Solvation parameters for amino acids

Atomic radii have been derived for the common amino acid side chains using a solvent interaction potential (SIP) based on quantum mechanically derived charges. Solvation energies calculated using these parameters are compared with those obtained using other sets of radii and charges, and from alternative methods. The differences from the experimental solvation energies for the nonionizable residues are all less than 10 kJ mol⁻¹. The largest error in the solvation energy occurs for acetic acid (−16.0 kJ mol⁻¹). For the charged side chain systems the difference from experiment are all less than 10 kJ mol⁻¹. SIP parameters for the aminoacetaldehyde derivatives of the common amino acids are presented. These are used in the calculation of the relative binding energies of six benzamidine inhibitors with trypsin. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 428–442, 1999