CONFORMATIONAL FREE-ENERGIES FROM SIMULATION - STOCHASTIC DYNAMICS MONTE-CARLO SIMULATIONS OF A HOMOLOGOUS SERIES OF GELLMANS DIAMIDES

We report simulations using the recently described Monte Carlo/stochastic dynamics (MC/SD) simulation method to examine the conformational thermodynamics for a homologous series of diamides. The simulations use the AMBER* force field and the GB/SA model for CHCl3 and are able to reproduce experimental observations of the degree of hydrogen bonding in the series. By carrying out simulations at different temperatures, we are able to obtain thermodynamic parameters for the equilibrium between hydrogen-bonded and non-hydrogen-bonded states. These parameters are found to be in general agreement with experiment. We also discuss the importance of the gas phase force field parameters, the solvation model, and the simulation methodology on the calculated results. One of the more surprising findings is that converged results are sensitive not only to the relative potential energies of conformational minima, but also to the heights of the barriers between conformations.