Structural And Spectroscopic Studies Of Weak Interactions In Bio-molecules

Amino acids,as elements of proteins,have extensive research value in the fields of biology and chemistry.Analyzing the structure and function of amino acids is one of the important ways tounderstand and explore the origin of life on earth.In the research,it is necessary to fully characterize the structural and functional relationships of amino acid oligomers,and this is often performed by means of spectroscopy methodologies.The structure and properties of a molecule depend on the combination of specific and non-specific interactions within it,such as covalent bonds,ionic bonds,van der Waals forces,hydrogen bonds,etc.The study of weak interactions including the hydrogen bonding is often challenging for quantum chemical（QM）modeling.In this work,we selected a typical representative amino acid case—serine as the research object.The serine structure has a variety of conformations,of which the two conformerswith lowest-energy used in our research are named as serine Ⅰ（Ser Ⅰ）and serine Ⅱ（Ser Ⅱ）.This amino acid consists of 14 atoms and contains 4 typical hydrogen bond types in the selected two conformers:NH···O=C,OH···N,OH···O=C,and NH···OH.This work provides high level theoretical results for structure and properties of serine,including the weak interaction ashydrogen bonds,which are a reference to benchmark density functional methods used in QM modelling.The first chapter introduces the research background,research purpose,research significance and research content of this thesis.The second chapter describesthe theoretical calculation framework and specific research methods.It mainly includes an introduction of the Hartree-Fock self-consistent field（SCF）method,perturbation theory,coupled cluster theory and density functional theory（DFT）.In addition,on the basis of these theoretical calculation methods,a"composite scheme"based on the coupled cluster theory with single,doubles and approximately treated triple excitations（CCSD（T））is introduced in more detail.This scheme has been shown to represent good calculation accuracy and efficiency forthe smaller amino-acid glycine.In this work,the"best estimated"structural and spectroscopic parameters are derived by the composite scheme and are used as a reference subsequently to compare and benchmark DFT methods.Chapter Ⅲ focuses on the structural parameters of serine.In the study of the structure of serine,we analyzed its bond lengths,bond angles,dihedral angles,as well as non-bonding distances and hydrogen bonding characteristics,comparing the―best estimated‖results with ones obtained at CCSD（T）,MP2 and DFT levels.Chapter Ⅳ focuses on energetic and spectroscopic properties computed at equilibrium.It contains analysis of electronic energies as well as the basic spectroscopic parameters,including the rotational constants,the ¹⁴N nuclear quadrupole coupling constants,quartic centrifugal distortion constants and harmonic vibrational frequencies.For the latter,"Best Estimates"are compared with DFT results,considering also a detailed analysis,focused on the OH stretching vibrations.Chapter Ⅴ introduced thermodynamics and spectroscopy beyond the harmonic approximation,mainly focusing on thermodynamic properties and anharmonic frequencies,which allow direct comparison with the experimental results.Chapter Ⅵ makes summary and prospect,and proposes extensions for further studies.