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Top 20 Most Read Articles
April 2013
The 20 articles with the most full-text downloads during the month, in descending order.
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J. Chem. Phys. 138, 054106 (2013); http://dx.doi.org/10.1063/1.4775807 (13 pages) Online Publication Date: 1 February 2013
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We propose a method for identifying accurate reaction coordinates among a set of trial coordinates. The method applies to special cases where motion along the reaction coordinate follows a one-dimensional Smoluchowski equation. In these cases the reaction coordinate can predict its own short-time dynamical evolution, i.e., the dynamics projected from multiple dimensions onto the reaction coordinate depend only on the reaction coordinate itself. To test whether this property holds, we project an ensemble of short trajectory swarms onto trial coordinates and compare projections of individual swarms to projections of the ensemble of swarms. The comparison, quantified by the Kullback-Leibler divergence, is numerically performed for each isosurface of each trial coordinate. The ensemble of short dynamical trajectories is generated only once by sampling along an initial order parameter. The initial order parameter should separate the reactants and products with a free energy barrier, and distributions on isosurfaces of the initial parameter should be unimodal. The method is illustrated for three model free energy landscapes with anisotropic diffusion. Where exact coordinates can be obtained from Kramers-Langer-Berezhkovskii-Szabo theory, results from the new method agree with the exact results. We also examine characteristics of systems where the proposed method fails. We show how dynamical self-consistency is related (through the Chapman-Kolmogorov equation) to the earlier isocommittor criterion, which is based on longer paths. |
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Equation of State Calculations by Fast Computing Machines J. Chem. Phys. 21, 1087 (1953); http://dx.doi.org/10.1063/1.1699114 (6 pages) Online Publication Date: 23 December 2004
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A general method, suitable for fast computing machines, for investigating such properties as equations of state for substances consisting of interacting individual molecules is described. The method consists of a modified Monte Carlo integration over configuration space. Results for the two‐dimensional rigid‐sphere system have been obtained on the Los Alamos MANIAC and are presented here. These results are compared to the free volume equation of state and to a four‐term virial coefficient expansion. |
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J. Chem. Phys. 53, 1126 (1970); http://dx.doi.org/10.1063/1.1674108 (5 pages) Online Publication Date: 18 September 2003
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Raman spectra are reported from single crystals of graphite and other graphite materials. Single crystals of graphite show one single line at 1575 cm−1. For the other materials like stress‐annealed pyrolitic graphite, commercial graphites, activated charcoal, lampblack, and vitreous carbon another line is detected at 1355 cm−1. The Raman intensity of this band is inversely proportional to the crystallite size and is caused by a breakdown of the k‐selection rule. The intensity of this band allows an estimate of the crystallite size in the surface layer of any carbon sample. Two in‐plane force constants are calculated from the frequencies. |
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Density‐functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 98, 5648 (1993); http://dx.doi.org/10.1063/1.464913 (5 pages)
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Despite the remarkable thermochemical accuracy of Kohn–Sham density‐functional theories with gradient corrections for exchange‐correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact‐exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange‐correlation functional containing local‐spin‐density, gradient, and exact‐exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first‐ and second‐row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol. |
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J. Chem. Phys. 132, 154104 (2010); http://dx.doi.org/10.1063/1.3382344 (19 pages) Online Publication Date: 16 April 2010
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The method of dispersion correction as an add-on to standard Kohn–Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%–40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C6 coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.
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Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79, 926 (1983); http://dx.doi.org/10.1063/1.445869 (10 pages)
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Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint. |
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Modified Z method to calculate melting curve by molecular dynamics J. Chem. Phys. 138, 134101 (2013); http://dx.doi.org/10.1063/1.4798225 (6 pages) Online Publication Date: 1 April 2013
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We extend the recently proposed Z method of estimating the melting temperature from a complete liquid and propose a modified Z method to calculate the melting temperature from a solid-liquid coexistence state. With the simulation box of rectangular parallelepiped, an initial structure of perfect lattice can run in the microcanonical ensemble to achieve steady solid-liquid coexistence state. The melting pressure and temperature are estimated from the coexistence state. For the small system with 1280 atoms, the simulation results show that the melting curve of copper has a good agreement with the experiments and is identical in accuracy with the results of the two-phase coexistence method with 24 000 atoms in the literature. Moreover, the method is conceptually simpler than the two-phase coexistence method.
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Perspective on density functional theory J. Chem. Phys. 136, 150901 (2012); http://dx.doi.org/10.1063/1.4704546 (9 pages) Online Publication Date: 17 April 2012
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Density functional theory (DFT) is an incredible success story. The low computational cost, combined with useful (but not yet chemical) accuracy, has made DFT a standard technique in most branches of chemistry and materials science. Electronic structure problems in a dazzling variety of fields are currently being tackled. However, DFT has many limitations in its present form: too many approximations, failures for strongly correlated systems, too slow for liquids, etc. This perspective reviews some recent progress and ongoing challenges.
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Communication: Covalent nature of X⋯H2O (X = F, Cl, and Br) interactions J. Chem. Phys. 138, 141102 (2013); http://dx.doi.org/10.1063/1.4801872 (3 pages) Online Publication Date: 12 April 2013
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Open-shell halogen (X = F, Cl, Br) atoms form entrance-channel complexes with H2O, which play an important role in the X + H2O reactions. To understand their structures and origin of stability, we report an extensive ab initio study of such complexes and contrast them with complexes between H2O and H/O(3P). Evidence is presented to show that the interaction between a halogen atom and H2O is dominated by a weak but covalent bond, rather than dispersion and/or electrostatic interactions. |
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Molecular dynamics with coupling to an external bath J. Chem. Phys. 81, 3684 (1984); http://dx.doi.org/10.1063/1.448118 (7 pages)
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In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD. A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling. The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints. The influence of coupling time constants on dynamical variables is evaluated. A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath. |
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Free Energy of a Nonuniform System. I. Interfacial Free Energy J. Chem. Phys. 28, 258 (1958); http://dx.doi.org/10.1063/1.1744102 (10 pages) Online Publication Date: 13 August 2004
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It is shown that the free energy of a volume V of an isotropic system of nonuniform composition or density is given by : NV∫V [f0(c)+κ(▽c)2]dV, where NV is the number of molecules per unit volume, ▽c the composition or density gradient, f0 the free energy per molecule of a homogeneous system, and κ a parameter which, in general, may be dependent on c and temperature, but for a regular solution is a constant which can be evaluated. This expression is used to determine the properties of a flat interface between two coexisting phases. In particular, we find that the thickness of the interface increases with increasing temperature and becomes infinite at the critical temperature Tc, and that at a temperature T just below Tc the interfacial free energy σ is proportional to (Tc−T  .The predicted interfacial free energy and its temperature dependence are found to be in agreement with existing experimental data. The possibility of using optical measurements of the interface thickness to provide an additional check of our treatment is briefly discussed. |
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Perspective: The glass transition J. Chem. Phys. 138, 12A301 (2013); http://dx.doi.org/10.1063/1.4795539 (13 pages) Online Publication Date: 26 March 2013
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We provide here a brief perspective on the glass transition field. It is an assessment, written from the point of view of theory, of where the field is and where it seems to be heading. We first give an overview of the main phenomenological characteristics, or “stylised facts,” of the glass transition problem, i.e., the central observations that a theory of the physics of glass formation should aim to explain in a unified manner. We describe recent developments, with a particular focus on real space properties, including dynamical heterogeneity and facilitation, the search for underlying spatial or structural correlations, and the relation between the thermal glass transition and athermal jamming. We then discuss briefly how competing theories of the glass transition have adapted and evolved to account for such real space issues. We consider in detail two conceptual and methodological approaches put forward recently, that aim to access the fundamental critical phenomenon underlying the glass transition, be it thermodynamic or dynamic in origin, by means of biasing of ensembles, of configurations in the thermodynamic case, or of trajectories in the dynamic case. We end with a short outlook.
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On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method J. Chem. Phys. 138, 084107 (2013); http://dx.doi.org/10.1063/1.4792208 (8 pages) Online Publication Date: 27 February 2013
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An issue of general interest in computer simulations is to incorporate information from experiments into a structural model. An important caveat in pursuing this goal is to avoid corrupting the resulting model with spurious and arbitrary biases. While the problem of biasing thermodynamic ensembles can be formulated rigorously using the maximum entropy method introduced by Jaynes, the approach can be cumbersome in practical applications with the need to determine multiple unknown coefficients iteratively. A popular alternative strategy to incorporate the information from experiments is to rely on restrained-ensemble molecular dynamics simulations. However, the fundamental validity of this computational strategy remains in question. Here, it is demonstrated that the statistical distribution produced by restrained-ensemble simulations is formally consistent with the maximum entropy method of Jaynes. This clarifies the underlying conditions under which restrained-ensemble simulations will yield results that are consistent with the maximum entropy method.
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J. Chem. Phys. 138, 064104 (2013); http://dx.doi.org/10.1063/1.4790583 (9 pages) Online Publication Date: 13 February 2013
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In this paper we present a time-domain time-dependent density functional theory (TDDFT) approach to calculate frequency-dependent polarizability and hyperpolarizabilities. In this approach, the electronic degrees of freedom are propagated within the density matrix based TDDFT framework using the efficient modified midpoint and unitary transformation algorithm. We use monochromatic waves as external perturbations and apply the finite field method to extract various orders of the time-dependent dipole moment. By fitting each order of time-dependent dipole to sinusoidal waves with harmonic frequencies, one can obtain the corresponding (hyper)polarizability tensors. This approach avoids explicit Fourier transform and therefore does not require long simulation time. The method is illustrated with application to the optically active organic molecule para-nitroaniline, of which the frequency-dependent polarizability α(−ω; ω), second-harmonic generation β(−2ω; ω, ω), optical rectification β(0; −ω, ω), third-harmonic generation γ(−3ω; ω, ω, ω), and degenerate four-wave mixing γ(−ω; ω, ω, −ω) are calculated.
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Kinetics of Phase Change. I General Theory J. Chem. Phys. 7, 1103 (1939); http://dx.doi.org/10.1063/1.1750380 (10 pages) Online Publication Date: 22 December 2004
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The theory of the kinetics of phase change is developed with the experimentally supported assumptions that the new phase is nucleated by germ nuclei which already exist in the old phase, and whose number can be altered by previous treatment. The density of germ nuclei diminishes through activation of some of them to become growth nuclei for grains of the new phase, and ingestion of others by these growing grains. The quantitative relations between the density of germ nuclei, growth nuclei, and transformed volume are derived and expressed in terms of a characteristic time scale for any given substance and process. The geometry and kinetics of a crystal aggregate are studied from this point of view, and it is shown that there is strong evidence of the existence, for any given substance, of an isokinetic range of temperatures and concentrations in which the characteristic kinetics of phase change remains the same. The determination of phase reaction kinetics is shown to depend upon the solution of a functional equation of a certain type. Some of the general properties of temperature‐time and transformation‐time curves, respectively, are described and explained. |
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Communication: New insight into electronic shells of metal clusters: Analogues of simple molecules J. Chem. Phys. 138, 141101 (2013); http://dx.doi.org/10.1063/1.4801860 (4 pages) Online Publication Date: 12 April 2013
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A new concept of super valence bond is proposed, of which superatoms can share both valence pairs and nuclei for shell closure thus forming delocalized super bonding. Using Li clusters as a test case, we theoretically find that metal clusters can mimic the behavior of simple molecules in electronic shells. It is found that Li14, Li10, and Li8 clusters are analogues of F2, N2, and CH4 molecules, respectively, in molecular orbital diagrams and bonding patterns. This new concept shows new insights in understanding the stability of clusters and designing the cluster-assembling materials. |
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J. Chem. Phys. 138, 134102 (2013); http://dx.doi.org/10.1063/1.4796545 (6 pages) Online Publication Date: 1 April 2013
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This paper explores the possibility of combining projected Hartree-Fock and density functional theories for treating static and dynamic correlations in molecular systems with mean-field computational cost. The combination of spin-projected unrestricted Hartree-Fock (SUHF) with the TPSS correlation functional (SUHF+TPSS) yields excellent results for non-metallic molecular dissociations and singlet-triplet splittings. However, SUHF+TPSS fails to provide the qualitatively correct dissociation curve for the notoriously difficult case of the chromium dimer. By tuning the TPSS correlation parameters and adding complex conjugation symmetry breaking and restoration to SUHF, the right curve shape for Cr2 can be obtained; unfortunately, such a combination is found to lead to overcorrelation in the general case.
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Sparse tensor framework for implementation of general local correlation methods J. Chem. Phys. 138, 144101 (2013); http://dx.doi.org/10.1063/1.4798940 (9 pages) Online Publication Date: 8 April 2013
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Coupled-cluster methods offer unprecedented accuracy for a wide range of chemically important properties, but the steep scaling of computational cost with system size makes widespread use challenging. Local approximations, building on the short-range nature of electron correlation effects in insulators, help a great deal, but are much more complicated than their canonical counterparts. In this work we discuss an automated implementation scheme for local coupled-cluster methods, based on an interpreter and an underlying representation of sparse tensors. We demonstrate the efficacy of the approach through implementation of a very wide range of singles-and-doubles-based coupled-cluster schemes.
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J. Chem. Phys. 137, 134102 (2012); http://dx.doi.org/10.1063/1.4755818 (11 pages) Online Publication Date: 2 October 2012
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The concept of a “consistent,” Kohn-Sham (KS) density functional theory (DFT) is discussed, where the functional is able to provide good total energies and its self-consistent potential is such that the KS eigenvalues correspond to accurate approximations to the principal ionization potentials for the molecule. Today, none of the vast number of DFT approximations show this property. The one exception is the ab initio dft method built upon the optimized effective potential strategy for exchange and correlation. This qualifies as a DFT method because it represents the correlated density as a single determinant and by imposing that condition, generates local exchange and correlation operators which are used in self-consistent solutions of the orbitals and eigenvalues. Such a “consistent” DFT shares many of the properties of the Dyson equation, but without its frequency dependence and associated complications. The relationship between ab initio dft based on MBPT2 functional and GW method is discussed. Ab initio dft provides a self-consistent, frequency independent, effective independent particle alternative with a local correlation potential.
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J. Chem. Phys. 138, 104501 (2013); http://dx.doi.org/10.1063/1.4793311 (11 pages) Online Publication Date: 8 March 2013
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In this (Paper I) and the companion paper (Paper II; R. May, R. Smith, and B. Kay, J. Chem. Phys. 138, 104502 (2013)10.1063/1.4793312), we investigate the mechanisms for the release of trapped gases from underneath amorphous solid water (ASW) films. In prior work, we reported the episodic release of trapped gases in concert with the crystallization of ASW, a phenomenon that we termed the “molecular volcano.” The observed abrupt desorption is due to the formation of cracks that span the film to form a connected pathway for release. In this paper, we utilize the “molecular volcano” desorption peak to characterize the formation of crystallization-induced cracks. We find that the crack length distribution is independent of the trapped gas (Ar, Kr, Xe, CH4, N2, O2, or CO). Selective placement of the inert gas layer is used to show that cracks form near the top of the film and propagate downward into the film. Isothermal experiments reveal that, after some induction time, cracks propagate linearly in time with an Arrhenius dependent velocity corresponding to an activation energy of 54 kJ/mol. This value is consistent with the crystallization growth rates reported by others and establishes a direct connection between crystallization growth rate and the crack propagation rate. A two-step model in which nucleation and crystallization occurs in an induction zone near the top of the film followed by the propagation of a crystallization/crack front into the film is in good agreement with the temperature programmed desorption results. |
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