Quantum chemical characterization of Biomolecules in the gas phase and on surfaces of metal oxides

Abstract

During the four years of my PhD study, I performed systematic studies of the conformations of biomolecules ranging from a small amino acid (e.g. glycine) to a medium-sized nucleoside (e.g. 2’-deoxycytidine). To better account for possible effects brought by explicit environments (e.g. radiation, aqueous solution, and so on), we studied biomolecules in different phases, including neutral and charged species, in the gas phase and solid state, and neutral on solid surface. The work being presented in this thesis is original as: (1) A tool which can automatically generate libraries of conformations for a systematic search of the conformational space of a molecule was developed. When combined with tools developed by our colleagues, our toolbox facilitates a combinatorial computational chemical study of some small biomolecules; (2) A new method which can suppress barriers between different local minima on a molecular potential energy surface (PES) was developed, and with this new deformed PES, a lot of other techniques (e.g. Monte Carlo and simulated annealing) could be adopted to search for the global minima structure in a much more efficient way; (3) We performed a highly accurate study of two conformers of glycine up to the coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) with basis sets up to aug-cc-pVQZ level of theory, and we found that the treatment at the CCSD(T) level of theory is necessary to achieve numerical stability of the relative energies with respect to different basis sets at different geometries; (4) Through a thorough search of the conformational space of 2’-deoxycytidine, we found that its conformations in the gas phase are quite different from those in the solid state, and hopefully this finding could correct some of the previous approaches, in which structural information extracted from solid state experiments was used in computational studies of molecules in the gas phase; (5) Adsorptions of hydrogen, methanol and glycine on different types of solid surfaces (conductive and semiconductive) were studied, and catalytic performances of these surfaces on breaking chemical bonds were discussed. The current thesis not only covers the main applications of computational chemistry tools in the conformational study of biomolecules, it also includes discussions on accuracy and methodology which is involved in these studies. We definitely did not intend to solve all of the problems which people have met in their conformational studies of biomolecules. We just hope that the work being presented here was performed in a much more systematic way, and we hope these studies can give people some insights which might be helpful in their further studies.