Theoretical Studies On Conformations And Spectral Properties Of Amino Acids And Short-Peptides

As the fundamental building block of protein, the structures and properties of amino acids and short-pep tides are very important for the deep understanding of its various biological functions and life phenomena. The theoretical calculation on such small biological molecules can help us to explain the relative experimental results and also give proper directions to the experiments that can not be done up to now. Spectroscopy, as a sensitive tool for the detection of electronic structure of molecules and the outer environment, has been widely used in theory and experiments. Based on the density functional theory and various ab initio methods, this thesis mainly focused on the chemical structure and electronic structure of amino acids and some short-peptides in the gas-phase, especially the infrared and X-ray spectra of them for the test of future experiments.In the first chapter, we introduce the basic theory of quantum chemistry calculation and the different kinds of theoretical methods, such as the ab initio method, the semi-experiential method and the density functional theory (DFT) et al. we also introduce the physical figures and the calculation theory of infrared spectroscopy (IR) and X-ray calculation, including near-edge X-ray absorption fine-structure (NEXAFS) and X-ray photoelectron spectroscopy (XPS). At last we briefly introduce the softwares that we used in the dissertation.In chapter2, the main contents of our research area on amino acids and short-peptides were given. Then the goals and the research status of such research in the gas-phase were given and the advantages of spectroscopy research for such small biological molecules were included and the main content of this thesis were also given.In chapter3, we take a systematic search on the potential energy surface (PES) of deprotonated arginine in the gas-phase based on the DFT and many-body perturbation theory (MP) methods. The global minimum in our results is1.57kcal/mol lower in energy than before at B3LYP/6-31G(d, p) level. The IR spectra of the canonical, zwitterionic, protonated and deprotonated aiginine have been compared with each other and depending on the previous results about the neutral arginine, the proton dissociation energy (PDE) and gas-phase acidity (GA) were calculated and in good agreement with the experimental values. In chapter4, the potential energy surface of gaseous arginine (canonical, zwittwrionic and protonated form) was systematically searched based on semi-experiential and DFT method. The results are in good agreement with the previous ones which were got by "step-by-step" strategy. By comparing the different algorithms for the study of aiginine, we found that the "step-by-step" strategy is much effective. Through the application of this strategy to four single amino acids, three dipeptides and one tripeptide, we believe that it can be used as a powerful tool for the search on the potential energy surface and more good results were produced even with less trial structures. A t last, this strategy were further extended and can be effectively used for large molecules with long chains.In chapter5, based on a series of infrared multiple photon dissociation (IRMPD) spectra of deprotonated amino acids and DFT theory, the details of deprotonation process were studied. Through the comparison between the theoretical and experimental results, the influence of the various side chains on the deprotonation process was found and the interesting relationship between the global minimum of neutral amino acids and that of its deprotonated form was also found. For tryptophan, phenylalanine and serine, the spectra of the global minimum of the deprotonated anions which occurred in the carboxylate group can match excellently with the experiments. In contrast, for tyrosine and cysteine, the spectra of the global minima of the deprotonated anions that occurred in the side-chain group match poorly with the experiments, however, another anions with a higher energies in which the deprotonated process occurred in the carboxylate group give much good results. For the complicated aspartic and glutamic acid molecules, a detail description of the broad, hardly resolved spectral features was given and even some dimmers were constructed and used to solve the problem.In chapter6, first principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra of neutral arginine at different K-edges in the solid phase as well as the X-ray photoelectron spectra (XPS) of neutral, deprotonated, and protonated arginines in the gas phase. The results in the solid state are in good agreement with the experiments. Through the analysis of features of XPS and NEXAFS, the canonical influences of the intra-and inter-molecular hydrogen bonds (HBs) and different charge states have been carefully examined to obtain useful structure-property relationships. Our calculations show noticeable difference in the NEXAFS/XPS spectra of the canonical and zwitterionic species that can be used for unambiguously identifying the dominant form in the gas phase. The results indicated that different temperatures have no influence on the positions of the peaks but change the transition strength,In chapter7, first principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra as well as the X-ray photoelectron spectra (XPS) at different K-edges and the infrared spectroscopy (IR) of neutral arginylglycine (RG) in the gas-phase. The theoretical study indicated that maybe arginylglycine is the smallest molecule in the gas phase that the zwitterionic form is dimonant, other than the canonical form. Through the analysis of the IR spectra and XPS/NEXAFS spectra, the differences in their chemical and electronic structures were given and can be helpful to future experiment. Finally, the relationship between the absorption spectra of arginylglycine, arginine and glycine were studied and the influence of the formation of dipeptide bond on the absorption spectra was found and the "building-block principle" was deeply understood,In chapter8, the summation of the work in this thesis was given.