The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostatic free energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene, water, , and octanol are compared with experimental data. We found an excellent correlation between the experimental and computed free energies of solvation for all the solvents. In addition, the employed algorithm for the cavity creation by Voronoi-Delaunay triangulation is compared with the GEPOL algorithm and is shown to predict more accurate free energies of solvation, especially in solvents composed by molecules with nonspherical molecular shapes.
REFERENCES
Typical examples in the quantum-mechanical approach to molecular surfaces are represented by Bondi and Pauling radii.
In cases where the atom-atom pair distribution functions are statistically too noisy, one might obtain these functions from a short MD simulations averaging over several configurations.
We also tried to apply the alpha- and convex-hull filtering (Ref. 19). However, we obtained worse molecular cavities in all the investigated cases by these filtering processes.
We have used the radius for the solvent molecule as implemented in the GAUSSIAN98REVA9 program (Ref. 49).