Molecular simulations of organic and biological molecules

The main purpose of this thesis is to study chemical reactivity and molecular interactions in organic and biological systems using quantum mechanical and Monte Carlo, and molecular dynamics simulation methods. The thesis consists of three chapters. The first chapter introduces Monte Carlo simulation combined with quantum mechanics, with emphasis at the semi-empirical AM1 level. The method is applied to the nucleophilic addition of methyl thiolate to N-methylacetamide in water. The second chapter describes a hybrid ab initio QM/MM method to study conformational isomerization of methyl acetate and the solvent effect on the conformational change and acidity. In chapter 3, quantum mechanical method (AM1) is combined with the CHARMM force field to probe differential nitric oxide (NO) affinity in the oxy- and deoxy-hemoglobin, along with analyses of residual contribution to the stability of the nitroso-hemolglobin. Finally, several papers from publications will be reprinted as an appendix to show interesting computational applications in chemistry.