A Special Hydrogen Method For Predicting Conformation Stability Of Alanine-α-polypeptide

The features of the conformers' structures have been analyzed and a new method has been proposed based on the density functional theory to determine the conformer's relative stability of the alanine-a-polypeptide. The special hydrogen atom was defined in this paper and the special hydrogen method was then proposed to predict the conformer's relative stability of the alanine-a-polypeptide. Total 239 conformers of alanine di-, tri-, tetra- , penta- and hexa- peptide molecules have been completely optimized at B3LYP/6-31G~* level. The parameters of twelve non-bonded interactions have been determined from 28 conformers of alanine polypeptides.In this work, comparing with the relative energies of total 239 alanine-a-polypeptide conformers obtained by B3LYP/6-31G~* method, it can be concluded that the special hydrogen method is quite reasonable for prediction of the conformation stability of alanine-α-polypeptides. The linear correlation equation between the relative energies Y(kJ/mol) obtained by the special hydrogen method and the relative energies X(kJ/mol) obtained by the B3LYP/6-31G~* is Y=0.9365X+1.7298. The correlation coefficient is R=0.9608. The standard deviation is 4.3kJ/mol. The population of the conformations with deviation smaller than 2kcal/mol is up to 95.0%. Through comparing the 239 conformers' relative energies obtained by the new scheme and B3LYP/6-31G~* ones, it can be concluded that the new method and the interaction parameters are reasonable for the determination of the conformation stability of alanine polypeptides.