Theoretical Studies On Conformations And Properties Of Amino Acids And Oligopeptides

Amino acids and oligopeptides are important biomolecules.Theoretical investigations on these molecules are critically important not only for its crucial role in explanations of experimental results but also because it can provide valuable structural insights into large biomolecules such as proteins.This dissertation is devoted to the theoretical studies on conformations and properties of representative amino acids and oligopeptides utilizing density functional theory(DFT) and wave function theory(WFT) based methods.The dissertation includes method development,method test and method application studies and covers several aspects in theoretical research area on amino acids and oligopeptides.In chapter 1,the basic theory of several computational methods including various ab initio,semiempirical and DFT methods were introduced.Some methods used to describe classical images such as orbitals and charges also been refered. Common software package used in this work were also described.In chapter 2,the main research contents and typical works in theoretical research area on amino acids and oligopeptides were introduced.This includes studies performed on structures,electronic properties,weak intramolecular interactions,protonation and deprotonation,conformer conversion,metal ion binding,solution effects and etc.This chapter provides us the research background in the area.In chapter 3,conformers of valine are explored using DFT method.The stable conformers we located complement the potential energy surface information given by others formerly.Distribution calculation on these conformers provides important information about the tempreture under which the previous experiment was performed.Systematic analyses on intramolecular hydrogen bonds in valine conformers were also carried out ultilizing atoms in molecule theory,natural bond orbital theory,geometric criteria and infrared spectra criteria.Normal,blue-shifting and dihydrogen hydrogen bonds which comprise all hydrogen bond types were found to coexist in a valine conformer.The coexistence of different hydrogen bonds indicates their coherent forming mechanism.The N-H…H-C dihydrogen bond we found is a new type one and broaden the definition of dihydrogen bonds. In chapter 4,taking the CCSD results as references,the performances of five DFT(BHandHLYP,MPWB1K,B3LYP,B3PW91 and SVWN) and two WFT(HF and MP2) methods for describing relative conformer energies,vertical electron detachment energies,deprotonation energies,and proton affinities of 22 amino acids were determined.The dependencies of the seven methods on the basis sets were also examined.BHandHLYP functional with the 6-311++G(d,p) basis set is the best choice for molecule systems that are rich in hydrogen bonds.This study provides the best method for studies carried out on similar systems by others.In chapter 5,thorough searches on the potential energy surfaces of 13 representative dipeptides are performed and structure characteristics of the stable conformers located were analyzed.Careful analyses reveal the connections between the structures of dipeptide and amino acids.A method for finding all important dipeptide conformers utilizing amino acid conformers is thus proposed.Applying the method to other dipeptides carefully examined by others shows that the new approach is not only more efficient but also more reliable by providing the most complete ensembles of dipeptide conformers and much improved agreements between the theoretical and experimental infrared spectra.In chapter 6,thorough searches on the potential energy surfaces of 5 representative tripeptides are performed and structure characteristics of the stable conformers located were analyzed and compared with that of dipeptides.Careful analyses reveal the connections between the structures of tripeptide and dipeptides or amino acids.Based on the method proposed for dipeptides,a method for finding all important tripeptide conformers utilizing dipeptide and amino acid conformers is put forward.Applying the method to other tripeptides carefully examined by others shows that the new approach is not only more efficient but also more reliable.The method is then broadened with genetic algorithm,and applying it to alanine tetrapeptides,conformers with important secondary structures of proteins were located.This establishes solid groundwork for the method being applied to larger peptides.