Polarizable continuum model of solvation for biopolymers

Abstract

AbstractThe original polarizable continuum model (PCM) of solvation based on the boundary element method for the numerical solution of the Poisson equation for a realistic molecular shape is modified through a classical description of solute charge distribution and solute polarization. In this approach, the solute charge distribution is represented by point charges and polarizabilities and the solute–solvent polarization is evaluated. The solvent–solute back polarization is also considered. The effect of electrolyte ionic strength is included via a dielectric function based on the Debye–Hückel model. A more realistic description of molecular cavity boundaries is introduced with the help of variable van der Waals radii. Approaches of evaluation of dispersion–repulsion and cavitation contributions to solvation Gibbs free energy suitable for large biopolymers are also presented. Test calculations illustrating the performance of the model are given together with examples of its application for larger biopolymer structures.