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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 360-364 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The average solvent distribution near complex solid substrates of arbitrary geometry is calculated by solving the hypernetted chain (HNC) integral equation on a three-dimensional discrete cubic grid. A numerical fast Fourier transform in three dimensions is used to calculate the spatial convolutions appearing in the HNC equation. The approach is illustrated by calculating the average solvent density in the neighborhood of small clusters of Lennard-Jones particles and inside a periodic array of cavities representing a simplified model of a porous material such as a zeolite. Molecular dynamics simulations are performed to test the results obtained from the integral equation. It is generally observed that the average solvent density is described accurately by the integral equation. The results are compared with those obtained from a superposition approximation in terms of radial pair correlation functions, and the reference interaction site model (RISM) integral equations. The superposition approximation significantly overestimates the amplitude of the density peaks in particular cases. Nevertheless, the number of the nearest neighbors around the clusters is well reproduced by all approaches. The present calculations demonstrate the feasibility of a numerical solution of HNC-type integral equations for arbitrarily complex geometries using a three-dimensional discrete grid. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 8678-8689 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A statistical mechanical integral equation theory is developed to describe the average structure of a polar liquid around a complex molecular solute of irregular shape. The integral equation is formulated in three-dimensional Cartesian coordinates from the hypernetted chain (HNC) equation for a solute at infinite dilution. The direct correlation function of the pure solvent used in the theory is taken from the analytical solution of the mean spherical approximation (MSA) equation for a liquid constituted of nonpolarizable hard spheres with an embedded dipole at their center. It is demonstrated explicitly that, in the limit where the size of the solvent particles becomes very small, the present theory reduces to the well-known equations for macroscopic electrostatics in which the solvent is represented in terms of a dielectric continuum. A linearized version of the integral equation corresponds to a three-dimensional extension of the familiar MSA equation. This 3D-MSA integral equation is illustrated with numerical applications to the case of an ion, a water molecule, and N-methylacetamide. The numerical solution, obtained on a discrete three-dimensional cubic grid in Cartesian coordinates, yields the average solvent density and polarization density at all the points x,y,z around the solute. All spatial convolutions appearing in the theory are calculated using three-dimensional numerical fast Fourier transforms (FFT). © 1996 American Institute of Physics.
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 3567-3577 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The intramolecular proton transfer in the enol form of acetylacetone is investigated at various temperatures both classically and quantum-mechanically using computer simulations. The potential energy surface is modeled using the empirical valence bond (EVB) approach of Warshel and fitted to the results of ab initio calculations. Quantum-statistical results are obtained via discretized Feynman path integral simulations. The classical and centroid potential of mean force for the reaction coordinate is obtained using umbrella sampling. The proton transfer rate is calculated based on classical and on Feynman path integral quantum transition state theory. For the classical system, the transmission coefficient is obtained from activated dynamics. Two different reaction coordinates are compared, the first one involving explicitly the transferring proton and the second one involving only heavy atoms in the molecules. The influence of isotopic substitutions is investigated by considering a fully deuterated version of acetylacetone. It is observed that there are significant differences between classical and quantum-mechanical calculations caused mainly by the lack of tunneling effects in the former. The quantum fluctuations of heavy atoms are found to have a considerable influence on the magnitude of the proton transfer rate. © 1997 American Institute of Physics.
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  • 4
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 35 (1995), S. 171-178 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple approximation is developed to account for the dominant effects of solvation in molecular dynamics simulations of biopolymers. A small number of water molecules are included explicitly in the primary hydration shell around the biopolymer. A nonspherical confining potential responding dynamically to the conformational changes of the biopolymer is applied to prevent evaporation and to approximate the conditions of constant pressure of a bulk solution. Simulations of a spherical system of 25 water molecules are lined to adjust the empirical restraining potential to yield a uniform density distribution close to that in the bulk liquid. The primary hydration shell approach is tested with molecular dynamics simulations of simple hydrated peptides. The conformational equilibrium of alanine dipeptide and alanine tripeptide is examined using umbrella sampling calculations. The relative free energies of the C7ax (φ = 60, ψ = -80) and αL (φ = 60, ψ = 60) conformations of the alanine dipeptide and the opened and closed conformations of a reversed β-turn modeled with the alanine tripeptide were calculated. The results indicate that the primary hydration shell can reproduce the influence of solvent on small peptides that was observed in simulations involving a much larger number of water molecules. © 1995 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 368-380 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A potential energy model is developed to study the intramolecular proton transfer in the enol form of acetylacetone. It makes use of the empirical valence bond approach developed by Warshel to combine standard molecular mechanics potentials for the reactant and product states to reproduce the interconversion between these two states. Most parameters have been fitted to reproduce the key features of an ab initio potential surface obtained from 4-31G* Hartree-Fock calculations. The partial charges have been fitted to reproduce the electrostatic potential surface of 6-31G* Hartree-Fock wave functions, subject to total charge and symmetry constraints, using a fitting procedure based on generalized inverses. The resulting potential energy function reproduces the features most important for proton transfer simulations, while being several orders of magnitude faster in evaluation time than ab initio energy calculations. © 1997 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1760-1772 
    ISSN: 0192-8651
    Keywords: computer simulations ; wavepacket ; zero-point vibration ; activation energy ; reaction coordinate ; empirical valence bond ; Fourier transform ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present results of mixed quantum-classical molecular dynamics simulations of the intramolecular proton transfer in acetylacetone. Simulations are performed starting from the reactant and transition state configurations with initial velocities at each configuration chosen from an ensemble at 300 K. The proton motion is treated quantum mechanically and the remaining degrees of freedom are treated classically. Two mixed quantum-classical molecular dynamics methods are implemented. In the first, a quantum-classical time-dependent self-consistent field method (QC/TDSCF), the time-dependent Schrödinger equation for the proton is solved using the split operator approach and a plane-wave basis. In the second, a mixed quantum-classical adiabatic method (QC/A), the instantaneous ground state wave function is calculated by solving the time-independent Schrödinger equation for the configurations of the classical particles by propagating in imaginary time using the split operator approach and the same plane-wave basis. A comparison of the two approaches with classical trajectories is presented. The QC/TDSCF and QC/A results are very similar for trajectories started from the reactant configuration. The two methods, however, yield somewhat different results when the trajectories are started from the transition state configuration. The proton wave function of the QC/A method adjusts instantaneously to the position of the classical particles, whereas the motion of the QC/TDSCF wavepacket more faithfully represents the true proton dynamics.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1760-1772, 1997
    Additional Material: 6 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 690-704 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A potential energy function is developed to represent the interaction of small monovalent cations, Li+, Na+, and K+, with the backbone of polypeptides. The results are based on ab initio calculations up to the 6-31G* level of the interactions of the ions with acetamide and N-methylacetamide. Basis set superposition errors are corrected with the counterpoise method. A systematic overestimate of the bond polarities is taken into account by an empirical scaling procedure that uses the ratio of the experimental to ab initio dipole moment. The calculated binding energies obtained with this procedure show consistent convergence with different basis sets and are in good agreement with experimental data on cation-water and cation-dimethylformamide systems. Investigations of the calculated ab initio potential energy surface indicate that the cation-peptide interaction is dominated by electrostatics and includes a nonnegligible contribution from polarization of the peptide group by the ion. The induced polarization results in a steeper-than-Coulombic interaction and cannot be described by fixed ion-peptide partial charges electrostatics. Atomic polarizabilities located on the atoms of the ligand molecule are introduced to account for the induced polarization in the empirical energy function. A ∼1/r4 attractive interaction appears in the potential function. The resulting radial and angular dependence of the potential energy surface is well reproduced. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 15 Ill.
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  • 8
    Publication Date: 1997-09-01
    Print ISSN: 1520-6106
    Electronic ISSN: 1520-5207
    Topics: Chemistry and Pharmacology , Physics
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  • 9
    Publication Date: 1997-03-01
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 10
    Publication Date: 1995-07-01
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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