Theoretical Studies On Structures And Propeities Of Amino Acid And Peptide Related Systems

Amino acids and peptides are significant biomolecules either as the building blocks of proteins or as the individual molecules. Theoretical studies on the amino acids and peptides have critically important significance both in theories and practices, and have been the focus of a large panel of the contemporary researches. This dissertation is devoted to the theoretical studies on the conformations and properties of representative amino acid and peptide systems utilizing quantum chemical calculations based molecular orbital and density functional theories. The dissertation covers several representative areas and focal issues in the theoretical research field on these systems.In chapter1, the basic theories and conceptions of several quantum chemical calculations including several ab initio methods, DFT methods, empirical approaches, gaussian basis sets and solution models are introduced. The main software packages adopted in this dissertation are also refered in the end of the chapter.In chapter2, the main research contents, typical works and important issues in the theoretical research field on amino acids and peptides are briefly introduced and summarized. This chapter provides the research background and direction of this dissertation.In chapter3, the structure and properties of glutamic acid molecules are studied in detail by ab initio and density functional methods. Extensive conformational searches are performed in order to more fully characterize the potential energy surfaces of the neutral, protonated and deprotonated glutamic acids. Conformations, intermolecular hydrogen bonding configurations and IR spectra are characterized. Rotational constants, dipole moments, IR spectra, and vertical ionization energies of conformers and the conformer distributions at various temperatures are provided. Several popular quantum chemistry methods are used to recalculate and determine the PDE, PA, GA, and GB of glutamic acid. The theoretical results are compared each other and with the experimental data, and the best theoretical estimates and the most effective computational method for the determination of the thermochemical properties are addressed.Chapter4thoroughly analyzes the coordination properties of representative alkali, alkaline earth and transition metal cations as well as water molecules with glutamic acid in gas phase by means of first principle calculations. Systemic structural searches are considered to explore the coordination spaces. The coordination effect of the cationic species and water molecular amount to the conformations and stabilities of glutamic acid are addressed. Binding energies of the metal ions are determined by high-level DFT calculations, and the relavant experimental issues are explained in connection with the theoretical calculations. Moreover, some elementary tests and analyses of the qualities of several theories on the description of the Fe+spin states are referred.In chapter5, according to relevant quantum theory, possible physical pictures for the hydrogen bonding interactions of glycine and water molecules in aqueous solution is analyzed and proposed, and a new structural determination strategy for discrete mode is presented. On the basis of them the solution-phase vibrational IR spectra of glycine are detailly investigated by a combined protocol of and density functional calculations. From the structural, vibrational IR spectral and energetic points of view, the above assumption of the hydrogen bonding interactions are analysed and demonstrated, which establishes valuable groundwork for the theoretical studies of relevant porperities of large biomolecular systems in solution.In chapter6, thorough conformational searches on the potential energy surfaces of11representative tri-, tetra-and penta-peptides are performed and structural characteristics of the stable conformers located are carefully analyzed. The analyses reveal the intrinsic characterizations and the connections between the conformations of different level peptides. Followed by the results obtained above and proposed in previously relevant studies, an efficient method for finding all important polypeptide conformations utilizing amino acid and oligopeptide conformations is deduced. The method illustrates a new aspect of theoretical studies on the structures for large peptide systems.Chapter7presents a brief summary of the research results in this dissertation.