Specifically, we let the Wang–Landau update method take care of the early stage recursion: the location of target free energy regions, and let the adaptive reweighting method take care of the late stage recursion: the refinements of free energy values. As comparably studied in the model systems, among three possible recursion procedures, the adaptive reweighting recursion approach is the least favorable one because of its low recursion efficiency during free energy region locations; and compared to the original Wang–Landau recursion approach, the proposed hybrid recursion technique can be more robust to guarantee free energy simulation efficiencies.
Show PACS
05.70.Ce Thermodynamic functions and equations of state
71.15.-m Methods of electronic structure calculations

Analytic derivatives for the Cholesky representation of the two-electron integrals

Francesco Aquilante, Roland Lindh, and Thomas Bondo Pedersen

J. Chem. Phys. 129, 034106 (2008); http://dx.doi.org/10.1063/1.2955755 (7 pages) | Cited 14 times

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We propose a formalism for calculating analytic derivatives of the electronic energy with respect to nuclear coordinates using Cholesky decomposition of the two-electron integrals. The formalism is derived by exploiting the equivalence of Cholesky decomposition and density fitting when a suitable auxiliary basis set is used for expanding atomic orbital product densities in the latter. An implementation of gradients at the nonhybrid density functional theory level is presented, and sample calculations demonstrate that the errors in equilibrium geometries due to the Cholesky representation of the integrals can be controlled by adjusting the decomposition threshold.
Show PACS
31.15.E- Density-functional theory

Simultaneous benchmarking of ground- and excited-state properties with long-range-corrected density functional theory

Mary A. Rohrdanz and John M. Herbert

J. Chem. Phys. 129, 034107 (2008); http://dx.doi.org/10.1063/1.2954017 (9 pages) | Cited 38 times

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We present benchmark calculations using several long-range-corrected (LRC) density functionals, in which Hartree–Fock exchange is incorporated asymptotically using a range-separated Coulomb operator, while local exchange is attenuated using an ansatz introduced by Iikura et al. [J. Chem. Phys. 115, 3540 (2001)]. We calculate ground-state atomization energies, reaction barriers, ionization energies, and electron affinities, each as a function of the range-separation parameter μ. In addition, we calculate excitation energies of small- and medium-sized molecules, again as a function of μ, by applying the LRC to time-dependent density functional theory. Representative examples of both pure and hybrid density functionals are tested. On the basis of these results, there does not appear to be a single range-separation parameter that is reasonable for both ground-state properties and vertical excitation energies. Reasonable errors in atomization energies and barrier heights are achieved only at the expense of excessively high excitation energies, at least for the medium-sized molecules, whereas values of μ that afford reasonable excitation energies yield some of the largest errors for ground-state atomization energies and barrier heights in small molecules. Notably, this conclusion is obscured if the database of excitation energies includes only small molecules, as has been the case in previous benchmark studies of LRC functionals.
Show PACS
31.15.ee Time-dependent density functional theory
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.50.Df Potential energy surfaces for excited electronic states
31.15.xr Self-consistent-field methods

Stochastic surrogate Hamiltonian

Gil Katz, David Gelman, Mark A. Ratner, and Ronnie Kosloff

J. Chem. Phys. 129, 034108 (2008); http://dx.doi.org/10.1063/1.2946703 (6 pages) | Cited 13 times

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The surrogate Hamiltonian is a general scheme to simulate the many body quantum dynamics composed of a primary system coupled to a bath. The method has been based on a representative bath Hamiltonian composed of two-level systems that is able to mimic the true system-bath dynamics up to a prespecified time. The original surrogate Hamiltonian method is limited to short time dynamics since the size of the Hilbert space required to obtain convergence grows exponentially with time. By randomly swapping bath modes with a secondary thermal reservoir, the method can simulate quantum dynamics of the primary system from short times to thermal equilibrium. By averaging a small number of realizations converged values of the system observables are obtained avoiding the exponential increase in resources. The method is demonstrated for the equilibration of a molecular oscillator with a thermal bath.
Show PACS
03.65.Ge Solutions of wave equations: bound states
02.50.Ey Stochastic processes

A direct relativistic four-component multiconfiguration self-consistent-field method for molecules

Jørn Thyssen, Timo Fleig, and Hans Jørgen Aa. Jensen

J. Chem. Phys. 129, 034109 (2008); http://dx.doi.org/10.1063/1.2943670 (14 pages) | Cited 8 times

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
A new direct relativistic four-component Kramers-restricted multiconfiguration self-consistent-field (KR-MCSCF) code for molecules has been implemented. The program is based upon Kramers-paired spinors and a full implementation of the binary double groups (D2h* and subgroups). The underlying quaternion algebra for one-electron operators was extended to treat two-electron integrals and density matrices in an efficient and nonredundant way. The iterative procedure is direct with respect to both configurational and spinor variational parameters; this permits the use of large configuration expansions and many basis functions. The relativistic minimum-maximum principle is implemented in a second-order restricted-step optimization algorithm, which provides sharp and well-controlled convergence. This paper focuses on the necessary modifications of nonrelativistic MCSCF methodology to obtain a fully variational KR-MCSCF implementation. The general implementation also allows for the use of molecular integrals from a two-component relativistic Hamiltonian as, for example, the Douglas–Kroll–Hess variants. Several sample applications concern the determination of spectroscopic properties of heavy-element atoms and molecules, demonstrating the influence of spin-orbit coupling in MCSCF approaches to such systems and showing the potential of the new method.
Show PACS
31.15.vn Electron correlation calculations for diatomic molecules
31.15.xr Self-consistent-field methods
31.30.jd Relativistic corrections due to negative-energy states or processes

Non-normal Lanczos methods for quantum scattering

Reza Rajaie Khorasani and Randall S. Dumont

J. Chem. Phys. 129, 034110 (2008); http://dx.doi.org/10.1063/1.2940733 (13 pages) | Cited 2 times

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
This article presents a new complex absorbing potential (CAP) block Lanczos method for computing scattering eigenfunctions and reaction probabilities. The method reduces the problem of computing energy eigenfunctions to solving two energy dependent systems of equations. An energy independent block Lanczos factorization casts the system into a block tridiagonal form, which can be solved very efficiently for all energies. We show that CAP-Lanczos methods exhibit instability due to the non-normality of CAP Hamiltonians and may break down for some systems. The instability is not due to loss of orthogonality but to non-normality of the Hamiltonian matrix. While use of a Woods–Saxon exponential CAP—as opposed to a polynomial CAP—reduced non-normality, it did not always ensure convergence. Our results indicate that the Arnoldi algorithm is more robust for non-normal systems and less prone to break down. An Arnoldi version of our method is applied to a nonadiabatic tunneling Hamiltonian with excellent results, while the Lanczos algorithm breaks down for this system.
Show PACS
03.65.Nk Scattering theory
03.65.Fd Algebraic methods

Basis set limit Hartree–Fock and density functional theory response property evaluation by multiresolution multiwavelet basis

Hideo Sekino, Yasuyuki Maeda, Takeshi Yanai, and Robert J. Harrison

J. Chem. Phys. 129, 034111 (2008); http://dx.doi.org/10.1063/1.2955730 (6 pages) | Cited 7 times

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We describe the evaluation of response properties using multiresolution multiwavelet (MRMW) basis sets. The algorithm uses direct projection of the perturbed density operator onto the zeroth order density operator on the real space spanned by the MRMW basis set and is applied for evaluating the polarizability of small molecules using Hartree–Fock and Kohn–Sham density functional theory. The computed polarizabilities can be considered to be converged to effectively complete space within the requested precision. The efficiency of the method against the ordinary Gaussian basis computation is discussed.
Show PACS
31.15.xr Self-consistent-field methods
31.15.E- Density-functional theory
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
31.15.xp Perturbation theory

Quantum theory of chemical reactions in the presence of electromagnetic fields

T. V. Tscherbul and R. V. Krems

J. Chem. Phys. 129, 034112 (2008); http://dx.doi.org/10.1063/1.2954021 (16 pages) | Cited 6 times

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We present a theory for rigorous quantum scattering calculations of probabilities for chemical reactions of atoms with diatomic molecules in the presence of an external electric field. The approach is based on the fully uncoupled basis set representation of the total wave function in the space-fixed coordinate frame, the Fock–Delves hyperspherical coordinates, and the adiabatic partitioning of the total Hamiltonian of the reactive system. The adiabatic channel wave functions are expanded in basis sets of hyperangular functions corresponding to different reaction arrangements, and the interactions with external fields are included in each chemical arrangement separately. We apply the theory to examine the effects of electric fields on the chemical reactions of LiF molecules with H atoms and HF molecules with Li atoms at low temperatures and show that electric fields may enhance the probability of chemical reactions and modify reactive scattering resonances by coupling the rotational states of the reactants. Our preliminary results suggest that chemical reactions of polar molecules at temperatures below 1 K can be selectively manipulated with dc electric fields and microwave laser radiation.
Show PACS
03.65.-w Quantum mechanics
82.30.-b Specific chemical reactions; reaction mechanisms
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

The 2-naphthol-water2 cluster: Two competing types of hydrogen-bonding arrangements

Dominik Schemmel and Martin Schütz

J. Chem. Phys. 129, 034301 (2008); http://dx.doi.org/10.1063/1.2952271 (10 pages) | Cited 7 times

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The potential energy surfaces of the S0 and S1(π∗←π) states of the 2-naphthol(H2O)n, n ∊ {1,2} clusters were explored at the level of coupled cluster (CC2) response theory. In the electronic ground state two different types of hydrogen-bonding networks coexist for n = 2, (i) a cyclic one [similar to those of the water trimer and phenol(H2O)2] where the hydroxy group of the aryl alcohol acts simultaneously as H donor for the first, and as H acceptor for the second water molecule, and (ii) a hydrogen-bonding arrangement where the aromatic π system is taking over the role as H acceptor. In the S1 state, on the other hand, the cyclic conformers are unstable. Consequently, the first group of cyclic ground state conformers gives rise to broad unstructured band shapes in the absorption spectrum, whereas the second group of conformers involving the aromatic π system gives rise to nicely structured band shapes. Based on these results the puzzling absorption spectrum of the n = 2 cluster can properly be interpreted.
Show PACS
36.40.Mr Spectroscopy and geometrical structure of clusters
31.50.Bc Potential energy surfaces for ground electronic states
31.15.bw Coupled-cluster theory
34.70.+e Charge transfer
33.70.Jg Line and band widths, shapes, and shifts

Single switch surface hopping for a model of pyrazine

Caroline Lasser and Torben Swart

J. Chem. Phys. 129, 034302 (2008); http://dx.doi.org/10.1063/1.2954019 (8 pages) | Cited 9 times

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The single switch trajectory surface hopping algorithm is tested for numerical simulations of a two-state three-mode model for the internal conversion of pyrazine through a conical intersection of potential energy surfaces. The algorithm is compared to two other surface hopping approaches, namely, Tully’s method of the fewest switches [J. Chem. Phys. 93, 1061 (1990)] and the method by Voronin et al. [J. Phys. Chem. A 102, 6057 (1998)] . The single switch algorithm achieves the most accurate results. Replacing its deterministic nonadiabatic branching condition by a probabilistic accept-reject criterion, one obtains the method of Voronin et al. without momentum adjustment. This probabilistic version of the single switch approach outperforms the considered algorithms in terms of accuracy, memory requirement, and runtime.
Show PACS
73.25.+i Surface conductivity and carrier phenomena
72.20.Ee Mobility edges; hopping transport
72.80.Le Polymers; organic compounds (including organic semiconductors)

H4+: What do we know about it?

Alexander Alijah and António J. C. Varandas

J. Chem. Phys. 129, 034303 (2008); http://dx.doi.org/10.1063/1.2953571 (5 pages)

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The potential energy surface of H4+ has been analyzed and stationary points and minima of intersections characterized by benchmark multireference configuration interaction calculations with basis sets as large as augmented septuble zeta. No evidence for minima other than those of the well established stable C2v configuration has been found. Some of the results obtained previously at a lower level of ab initio theory had to be revised.
Show PACS
31.50.-x Potential energy surfaces
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
33.15.Bh General molecular conformation and symmetry; stereochemistry
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Site-directed electronic tunneling in a dissipative molecular environment

Roie Volkovich, Maytal Caspary Toroker, and Uri Peskin

J. Chem. Phys. 129, 034501 (2008); http://dx.doi.org/10.1063/1.2951449 (8 pages) | Cited 6 times

Online Publication Date: 15 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The ability to control electronic tunneling in complex molecular networks of multiple donor/acceptor sites is studied theoretically. Our past analysis, demonstrating the phenomenon of site-directed transport, was limited to the coherent tunneling regime. In this work we consider electronic coupling to a dissipative molecular environment including the effect of decoherence. The nuclear modes are classified into two categories. The first kind corresponds to the internal molecular modes, which are coupled to the electronic propagation along the molecular bridges. The second kind corresponds to the external solvent modes, which are coupled to the electronic transport between different segments of the molecular network. The electronic dynamics is simulated within the effective single electron picture in the framework of the tight binding approximation. The nuclear degrees of freedom are represented as harmonic modes and the electronic-nuclear coupling is treated within the time-dependent Redfield approximation. Our results demonstrate that site-directed tunneling prevails in the presence of dissipation, provided that the decoherence time is longer than the time period for tunneling oscillations (e.g., at low temperatures). Moreover, it is demonstrated that the strength of electronic coupling to the external nuclear modes (the solvent reorganization energy) controls the coherent intramolecular tunneling dynamics at short times and may be utilized for the experimental control of site-directed tunneling in a complex network.
Show PACS
73.40.Gk Tunneling
85.65.+h Molecular electronic devices

The isotropic nuclear magnetic shielding constants of acetone in supercritical water: A sequential Monte Carlo/quantum mechanics study including solute polarization

Tertius L. Fonseca, Kaline Coutinho, and Sylvio Canuto

J. Chem. Phys. 129, 034502 (2008); http://dx.doi.org/10.1063/1.2951995 (9 pages) | Cited 5 times

Online Publication Date: 15 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The nuclear isotropic shielding constants σ(17O) and σ(13C) of the carbonyl bond of acetone in water at supercritical (P = 340.2 atm and T = 673 K) and normal water conditions have been studied theoretically using Monte Carlo simulation and quantum mechanics calculations based on the B3LYP/6-311++G(2d,2p) method. Statistically uncorrelated configurations have been obtained from Monte Carlo simulations with unpolarized and in-solution polarized solute. The results show that solvent effects on the shielding constants have a significant contribution of the electrostatic interactions and that quantitative estimates for solvent shifts of shielding constants can be obtained modeling the water molecules by point charges (electrostatic embedding). In supercritical water, there is a decrease in the magnitude of σ(13C) but a sizable increase in the magnitude of σ(17O) when compared with the results obtained in normal water. It is found that the influence of the solute polarization is mild in the supercritical regime but it is particularly important for σ(17O) in normal water and its shielding effect reflects the increase in the average number of hydrogen bonds between acetone and water. Changing the solvent environment from normal to supercritical water condition, the B3LYP/6-311++G(2d,2p) calculations on the statistically uncorrelated configurations sampled from the Monte Carlo simulation give a 13C chemical shift of 11.7±0.6 ppm for polarized acetone in good agreement with the experimentally inferred result of 9–11 ppm.
Show PACS
61.20.Ja Computer simulation of liquid structure
76.60.Cq Chemical and Knight shifts

Refinements in the characterization of the heterogeneous dynamics of Li ions in lithium metasilicate

J. Habasaki and K. L. Ngai

J. Chem. Phys. 129, 034503 (2008); http://dx.doi.org/10.1063/1.2951463 (11 pages) | Cited 5 times

Online Publication Date: 15 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We have performed the molecular dynamics simulations of ionically conducting lithium metasilicate, Li2SiO3, to get a more in depth understanding of the heterogeneous ion dynamics by separating out the partial contributions from localized and diffusive ions to the mean square displacement (MSD) 〈r2(t)〉, the non-Gaussian parameter α2(t), and the van Hove function Gs(r,t). Several different cage sizes lc have been used for the definition of localized ions. Behaviors of fast ions are obtained by the subtraction of the localized component from the 〈r2(t)〉 of all ions, and accelerated dynamics is found in the resultant subensemble. The fractional power law of MSD is explained by the geometrical correlation between successive jumps. The waiting time distribution of jumps also plays a role in determining 〈r2(t)〉 but does not affect the exponent of its fractional power law time dependence. Partial non-Gaussian parameters are found to be instructive to learn how long length-scale motions contribute to various quantities. As a function of time, the partial non-Gaussian parameter for the localized ions exhibits a maximum at around tx2, the onset time of the fractional power law regime of 〈r2(t)〉. The position of the maximum is slightly dependent on the choice of lc. The power law increases in the non-Gaussian parameter before the maximum are attributed to the Lévy distribution of length scales of successive (long) jumps. The decreases with time, after the maximum has been reached, are due to large back correlation of motions of different length scales. The dynamics of fast ions with superlinear dependence in their MSD also start at time around the maximum. Also investigated are the changes of the characteristic times demarcating different regimes of 〈r2(t)〉 on increasing temperatures from the glassy state to the liquid state. Relation between the activation energies for short time and long time regimes of 〈r2(t)〉 is in accord with interpretation of ion dynamics by the coupling model.
Show PACS
66.30.H- Self-diffusion and ionic conduction in nonmetals
64.70.P- Glass transitions of specific systems
66.10.C- Diffusion and thermal diffusion
61.43.Fs Glasses
61.20.Ja Computer simulation of liquid structure
61.43.Bn Structural modeling: serial-addition models, computer simulation

POLIR: Polarizable, flexible, transferable water potential optimized for IR spectroscopy

Parminder K. Mankoo and Thomas Keyes

J. Chem. Phys. 129, 034504 (2008); http://dx.doi.org/10.1063/1.2948966 (9 pages) | Cited 12 times

Online Publication Date: 17 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
A polarizable, flexible and transferable potential for water, POLIR, is presented. In addition to providing a good description of the usual structural and kinetic properties, POLIR correctly describes the vibrational frequencies, absolute infrared intensities, and HOH angle in clusters, liquid water, and ice, offering the possibility of a comprehensive classical theory of vibrational spectroscopy. The high degree of transferability suggests applications to solvation and to water that is confined, interfacial, and under the extreme conditions encountered in the geological and planetary sciences.
Show PACS
78.30.C- Liquids

The microscopic structure of an exactly solvable model binary solution that exhibits two closed loops in the phase diagram

Radu P. Lungu and Dale A. Huckaby

J. Chem. Phys. 129, 034505 (2008); http://dx.doi.org/10.1063/1.2953319 (11 pages)

Online Publication Date: 18 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
An exactly solvable lattice model describing a binary solution is considered where rodlike molecules of types AA and BB cover the links of a honeycomb lattice, the neighboring molecular ends having three-body and orientation-dependent bonding interactions. At phase coexistence of AA-rich and BB-rich phases, the average fraction of each type of triangle of neighboring molecular ends is calculated exactly. The fractions of the different types of triangles are then used to deduce the local microscopic structure of the coexisting phases for a case of the model that contains two closed loops in the phase diagram.
Show PACS
64.70.D- Solid-liquid transitions
64.75.Bc Solubility

Fundamental measure density functional theory studies on the freezing of binary hard-sphere and Lennard-Jones mixtures

Vadim B. Warshavsky and Xueyu Song

J. Chem. Phys. 129, 034506 (2008); http://dx.doi.org/10.1063/1.2953329 (8 pages) | Cited 2 times

Online Publication Date: 18 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Free energies and correlation functions of liquid and solid hard-sphere (HS) mixtures are calculated using the fundamental measure density functional theory. Using the thermodynamic perturbation theory the free energies of solid and liquid Lennard-Jones (LJ) mixtures are obtained from correlation functions of HS systems within a single theoretical approach. The resulting azeotrope- and spindle-type solid-liquid phase diagrams of HS and LJ binary mixtures are in good agreement with the corresponding ones from computer simulations.
Show PACS
64.70.D- Solid-liquid transitions
65.20.-w Thermal properties of liquids
64.75.Ef Mixing

The effect of the order of the autocatalysis on the transverse stability of reaction fronts

J. H. Merkin

J. Chem. Phys. 129, 034507 (2008); http://dx.doi.org/10.1063/1.2953313 (7 pages) | Cited 1 time

Online Publication Date: 21 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
A linear stability analysis of planar reaction fronts to transverse perturbations is considered for a system based on an autocatalytic reaction of general order p. Dispersion curves, plots of the growth rate σ against a transverse wavenumber k, are obtained for a range of values of p and D, where D is the ratio of the diffusion coefficients of autocatalyst and substrate. A value D0 of D, dependent on p, is found at which σmax, the maximum value of σ in the unstable regime, is largest, with D0 increasing as p is increased. An asymptotic analysis for small wavenumbers is derived, which enables the region in the (p,D) parameter space for instability to be determined. An analysis for D small is undertaken, which leads to upper bounds on the wavenumber for a possible instability.
Show PACS
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
82.20.Hf Product distribution
back to top Surfaces, Interfaces, and Materials

The effect of the water/methane interface on methane hydrate cages: The potential of mean force and cage lifetimes

Ethan A. Mastny, Clark A. Miller, and Juan J. de Pablo

J. Chem. Phys. 129, 034701 (2008); http://dx.doi.org/10.1063/1.2925680 (8 pages) | Cited 12 times

Online Publication Date: 15 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Molecular dynamics simulations were used to determine the influence of a methane-water interface on the position and stability of methane hydrate cages. A potential of mean force was calculated as a function of the separation of a methane hydrate cage and a methane-water interface. The hydrate cages are found to be strongly repelled from the methane gas into the water phase. At low enough temperatures, however, the most favorable location for the hydrate cage is at the interface on the water side. Cage lifetime simulations were performed in bulk water and near a methane-water interface. The methane-water interface increases the cage lifetime by almost a factor of 2 compared to cage lifetimes of cages in bulk water. The potential of mean force and the cage lifetime results give additional explanations for the proposed nucleation of gas hydrates at gas-water interfaces.
Show PACS
68.03.-g Gas-liquid and vacuum-liquid interfaces

On the role of the nonlocal Hartree–Fock exchange in ab initio quantum transport: H2 in Pt nanocontacts revisited

Y. García and J. C. Sancho-García

J. Chem. Phys. 129, 034702 (2008); http://dx.doi.org/10.1063/1.2953459 (5 pages) | Cited 1 time

Online Publication Date: 17 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We propose a practical way to overcome the ubiquitous problem of the overestimation of the zero-bias and zero-temperature conductance, which is associated with the use of local approximations to the exchange-correlation functional in density-functional theory when applied to quantum transport. This is done through partial substitution of the local exchange term in the functional by the nonlocal Hartree–Fock exchange. As a nontrivial example of this effect we revisit the smallest molecular bridge studied so far: a H2 molecule placed in between Pt nanocontacts. When applied to this system the value of the conductance diminishes as compared to the local-exchange-only value, which is in close agreement with the results predicted from time-dependent current-density-functional theory. Our results issue a warning message on recent claims of perfect transparency of a H2 molecule in Pt nanocontacts.
Show PACS
73.63.Rt Nanoscale contacts
73.40.Ns Metal-nonmetal contacts
73.22.-f Electronic structure of nanoscale materials and related systems
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.45.Gm Exchange, correlation, dielectric and magnetic response functions, plasmons

Structure versus electron effects in the growth mode of pentacene on metal-induced Si(111)-math×math surfaces

Jing Teng, Jiandong Guo, Kehui Wu, and Enge Wang

J. Chem. Phys. 129, 034703 (2008); http://dx.doi.org/10.1063/1.2953470 (7 pages) | Cited 1 time

Online Publication Date: 17 July 2008

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The growth of pentacene films on different metal (Ga, Pb, Bi, Ag) induced Si(111)-(math×math)R30° surfaces is investigated by scanning tunneling microscopy. On surfaces with high atomic surface roughness, such as Ga/Si-math, β-Pb/Si-math, and α-Bi/Si-math, pentacene forms an initial disordered wetting layer followed by the growth of crystalline thin films. The growth behavior is independent of the metallicity of the substrate surface in this regime. On the other hand, on surfaces with low adatom surface roughness, pentacene molecules form self-organized structures without forming a wetting layer. Moreover, the molecular orientation is critically dependent on the surface metallicity. This work reveals that the growth mode of pentacene on solid surfaces is determined by the combined effects of structural and electronic properties of the substrate.
Show PACS
68.55.ag Semiconductors
68.43.-h Chemisorption/physisorption: adsorbates on surfaces
68.35.B- Structure of clean surfaces (and surface reconstruction)
Page 1 of 2 Pages Next Page | Jump to Page
Close

Google Calendar

ADVERTISEMENT

Your Recent History Recent History Help

Recently Viewed

  1. Multifunctional metal-doped carbon nanocapsules
  2. Erratum: “Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration” [ J. Chem. Phys. 122, 144107 (2005) ]
  3. Coupled cluster calculations for static and dynamic polarizabilities of C60
  4. Optimal nuclear magnetic resonance excitation schemes for the central transition of a spin 3/2 in the presence of residual quadrupolar coupling
  5. Molecular dynamics with time dependent quantum Monte Carlo
Go to AIP Home
Copyright © American Institute of Physics
close