Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation

• Published in: Journal of chemical information and modeling Vol. 61; no. 6; pp. 2686 - 2696
• Main Authors: Liu, Mengjie, Grinberg Dana, Alon, Johnson, Matthew S, Goldman, Mark J, Jocher, Agnes, Payne, A. Mark, Grambow, Colin A, Han, Kehang, Yee, Nathan W, Mazeau, Emily J, Blondal, Katrin, West, Richard H, Goldsmith, C. Franklin, Green, William H
• Format: Journal Article
• Language: English
• Published: Washington American Chemical Society 28.06.2021
• Subjects: Algorithms; Chemical Information; Chemistry; Computer science; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Isomorphism; Liquid phases; Machine learning; Mathematical models; Molecules; Parallel processing; Parameter sensitivity; Pharmacology & pharmacy; Reaction kinetics; Reaction mechanisms; Resonance structures; Sensitivity analysis; Surface reactions; Thermochemistry; Uncertainty analysis
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/acs.jcim.0c01480

In chemical kinetics research, kinetic models containing hundreds of species and tens of thousands of elementary reactions are commonly used to understand and predict the behavior of reactive chemical systems. Reaction Mechanism Generator (RMG) is a software suite developed to automatically generate such models by incorporating and extrapolating from a database of known thermochemical and kinetic parameters. Here, we present the recent version 3 release of RMG and highlight improvements since the previously published description of RMG v1.0. Most notably, RMG can now generate heterogeneous catalysis models in addition to the previously available gas- and liquid-phase capabilities. For model analysis, new methods for local and global uncertainty analysis have been implemented to supplement first-order sensitivity analysis. The RMG database of thermochemical and kinetic parameters has been significantly expanded to cover more types of chemistry. The present release includes parallelization for faster model generation and a new molecule isomorphism approach to improve computational performance. RMG has also been updated to use Python 3, ensuring compatibility with the latest cheminformatics and machine learning packages. Overall, RMG v3.0 includes many changes which improve the accuracy of the generated chemical mechanisms and allow for exploration of a wider range of chemical systems.