Theoretical Study On Molecular Faces For Amino Acid Dipeptide And HIV Protease Inhibitor

In recent years,the molecular face theory developed by Yang et al.has gradually become a new tool for studying the shape of molecules,it can display the shape,size and distribution of frontier electron density,and can predict the sites of molecular stereoselectivity.However,this theory contains a large number of complex molecular integral terms in the calculation process,and the research on biological macromolecular systems takes a long time.Based on the theory of molecular morphology,this paper develops a potential method for quickly predicting the potential of single-electron potential--D_pband semi-empirical depiction of molecular morphology.Through the study of a series of small organic molecules,it is verified that the new method is not only time-saving but also highly accurate.The specific research work are as follows:（1）Taking the C-H bond of methane molecule and the isolated C and H atoms as the research objects,we determined the approximate formula for quickly predicting D_pbunder semi-empirical method.Firstly,under the theoretical level of B3LYP/6-311++G（d,p）,the D_pbvalues of the chemical bonds in some organic small molecules are calculated and compared by the ab initio and semi-empirical methods respectively,the results are very close.Secondly,the D_pbvalues of some chemical bonds in the 20 amino acid dipeptides and 9 HIV protease inhibitor molecules were calculated by using a new method.According to the smaller the value of D_pband the weaker chemical bond,the strength of chemical bonds is compared,which provides a new idea for studying their related properties.（2）Based on the point charge model,we established a new semi-empirical approximation method to quickly construct the MF.In order to judge whether the distribution of the electron density calculated by the new method on the molecular boundary is consistent with the ab initio result,we select some common organic small molecules and calculate their intrinsic characteristic parameters,including the boundary distance and the electron density near the boundary,etc.The results show that the error of each physical quantity calculated by the two methods is less than 6%.On this basis,we have drawn the face of these small molecules under two methods.The distribution of electron density on the face and the shape and size of the molecules are basically the same.As a new method,at the same theoretical level,we have mapped the topography of 20 amino acid dipeptide molecules and 9 HIV protease inhibitor molecules,laying the foundation for the application of molecular morphology theory to biomacromolecular systems.In summary,this paper develops a new method for rapidly predicting D_pband semi-empirical depiction of molecular morphology based on molecular morphology theory.Taking the small organic molecules as the research objects,the credibility of the new method was confirmed,and the molecular face of 20 amino acid dipeptide molecules and 9 protease inhibitor molecules was delineated by new methods,and the related properties were studied.