Anomeric free energy of d-mannose in water: A comparison of free energy perturbation, potential of mean force, and mc (jbw)/sd simulations

The anomeric free energy difference between the α (axial) and β (equatorial) anomers of d-mannose was calculated using standard free energy methods (free energy perturbation (FEP) and potential of mean force (PMF)) and with the recently described MC(JBW)/SD simulation technique. The final results obtained with our new united atom AMBER* force field and GB/SA continuum water are FEP 0.28 ± 0.10, PMF 0.20 ± 0.10, MC(JBW)/SD, and 0.25 ± 0.02 kcal/mol in favor of the α anomer, all in good agreement with the experimental value (0.34−0.45 kcal/mol). Convergence, as measured by the stability of the results and the standard deviations, is reached at least an order of magnitude faster with MC(JBW)/SD than with the other two methods.