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  • 1
    ISSN: 1432-2234
    Keywords: Key words: Solvation ; Electrostatics ; Generalised Born theory ; Salt effects ; Continuum solvent
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. The Poisson–Boltzmann (PB) continuum solvent model shows considerable promise in providing a description of electrostatic solvation effects in biomolecules, but it can be computationally expensive to obtain converged results for large systems. Here we examine the performance of a pairwise generalized Born approximation (GB) method on multiple conformations of a small peptide, three proteins (protein A, myoglobin, and rusticyanin) and four RNA and DNA duplexes and hairpins containing 20–24 nucleotides. Charge and dielectric radii models were adapted from the CHARMM and Amber force fields. Finite difference PB calculations were carried out with the Delphi and PEP programs, and for several examples the matrix of all pairwise interaction energies was determined. In general, this parameterization of the GB model does an excellent job of reproducing the PB solvation energies for small molecules and for groups near the surface of larger molecules. There is a systematic tendency for this GB model to overestimate the effects of solvent screening (compared to PB) for pairs of buried atoms, but individual errors tend to cancel, and a good overall account of conformational energetics is obtained. A simple extension to the GB model to account for salt effects (in the linearized Debye–Hückel approximation) is proposed that does a good job of reproducing the salt dependence of the PB calculations. In many cases, it should be possible to replace PB calculations with much simpler GB models, but care needs to be taken for systems with extensive burial of charges or dipoles.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 56 (1995), S. 95-102 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present nonlocal density-functional calculations for a model of the [Fe4S4]3+ cluster found in high potential iron proteins, which consists formally of a ferric pair Fe 3+Fe3+ and a mixed-valence pair Fe 2.5+—Fe2.5+. Three Spin Hamiltonian parameters, J (the interlayer Heisenberg interaction), B (a resonance delocalization term) and ΔJ12 (associated with the ferric pair) have been estimated using density-functional energies of a high-spin state as well as two different broken symmetry states. We obtain J=673 cm-1, B=878 cm-1, and Δ J12=160 cm-1. These results are discussed in the light of experimental work on a model compound in the same oxidation state, in which the temperature dependence of the magnetic susceptibility was analyzed with this sort of spin Hamiltonian. Good overall agreement between theory and experiment (J=652 cm-1, B=592 cm-1), and ΔJ12=145 cm-1 is found. In particular, the antiferromagnetic spin coupling constant for the ferric pair exceeds in magnitude all other Heisenberg-type interactions (ΔJ12 〉 0) as expected from previous theoretical and experimental work; this is the first time that the broken symmetry method has been used to analyze a spin Hamiltonian with multiple coupling constants in an Fe4S4 cluster. © 1995 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 18 (1980), S. 1091-1099 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solutions to some practical problems that arise in multiple scattering calculations on large molecules are discussed. (1) Numerical instabilities near the zero of energy can be removed by rescaling the secular matrix. (2) The calculation of structure factors can be made much more efficient by the application of symmetry projection operators. (3) An energy search procedure is described that ensures that no states are inadvertently neglected. Test calculations incorporating these changes illustrate the improved numerical stability, and show decreases in computation time of 30-60%, when compared to previous codes. The procedures suggested here are applicable to both relativistic and nonrelatitistic calculations.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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