| This dissertation presents results of investigations aimed at developing and applying methods for computing inter- and intramolecular interaction energies to be used in Monte Carlo, molecular mechanics, and molecular dynamics simulations. Modeling of molecular systems in condensed phase was the primary target because of their importance in organic and biochemical research. First, Lennard-Jones and Coulomb formalism has been considered with an emphasis on obtaining the most adequate interaction parameters and using them to compute energetic and structural properties of pure liquid saturated hydrocarbons and their dilute aqueous solutions. Second, liquid methanol, butane, and NMA have been used to compare performance of three existing molecular force fields, OPLS-AA, MMFF94, and AMBER94. OPLS-AA potential functions were found to yield the best representation of the systems involved. Next, a non-additive electrostatic polarization term has been included in the total classical energy expression for four rotaxane- and catenane-type compounds in acetonitrile (cyclobis(paraquat-p-phenylene) complexes with benzidine, biphenol, 1,4-diaminobenzene, and hydrobenzoquinone) to investigate the importance of taking into account such polarization interactions in simulating systems which contain aromatic fragments and highly charged atomic sites. Finally, a combined quantum mechanical and molecular mechanical approach has been explored with QM/MM coupling evaluation based on scaled CM1A electrostatic charges. The method was employed in assessing free energies of hydration and solvent effects on reaction rates and equilibria and has been found to perform very well compared with more resource-consuming methods. |
