J. Phys. Chem. B, 108 (41), 16250 -16254, 2004. 10.1021/jp048788l S1089-5647(04)08788-7

Statistical Mechanical Modeling of Chemical Reactions in Complex Systems: The Reaction Free Energy Surface

A. Amadei,* M. D'Alessandro, and M. Aschi

Dipartimento di Scienze e Tecnologie Chimiche, Universita' di Roma "Tor Vergata", via della Ricerca Scientifica 1, 00133 Roma, Italy, Dipartimento di Chimica, Universita' di Roma "La Sapienza", P.le Aldo Moro 5, 00185 Roma, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita' dell'Aquila, via Vetoio 67010, l'Aquila, Italy

Received: March 18, 2004

In Final Form: June 21, 2004

FULL TEXT

Abstract

In this paper, the perturbed matrix method (PMM) is used in combination with basic statistical mechanics, to develop a general theoretical method to model chemical reactions and related molecular processes in complex systems, i.e., liquids, biochemical systems, macromolecules, etc. The main feature of this approach consists of the explicit treatment of the coupling between the reaction center and the fluctuating atomic-molecular environment, providing a rigorous statistical mechanical description of the chemical event. A special attention is dedicated to the approximations and assumptions necessary to use such a theoretical procedure in combination with simulation data.