Hydrogen Bond Interaction Between The Bases And Amino Acid Dipeptide

It is very important for all kinds of life activities that the interaction performs betweennucleic acids and protein, the interaction depends mostly on the formation and fracture of thehydrogen bond between bases of nucleic and protein.The minimum unit of protein is amino acid, amino acids perform polypeptide chains bydehydration synthesis. Large numbers of studies provide that the most part of protein isabsorbed in the form of the peptide after organism takes protein. There are five kinds of basesin nucleic acid, this paper selects single hydrogen bond that is formed between three kinds ofbases(adenine、guanine、cytosine)and nine kinds of amino acid dipeptide as the studied objects.The geometry optimizations and the energy calculations are performed by ABEEMσπ/MM.Besides, the geometry optimizations are performed at the ab initio B3LYP/6-311++G(d,p)level, and the energy calculations are performed at the MP2/6-311++G(d,p) level for the samesystem. The electrostatic interaction parameter kH-bondin the hydrogen bond interaction region(HBIR) is changed through the comparison of binding energy from two methods, then, we fitthe functions kH-bond(Rlp,H) of parameter kH-bondand the distance Rlp,Hbetween the H that formshydrogen bond and the lone pair electrons of its receptor atom.We classify by the labels of atoms and lone pairs formed hydrogen, For hydrogen bondof the same labels, we change the four coefficient A、B、C、D of the functions kH-bond(Rlp,H),and make the functions kH-bond(Rlp,H) of the same labels consistent. Using the functions tocalculate the binding energy of the complexes, Comparing to the binding energy of ab initio,the binding energy’ absolute deviation is basically under1kcal/mol, the minimum is0.0143kcal/mol. the liner correlation coefficient is0.9570. The results illustrateABEEMσπ/MM method correspond to ab initio method very well, and the functionskH-bond(Rlp,H) make preparations for nucleic acid-protein interactions’ study byABEEMσπ/MM method.