First Principle Investigations On Structures And Properties Of Amino Acids And Amino Acid Complexes

Amino acids are basic building blocks for a large group of biomolecules. The structure of amino acids and the interaction from other fragments in the envi-ronment with amino acids are basic topics in computational biology. Meanwhile, amino acids are systems of multi-conformer, multi-hydrogen bond and strong charge transfer, which, are hot areas of modern computational chemistry. This thesis systemically reviewed the basic methods used in this area and used three different methods to investigate the structures and corresponding properties of three different subsystems.In chapter Ⅰ, the basic methods and concepts of quantum chemistry involved in this thesis were introduced at the essential level.In chapter Ⅱ, the results of our investigation on glutamine were present-ed. We used the systemic method to research the structures of three forms of glutamine. Different theoretical methods were employed to calculate the cor-responding distribution, vertical ionization energies, rotational constants and dipole moments. The previous reported experimental and theoretical gaseous acidities/basicities and proton affinities/dissociation energies were systemically reviewed and compared with our results to judge the reliability of each date and to analyse possible error sources inside. A comment on the performance of various theoretical methods on this system was also presented.In chapter Ⅲ, we designed a systemic method of searching structures of complexes according to the structure characters of amino acid metal ion com-plexes and tried it on the investigation of the structures of Ⅰ\Ⅱ main group ion binding with glutamine. We compared the published theoretical results with ours and updated several new structures. The metal ion binding energies and in-frared spectrum were calculated and compared with some published results. We found B3LYP overestimated the binding energies of some ions and the stability of zwitterion complexes while MP2results highly coincided with experiment. We believed that this phenomenon could be interpreted by the so-called delocalized error. The difference on the intensity of IR spectrum can be possibly attributed to the non-equilibrium condition in the multiphoton dissociation process.In chapter Ⅳ, a new strategy of exploring the low energy structure of small hydrated amino acid cluster was present. This method tried to be insensitive to the detail condition of the empirical potential, therefore might be suitable for systems of strong charge transfer. This method was applied to glycine(H2O)8and obtained much better results than the reported results got by simulated annealing algorithms. The glycine(H2O)8is believed to be competent at repre-senting the short range solvent interaction after analysing the radius distribution of the solvents to the polar sites in the glutamine. The infrared and NEXAFS spectra were calculated and added by the thermal distribution weighted method. The above deduction was confirmed by comparing those with the solution and gaseous spectrum. We believed this work could be served as a solid foundation of ab initio predicting of the solvent effects of biomolecule.In chapter Ⅴ, The investigations published on proton affinities and pro-ton dissociation energies of20nature amino acids were reviewed. The systemic method was applied to all these20systems and the corresponding thermody-namical values were reevaluated. After analysing these data, we confirmed that the traditional simple kinetic method (SKM) was not as reliable as extended kinetic method (EKM) in these systems. G4MP2got the closest results to the experimental values in all the quantum chemistry theories employed. B2PLYPD provided reliable results in neutral and cationic systems but seemed to have slight tendency to underestimate the energies of anionic system. B3LYP was the one which gets well balance between the speed and accuracy.In chapter VI, we gave a brief summary of this thesis.