Implementation of the solvent effect in molecular mechanics. 1. Model development and analytical algorithm for the solvent-accessible surface area

Abstract A short review is given on the treatment of the solvent effect based on the continuum medium theory. A new modification is proposed which extends Still's recent breakthrough. Essential points of our modification are (1) separation of cavity and intrinsic terms and (2) relating the cavity term to the molecular volume. Several technical problems that occurred in the algorithm of solvent-accessible molecular surface-area calculations and that concerning the discontinuity in the surface-area derivatives are discussed. Results of critical tests on the extensively revised algorithm are described. The most crucial situation arises when the function for calculating surface-area must be switched, in the course of geometry optimization, from the two-spheres intersection case to three-spheres case. A test using a simple three-spheres model indicates that the switching of the function will not be hazardous.

[1]  P. Claverie,et al.  Calculation of the interaction energy of one molecule with its whole surrounding. I. Method and application to pure nonpolar compounds , 1972 .

[2]  C. Cramer,et al.  General parameterized SCF model for free energies of solvation in aqueous solution , 1991 .

[3]  D. Oakenfull,et al.  Effect of ethanol on hydrophobic interactions. Conductometric study of ion-pair formation by double-long-chain electrolytes , 1974 .

[4]  Arieh Ben-Naim,et al.  Solvation thermodynamics of nonionic solutes , 1984 .

[5]  Barry Honig,et al.  Reevaluation of the Born model of ion hydration , 1985 .

[6]  T. Richmond,et al.  Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. , 1984, Journal of molecular biology.

[7]  Robert B. Hermann,et al.  Theory of hydrophobic bonding. II. Correlation of hydrocarbon solubility in water with solvent cavity surface area , 1972 .

[8]  A. Y. Meyer.  Molecular mechanics of organic halides. V. Conformational equilibria in solution , 1981 .

[9]  H. Berendsen,et al.  THERMODYNAMICS OF CAVITY FORMATION IN WATER - A MOLECULAR-DYNAMICS STUDY , 1982 .

[10]  Amatzya Y. Meyer,et al.  Molecular mechanics and molecular shape. Part 1. van der Waals descriptors of simple molecules , 1985 .

[11]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[12]  J. Janin,et al.  Analytical approximation to the accessible surface area of proteins. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[13]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[14]  R. B. Hermann.  Theory of hydrophobic bonding. III. Method for the calculation of the hydrophobic interaction based on liquid state perturbation theory and a simple liquid model , 1975 .

[15]  J. Tomasi,et al.  Dispersion and repulsion contributions to the solvation energy: Refinements to a simple computational model in the continuum approximation , 1991 .

[16]  W. C. Still,et al.  A rapid approximation to the solvent accessible surface areas of atoms , 1988 .

[17]  R. Pierotti,et al.  A scaled particle theory of aqueous and nonaqueous solutions , 1976 .

[18]  S. I. Grossman.  Multivariable Calculus, Linear Algebra and Differential Equations , 1982 .

[19]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[20]  D. Rinaldi,et al.  Influence of dispersion forces on the electronic structure of a solvated molecule , 1986 .

[21]  D. D. Yue,et al.  Theory of Electric Polarization , 1974 .

[22]  Masao Doyama,et al.  Computer Aided Innovation of New Materials , 1991 .

[23]  Cyrus Levinthal,et al.  A vectorized algorithm for calculating the accessible surface area of macromolecules , 1991 .

[24]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[25]  A. Ben-Naim.  Water and Aqueous Solutions: Introduction to a Molecular Theory , 1974 .

[26]  W. J. Orville-Thomas,et al.  Internal rotation in molecules , 1974 .

[27]  Douglas A. Smith,et al.  Molecular modeling of intramolecular hydrogen bonding in simple oligoamides 2. GB/SA CH2Cl2. , 1991 .

[28]  A. Bondi.  van der Waals Volumes and Radii , 1964 .

[29]  H. Hosoya,et al.  Investigation of intramolecular interactions in n-alkanes. Cooperative energy increments associated with GG and GTG' [G = gauche, T = trans] sequences , 1991 .

[30]  K. D. Gibson,et al.  Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii , 1987 .

[31]  Hitoshi Goto,et al.  FAST ALGORITHM FOR COVERING CONFORMATIONAL SPACE BY MOLECULAR MECHANICS , 1991 .

[32]  G. Chang,et al.  Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics , 1990 .

[33]  Robert F. Hout,et al.  Representation of electron densities. 1. Sphere fits to total electron density surfaces , 1984 .