Solvent, structure, and spectroscopy: the role of dynamics in chemical reactions and s-nitrosylated proteins

Understanding the motions of atoms in a chemical system is core to chemistry. The dynamic motions of chemical events can occur at different time scales, ranging from a bond formation which occurs at the femtosecond timescale, or a displacement of a protein β-sheet which occurs over nanoseconds. Experimental characterization of such events at the atomistic level, especially in a condensed phase, requires refined temporal and spatial resolutions which still remains a challenge. Molecular Dynamic simulations can bring molecular-level insight into the dynamics and energetics of chemical processes for systems ranging from small molecules to proteins in the condensed phase.
The first part of the thesis emphasizes the chemical background of the conducted studies and the theoretical basis of the applied methods. In Chapter 3, the energetics and solvent distributions for the NH3+MeCl and Pyr+MeBr reactions were investigated in explicit solvent (water, methanol, acetonitrile, benzene, cyclohexane) by means of reactive molecular dynamics simulations. In Chapter 4, The structural dynamics and vibrational spectroscopy of S-Nitrosylation in the condensed phase are investigated for the methyl-capped cysteine model system and for myoglobin using conventional point charge and physically more realistic multipolar force fields for the -SNO group. In Chapter 5, the structural dynamics and hydration of the S Nitrosylated KRAS protein with and without GDP binding are studied in the condensed phase. The detailed abstracts of each study are provided in their respective chapters. Finally, conclusions are drawn in Chapter 6.