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Vol 44(2010) N 2 p. 303-316;
L.B. Pereyaslavets, A.V. Finkelstein*

Atomic Force Field FFsol for Calculating Molecular Interactions in Water Environment

Institute of Protein Reseach, Russian Academy of Sciences, Pouschino, 142290 Russia

*afinkel@vega.protres.ru
Received - 2009-08-18; Accepted - 2009-09-21

A detailed calculation of the protein interactions with explicitly considered water takes enormous computer time. The calculation becomes faster if water is implicitly considered (as a continuous media rather than as molecules); however, these calculations are much less precise, unless using an additional (and also time-consuming) computation of the solvent-accessible areas of all protein atoms. The goal of this work was to obtain the parameters for noncovalent atom--atom interactions for the case of implicitly considered water environment avoiding the computation of solvent-accessible areas. Since the interactions of atoms in a "vacuum" environment are obtained from experimental structures of crystals and the enthalpies of their sublimation, the sublimation enthalpies in water environment require adjustment by the value of solvation free energies of molecules calculatable from the Henry constants. Having processed 58 structures of crystals and the thermodynamic data on their sublimation and solubility, we got the attraction and repulsion parameters for the atoms characteristic of proteins (H, C, N, O, and S) in various covalently bound states as well as the parameters for electrostatic interactions. In these computations, all the parameters for covalent interactions were taken from the ENCAD force field, while all the partial changes were obtained by quantum mechanical calculations. The required parameters of van der Waals and electrostatic interactions in water were optimized to achieve the best description of equilibrium crystal structures, their sublimation, and solvation at room temperature. The mean error in calculation of the cohesion energy of molecules in crystals using the optimized parameters was less than 10% for both vacuum and water environments.

noncovalent atom-atom interactions, implicit water surrounding, structures of molecular crystals, sublimation, solvation



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