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  • 1
    Electronic Resource
    Electronic Resource
    Calculating electrostatic forces from grid-calculated potentials (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 401-409 
    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 accurate calculation of forces from finite difference potentials is very important, especially in the area of Brownian dynamics simulations. Test charge methods are typically used to calculate these forces. In these methods, the potential is calculated with one group of charges present, then the force on a second set of charges is calculated as the negative of the gradient of the potential times the charge. The test charge methods for calculating forces between solute molecules have been compared with more accurate methods and then regions of validity of the test charge methods explored. The test charge methods neglect certain reaction field effects. It is found for the simple charged systems studied that beyond a center-to-center separation of about twice the sum of the molecular radii the test charge approximations can be quite good. For polar molecules with no net charges, however, the corrections can be significant to even longer ranges.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110315
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  • 2
    Electronic Resource
    Electronic Resource
    Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 909-912 
    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: Finite difference methods are becoming very popular for calculating electrostatic fields around molecules. Due to the large amount of computer memory required, grid spacings cannot be made extremely small in relation to the size of the van der Waals radii of the atoms. As a result, the calculations make a rather crude approximation to the molecular surface by defining grid line midpoints discontinuously as either interior or exterior. We present a method which “smoothes” the boundary, but more accurately models the potential from the analytic solution of the discontinuous dielectric problem and improves convergence in electrostatic energy calculations. In addition, a small improvement in convergence rate is observed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540120718
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  • 3
    Electronic Resource
    Electronic Resource
    Hydration of small anions: Calculations by the AM1 semiempirical method (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 350-358 
    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 AM1 semiempirical molecular orbital method has been used to calculate successive heats of hydration of small anions, including hydride, hydroxide, and the halogen ions, for cluster sizes up to 11 water molecules surrounding the central anion. Heats of hydration agree with available experimental data to within a few kcal/mol. Structures, however, do not always agree well with available ab initio calculations on clusters with one or two water molecules. The results indicate that the AM1 semiempirical technique applied to finite-sized clusters must be used with caution in understanding how hydration affects the chemical reactions of anions.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540120308
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  • 4
    Electronic Resource
    Electronic Resource
    Electrostatic energy calculations by a Finite-difference method: Rapid calculation of charge-solvent interaction energies (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 768-771 
    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: Finite-difference Poisson-Boltzmann (FDPB) methods allow a fast and accurate calculations of the reaction field (charge-solvent) energies for molecular systems. Unfortunately, the energy in the FDPB calculations includes the self-energies and the finite-difference approximation to the Coulombic energies as well as the reaction field energy. A second finite-difference calculation, in a uniform dielectric, is therefore necesssary to eliminate these contributions. In this article we describe a rapid and accurate method to calculate the self energy and finite-difference Coulombic energies in a uniform dielectric thus eliminating the need for a second finite-difference calculation. The computational savings for this method range from a factor of 4 for a typical protein to a factor of 103 for small molecules. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130610
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  • 5
    Electronic Resource
    Electronic Resource
    Solving the finite-difference non-linear Poisson-Boltzmann equation (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1114-1118 
    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 Poisson-Boltzmann equation can be used to calculate the electrostatic potential field of a molecule surrounded by a solvent containing mobile ions. The Poisson-Boltzmann equation is a non-linear partial differential equation. Finite-difference methods of solving this equation have been restricted to the linearized form of the equation or a finite number of non-linear terms. Here we introduce a method based on a variational formulation of the electrostatic potential and standard multi-dimensional maximization methods that can be used to solve the full non-linear equation. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130911
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