ISSN:
0192-8651
Keywords:
Computational Chemistry and Molecular Modeling
;
Biochemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
An algorithm for the analytical computation of solvent-excluded volume is presented as part of our efforts to develop an improved computational model for a solvent effect term, in which the work required to create a cavity in the solvent is expressed as a function of the solvent-excluded volume. In this article we describe mathematical developments in the analytical integration of solvent-accessible surface (SAS) area, the singularities in SAS area and volume functions, and the procedures required to detect and treat singularities. Techniques to increase algorithm performance are presented, which improve computational speed by about five times, on the average. The accuracy of the analytical method for volume computation is compared with the accuracy of two numerical methods: the numerical integration of SAS area and the point-by-point scanning method. This algorithm calculates the volume of the spheres confined among their intersection planes and resembles a numerical integration of surface area by summing up volume layers. These characteristics make the algorithm useful in analytically calculating the work required to create a convex cavity in a solvent and the work (pΔV) associated with a change in the solvent-excluded volume of the solute due to solvent pressure. © 1995 by John Wiley & Sons, Inc.
Additional Material:
13 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/jcc.540160703
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