Monte Carlo Determination of the Free Energy and Internal Energy of Hydration for the Ala Dipeptide at 25oC
Abstract: The differences in free energy and internal energy of hydration of the Ala dipeptide in the C7, aR, C5, and PII conformations were computed with the Monte Carlo method in the (T,V,N) ensemble at 25o. The free-energy differences were obtained by determining the relative probabilities of the conformations that lie on a line that connects two conformations in the (y,f) space. The determinantion of one free-energy difference required three to five separate Monte Carlo runs using non-Boltzmann sampling. The results indicate that both the aR and PII conformations are preferentially stabilized by hydration. The major contributing factor for the stability of internal energy of hydration for these conformations can be traced to the hydration of the carbonyl group.