Search Of The Stable Conformations Of Different Types Of Organic Small Molecules And Thr-tripeptide Using ABEEM??/MM Method

Exploring the stable conformation of molecules can provide theoretical guidance for the study of its thermodynamic kinetic properties.The analysis of the conformation is important for the computational simulation of the biological system,the main research work of this paper is the calibration of molecular force field method accuracy and the parameter construction of various systems,this thesis is divided into two parts.(?)We have selected 17 organic small molecules with different chemical functions(including alkanes,alkenes,ethers,alcohols,aldehydes,amines,amides,electrically neutral and negatively charged carboxylic acids)as the research objects and conducted a rapid search for the stable conformation.Gaussian09 software,high-level B3LYP/6-311++G(d,p)method were used to scan the potential energy surfaces of two characteristics dihedral angles that reflect different molecular,at the same time the structural optimization was adopted for the stable conformation.Based on the stable conformations obtained from ab initio,Atom-Bond Electronegativity Equalization Fluctuating Charge Force Field(ABEEM??/MM)and other force field methods were used to search the molecules' conformations.The results were compared,the data shows that the ABEEM??/MM method is in good agreement with the ab initio and can find all the conformations accurately.The MAD(mean absolute deviation)of the molecules in this force field is optimal and has the best agreement with the ab initio data.(?)Taking the polar amino acid,threonine dipeptide as a model molecule,the predecessor has fixed the backbone and scanned it to obtain ten different kinds of stable conformations.Due to a hydroxyl group on the branch of threonine,which has an remarkable influence of the conformation,we scanned and optimized its brancheand then investigated the threonine dipeptide molecules by ABEEM??/MM,OPLS/AA,AMBER99 sb,CHARMM27and AMOEBA force field methods.The ab initio data were used as the reference standard.By comparing the results of contrast calulation,we find that ABEEM??/MM method can obtain the same numbers of the stable conformations as ab initio,and the MAD of the dihedral angles between the two methods is only 3.08°.However,the correlation properties of stable conformations obtained by other force fields only partially the same as ab initio results.In summary,the ABEEM??/MM fluctuating charge polarizable force field can quickly and accurately search for molecular stable conformations.The calculated results are in good agreement with ab initio results and have an outstanding coincidence degree.TheABEEM??/MM has advantages in the field of molecular conformations,laying a solid foundation for future research on biological macromolecular systems.