ISSN:
0192-8651

Keywords:
Computational Chemistry and Molecular Modeling
;
Biochemistry

Source:
Wiley InterScience Backfile Collection 1832-2000

Topics:
Chemistry and Pharmacology
,
Computer Science

Notes:
We present improved algorithms for the SMx (x = 1, 1a, 2, 3) solvation models presented previously [see the overview in C. J. Cramer and D. G. Truhlar, J. Comp.-Aided Mol. Design, 6, 629 (1992)]. These models estimate the free energy of solvation by augmenting a semiempirical Hartree-Fock calculation on the solute with the generalized Born (GB) model for electric polarization of the solvent and a surface tension term based on solvent-accessible surface area. This article presents three improvements in the algorithms used to carry out such calculations, namely (1) an analytical accessible surface area algorithm, (2) a more efficient radial integration scheme for the dielectric screening computation in the GB model, and (3) a damping algorithm for updating the GB contribution to the Fock update during the iterations to achieve a self-consistent field. Improvements (1) and (2) decrease the computer time, and improvement (3) leads to more stable convergence. Improvement (2) removes a small systematic numerical error that was explicitly absorbed into the parameterization in the SMx models. Therefore, we have adjusted the parameters for one of the previous models to yield essentially identical performance as was obtained originally while simultaneously taking advantage of improvement (2). The resulting model is called SM2.1. The fact that we obtain similar results after removing the systematic quadrature bias attests to the robustness of the original parameterization. © 1995 by John Wiley & Sons, Inc.

Additional Material:
13 Ill.

Type of Medium:
Electronic Resource

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