Search Of The Conformations Of Asp-dipeptide And Asp-tripeptide With ABEEMσπ/MM Method

This paper mainly discusses two aspects.First,the Gaussian09 package was applied to scan the backbone dihedral angle of aspartic acid dipeptide and tripeptide.We find out the most suitable method,basis sets and time step of scanning and obtain the stable conformation of aspartic acid.The scan of conformations of charged and neutral Asp-dipeptide are performed in the gas phase and liquid phase,respectively.By this way,the influence of the environment can be obtained.It was found that the intramolecular hydrogen bond made the conformation stable.Second,the scan and optimization of aspartic acid dipeptide and tripeptide were performed by using ABEEMσπ polarizable force field.Then,we got 9 kinds of the stable conformations of aspartic acid dipeptide and 50 kinds of the stable conformations of aspartic acid tripeptide.The results obtained from ABEEMσπ polarizable force filed are very close to those of ab initio B3LYP/6-311++G(d,p)method.ABEEMσπ polarizable force filed can not only find out all the stable conformations with accuracy,but also produce small MADs(mean absolute derivations)which are only 2.29° and 2.76° for Asp-dipeptide and tripeptide,respectively.The results obtained from ABEEMσπ are better than those of other fixed charge force fields,such as OPLS/AA,AMBER99 sb and CHARMM27.Compared with AMOERA polarizable force field,our method can not only find out the same number of stable conformations which are consistent with those of ab initio with high efficiency,but also obtain smaller MADs.For the scan of conformation of amino acid dipeptide or polypeptide,we can conclude that the shorter the time step of scanning is,the more accurate conformation we obtain.These results indicate that ABEEMσπ polarizable force field can be used in conformational scanning with high efficiency and accuracy,which establishes the foundation for studying larger biomolecules.