Structures And Properties Of Amino Acids

The dissertation is devoted to the study of conformations and properties of amino acids in the gas phase using the DFT and ab initio calculations. With the progress in computational methods and enhancement of computational ability, molecular electronic structure theory and computational method based first-principles calculation have been widely used in chemistry, biochemistry, environmental science and material science. Meanwhile, amino acids have become a research focus as they are the units of building blocks of proteins and peptides. We thorough search the stable conformers of aromatic amino acids and arginine and examine the properties of the stable conformers using ab initio and DFT methods. The properties examined include the characteristics of intramolecular interactions, IR and UV spectra, temperature dependent conformer distributions, electron attachment and ionization energies, protonation/deprotonation processes.In chapter 1, we introduce the basic principles of quantum chemistry and computational methods including Many-Body Perturbation Theory, Configuration Interaction, Coupled Cluster and Density Functional Theory. We also introduce the Time-dependent DFT, Atoms in Molecules and Natural Bond Orbital. At the end of this chapter, we briefly introduce two simulation packages used in the dissertation and the aim of the study.In chapter 2, we first introduce the physical and chemical properties of amino acids. Tryptophan, tyrosine, phenylalanine and histidine have aromatic UV chromophores, and thus have been the subject of most laser spectroscopic studies on amino acids. We systematically explore the conformational potential energy surfaces of aromatic amino acids and calculate the conformational properties, explaining the experimental UV spectra of aromatic amino acids. In addition, the intramolecular interactions of aromatic amino acids are characterized using AIM theory. In chapter 3, we study the conformations and properties of arginine in the gas phase. The conformational study of arginine is the most challenging due to its large number of rotational degrees of freedom. Arginine is also the most basic natural amino acid due to its extremely basic guanidine side chain. It is speculated that the zwitterionic form of arginine exists in the gas phase. Due to a large number of hydrogens in the molecule, the study of the intramolecular interaction of arginine is very interesting. We reveal the intramolecular interaction of arginine using the ab initio and DFT calculations as well as AIM and NBO.In chapter 4, we study the conformations and properties of histidine and its related ions. The imidazole side chain of histidine frequently serves as a general acid or base in catalysis and in ligation of essential metal ions. Detailed knowledge of the structures and properties of histidine and the related molecules is important for our understanding of their static and dynamic properties in larger bio-systems. We reveal the protonation and deprotonation processes of gaseous histidine molecule using the DFT calculations. In addition, we calculated the electronic spectra of neutral and protonated histidine using the TDDFT method in order to understand the UV feature spectra of histidine residue in solution and protein and the dissociation processes of protonated histidine on UV excitation.