Theoretical study on the structural variations of alanine dipeptide conformers by hydration

Abstract

The effects in structural variations and relative stabilities of the hydration of Alanine dipeptide in the $C^{eq}_7$, $C^{ax}_7$, $C_5$, $\alpha_R$, and $P_{II}$ conformations were investigated by the method of SUMSL(Secant-type Unconstrained minimization Solver) energy Minimization technique with the empirical four-term potential energy function of the solute, and with the ST2 water model. We thought the hydration, imaginarily, as the discrete addition of water molecules to the solute. The binding sites of water molecules in the solute are selected from spherical interaction energy maps. As a function of the number of added water molecules, we traced the structural variations mainly in the (Φ,Ψ) torsion angle space, and calculated the total internal energies of each solute-waters systems to evaluate the relative probabilities between those five conformers. The results indicate that the conformers having no intramolecular hydrogen-bondings, such as $\alpha_R$, $C_5$, $P_{II}$, show larger structural variations than the conformers of $C^{ax}_7$, $C^{eq}_7$ which have intramolecular hydrogen-bondings. The torsion angle of Ψ fluctuated more than Φ for all the examined conformers. Probably this fact was caused by the presence of the repulsive interaction over the dihedral angle of $C_\beta^-C_\alpha^-C``_R-O_R$ in the solute. The energetically dominant conformation is shifted from $C^{eq}_7$ to $\alpha_R$ as the hydration is proceeded.