A Monte Carlo quantum mechanical-molecular mechanical (QM-MM) simulation method was used to determine the contributions of the solvent polarization effect to the total interaction energies between solute and solvent for amino acid side chains and nucleotide bases in aqueous solution. In the present AM1-TIP3P approach, the solute molecule is characterized by valence electrons and nucleus cores with Hartree-Fock theory incorporating explicit solvent effects into the total Hamiltonian, while the solvent is approximated by the three-point charge TIP3P model. The polarization energy contributes 10 to 20 percent of the total electrostatic energy in these systems. The performance of the hybrid AM1-TIP3P model was further validated by consideration of bimolecular complexes with water and by computation of the free energies of solvation of organic molecules using statistical perturbation theory. Excellent agreement with ab initio 6-31G(d) results and experimental solvation free energies was obtained.

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A four-site intermolecular potential function for NH3 has been developed and tested in Monte Carlo statistical mechanics simulations of the liquid at its boiling point (-33.35 "C) and 1 atm. The potential yields good thermodynamic results for liquid ammonia, while the structures of the liquid are characterized through radial distribution functions and hydrogen-bonding analyses. The results indicate that each ammonia forms on average three hydrogen bonds and the liquid contains winding chains of hydrogen bonded monomers. Roughly linear hydrogen bonds predominates in the liquid. The results were also compared with those obtained using the five-site model developed by Ferrario et al. Although the computed heat of vaporization, liquid density, and the radial distribution functions are in good accord with our results and experimental data, to our surprise, a significant difference in the dimer and liquid structures exists between the two theoretical models. The structural difference is due to the Occurrence of unrealistic dimer structures with donation of hydrogen bonds to the opposite side of the ammonia lone pair in the liquid from the model of Ferrario et al. In contrast, both ab initio calculations and the present four-site model predict no stable complexes for these structures. These findings emphasize the importance of specific consideration of bimolecular interactions in developing potential functions for fluid simulations and suggest that erroneous results might be obtained if the potential functions are fitted to reproduce the condensed-phase properties alone.

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