Theoretical Study On Molecular Face For Amino Acid Fragments And The Interaction Between Inert Gas Atoms And An HX Molecule

Molecular face?MF?is a theory that can describe not only the shape and size of a molecule but also the frontier electron density.It can be used to indicate the intermolecular interaction or directional recognition and reactive regions of a molecule.In this paper,MF is used to investigate the dynamic changes of the molecular faces when inert gas atoms Rg?Rg=He,Ne,Ar,Kr?gradually approach to HX?X=F,Cl?at the H or X side.The potential acting on an electron in a molecule?PAEM?of basic amino acid fragments is calculated by the semi-empirical simulation of the MF,and then their molecular faces are constructed rapidly.Specific research contents are as follows:?1?At the level of MP2/6-311++G?2d,2p?,the dimers XH---Rg and HX---Rg are optimized.We obtained the stable conformation of the dimmers,when distances between H or X atom and Rg atom gradually decrease from 8.0?to 2.0?.And the PAEM is calculated at the CISD/6-311++G?2d,2p?level with MELD package and our in-house programs.Firstly,in this thesis,the distance between the intrinsic characteristic point of the molecular plane and the nucleus as well as the frontier electron densities of the dimers XH---Rg and HX---Rg are calculated.Then,the molecular faces of the respective model molecules are obtained.It is demonstrated that the D_pb values between the inert gas atom Rg and the H or X atom in the HX molecule exhibit exponential decay when their distances get longer.When the inert gas atoms Rg gradually approach to the H or X atom from far away,both of them stretch their hands to welcome each other in the adjacent medial direction,and boundary distance of atoms in molecules and electron density at the interface change a little.?2?In this paper,we choose the amino acid fragments as the model molecules.Firstly,these fragments were optimized at the MP2/6-311++G?2d,2p?level.Then,the semi-empirical simulation of the MF was performed to obtain the PAEM values which were equal to the negatives of the first ionization energies.The molecular intrinsic characteristic contour?MICC?was built and combined with the electron density obtained by ab initio method,and then the molecular face was constructed rapidly.The surface area and volume of MICC interface,the boundary distance and the electron density at the interface were calculated by both ab initio and the semi-empirical simulation methods.It is found that the contours of molecular face which are obtained by both methods are similar and the absolute errors of the corresponding electron density on the interface are small.Through the research of the semi-empirical simulation of the MF,it is found that the MF can provide a new knowledge about covalent interaction,non-covalent interaction and the reactive properties of many biological macromolecules.