Modifying Poisson equation for near-solute dielectric polarization and solvation free energy

- We modify the Poisson equation.
- The dielectric polarization was calculated from the modified Poisson equation.
- The solvation free energies of the solutes were calculated from the dielectric polarization.
- The calculated solvation free energies were similar to those obtained from MD simulations.

The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein-protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density Nbulk; and relative solvent molecular density g. For a molecular solute, 4πr2p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss's law of Maxwell's equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.

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