Fast Calculation Of Molecular Total Energy With ABEEM??/MM Method—for Some Series Of Organic Molecules And Peptides And Search Of Conformations Ser-dipeptide And Ser-tripeptide

This paper is divided into two parts:The first part is that a new ABEEM??/MM method for fast calculation of molecular total energy is established by combining ABEEM?? model with force field representation,where ABEEM?? is the atom-bond electronegativity equalization model at the ?? level.The calibrated parameters are suitable and transferable.This paper demonstrates that the total molecular energies for series of alcohols,aldehydes,carboxylic acids and peptides calculated by ABEEMa??/MM method are in fair agreement with those obtained from calculations of ab initio MP2/6-311++G(d,p)method with root mean square deviation(RMSD)being 2.00 kcal/mol,mean absolute deviation(MAD)being 1.45 kcal/mol and their linear correlation coefficients being 1.0000.The relative energies between different isomers by using ABEEM??/MM method are close to those obtained by MP2/6-311++G(d,p).What's more,these energies would no longer be correlated for MP2 energies alone(versus number of C atoms).However,the fitness maintains goodness when changing R to be-N02,-OH,-Ph,-CO.The second part is to search stable conformations of serine dipeptide and tripeptide obtained by ABEEM??/MM method.34 kinds of stable conformations for serine dipeptide and 44 kinds of stable conformations for serine tripeptide can be quickly obtained by ABEEM??/MM method that is in fair agreement with those obtained by initio B3LYP/6-311++G(d,p)method,and the backbone dihedral angles and branched chain dihedral Angles of the stable conformations obtained by the two methods are similar.However,all of stable conformations of serine dipeptide and serine tripeptide can not be found by OPLS/AA and AMBER 99sb.For serine dipeptide,The average absolute deviation(MAD)of dihedral Angles(????x1and x2)obtained by ABEEM??/MM,OPLS/AA and AMBER 99sb is 4.8°,8.9° and 12.00 respectively;For serine tripeptide,The average absolute deviation(MAD)of dihedral Angles obtained by ABEEM??,OPLS/AA and AMBER 99sb is 2.9°,15.6° and 11.0° respectively.Thus it opens good prospects for wide applications to chemical and biological systems.