Molecular dynamics simulations of free energy and conformational transition rates of calix[4]arene in chloroform

In a previous article we introduced a reaction coordinate based on the unstable normal mode at the saddle point of the potential energy surface. We here calculate the free-energy distribution along this coordinate for the isomerization of calix[4]arene in vacuo and in chloroform using umbrella sampling, with one umbrella covering the entire range of the reaction coordinate. An excellent first guess at this umbrella is obtained by performing a normal-mode analysis at various points along the reaction path. The isomerization rate constant of this reaction is determined using the reactive flux method and is found to be in good agreement with experimental data. The rate was found to be independent of the location of the transition state, as it should be.