Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Electrolytes and interphases in Li-ion batteries and beyond.

Renewable Resources Robert-Jan van Putten,†,‡ Jan C. van der Waal,† Ed de Jong,*,† Carolus B. Rasrendra,‡,⊥ Hero J. Heeres,*,‡ and Johannes G. de Vries* †Avantium Chemicals, Zekeringstraat 29, 1014 BV Amsterdam, the Netherlands ‡Department of Chemical Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands DSM Innovative Synthesis BV, P.O. Box 18, 6160 MD Geleen, the Netherlands Department of Chemical Engineering, Institut Teknologi Bandung, Ganesha 10, Bandung 40132, Indonesia

Hydroxymethylfurfural, A Versatile Platform Chemical Made from Renewable Resources

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

This review gives a survey on the latest most representative developments and progress concerning ionic liquids, from their fundamental properties to their applications in catalytic processes. It also highlights their emerging use for biomass treatment and transformation.

Ionic liquids and catalysis: Recent progress from knowledge to applications

The proton chemical shift of water is measured at temperatures up to 400°C and densities of 0.19, 0.29, 0.41, 0.49, and 0.60g/cm3. The magnetic susceptibility correction is made in order to express the chemical shift relative to an isolated water molecule in dilute gas. The chemical shift is related to the average number of hydrogen bonds in which a water molecule is involved. It is found that the hydrogen bonding persists at supercritical temperatures and that the average number of hydrogen bonds is more than one for a water molecule in the supercritical densities. The density and temperature dependence of the chemical shift at supercritical temperatures are analyzed on the basis of statistical thermodynamics. It is shown that the hydrogen bonding is spatially more inhomogeneous at lower densities.

Structural study of supercritical water. I. Nuclear magnetic resonance spectroscopy

The energetic representation of the molecular configuration in a dilute solution is introduced to express the solvent distribution around the solute over a one-dimensional coordinate specifying the solute–solvent interaction energy. In this representation, the correspondence is shown to be one-to-one between the set of solute–solvent interaction potentials and the set of solvent distribution functions around the solute. On the basis of the one-to-one correspondence, the Percus–Yevick and hypernetted-chain integral equations are formulated over the energetic coordinate through the method of functional expansion. It is then found that the Percus–Yevick, hypernetted-chain, and superposition approximations in the energetic representation determine the solvent distribution functions correctly to first-order with respect to the solute–solvent interaction potential and to the solvent density. The expressions for the chemical potential of the solute are also presented in closed form under these approximations and are shown to be exact to second-order in the solute–solvent interaction potential and in the solvent density.

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Theory of solutions in the energetic representation. I. Formulation

An approximate functional for the chemical potential of a solute in solution is presented in the energy representation. This functional is constructed by adopting the Percus–Yevick-like approximation in the unfavorable region of the solute–solvent interaction and the hypernetted-chain-like approximation in the favorable region. The chemical potential is then expressed in terms of energy distribution functions in the solution and pure solvent systems of interest, and is given exactly to second order with respect to the solvent density and to the solute–solvent interaction. In the practical implementation, computer simulations of the solution and pure solvent systems are performed to provide the energy distribution functions constituting the approximate functional for the chemical potential. It is demonstrated that the chemical potentials of nonpolar, polar, and ionic solutes in water are evaluated accurately and efficiently from the single functional over a wide range of thermodynamic conditions.

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Theory of solutions in the energy representation. II. Functional for the chemical potential

The method of energy representation for evaluating the solvation free energy is extended to a solute molecule with structural flexibility. When the intramolecular structure of the solute molecule exhibits a strong response to the solute–solvent interaction, the approximate functional for the solvation free energy needs to be modified from the original form presented previously [J. Chem. Phys. 117, 3605 (2002); 118, 2446 (2003)]. In the modification of the functional, the solvation-induced change in the distribution function of the solute structure is taken into account with respect to the intramolecular energy of the solute. It is then demonstrated over a wide range of thermodynamic conditions that the modified form of functional provides an accurate and efficient route to the solvation free energy of a flexible solute molecule even when the structural distribution function of the solute in solution overlaps barely with that of the solute at isolation.

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Theory of solutions in the energy representation. III. Treatment of the molecular flexibility

The hydration shell model for excess thermodynamic quantities is examined. A simple formula for the excess energy of a solute in solution is presented which is expressed as an integral of the solvent binding energy over the hydration shell. For methane in water, which is chosen as the first application, the binding energy of a water molecule around the solute is calculated from a Monte Carlo simulation as a continuous function of the distance from the solute. The localization of the excess energy within the hydration shell is then analyzed in terms of the deviation of the binding energy from the bulk value. About 70% of the total excess energy of methane in water is accounted for by the hydration shell formula using the first minimum in the methane-water radial distribution function to define the shell. The dependence of the excess energy on the solution process is investigated. The difference between the excess energy in the constant-volume process and that in the constant-pressure process is estimated for a variety of water models and compared with experiments. The hydration shell formula is shown to correspond to the excess energy at constant pressure. The contribution of the solvent reorganization energy to the total excess energy and to the free energy of solvation is discussed.

Nobuyuki Matubayasi

Papers

Structural study of supercritical water. I. Nuclear magnetic resonance spectroscopy

Theory of solutions in the energetic representation. I. Formulation

Theory of solutions in the energy representation. II. Functional for the chemical potential

Theory of solutions in the energy representation. III. Treatment of the molecular flexibility

Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute