Solvation Free Energies and Transfer Free Energies for Amino Acids from Hydrophobic Solution to Water Solution from a Very Simple Residue Model

Abstract

Solvation free energies of neutral amino acids in water and in chloroform were computed from extensive molecular dynamics simulations using multiconfiguration thermodynamic integration. The values computed for the AMBER force field are in very good agreement with available experimental data (rms differences of 5.1 kJ mol-1 for the solvation free energies and 6.4 kJ mol-1 for the transfer free energies of amino acids between water and chloroform) and with existing calculations. We derived an additive residue-scale solvation model formulated as the sum of a nonpolar term that is proportional to the molecular surface area and an electrostatic term (Kirkwood−Onsager model) for the hydration free energy of a dipole in a solvated cavity. This model can surprisingly well describe the solvation free energies in water and chloroform as well as the transfer free energies of amino acids between the two solvents when suitably adapted cavity radii are used. Root-mean-square differences of the predicted values with res...