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Ramon Crehuet

Publications and source records attributed to Ramon Crehuet.

4 recordsLinked to original sources

The reaction path intrinsic reaction coordinate method and the Hamilton-Jacobi theory.

The definition and location of an intrinsic reaction coordinate path is of crucial importance in many areas of theoretical chemistry. Differential equations used to define the path hitherto are complemented in this study with a variational principle of Fermat type, as Fukui [Int. J. Quantum Chem., Quantum Chem. Symp. 15, 633 (1981)] reported in a more general form some time ago. This definition is more suitable for problems where initial and final points are given. The variational definition can naturally be recast into a Hamilton-Jacobi equation. The character of the variational solution is studied via the Weierstrass necessary and sufficient conditions. The characterization of the local minima character of the intrinsic reaction coordinate is proved. Such result leads to a numerical algorithm to find intrinsic reaction coordinate paths based on the successive minimizations of the Weierstrass E-function evaluated on a guess curve connecting the initial and final points of the desired path.

Algorithms↗

An implementation of the nudged elastic band algorithm and application to the reaction mechanism of HGXPRTase from Plasmodium falciparum.

The understanding of transition processes, such as chemical reactions, is a central topic in theoretical molecular science. A common approach for investigating such processes is to calculate paths between reactant and product structures that are representative of the transition. Many approaches have been proposed to determine such paths but, in this paper, we examine the nudged elastic band algorithm which was recently introduced by Jónsson and co-workers and has been used to study a wide range of transition problems. We describe our implementation of the method in the simulation program Dynamo and some modifications to the original algorithm that we found improve its efficiency. The use of the method is illustrated by an application to the reaction mechanism of the enzyme hypoxanthine-guanine-xanthine phosphoribosyltransferase from Plasmodium falciparum.

Alanine↗

Transition events in one dimension.

The instanton or stationary-phase formula has received much attention recently as a way of determining transition paths in reacting systems. In this paper, we analyze the instanton approach for some one-dimensional problems and compare the results it gives with data from a numerical simulation. We show that a proper comparison of the analytic and numerical results must take into account the boundary conditions used in the numerical simulations and also suggest values for the integration constant in the instanton formula that gives the best agreement with the simulated results.

Journal Article↗