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  • 1
    Electronic Resource
    Electronic Resource
    Ability of the PM3 quantum-mechanical method to model intermolecular hydrogen bonding between neutral molecules (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 89-104 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-1 suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-1 imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 Å for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-1. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and O predict that donor strength follows the order F 〉 O 〉 N and acceptor strength follows the order N 〉 O 〉 F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H---N bond to be the strongest and the N-H---F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems. © 1993 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540140113
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    On velocity scaling in molecular dynamics simulations (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 200-203 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effect of scaling the molecular velocities to a fixed total energy in molecular dynamics simulations within the (N,V,E) ensemble has been investigated. The effect of using different time steps is also discussed. It is found that, even for small time steps, velocity scaling has a substantial influence on the resulting molecular trajectories, velocities, and forces. Furthermore, velocity rescaling and larger time step seem to have an additive effect on the calculated trajectories, but not on the average thermodynamic properties, such as temperature, pressure, and energy.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090303
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Modeling of magic water clusters (H2O)20 and (H2O)21H+ with the PM3 quantum-mechanical method (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1326-1332 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The PM3 quantum-mechanical method is able to model the magic water clusters (H2O)20 and (H2O)21H+. Results indicate that the H3O+ ion is tightly bound within the (H2O)20 cluster by multiple hydrogen bonds, causing deformation to the symmetric (H2O)20 pentagonal dodecahedron structure. The structures, energetics, and hydrogen bond patterns of six local minima (H2O)21H+ clusters are presented. © John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540141109
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    Paper (German National Licenses)
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