Hydration Thermodynamics of Biomolecules. IV. Hydration Free Energy of Amino Acid Related Molecules

Abstract

Analysis of the free energy of transfer from gas phase to water has been made on forty organic molecules carrying the same atomic group as natural amino acids, where their conformation distribution and the effect of intramolecular interactions are explicitly considered. The best model is presented for classifying all the constituent atoms into hydration-thermodynamically different groups. The atomic hydration parameter, i.e. the transfer free energy per unit accessible surface area, is determined for each group. The intrinsic hydration energies of sulfur, oxygen and nitrogen atoms are estimated. Applicability to polar atoms of the assumption that the hydration free energy of a molecule can be given by a linear combination of accessible surface areas of the constituent atoms, is examined. The transfer free energy of an amino acid is shown to be significantly affected by the spatial interference between its main chain and side chain atoms.