tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics

• Published in: Journal of computational chemistry Vol. 39; no. 23; pp. 1922 - 1930
• Main Authors: Rodríguez, Aurelio, Rodríguez-Fernández, Roberto, A Vázquez, Saulo, L Barnes, George, J P Stewart, James, Martínez-Núñez, Emilio
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 05.09.2018
• Subjects: accelerated dynamics simulations; automated method; Automation; Chemical reactions; Computer simulation; Graph Theory; Kinetic Monte Carlo; Kinetics; Organic chemistry; Potential energy; Reaction kinetics; Reaction mechanisms; reaction network; Source code; accelerated dynamics simulations; automated method; reaction network; Kinetic Monte Carlo; Graph Theory
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.25370

A new software, called tsscds2018, has been developed to discover reaction mechanisms and solve the kinetics in a fully automated fashion. The program employs algorithms based on Graph Theory to find transition state (TS) geometries from accelerated semiempirical dynamics simulations carried out with MOPAC2016. Then, the TSs are connected to the corresponding minima and the reaction network is obtained. Kinetic data like populations vs time or the abundancies of each product can also be obtained with our program thanks to a Kinetic Monte Carlo routine. Highly accurate ab initio potential energy diagrams and kinetics can also be obtained using an interface with Gaussian09. The source code is available on the following site: http://forge.cesga.es/wiki/g/tsscds/HomePage © 2018 Wiley Periodicals, Inc. Our computer program was designed to find reaction mechanisms with minimal human intervention. Starting from a given structure of our system, tsscds2018 builds the reaction network by running accelerated direct dynamics simulations, which are analyzed with tools from Graph Theory. The obtained network of minima and transition states is fed into a Kinetic Monte Carlo simulator to provide populations of all chemical species as a function of time, for the desired experimental conditions.