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Top 20 Most Read Articles
October 2010
The 20 articles with the most full-text downloads during the month, in descending order.
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Communication: Thermodynamics of water modeled using ab initio simulations J. Chem. Phys. 133, 141101 (2010); http://dx.doi.org/10.1063/1.3499315 (4 pages) Online Publication Date: 8 October 2010
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We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. Assuming classical statistical mechanical simulations at 350 K model the liquid at 298 K, the calculated free energy is found in fair agreement with experiments, but the excess internal energy and hence also the excess entropy are not. The utility of thermodynamic characterization in understanding the role of high temperatures to mimic nuclear quantum effects and in evaluating ab initio simulations is noted.
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Communication: ROHF theory made simple J. Chem. Phys. 133, 141102 (2010); http://dx.doi.org/10.1063/1.3503173 (4 pages) Online Publication Date: 13 October 2010
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Restricted open-shell Hartree–Fock (ROHF) theory is formulated as a projected self-consistent unrestricted HF (UHF) model by mathematically constraining spin density eigenvalues. This constrained UHF (CUHF) wave function is identical to that obtained from Roothaan’s effective Fock operator. The α and β CUHF Fock operators are parameter-free and have eigenvalues (orbital energies) that are physically meaningful as in UHF, except for eliminating spin contamination. This new way of solving ROHF leads to orbitals that turn out to be identical to semicanonical orbitals. The present approach removes ambiguities in ROHF orbital energies.
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J. Chem. Phys. 133, 104103 (2010); http://dx.doi.org/10.1063/1.3475563 (9 pages) Online Publication Date: 9 September 2010
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This work proposes a new term on the “Jacob’s ladder” of approximate exchange-correlation functionals in Kohn–Sham density functional theory. In these Rung 3.5 functionals, the exchange-correlation energy density at a point depends linearly (rather than quadratically) on the nonlocal Kohn–Sham one-particle density matrix in a finite neighborhood around the point. These functionals are intermediate in complexity between the semilocal approximations of Rungs 1–3, and fully nonlocal Rung 4 approximations such as global hybrids. Rung 3.5 functionals built on the model for exchange in [
B. G. Janesko, J. Chem. Phys. 131, 234111 (2009)
] predict molecular thermochemistry and kinetics with accuracy intermediate between their “parent” semilocal functional and the corresponding global hybrid. The best Rung 3.5 functional presented here gives mean absolute errors of 5.7 kcal/mol for G3/99 thermochemistry, 5.2 kcal/mol for HTBH38/04 hydrogen-transfer reaction barriers, and 5.7 kcal/mol for NHTBH38/04 nonhydrogen-transfer reaction barriers, while incorporating only two empirical parameters.
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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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Communication: Second-order multireference perturbation theory with explicit correlation: CASPT2-F12 J. Chem. Phys. 133, 141103 (2010); http://dx.doi.org/10.1063/1.3489000 (4 pages) Online Publication Date: 13 October 2010
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An explicitly correlated complete active space second-order perturbation (CASPT2-F12) method is presented which strongly accelerates the convergence of CASPT2 energies and properties with respect to the basis set size. A Slater-type geminal function is employed as a correlation factor to represent the electron-electron cusp of the wave function. The explicitly correlated terms in the wave function are internally contracted. The required density matrix elements and coupling coefficients are the same as in conventional CASPT2, and the additional computational effort for the F12 correction is small. The CASPT2-F12 method is applied to the singlet-triplet splitting of methylene, the dissociation energy of ozone, and low-lying excited states of pyrrole.
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Sequence composition and environment effects on residue fluctuations in protein structures J. Chem. Phys. 133, 155101 (2010); http://dx.doi.org/10.1063/1.3498743 (7 pages) Online Publication Date: 15 October 2010
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Structure fluctuations in proteins affect a broad range of cell phenomena, including stability of proteins and their fragments, allosteric transitions, and energy transfer. This study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per-residue elastic network model accounting for the nonhomogeneous protein mass distribution and the interatomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues in agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups: (i) highly fluctuating-Gly, Ala, Ser, Pro, and Asp, (ii) moderately fluctuating-Thr, Asn, Gln, Lys, Glu, Arg, Val, and Cys, and (iii) weakly fluctuating-Ile, Leu, Met, Phe, Tyr, Trp, and His. The structural instability in proteins possibly relates to the high content of the highly fluctuating residues and a deficiency of the weakly fluctuating residues in irregular secondary structure elements (loops), chameleon sequences, and disordered proteins. Strong correlation between residue fluctuations and the sequence composition of protein loops supports this hypothesis. Comparing fluctuations of binding site residues (interface residues) with other surface residues shows that, on average, the interface is more rigid than the rest of the protein surface and Gly, Ala, Ser, Cys, Leu, and Trp have a propensity to form more stable docking patches on the interface. The findings have broad implications for understanding mechanisms of protein association and stability of protein structures.
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J. Chem. Phys. 133, 095103 (2010); http://dx.doi.org/10.1063/1.3478224 (9 pages) Online Publication Date: 7 September 2010
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Fluorescence correlation spectroscopy (FCS) was applied to the crystallization processes of egg-white lysozyme. Utilizing FCS’s high spatial resolution of about the laser wavelength used, the molecular dynamics close to crystal surfaces was investigated for both tetragonal single crystals and needlelike spherulites. When the FCS measurement was done at the point closer than 1 μm to the surface of a tetragonal single crystal, the relaxation time became several times longer than that in bulk solution, but the fluorescence intensity (thus concentration) was similar to that observed in bulk solution. On the other hand, the peculiar slow dynamics (a few orders of magnitude slower than that in bulk solution) of concentrated liquid states of the lysozyme molecules was observed in needlelike spherulites. We suggested that these observations could be explained by the formation of softly connected aggregates accumulating around the needlelike crystals, which could cause the instability of the crystal growth and thus the formation of spherulites. These aggregates gradually disappeared as the crystallization further proceeded. After the disappearance of the aggregates, the spherulites started to mature.
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Curvature dependence of surface free energy of liquid drops and bubbles: A simulation study J. Chem. Phys. 133, 154702 (2010); http://dx.doi.org/10.1063/1.3493464 (12 pages) Online Publication Date: 18 October 2010
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We study the excess free energy due to phase coexistence of fluids by Monte Carlo simulations using successive umbrella sampling in finite L×L×L boxes with periodic boundary conditions. Both the vapor-liquid phase coexistence of a simple Lennard-Jones fluid and the coexistence between A-rich and B-rich phases of a symmetric binary (AB) Lennard-Jones mixture are studied, varying the density ρ in the simple fluid or the relative concentration xA of A in the binary mixture, respectively. The character of phase coexistence changes from a spherical droplet (or bubble) of the minority phase (near the coexistence curve) to a cylindrical droplet (or bubble) and finally (in the center of the miscibility gap) to a slablike configuration of two parallel flat interfaces. Extending the analysis of
Schrader et al., [Phys. Rev. E 79, 061104 (2009)]
, we extract the surface free energy γ(R) of both spherical and cylindrical droplets and bubbles in the vapor-liquid case and present evidence that for R→∞ the leading order (Tolman) correction for droplets has sign opposite to the case of bubbles, consistent with the Tolman length being independent on the sign of curvature. For the symmetric binary mixture, the expected nonexistence of the Tolman length is confirmed. In all cases and for a range of radii R relevant for nucleation theory, γ(R) deviates strongly from γ(∞) which can be accounted for by a term of order γ(∞)/γ(R)−1∝R−2. Our results for the simple Lennard-Jones fluid are also compared to results from density functional theory, and we find qualitative agreement in the behavior of γ(R) as well as in the sign and magnitude of the Tolman length.
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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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J. Chem. Phys. 116, 8015 (2002); http://dx.doi.org/10.1063/1.1468885 (13 pages) Online Publication Date: 25 April 2002
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In order to improve the experimental database about the additional nonrotational broadening of vibrational line shapes observable when a simple fluid approaches its gas–liquid critical point, we improved the pioneering measurements of Clouter and Kiefte [for their own review see Phys. Rev. A 33, 2749 (1986)] on the critical behavior of the polarized Raman line of fluid nitrogen by using the isotopic mixture (14N2).975−(14N15N).025, giving special attention to the fact that the isotropic line shape of liquid N2 (  ≈ 2327 cm−1) is affected by intermolecular vibrational resonance couplings. Using a highest-resolution double monochromator and modern CCD detection techniques, we were able to follow the temperature dependencies of the line shape parameters (i.e., shift, width, and asymmetry) of the coupled 14N2 and, depending on the S/N ratio available, of the uncoupled 14N15N in the range 45 K≲T≲300 K with up to mK resolution (1) in the β-solid phase, (2) in the coexisting liquid and gas phases, and (3) along the critical isochore. Comparing the line shifts of both isotopic species, clear evidence was found that vibrational resonance couplings are present in all dense phases studied, the line position 0 being more density than temperature dependent. Additionally, the existence of (negative) cross correlations between resonant and nonresonant dephasing mechanisms has been confirmed by the change in sign observed for the small but non-negligible difference in the linewidths between coupled 14N2 and uncoupled 14N15N around 90 K. The λ-shaped dependencies of the width parameters, observed when moving along the coexistence line through the critical point, Tcrit = 126.192 K, and along the critical isochore, is much more evident in the line asymmetry than in the usually considered linewidth. Clear proof was found that, in accordance with theoretical predictions, the linewidth converges to a constant maximum value regardless if the critical point is reached along the coexistence line or along the critical isochore, i.e., it does not diverge approaching the critical temperature up to our closest value ∣T/Tcrit−1∣ ≈ 10−5. © 2002 American Institute of Physics. |
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Communication: Conditions for one-photon coherent phase control in isolated and open quantum systems J. Chem. Phys. 133, 151101 (2010); http://dx.doi.org/10.1063/1.3491366 (3 pages) Online Publication Date: 15 October 2010
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Coherent control of observables using the phase properties of weak light that induces one-photon transitions is considered. Measurable properties are shown to be categorizable as either class A, where control is not possible, or class B, where control is possible. Using formal arguments, we show that phase control in open systems can be environmentally assisted.
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J. Chem. Phys. 133, 164101 (2010); http://dx.doi.org/10.1063/1.3499947 (9 pages) Online Publication Date: 22 October 2010
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We present a new method for introducing stable nonequilibrium velocity and temperature gradients in molecular dynamics simulations of heterogeneous systems. This method extends earlier reverse nonequilibrium molecular dynamics (RNEMD) methods which use momentum exchange swapping moves. The standard swapping moves can create nonthermal velocity distributions and are difficult to use for interfacial calculations. By using nonisotropic velocity scaling (NIVS) on the molecules in specific regions of a system, it is possible to impose momentum or thermal flux between regions of a simulation while conserving the linear momentum and total energy of the system. To test the method, we have computed the thermal conductivity of model liquid and solid systems as well as the interfacial thermal conductivity of a metal-water interface. We find that the NIVS-RNEMD improves the problematic velocity distributions that develop in other RNEMD methods.
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J. Chem. Phys. 133, 134301 (2010); http://dx.doi.org/10.1063/1.3487736 (9 pages) Online Publication Date: 1 October 2010
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The photodissociation dynamics of H2O via the
 state by two-photon excitation has been investigated using the H atom Rydberg tagging time-of-flight technique. The rotational resolved action spectrum of the ← transition band has been measured. The line widths show a pronounced dependence on the parent rotational excitation in the state. The quantum state resolved OH product translational energy distributions and angular distributions have also been obtained. By carefully simulating these distributions, quantum state distributions of the OH product as well as the state-resolved angular anisotropy parameters were determined. The experimental results confirm the variation of two competitive predissociation pathways. A heterogeneous predissociation channel is mediated by rotational coupling to the  1A1 state associated with the a-axis (ka′), and a homogeneous pathway arises from purely electronic coupling to the  1B1 state. We have also obtained the branching ratios of the OH(X) and OH(A) products, and related these to the → and → pathways. The branching ratios display a strong ka′ dependence. |
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Frontiers in electronic structure theory J. Chem. Phys. 132, 110902 (2010); http://dx.doi.org/10.1063/1.3369628 (7 pages) Online Publication Date: 18 March 2010
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Current and emerging research areas in electronic structure theory promise to greatly extend the scope and quality of quantum chemical computations. Two particularly challenging problems are the accurate description of electronic near-degeneracies (as occur in bond-breaking reactions, first-row transition elements, etc.) and the description of long-range dispersion interactions in density functional theory. Additionally, even with the emergence of reduced-scaling electronic structure methods and basis set extrapolation techniques, quantum chemical computations remain very time-consuming for large molecules or large basis sets. A variety of techniques, including density fitting and explicit correlation methods, are making rapid progress toward solving these challenges.
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J. Chem. Phys. 133, 131101 (2010); http://dx.doi.org/10.1063/1.3490795 (4 pages) Online Publication Date: 1 October 2010
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The effects of the reactant bending excitations in the F+CHD3 reaction are investigated by crossed molecular beam experiments and quasiclassical trajectory (QCT) calculations using a high-quality ab initio potential energy surface. The collision energy (Ec) dependence of the cross sections of the F+CHD3(vb = 0,1) reactions for the correlated product pairs HF(v′)+CD3(v2 = 0,1) and DF(v′)+CHD2(v4 = 0,1) is obtained. Both experiment and theory show that the bending excitation activates the reaction at low Ec and begins to inactivate at higher Ec. The experimental F+CHD3(vb = 1) excitation functions display surprising peak features, especially for the HF(v′ = 3)+CD3(v2 = 0,1) channels, indicating reactive resonances (quantum effects), which cannot be captured by quasiclassical calculations. The reactant state-specific QCT calculations predict that the v5(e) bending mode excitation is the most efficient to drive the reaction and the v6(e) and v5(e) modes enhance the DF and HF channels, respectively.
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Efficient on the fly calculation of time correlation functions in computer simulations J. Chem. Phys. 133, 154103 (2010); http://dx.doi.org/10.1063/1.3491098 (12 pages) Online Publication Date: 15 October 2010
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Time correlation functions yield profound information about the dynamics of a physical system and hence are frequently calculated in computer simulations. For systems whose dynamics span a wide range of time, currently used methods require significant computer time and memory. In this paper, we discuss the multiple-tau correlator method for the efficient calculation of accurate time correlation functions on the fly during computer simulations. The multiple-tau correlator is efficacious in terms of computational requirements and can be tuned to the desired level of accuracy. Further, we derive estimates for the error arising from the use of the multiple-tau correlator and extend it for use in the calculation of mean-square particle displacements and dynamic structure factors. The method described here, in hardware implementation, is routinely used in light scattering experiments but has not yet found widespread use in computer simulations.
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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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Imaging mesoscopic nuclear spin noise with a diamond magnetometer J. Chem. Phys. 133, 124105 (2010); http://dx.doi.org/10.1063/1.3483676 (8 pages) Online Publication Date: 27 September 2010
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Magnetic resonance imaging can characterize and discriminate among tissues using their diverse physical and biochemical properties. Unfortunately, submicrometer screening of biological specimens is presently not possible, mainly due to lack of detection sensitivity. Here we analyze the use of a nitrogen-vacancy center in diamond as a magnetic sensor for nanoscale nuclear spin imaging and spectroscopy. We examine the ability of such a sensor to probe the fluctuations of the “classical” dipolar field due to a large number of neighboring nuclear spins in a densely protonated sample. We identify detection protocols that appropriately take into account the quantum character of the sensor and find a signal-to-noise ratio compatible with realistic experimental parameters. Through various example calculations we illustrate different kinds of image contrast. In particular, we show how to exploit the comparatively long nuclear spin correlation times to reconstruct a local, high-resolution sample spectrum.
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A transferable classical potential for the water molecule J. Chem. Phys. 133, 144109 (2010); http://dx.doi.org/10.1063/1.3490660 (10 pages) Online Publication Date: 12 October 2010
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We developed a new model for the water molecule which contains only three Gaussian charges. Using the gas-phase geometry the dipole moment of the molecule matches, the quadrupole moment closely approximates the experimental values. The negative charge is connected by a harmonic spring to its gas-phase position. The polarized state is identified by the equality of the intermolecular electrostatic force and the spring force acting on the negative charge. In each timestep the instantaneous position of the massless negative charge is determined by iteration. Using the technique of Ewald summation, we derived expressions for the potential energy, the forces, and the pressure for Gaussian charges. The only properties to be fitted are the half-width values of the Gaussian charge distributions and the parameters of the nonelectrostatic repulsion-attraction potential. We determined the properties of gas-phase clusters up to six molecules, the internal energy and density of ambient water and hexagonal ice. We calculated the equilibrium density of ice VII as a function of pressure. As an additional test, we calculated the pair-correlation function, the isotherm compressibility, the heat capacity, and the self-diffusion coefficients for ambient water. As far as we know, this is the first classical model of water which is able to estimate both ends of the phase diagram, the high pressure ice VII, and the gas clusters of water with excellent accuracy.
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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
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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.
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