THE GB SA CONTINUUM MODEL FOR SOLVATION - A FAST ANALYTICAL METHOD FOR THE CALCULATION OF APPROXIMATE BORN RADII/

Atomic Born radii (alpha) are used in the generalized Born (GB) equati on to calculate approximations to the electrical polarization componen t (G(pol)) of solvation free energy. We present here a simple analytic al formula for calculating Born radii rapidly and with useful accuracy . The new function is based on an atomic pairwise r(ij)(-4) treatment and contains several empirically determined parameters that were estab lished by optimization against a data set of >10 000 accurate Born rad ii computed numerically using the Poisson equation on a diverse group of organic molecules, molecular complexes, oligopeptides, and a small protein. Coupling this new Born radius calculation with the previously described GB/SA solvation treatment provides a fully analytical solva tion model that is computationally efficient in comparison with tradit ional molecular solvent models and also affords first and second deriv atives. Tests with the GB/SA model and Born radii calculated with our new analytical function and with the accurate but more time-consuming Poisson-Boltzmann methods indicate that comparable free energies of so lvent like dielectric polarization can be obtained using either method and that the resulting GB/SA solvation free energies compare well wit h the experimental results on small molecules in water.