Studies Of The Interactions Between Urea And Water/Amino Acid Dipeptides By Quantum Chemical Methods And ABEEM/MM Fluctuating Charge Force Field

By using of the high level quantum chemical calculation method,MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p),the structure optimization and frequency calculation of Urea(H2O)n(n=1-8)and the complexes formed by urea with three kinds of amino acid dipeptides,Urea(Gly)2,Urea(Ala)2 and Urea(Val)2 were performed.The results show that Urea(H2O)n(n=1-8)formed stable complexes by hydrogen bonds,and six water molecules can be binded in the first hydration layer of urea with wo types of hydrogen bond:one is formed between the oxygen of urea and the hydrogen of water molecules and the other is between oxygen of water molecules and hydrogen of urea.,The former hydrogen bonding is stronger than the latter one.Three types of hydrogen bonds were formed between urea and amino acid dipeptide.The first is formed between the oxygen atom of amino acid dipeptide with of the urea hydrogen,the second between amide oxygen atoms urea and hydrogen connected to the nitrogen of amino acid dipeptide,and the third is between oxygen atom of urea and the hydrogen connected with the carbon atoms of amino acid dipeptide..According to the QM results,the fluctuating charge potential functions of the interaction between urea and water and urea and amino acid dipeptides were constructed based on the ABEEM/MM model.,And the potential functions were applied to calculate the geometric structures,charge distributions and binding energies of Urea(H2O)n(n=1-8),Urea(Gly)2,Urea(Ala)2 and Urea(Val)2,and the ABEEM/MM fixed charge model and OPLS/AA force field were also employed.Compared with the QM methods,for urea(H2O)n(n=1-8),of the linear correlation coefficient of the charge distributions of ABEEM/MM fluctuating charge model reaches 0.98,the average absolute deviation(AAD)of binding energies is 1.43 kcal/mol,the root mean square deviation(RMSD)of hydrogen bond length and angle are 0.1020A and 1.33°,respectively.For the ABEEM/MM fixed charge model,the AAD of binding energies is 2.08 kcal/mol,and the RMSD of bond length and angle are 0.2262A and 3.22°,respectively.For the OPLS/AA,the AAD of binding energis is 14.91 kcal/mol,and the RMSD of hydrogen bond length and angle are 0.0952A and 14.98°,respectively.For the Urea(Gly)2,Urea(Ala)2 and Urea(Val)2,compared to the QM results,the linear correlation coefficient of charge distributions of ABEEM/MM fluctuating charge model reaches 0.96.The AAD of binding energies of the ABEEM/MM fluctuating charge model,ABEEM/MM fixed charge model and OPLS/AA are 1.57,1.04 and 1.12kcal/mol;1.59,1.62 and 1.20kcal/mol;4.04,3.80 and 4.87kcal/mol,respectively.Compared between the structures from QM and the three force fields,the deviation of the ABEEM/MM fluctuating charge model is the smallest,and the results of ABEEM/MM fixed charge model is better than those of OPLS/AA.The deviation of some structures obtained by OPLS/AA are remarkable.