Theoretical Studies On Hydrogen Bonds Of The Amino-acids Hydration And ?H₂O?₂,?H_S?₂,?HF?₂

The hydrogen bond plays an important role in biological,chemical and physical properties of materials.The study of the hydrogen bond is an emerging field of topical interest.The interaction between amino acids and water is the hydrogen bond.Because amino acids are the primary building blocks for proteins,the study of amino acids hydrate will be helpful to the study on the interaction between water and large biological molecule.The dimers of?H₂O?₂,?H₂S?₂,and ?HF?₂ are also formed with the hydrogen bond.But the recognition of their vibrational spectra from hydrogen bonds is not well understood.In this thesis,by performing ab initio molecular dynamics simulations.The first principles calculations and methods we studied the properties of hydrogen bonds in the system of the hydration of amino acids and these dimers of?H₂O?₂,?H₂S?₂,and?HF?₂.In the first chapter,we first introduced the finding history,the research development of the hydrogen bond.Second the important role of the hydrogen bonds in water,DNA,and proteins were summarized.Last we showed the research content of this thesis.In the second chapter,we introduced the theoretical calculation methods.First of all,we introduce the first principles calculation and density functional theory?DFT?,and then the methods of the molecular dynamics?MD?simulation and the vibrational spectra obtained from the MD trajectories are presented.Finally we introduced the method of ab intio molecular dynamics.In the third chapter,the 1:1 complexes of glycine–water,serine-water,proline-water were studied respectively by performing the first principles calculation,and we obtained the rules on the relationship of the amino acid hydrate structure and the hydrogen bond strength.By comparing the results of the structure optimization,the binding energy,and the Bader analysis of atomic charge for the ground states of these three complexes,we got a law of the structure and the binding energy.For example,among these three complexes,the structures of the lowest energy conformers are similar.In this structure,the hydrogen of the carboxyl group forms a hydrogen bond with the oxygen of the water molecule,and one of the hydrogen atoms of the water molecule also forms a hydrogen bond with the oxygen of the C=O group.This rule will be appropriate for the other amino acids complexes.In the fourth chapter,the vibrational spectra of?H₂O?₂,?H₂S?₂,and ?HF?₂ were investigated.Firstly,we performed the first principle molecular dynamics calculation for these three dimers.The vibrational spectra were obtained by performing the Fourier transformation of velocity autocorrelation functions from the MD trajectories.The calculated vibrational spectra are in good agreement with the experiments.Secondly,by comparing the spectra of the monomer and the dimer,the peak of the stretching mode in the monomer is shifted to the lower energy area in the dimer with the effect of hydrogen bond.Finally,by analyzing the vibrational spectra of?H₂O?₂,?H₂S?₂,?HF?₂,we conclude that the larger the strength of hydrogen bonds,the larger the left shift of the stretching mode.The last part of the paper,we make a summary and prospect of this thesis.