AutoMeKin2021: An open-source program for automated reaction discovery

Emilio Martínez-Núñez; George L Barnes; David R Glowacki; Sabine Kopec; Daniel Peláez; Aurelio Rodríguez; Roberto Rodríguez-Fernández; Robin J Shannon; James J P Stewart; Pablo G Tahoces; Saulo A Vazquez

doi:10.1002/jcc.26734

AutoMeKin2021: An open-source program for automated reaction discovery

J Comput Chem. 2021 Oct 30;42(28):2036-2048. doi: 10.1002/jcc.26734. Epub 2021 Aug 13.

Affiliations

¹ Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela, Spain.
² Department of Chemistry and Biochemistry, Siena College, Loudonville, New York, USA.
³ Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
⁴ Institut de Sciences Moléculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, Orsay, France.
⁵ Galicia Supercomputing Center (CESGA), Santiago de Compostela, Spain.
⁶ Stewart Computational Chemistry, Colorado Springs, Colorado, USA.
⁷ Department of Electronics and Computer Science, University of Santiago de Compostela, Santiago de Compostela, Spain.

PMID: 34387374
DOI: 10.1002/jcc.26734

Abstract

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.

Keywords: MD simulations; graph theory; kinetics; reaction mechanisms.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.