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Top 20 Most Read Articles
January 2012
The 20 articles with the most full-text downloads during the month, in descending order.
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Communication: Quantum mechanics without wavefunctions J. Chem. Phys. 136, 031102 (2012); doi:10.1063/1.3680558 (4 pages) Online Publication Date: 19 January 2012
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We present a self-contained formulation of spin-free non-relativistic quantum mechanics that makes no use of wavefunctions or complex amplitudes of any kind. Quantum states are represented as ensembles of real-valued quantum trajectories, obtained by extremizing an action and satisfying energy conservation. The theory applies for arbitrary configuration spaces and system dimensionalities. Various beneficial ramifications—theoretical, computational, and interpretational—are discussed.
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Electronic structure calculations in arbitrary electrostatic environments J. Chem. Phys. 136, 024101 (2012); doi:10.1063/1.3670417 (14 pages) Online Publication Date: 9 January 2012
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Modeling of electronic structure of molecules in electrostatic environments is of considerable relevance for surface-enhanced spectroscopy and molecular electronics. We have developed and implemented a novel approach to the molecular electronic structure in arbitrary electrostatic environments that is compatible with standard quantum chemical methods and can be applied to medium-sized and large molecules. The scheme denoted CheESE (chemistry in electrostatic environments) is based on the description of molecular electronic structure subject to a boundary condition on the system/environment interface. Thus, it is particularly suited to study molecules on metallic surfaces. The proposed model is capable of describing both electrostatic effects near nanostructured metallic surfaces and image-charge effects. We present an implementation of the CheESE model as a library module and show example applications to neutral and negatively charged molecules.
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J. Chem. Phys. 135, 241102 (2011); doi:10.1063/1.3675629 (4 pages) Online Publication Date: 29 December 2011
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The ability to achieve sub-wavenumber resolution (0.6 cm−1) and a large signal-to-noise ratio in high-resolution broadband sum-frequency generation vibrational spectroscopy (HR-BB-SFG-VS) allows for the detailed SFG spectral lineshapes to be used in the unambiguous determination of fine spectral features. Changes in the structural spectroscopic phase in SFG-VS as a function of beam polarization and experimental geometry proved to be instrumental in the identification of an unexpected 2.78 ± 0.07 cm−1 spectral splitting for the two methyl groups at the vapor/dimethyl sulfoxide (DMSO, (CH3)2SO) liquid interface as well as in the determination of their orientational angles.
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J. Chem. Phys. 136, 021101 (2012); doi:10.1063/1.3675847 (4 pages) Online Publication Date: 11 January 2012
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Relaxation of a system to equilibrium is as ubiquitous, essential, and as poorly quantified as any phenomena in physics. For over a century, the most precise description of relaxation has been Boltzmann's H-theorem, predicting that a uniform ideal gas will relax monotonically. Recently, the relaxation theorem has shown that the approach to equilibrium can be quantified in terms of the dissipation function first defined in the proof of the Evans-Searles fluctuation theorem. Here, we provide the first demonstration of the relaxation theorem through simulation of a simple fluid system that generates a non-monotonic relaxation to equilibrium.
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An algebraic operator approach to electronic structure J. Chem. Phys. 135, 244111 (2011); doi:10.1063/1.3671388 (14 pages) Online Publication Date: 30 December 2011
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In this paper, we introduce an algebraic approach to electronic structure calculations. Our approach constructs a Jordan algebra based on the second-quantized electronic Hamiltonian. From the structure factor of this algebra, we show that we can calculate the energy of the ground electronic state of the Hamiltonian operator. We apply our method to several generalized Hubbard models and show that we can usually obtain a significant fraction of the correlation energy for low-to-moderate values of the electronic repulsion parameter while still retaining the O(L3) scaling of the Hartree-Fock algorithm. This surprising result, along with several other observations, suggests that our algebraic approach represents a new paradigm for electronic structure calculations which opens up many new directions for research.
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Stochastic simulation of chemically reacting systems using multi-core processors J. Chem. Phys. 136, 014101 (2012); doi:10.1063/1.3670416 (8 pages) Online Publication Date: 3 January 2012
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In recent years, computer simulations have become increasingly useful when trying to understand the complex dynamics of biochemical networks, particularly in stochastic systems. In such situations stochastic simulation is vital in gaining an understanding of the inherent stochasticity present, as these models are rarely analytically tractable. However, a stochastic approach can be computationally prohibitive for many models. A number of approximations have been proposed that aim to speed up stochastic simulations. However, the majority of these approaches are fundamentally serial in terms of central processing unit (CPU) usage. In this paper, we propose a novel simulation algorithm that utilises the potential of multi-core machines. This algorithm partitions the model into smaller sub-models. These sub-models are then simulated, in parallel, on separate CPUs. We demonstrate that this method is accurate and can speed-up the simulation by a factor proportional to the number of processors available.
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J. Chem. Phys. 53, 1126 (1970); doi: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); doi: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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Equation of State Calculations by Fast Computing Machines J. Chem. Phys. 21, 1087 (1953); doi: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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Local reactivity of O2 with Pt3 on Co3Pt and related backgrounds J. Chem. Phys. 128, 204701 (2008); doi:10.1063/1.2908824 (11 pages) Online Publication Date: 27 May 2008
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We study the local reactivity of molecular oxygen with bimetallic substrates of a platinum trimer island supported on nanotips of CoPt, Pt, Co, Ni, and Fe. Because of the reduced interatomic distances and varying interaction strengths with the substrates, the supported island interaction with oxygen can be tuned from stronger to weaker relative to the interaction of a freestanding island with oxygen despite that there is no well-behaved trend with the binding energy of the island to the substrates.
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J. Chem. Phys. 136, 041101 (2012); doi:10.1063/1.3678309 (4 pages) Online Publication Date: 23 January 2012
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Density functional theory (DFT) based approaches within the local-density approximation or generalized gradient approximation frameworks fail to predict the correct electron localization in strongly correlated systems due to the lack of cancellation of the Coulomb self-interaction. This problem might be circumvented either by using hybrid functionals or by introducing a Hubbard-like term to account for the on site interactions. This latter DFT+U approach is less expensive and therefore more practical for extensive calculations in solid-state computational simulations. By and large, the U term only affects the metal electrons, in our case the Ce 4f ones. In the present work, we report a systematic analysis of the effect of adding such a U term also to the oxygen 2p electrons. We find that using a set of Uf = 5 eV and Up = 5eV effective terms leads to improved description of the lattice parameters, band gaps, and formation and reduction energies of CeO2. |
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J. Chem. Phys. 136, 024103 (2012); doi:10.1063/1.3674992 (8 pages) Online Publication Date: 9 January 2012
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We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the Cs-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.
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J. Chem. Phys. 132, 154104 (2010); doi: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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O2-coverage-dependent CO oxidation on reduced TiO2(110): A first principles study J. Chem. Phys. 125, 144706 (2006); doi:10.1063/1.2354083 (6 pages) Online Publication Date: 11 October 2006
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First principles periodic slab calculations based on gradient-corrected density functional theory have been performed to investigate CO oxidation on rutile TiO2(110) at varying O2 coverages (θ = 1, 2, and 3, where θ is defined as the number of O2 per oxygen vacancy). For each coverage we only present the reaction of CO with oxygen species in the most stable configuration. Our results show a significant variation in the oxidation activation energy with O2 coverage.
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J. Chem. Phys. 136, 014501 (2012); doi:10.1063/1.3665140 (8 pages) Online Publication Date: 3 January 2012
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We have investigated the rotational dynamics of lithium thiocyanate (LiNCS) dissolved in various polar solvents with time and polarization resolved vibrational spectroscopy. LiNCS forms multiple distinct ionic structures in solution that can be distinguished with the CN stretch vibrational frequency of the different ionic assemblies. By varying the solvent and the LiNCS concentration, the number and type of ionic structures present in solution can be controlled. Control of the ionic structure provides control over the volume, shape, and dipole moment of the solute, critical parameters for hydrodynamic and dielectric continuum models of friction. The use of solutes with sizes comparable to or smaller than the solvent molecules also helps amplify the sensitivity of the measurement to the short-ranged solute-solvent interaction. The measured orientational relaxation dynamics show many clear and distinct deviations from simple hydrodynamic behavior. All ionic structures in all solvents exhibit multi-exponential relaxation dynamics that do not scale with the solute volume. For Lewis base solvents such as benzonitrile, dimethyl carbonate, and ethyl acetate, the observed dynamics strongly show the effect of solute-solvent complex formation. For the weak Lewis base solvent nitromethane, we see no evidence for solute-solvent complex formation, but still see strong deviation from the predictions of simple hydrodynamic theory. |
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Thermal fluctuations in shape, thickness, and molecular orientation in lipid bilayers J. Chem. Phys. 135, 244701 (2011); doi:10.1063/1.3660673 (22 pages) Online Publication Date: 22 December 2011
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We present a unified continuum-level model for bilayer energetics that includes the effects of bending, compression, lipid orientation (tilting relative to the monolayer surface normal), and microscopic noise (protrusions). Expressions for thermal fluctuation amplitudes of several physical quantities are derived. These predictions are shown to be in good agreement with molecular simulations.
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Structure and dynamics of nano-sized raft-like domains on the plasma membrane J. Chem. Phys. 136, 015103 (2012); doi:10.1063/1.3672704 (11 pages) Online Publication Date: 5 January 2012
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Cell membranes are constitutively composed of thousands of different lipidic species, whose specific organization leads to functional heterogeneities. In particular, sphingolipids, cholesterol and some proteins associate among them to form stable nanoscale domains involved in recognition, signaling, membrane trafficking, etc. Atomic-detail information in the nanometer/second scale is still elusive to experimental techniques. In this context, molecular simulations on membrane systems have provided useful insights contributing to bridge this gap. Here we present the results of a series of simulations of biomembranes representing non-raft and raft-like nano-sized domains in order to analyze the particular structural and dynamical properties of these domains. Our results indicate that the smallest (5 nm) raft domains are able to preserve their distinctive structural and dynamical features, such as an increased thickness, higher ordering, lower lateral diffusion, and specific lipid-ion interactions. The insertion of a transmembrane protein helix into non-raft, extended raft-like, and raft-like nanodomain environments result in markedly different protein orientations, highlighting the interplay between the lipid-lipid and lipid-protein interactions. |
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Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79, 926 (1983); doi: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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J. Chem. Phys. 136, 041103 (2012); doi:10.1063/1.3680256 (4 pages) Online Publication Date: 24 January 2012
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We report a chemically accurate global potential energy surface for the HOCO system based on high-level ab initio calculations at ∼35 000 points. The potential energy surface is shown to reproduce important stationary points and minimum energy paths. Quasi-classical trajectory calculations indicated a good agreement with experimental data. |
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Quantum entanglement between electronic and vibrational degrees of freedom in molecules J. Chem. Phys. 135, 244110 (2011); doi:10.1063/1.3671386 (11 pages) Online Publication Date: 30 December 2011
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We consider the quantum entanglement of the electronic and vibrational degrees of freedom in molecules with tendencies towards double welled potentials. In these bipartite systems, the von Neumann entropy of the reduced density matrix is used to quantify the electron-vibration entanglement for the lowest two vibronic wavefunctions obtained from a model Hamiltonian based on coupled harmonic diabatic potential-energy surfaces. Significant entanglement is found only in the region in which the ground vibronic state contains a density profile that is bimodal (i.e., contains two separate local maxima). However, in this region two distinct types of density and entanglement profiles are found: one type arises purely from the degeneracy of energy levels in the two potential wells and is destroyed by slight asymmetry, while the other arises through strong interactions between the diabatic levels of each well and is relatively insensitive to asymmetry. These two distinct types are termed fragile degeneracy-induced entanglement and persistent entanglement, respectively. Six classic molecular systems describable by two diabatic states are considered: ammonia, benzene, BNB, pyridine excited triplet states, the Creutz-Taube ion, and the radical cation of the “special pair” of chlorophylls involved in photosynthesis. These chemically diverse systems are all treated using the same general formalism and the nature of the entanglement that they embody is elucidated. |
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