Ramachandran surfaces for the alanine di- and tripeptides in gas phase and solution are mapped out using the recently introduced adiabatic free-energy dynamics (AFED) approach introduced by Rosso et al. (J. Chem. Phys. 2002, 116, 4389) as applied to the CHARMM22 force field. It is shown that complete surfaces can be mapped out with an order of magnitude of greater efficiency with the AFED approach than they can using the popular umbrella sampling method. In the alanine dipeptide, it is found, in agreement with numerous other studies using the CHARMM22 force field, that the lowest free-energy structure is the extended β conformation, (φ, ψ) = (-81, 81), while in solution, the extended β, (φ, ψ) = (-81, 153) and right-handed α-helical, (φ, ψ) = (-81, 63) conformations are nearly isoenergetic. In solution, a secondary minimum at (φ, ψ) = (63, -81), corresponding to a C 7 ax conformation, occurs approximately 2.3 kcal/mol above the global free-energy minimum. The alanine tripeptide, a system that has received considerably less attention in the literature, is found to exhibit a similar structure to the alanine dipeptide with the extended β conformation being the free-energy minimum in the gas phase and the β and right-handed α-helical conformations being isoenergetic in solution. These studies indicate that the AFED method can be a powerful tool for studying multidimensional free-energy surfaces in complex systems.
ASJC Scopus subject areas
- Physical and Theoretical Chemistry