Jump to Content
View Cart
Top 20 Most Read Articles
October 2007
The 20 articles with the most full-text downloads during the month, in descending order.
 |
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
Full Text:
|
Download PDF
|
||
|
Show Abstract
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. |
|||
|
|
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)
Full Text:
|
Download PDF
|
|||
|
Show Abstract
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. |
||||
|
Show PACS
|
||||
|
|
J. Chem. Phys. 127, 154102 (2007); http://dx.doi.org/10.1063/1.2790019 (11 pages) Online Publication Date: 16 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
The formic acid molecule, its dimers, and its molecular crystal are adopted as test systems to compare results obtained with plane wave (PW) basis sets and norm-conserving pseudopotentials to all-electron Gaussian-type orbital (GTO) calculations. The CPMD and CRYSTAL06 codes, respectively, are applied with the PBE, PW91, and BLYP density functionals. Hydrogen bonding is the leading interaction in the dimers and the crystal. In the latter, dispersive and weak C–H⋯O interactions are also relevant. Irrespective of the adopted functional, for all considered structures PW and GTO results converge smoothly as a function of the quality of the adopted basis sets to the same values for structures, energies of interaction, and harmonic vibrational features. To achieve a high level of mutual agreement the use of GTO basis sets of at least of triple-zeta quality including one set of polarization functions and PW basis sets with a kinetic energy cutoff higher than 110 Ry is recommended. Pros and cons of both approaches for studying molecular crystals are also discussed.
|
|||
|
Show PACS
|
|||
|
|
Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles J. Chem. Phys. 127, 154101 (2007); http://dx.doi.org/10.1063/1.2790421 (19 pages) Online Publication Date: 15 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
We introduce a “virtual-move” Monte Carlo algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an important realization being self-assembling particles endowed with strong, short-ranged, and angularly specific (“patchy”) attractions. Standard Monte Carlo techniques employ sequential updates of particles and can suffer from low acceptance rates when attractions are strong. In this event, collective motion can be strongly suppressed. Our algorithm avoids this problem by proposing simultaneous moves of collections (clusters) of particles according to gradients of interaction energies. One particle first executes a “virtual” trial move. We determine which of its neighbors move in a similar fashion by calculating individual bond energies before and after the proposed move. We iterate this procedure and update simultaneously the positions of all affected particles. Particles move according to an approximation of realistic dynamics without requiring the explicit computation of forces and without the step size restrictions required when integrating equations of motion. We employ a size- and shape-dependent damping of cluster movements, motivated by collective hydrodynamic effects neglected in simple implementations of Brownian dynamics. We discuss the virtual-move algorithm in the context of other Monte Carlo cluster-move schemes and demonstrate its utility by applying it to a model of biological self-assembly.
|
|||
|
Show PACS
|
|||
|
|
Local electrostatics algorithm for classical molecular dynamics simulations J. Chem. Phys. 127, 134104 (2007); http://dx.doi.org/10.1063/1.2769358 (9 pages) Online Publication Date: 3 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
An implementation of a local, linear scaling algorithm for computing electrostatic interactions in molecular dynamics simulations that was recently proposed [
J. Rottler and A. C. Maggs, Phys. Rev. Lett. 93, 170201 (2004)
] is presented. Coulombic forces are mediated by a propagating electric field that obeys Gauss’s law. A detailed description of the numerical implementation is presented, and the accuracy is calibrated by comparing the electrostatic force to that obtained from a standard Ewald summation. A parallelized implementation exhibits excellent scaling behavior on a contemporary low latency compute cluster, and therefore becomes an interesting alternative to existing algorithms for computing electrostatics in large-scale molecular dynamics. The approach opens new possibilities for the study of physical situations that are difficult or impossible to treat with standard reciprocal space methods, in particular nonperiodic boundary conditions and spatially heterogeneous dielectric environments in implicit solvent models.
|
|||
|
Show PACS
|
|||
|
|
J. Chem. Phys. 127, 141101 (2007); http://dx.doi.org/10.1063/1.2794032 (4 pages) Online Publication Date: 9 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
Designing an effective order parameter for the identification of geometries in atomic clusters is an important step toward understanding the structural transitions occurring in these systems. We propose a method that simultaneously utilizes the local and global bond orientational order parameters for structural transitions. When applied to Lennard–Jones clusters at finite temperature over the size range 30 ≤ N ≤ 146, this method identified all the major geometries: icosahedra with Mackay overlayers, icosahedra with anti-Mackay overlayers, decahedra, octahedra, and tetrahedra. From the distributions of these geometries as a function of temperatures on clusters containing 38, 75, and 98 atoms, we are able to interpret all transition types without ambiguity.
|
|||
|
Show PACS
|
|||
|
|
Molecular simulations of droplet coalescence in oil/water/surfactant systems J. Chem. Phys. 127, 134701 (2007); http://dx.doi.org/10.1063/1.2780865 (11 pages) Online Publication Date: 2 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
We report a molecular simulation study of the mechanism by which droplets covered with a surfactant monolayer coalesce. We study a model system where the rate-limiting step in coalescence is the rupture of the surfactant film. Our simulations allow us to focus on the stages at the core of the coalescence process: the initial rupture of the two surfactant monolayers, the rearrangement of the surfactant molecules to form a channel connecting the two droplets, and the expansion of the radius of the resulting channel. For our numerical study, we made use of the dissipative particle dynamics method. We used a coarse-grained description of the oil, water, and surfactant molecules. The rupture of the surfactant film is a rare event on the molecular time scale. To enhance the sampling of the rupture of the surfactant film, we used forward flux sampling (FFS). FFS not only allows us to estimate coalescence rates, it also provides insight into the molecular structure and free energy of the “transition” state. For an oil-water-oil film without surfactant, the rupture rate decreases exponentially with increasing film thickness. The critical state is different in thin and thick films: Thin films break following a large enough thickness fluctuation. Thicker films break only after a sufficiently large hole fluctuation—they can heal. Next, we designed surfactant molecules with positive, zero, and negative natural curvatures. For a water film between two surfactant-covered oil droplets, the rupture rate is highest when the surfactant has a negative natural curvature, lowest when it has zero natural curvature, and lying in between when it has a positive natural curvature. This nonmonotonic variation with curvature stems from two effects: First, the surfactants with a large absolute value of the natural curvature have lower interfacial tension and bending rigidity. This promotes the interfacial fluctuations required to nucleate a channel. Second, the sign of the natural curvature determines whether there is a critical channel radius at which the channel free energy has a maximum. The latter is in agreement with the hole-nucleation theory of
Kabalnov and Wennerström [Langmuir 12, 276 (1996)]
. Our simulations seriously overestimate the relative stability of surfactant free emulsions. We argue that this is due to the fact that our model does not allow for nanobubble formation and capillary evaporation—processes that are presumably of key importance in the coalescence of surfactant-free emulsions.
|
|||
|
Show PACS
|
|||
|
|
Resonance vibrational Raman optical activity: A time-dependent density functional theory approach J. Chem. Phys. 127, 134101 (2007); http://dx.doi.org/10.1063/1.2768533 (11 pages) Online Publication Date: 2 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
We present a method to calculate both on- and off-resonance vibrational Raman optical activities (VROAs) of molecules using time-dependent density functional theory. This is an extension of a method to calculate the normal VROA by including a finite lifetime of the electronic excited states in all calculated properties. The method is based on a short-time approximation to Raman scattering and is, in the off-resonance case, identical to the standard theory of Placzek. The normal and resonance VROA spectra are calculated from geometric derivatives of the different generalized polarizabilites obtained using linear response theory which includes a damping term to account for the finite lifetime. Gauge-origin independent results for normal VROA have been ensured using either the modified-velocity gauge or gauge-included atomic orbitals. For the resonance VROA only the modified-velocity gauge has been implemented. We present some initial results for H2O2 and (S)-methyloxirane and compare with predictions from a simple two-state approximation.
|
|||
|
Show PACS
|
|||
|
|
Umbrella sampling for nonequilibrium processes J. Chem. Phys. 127, 154112 (2007); http://dx.doi.org/10.1063/1.2784118 (8 pages) Online Publication Date: 18 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
The authors introduce an algorithm for determining the steady-state probability distribution of an ergodic system arbitrarily far from equilibrium. By enforcing equal sampling of different regions of phase space, as in umbrella sampling simulations of systems at equilibrium, low probability regions are explored to a much greater extent than in physically weighted simulations. The algorithm can be used to accumulate joint statistics for an arbitrary number of order parameters for a system governed by any stochastic dynamics. They demonstrate the efficiency of the algorithm by applying it to a model of a genetic toggle switch which evolves irreversibly according to a continuous time Monte Carlo procedure.
|
|||
|
Show PACS
|
|||
|
|
J. Chem. Phys. 127, 144104 (2007); http://dx.doi.org/10.1063/1.2794036 (5 pages) Online Publication Date: 10 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
|||
|
Show Abstract
We report second order Møller-Plesset (MP2) and MP2-F12 total energies on He, Ne, Ar, H2O, CH4, C2H2, C2H4, and C6H6, using the correlation consistent basis sets, aug-cc-pVXZ (X = D−7). Basis set extrapolation techniques are applied to the MP2 and MP2-F12/B methods. The performance of the methods is tested in the calculations of the atoms, He, Ne, and Ar. It is indicated that the two-point extrapolation of MP2-F12/B with the basis sets (X = 5,6) is the most reliable. Similar accuracy is obtained using two-point extrapolated conventional MP2 with the basis sets (X = 6,7). For the molecules investigated the valence MP2 correlation energy is estimated within 1 mEh.
|
||||
|
Show PACS
|
||||
|
|
Double-hybrid density functional theory for excited electronic states of molecules J. Chem. Phys. 127, 154116 (2007); http://dx.doi.org/10.1063/1.2772854 (18 pages) Online Publication Date: 19 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
Double-hybrid density functionals are based on a mixing of standard generalized gradient approximations (GGAs) for exchange and correlation with Hartree-Fock (HF) exchange and a perturbative second-order correlation part (PT2) that is obtained from the Kohn-Sham (GGA) orbitals and eigenvalues. This virtual orbital-dependent functional (dubbed B2PLYP) contains only two empirical parameters that describe the mixture of HF and GGA exchange (ax) and of the PT2 and GGA correlation (ac), respectively. Extensive testing has recently demonstrated the outstanding accuracy of this approach for various ground state problems in general chemistry applications. The method is extended here without any further empirical adjustments to electronically excited states in the framework of time-dependent density functional theory (TD-DFT) or the closely related Tamm-Dancoff approximation (TDA-DFT). In complete analogy to the ground state treatment, a scaled second-order perturbation correction to configuration interaction with singles (CIS(D)) wave functions developed some years ago by
Head-Gordon et al. [Chem. Phys. Lett. 219, 21 (1994)]
is computed on the basis of density functional data and added to the TD(A)-DFT∕GGA excitation energy. The method is implemented by applying the resolution of the identity approximation and the efficiency of the code is discussed. Extensive tests for a wide variety of molecules and excited states (of singlet, triplet, and doublet multiplicities) including electronic spectra are presented. In general, rather accurate excitation energies (deviations from reference data typically <0.2 eV) are obtained that are mostly better than those from standard functionals. Still, systematic errors are obtained for Rydberg (too low on average by about 0.3 eV) and charge-transfer transitions but due to the relatively large ax parameter (0.53), B2PLYP outperforms most other functionals in this respect. Compared to conventional HF-based CIS(D), the method is more robust in electronically complex situations due to the implicit account of static correlation effects by the GGA parts. The (D) correction often works in the right direction and compensates for the overestimation of the transition energy at the TD level due to the elevated fraction of HF exchange in the hybrid GGA part. Finally, the limitations of the method are discussed for challenging systems such as transition metal complexes, cyanine dyes, and multireference cases.
|
|||
|
Show PACS
|
|||
|
|
Comparison of double-ended transition state search methods J. Chem. Phys. 127, 134102 (2007); http://dx.doi.org/10.1063/1.2767621 (12 pages) Online Publication Date: 2 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
While a variety of double-ended transition state search methods have been developed, their relative performance in characterizing complex multistep pathways between structurally disparate molecular conformations remains unclear. Three such methods (doubly-nudged elastic band, a string method, and a growing string method) are compared for a series of benchmarks ranging from permutational isomerizations of the seven-atom Lennard-Jones cluster (LJ7) to highly cooperative LJ38 and LJ75 rearrangements, and the folding pathways of two peptides. A database of short paths between LJ13 local minima is used to explore the effects of parameters and suggest reasonable default values. Each double-ended method was employed within the framework of a missing connection network flow algorithm to construct more complicated multistep pathways. We find that in our implementation none of the three methods definitively outperforms the others, and that their relative effectiveness is strongly system and parameter dependent.
|
|||
|
Show PACS
|
|||
|
|
Topological building blocks of hydrogen bond network in water J. Chem. Phys. 127, 134504 (2007); http://dx.doi.org/10.1063/1.2772627 (9 pages) Online Publication Date: 4 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
|||
|
Show Abstract
Basic three-dimensional units of the network, called fragments, are introduced to characterize the hydrogen bond (HB) network structure of water. Topological differences among normal liquid water, water at low temperature, and water under high pressure are elucidated by their fragment statistics. Water at low temperature has almost defect-free network and is filled with stable fragments with small distortion. It is found that there exists a certain way on how fragments mutually aggregate. Well-formed aggregates heterogeneously constitute very stable network structures. HB network rearrangements occur scarcely inside these aggregated domains but take place in their surface areas. The heterogeneity of HB structure and rearrangement in water is thus explained in terms of the fragment structure and its rearrangements. The fragment analysis thus elucidates the intermediate-range order in water HB network.
|
||||
|
Show PACS
|
||||
|
|
First principles study of magnetism in nanographenes J. Chem. Phys. 127, 124703 (2007); http://dx.doi.org/10.1063/1.2770722 (5 pages) Online Publication Date: 27 September 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
|||||||||||||
|
Show Abstract
Magnetism in nanographenes [also known as polycyclic aromatic hydrocarbons (PAHs)] is studied with first principles density functional calculations. We find that an antiferromagnetic (AFM) phase appears as the PAH reaches a certain size. This AFM phase in PAHs has the same origin as the one in infinitely long zigzag-edged graphene nanoribbons, namely, from the localized electronic state at the zigzag edge. The smallest PAH still having an AFM ground state is identified. With increased length of the zigzag edge, PAHs approach an infinitely long ribbon in terms of (1) the energetic ordering and difference among the AFM, ferromagnetic, and nonmagnetic phases and (2) the average local magnetic moment at the zigzag edges. These PAHs serve as ideal targets for chemical synthesis of nanographenes that possess magnetic properties. Moreover, our calculations support the interpretation that experimentally observed magnetism in activated carbon fibers originates from the zigzag edges of the nanographenes.
|
||||||||||||||
|
Show PACS
|
||||||||||||||
|
|
J. Chem. Phys. 127, 134302 (2007); http://dx.doi.org/10.1063/1.2773726 (5 pages) Online Publication Date: 2 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
Buffer-gas pressure broadening for the ν1+ν3 band of H2O at 1.34–1.44 μm for a variety of buffer gases was investigated at room temperature using continuous-wave cavity ring-down spectroscopy. The effective interaction energy of water dimer under room temperature conditions was evaluated from the pressure broadening coefficients for rare gases using Permenter-Seaver’s relation. Monte Carlo simulations were performed using ab initio molecular orbital calculations to evaluate the interaction energies for the water dimer at 300 K. In this theoretical calculation, the orientations of the two water molecules were statistically treated.
|
|||
|
Show PACS
|
|||
|
|
J. Chem. Phys. 127, 141102 (2007); http://dx.doi.org/10.1063/1.2795693 (4 pages) Online Publication Date: 10 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
Calculations for the complex of thymine and adenine are used to show that the supermolecule second-order Møller-Plesset perturbation theory (MP2) approach for evaluating interaction energies fails in certain cases because of the behavior of one of its components: the uncoupled Hartree-Fock dispersion energy. A simple approach for correcting the MP2 supermolecule interaction energies is proposed. It focuses on correcting a relatively small difference between the MP2 and coupled cluster interaction energies, which is a very appealing feature of the new approach considering a benchmark role played by coupled cluster results.
|
|||
|
Show PACS
|
|||
|
|
J. Chem. Phys. 127, 144107 (2007); http://dx.doi.org/10.1063/1.2770718 (6 pages) Online Publication Date: 12 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
We investigate electron transport through single conjugated molecules—including benzenedithiol, oligophenylene ethynylenes of different lengths, and a ferrocene-containing molecule sandwiched between two gold electrodes with different contact structures—by using a single-particle Green function method combined with density functional theory calculation. We focus on the effect of the basis set in the ab initio calculation. It is shown that the position of the Fermi energy in the transport gap is sensitive to the molecule-lead charge transfer which is affected by the size of basis set. This can dramatically change, by orders of magnitude, the conductance for long molecules, though the effect is only minor for short ones. A resonance around the Fermi energy tends to pin the position of the Fermi energy and suppress this effect. The result is discussed in comparison with experimental data.
|
|||
|
Show PACS
|
|||
|
|
Accelerated entropy estimates with accelerated dynamics J. Chem. Phys. 127, 154105 (2007); http://dx.doi.org/10.1063/1.2794754 (5 pages) Online Publication Date: 16 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
Accelerated dynamics is applied to entropy calculations on a set of toy and molecular systems and is found to enhance the rate of convergence.
|
|||
|
Show PACS
|
|||
|
|
A unified density-functional treatment of dynamical, nondynamical, and dispersion correlations J. Chem. Phys. 127, 124108 (2007); http://dx.doi.org/10.1063/1.2768530 (8 pages) Online Publication Date: 27 September 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
In previous work we have introduced exact-exchange-based density-functional models of dynamical, nondynamical, and dispersion correlations. We have not yet, however, been able to combine these models into a single energy functional. The problem is that interaction curves in van der Waals complexes are too repulsive. A simple solution is proposed in the present work resulting in an exact-exchange-based energy functional for all chemical interactions, from the weakest (dispersion) to the strongest (molecular bonds).
|
|||
|
Show PACS
|
|||
|
|
What is the best definition of a liquid cluster at the molecular scale? J. Chem. Phys. 127, 154516 (2007); http://dx.doi.org/10.1063/1.2786457 (6 pages) Online Publication Date: 19 October 2007
Full Text:
Read Online (HTML)
|
Download PDF
|
||
|
Show Abstract
We investigate the ability of different cluster definitions to serve as a good reaction coordinate in molecular simulations of nucleation. In particular, the most commonly used Stillinger criterion [
J. Chem. Phys. 38, 1486 (1963)
] is compared with the cluster definition introduced by ten
Wolde and Frenkel [J. Chem. Phys. 109, 9901 (1998)
]. The accuracy of these two different cluster definitions is tested by using molecular dynamics to study the vapor-liquid nucleation of Lennard-Jones argon as a model system. We are able to compare the size of the critical cluster identified by each cluster definition with a completely model-independent value provided by the nucleation theorem, aided by a recently introduced method that accurately extracts the location of the transition state directly from the kinetics. It is found that the Stillinger definition strongly overestimates the size of small molecular clusters by up to a factor of 2. A simple change of the Stillinger radius is unable to rectify this deficiency. On the contrary, the ten Wolde-Frenkel definition, while being only slightly more elaborate than a simple Stillinger criterion, is remarkably successful in identifying the correct molecular excess of the small clusters if the parameters are chosen adequately. The method described here can also be generalized to identify a proper reaction coordinate in other activated processes.
|
|||
|
Show PACS
|
|||
This Publication
Scitation
Google Scholar
PubMed