Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde

The free energy profile and the (classical) kinetics of chemical reactions in (soft) condensed phase are modeled theoretically by means of molecular dynamics simulations, the Perturbed Matrix Method (PMM) and the quasi Gaussian entropy (QGE) theory. In this paper we describe the theoretical framework and apply the model to the intramolecular proton transfer reaction of aqueous malonaldehyde. Although in the present application we disregard the quantum effects for the proton dynamics along the reaction coordinate (i.e., tunneling), the classical-like view of the proton transition over the reaction free energy surface seems to properly describe the kinetic process and shows that water acts lowering the reaction free energy barrier. Moreover, a weak temperature dependence of the free energy surface is obtained, implying small entropy variations in the transition. Interestingly the activation entropy, as provided by the QGE model, is negative in the whole temperature range considered, thus indicating an entropy reduction at the transition structure. Finally, by comparing our results with theoretical and experimental literature data, we critically address the actual role of tunneling in this reaction and discuss the emerging kinetic scheme. Copyright (c) 2006 John Wiley & Sons, Ltd.