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

Abstract

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 calix͓4͔arene 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. © 1997 American Institute of Physics. ͓S0021-9606͑97͒50437-5͔

Solvent Effect on the Isomerization Rate of Calix[4]arene Studied by Molecular Dynamics Simulations

“…Once the molecule reached the 1,2-alternate conformation it never returned to the paco conformation. There are two ways for a paco to transform into a 1,2-alternate, depending on whether the second rotated phenol ring neighbors the first rotated phenol ring on the left or on the right . Both 1,2-alternates have the same energy, but the two paco to 1,2-alternate transition states have slightly different energies because of the orientation of the hydrogen bonds.…”

“…As a comparison, in Figure we have plotted the probability distribution of a calix[4]arene in chloroform. This distribution was calculated previously, using the same techniques as described here, but with a different umbrella . We converted this distribution into the distribution that we would have obtained in chloroform with the current vacuum umbrella, i.e.…”

“…The assumptions underlying this theory are that the amplitudes of the vibrations are small, and that there is no coupling between rotations and vibrations. As we have shown elsewhere, it is straightforward to calculate the free energy as a function of the reaction coordinate under the same conditions. The basic task is to calculate the lowest energy conformation and the 3 N − 7 eigenfrequencies of vibrations in the hyperplane of configurations with a prescribed value of the reaction coordinate.…”

“…This coefficient has been calculated for a number of isomerization reactions, as well as for a few chemical reactions. , A third important quantity in reaction rate theory is the reaction coordinate . We have recently introduced a convenient definition of this coordinate, based on the unstable normal mode at the saddle point of the potential energy surface. , This definition is computationally efficient, and can be applied to a wide variety of reactions.…”

Simulation of a Liquid State Photoinduced Enol-Keto Tautomerization Involving Long-Range Proton Transfer

“…Since then several improvements of the theory have been offered. Molecular descriptions of liquid-state chemical reactions are quite rare. − The proper choice between continuum and molecular theories can only be made if they are confronted with reactions whose mechanisms and dynamics are known experimentally with great certainty.…”