Search Of The Conformations Of Organic Molecules And Methionine Dipeptide With ABEEM/MM Method

In this thesis,ABEEM/MM method is used to search for the stable conformation of six types organic molecules and methionine dipeptide.The research shows that the result obtained by ABEEM/MM method is consistent and has high accuracy with ab initio.The specific research contents are as follows:(1)Taking pentane as an example,the characteristic dihedral angles of pentane are scanned in steps of 10°and 30°,respectively.By comparing the results of both,it is found that the result of 10°step is more accurate.Therefore,the stable conformations of the organic molecules are explored in step of 10°.Six types organic molecules(alkanes,alcohols,carboxylic acids,ethers,olefins,thioethers)are selected as research objects to study the stable conformations of organic molecules with linear structures of 2-10 carbon atoms.B3LYP/6-311++G(d,p)method is used to scan the two characteristics dihedral angles(Tor1,Tor2)of organic molecules in 10°steps,and the local minimum points are optimized;the optimized structures are calculated by MP2/6-311++G(d,p)method,and the optimized structures are taken as the standard.The stable conformations of six types organic molecules are searched by using ABEEM/MM,AMOEBA09,OPLS/AA,AMBER99sb and CHARMM force fields,respectively.Referring to the results of ab initio,the ABEEM/MM force field can find the same number of stable conformations as ab initio,the mean absolute deviation(MAD)of the resulting dihedral angle is relatively small;the data fitting consistency is good;the calculation speed is much faster than ab initio method,which lays a foundation for the study of biological macromolecules.(2)Uing methionine dipeptide as a model molecule,the main chain is fixed,and the side chain is scanned and analyzed to explore the effect of side chain on the stable conformations of methionine dipeptide.The predecessors searched 15 kinds of stable conformations by exploring the dihedral angle of the methionine skeleton.In order to find out more possible stable conformations of methionine dipeptide,based on previous studies,the dihedral angles(?₁??₂??₃)of 15 types of stable conformational side chains were scanned,taking the lowest energy and most stable structure as the research object,the scanning results are locally optimized and local minimer by B3LYP/6-311++G(d,p)method.The optimized structures are used as a standard to search for the stable conformations of methionine dipeptide by using ABEEM/MM,AMOEBAbio09,OPLS/AA,AMBER99sb and CHARMM force fields respectively to verify whether all force fields could find all stable conformations.In this paper,the localization and global optimization methods are used to explore the strength of interaction between the main chains and side chains.The data analysis shows that the main chains and side chains of the methionine dipeptide have little influence on each other,and the ABEEM/MM force field method can obtain the same number of stable conformations in local optimization and global optimization as ab initio.The MAD of the dihedral angle are 2.4°and1.0°,respectively.In summary,the number of stable conformations of six types organic molecules and methionine dipeptide in the ABEEM/MM force field are consistent with ab initio,and the MAD of the dihedral angle is the smallest.Due to accuracy of its calculation results and the efficiency of the calculation process,the ABEEM/MM method proves its feasibility for conformational studies,which lays a foundation for the study of oligopeptides,peptides and biological macromolecules.