Treatment of rotational isomers in free energy evaluations. Analysis of the evaluation of free energy differences by molecular dynamics simulations of systems with rotational isomeric states

Using 1,2-dimethoxy ethane in aqueous solution as an example, the applicability of the perturbation method and the thermodynamic integration technique to evaluate free energy differences is considered for systems with multiple rotational isomeric states. It is shown that the naive application of these methods to evaluate free energy differences for such systems, even in a simple case such as the free energy of hydration of 1,2-dimethoxy ethane, may lead to unreasonable results. This problem is due to the fact that, in a conventional simulation, it is unlikely that all isomeric states will be sampled with the appropriate equilibrium probabilities. A procedure is proposed to estimate the contributions of isomeric states in free energy difference calculations.