Theoretical Study Of Weak Interactions,Protonation And Proton Migration Of Short Peptides

As the basic components of proteins,the research of amino acids and short peptides on their structures,properties and spectra is conducive to understand the protein functions and biological phenomena of various organisms.With the development of computational simulation methods and computer technology,theoretical calculation plays an increasingly important role in the study of amino acids and short peptides.The theoretical calculation of these biological small molecules can be used to explain some experimental research results,which can also be applied to speculate and guide the unexplored experimental fields.In this paper,the competition between intramolecular hydrogen bond interaction and dispersive interaction was explored based on carrying out systematical study of the geometric and electronic structures of a series of short peptides,while the evolution and reasons of amino protonation and peptide protonation were also researched.In the first chapter,various calculation methods are introduced,including Hartree Fock method and density functional theory,as well as the calculation software used in this paper and some other commonly used calculation software.In addition,the infrared spectrum and XPS spectrum are briefly introduced.the potential energy surface and the important stagnation points on the potential energy surface are introduced.Finally,it elaborates the reasons for selecting short peptide,as well as discussing the significance and current situation of gas phase research.In second chapter,the potential energy surface of dipeptide benzyloxycarbonyl arginine was systematically researched.The infrared spectra,XPS and NEXAFS spectra of three different isomers were calculated and simulated,while the calculated energy ordering,molecular structure and spectra reasonably explain the experimental infrared spectra reported before.We conducted calculation and analysis on the intramolecular hydrogen bond interaction and dispersive interaction,whose results are different from the previous reports that the dispersive interaction plays a leading role.But this calculation results demonstrate that the conventional hydrogen bond interaction plays a leading role in the molecular stability.In third chapter,we systematically search the potential energy surfaces of eight kinds of peptides.The electron energies of eight short peptides after amino protonation and peptide bond protonation correction were calculated and sequenced based on three theoretical methods.Finally,glycyl proline(GPH)was found as the most stable conformation of short peptides.Thus the infrared spectra of different isomers of GPH were calculated and simulated.The conformation changes between amino and peptide bonds were analyzed,which reflected that the energy difference between amino and peptide bonds came from the energy difference in the process of proton transfer,while the energy difference caused by the change of interaction between molecules caused by the change of space structure.Finally,we made a summary and briefly explained the conclusions we reached.The calculation results of benzyloxycarbonyl arginine show that hydrogen bond interactions rather than dispersion interactions still play a dominant role in molecular stability in this molecule.We have found a dipeptide whose peptide bond protonation is more stable than amino protonation,and analyzed the proton transfer process.The results show that the energy difference between amino protonation and peptide bond protonation mainly comes from the proton transfer process.Poor energy.