A combined Monte Carlo quantum mechanical and molecular mechanical (QM/MM) simulation method is used to determine the free energy of hydration and the solvent polarization effect for the nucleotide bases. In the present AM1/TIP3P model, the solute molecule is characterized by valence electrons and effective nucleus cores with Hartree-Fock molecular orbital theory incorporating a solute-solvent interaction Hamiltonian. It is found that polarization energy contributes up to 37%-61% of the total solute-solvent interaction for the systems considered. The computed free energies of hydration are compared with previous theoretical results.
- Monte Carlo simulation
- Nucleotide bases