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

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.

doi:10.1021/acs.jcim.0c01480

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

Abstract

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.

Authors:

^[1];

^[2]; Johnson, Matthew S. ^[1];

^[1];

^[1]; Payne, A. Mark ^[1];

^[1];

^[1]; Yee, Nathan W. ^[1];

^[3];

^[4];

^[1];

^[4];

^[1]

Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Chemical Engineering
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Chemical Engineering; Technion-Israel Institute of Technology, Haifa (Israel). Wolfson Dept. of Chemical Engineering
Northeastern Univ., Boston, MA (United States). Dept. of Chemical Engineering
Brown Univ., Providence, RI (United States). School of Engineering

Publication Date:: 2021-05-28

Research Org.:: Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division; USDOE National Nuclear Security Administration (NNSA); National Science Foundation (NSF)

OSTI Identifier:: 1851973

Grant/Contract Number:: SC0014901; 122374

Resource Type:: Journal Article: Accepted Manuscript

Journal Name:: Journal of Chemical Information and Modeling

Additional Journal Information:: Journal Volume: 61; Journal Issue: 6; Journal ID: ISSN 1549-9596

Publisher:: American Chemical Society

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Pharmacology & pharmacy; Chemistry; Computer science; Algorithms; Surface reactions; Molecules; Thermochemistry; Resonance structures

Citation Formats


                    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, and Green, William H. Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation.  United States: N. p., 2021. 
        Web.  doi:10.1021/acs.jcim.0c01480.

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                    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. Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation.  United States.  https://doi.org/10.1021/acs.jcim.0c01480

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                    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, and Green, William H. 2021.  
        "Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation".  United States.  https://doi.org/10.1021/acs.jcim.0c01480.  https://www.osti.gov/servlets/purl/1851973.

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@article{osti_1851973,

  title        = {Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation},

  author       = {Liu, Mengjie and Grinberg Dana, Alon and Johnson, Matthew S. and Goldman, Mark J. and Jocher, Agnes and Payne, A. Mark and Grambow, Colin A. and Han, Kehang and Yee, Nathan W. and Mazeau, Emily J. and Blondal, Katrin and West, Richard H. and Goldsmith, C. Franklin and Green, William H.},

  abstractNote = {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.},

  doi          = {10.1021/acs.jcim.0c01480},

  url          = {https://www.osti.gov/biblio/1851973},
  journal      = {Journal of Chemical Information and Modeling},

  issn         = {1549-9596},

  number       = 6,

  volume       = 61,

  place        = {United States},

  year         = {2021},

  month        = {5}

}

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

Abstract

Citation Formats

Self-Evolving Machine: A Continuously Improving Model for Molecular Thermochemistry journal, February 2019

Automatic reaction network generation using RMG for steam cracking of n-hexane journal, January 2006

Automatic Generation of Microkinetic Mechanisms for Heterogeneous Catalysis journal, May 2017

Accurate Thermochemistry with Small Data Sets: A Bond Additivity Correction and Transfer Learning Approach journal, June 2019

A priori rate constants for kinetic modeling journal, October 2002

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First-principles based group additivity values for thermochemical properties of substituted aromatic compounds journal, August 2015

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Automated chemical resonance generation and structure filtration for kinetic modeling journal, July 2019

Group additive modeling of substituent effects in monocyclic aromatic hydrocarbon radicals journal, December 2016

Ethanol steam reforming over Ni/MxOyNi/MxOy–Al2O3Al2O3 (M=CeM=Ce, La, Zr and Mg) catalysts: Influence of support on the hydrogen production journal, July 2007

Uncertainty analysis of correlated parameters in automated reaction mechanism generation journal, February 2020

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Analyzing Learned Molecular Representations for Property Prediction journal, July 2019

Intramolecular 13C isotope distributions of butane from natural gases journal, May 2020

Thermochemistry Prediction and Automatic Reaction Mechanism Generation for Oxygenated Sulfur Systems: A Case Study of Dimethyl Sulfide Oxidation journal, February 2020

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms journal, June 2016

Rate-based screening of pressure-dependent reaction networks journal, August 2001

The predictive capability of an automatically generated combustion chemistry mechanism: Chemical structures of premixed iso-butanol flames journal, November 2013

Capturing pressure-dependence in automated mechanism generation: Reactions through cycloalkyl intermediates journal, January 2003

Computer-Generated Kinetics for Coupled Heterogeneous/Homogeneous Systems: A Case Study in Catalytic Combustion of Methane on Platinum journal, August 2019

Additivity Rules for the Estimation of Molecular Properties. Thermodynamic Properties journal, September 1958

Automatic Mechanism and Kinetic Model Generation for Gas- and Solution-Phase Processes: A Perspective on Best Practices, Recent Advances, and Future Challenges: AUTOMATIC MECHANISM GENERATION FOR GAS- AND SOLUTION-PHASE PROCESSES journal, January 2015

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Forty years of Clar's aromatic π-sextet rule journal, January 2013

Genesys: Kinetic model construction using chemo-informatics journal, October 2012

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Moving from postdictive to predictive kinetics in reaction engineering journal, October 2020

Reaction: System for Modeling Chemical Reactions journal, May 1995

An Extended Group Additivity Method for Polycyclic Thermochemistry Estimation: AN EXTENDED GROUP ADDITIVITY METHOD FOR POLYCYCLIC THERMOCHEMISTRY ESTIMATION journal, February 2018

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Automated Reaction Mechanism Generation Including Nitrogen as a Heteroatom: AUTOMATED REACTION MECHANISM GENERATION INCLUDING NITROGEN AS A HETEROATOM journal, February 2018

Rate-Based Construction of Kinetic Models for Complex Systems journal, May 1997

Self-Evolving Machine: A Continuously Improving Model for Molecular Thermochemistry
journal, February 2019

Automatic reaction network generation using RMG for steam cracking of n-hexane
journal, January 2006

Automatic Generation of Microkinetic Mechanisms for Heterogeneous Catalysis
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Accurate Thermochemistry with Small Data Sets: A Bond Additivity Correction and Transfer Learning Approach
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journal, October 2002

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journal, February 2018

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journal, August 2015

378. 1 : 12-2 : 3-10 : 11-Tribenzoperylene
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Automated chemical resonance generation and structure filtration for kinetic modeling
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Ethanol steam reforming over Ni/MxOyNi/MxOy–Al2O3Al2O3 (M=CeM=Ce, La, Zr and Mg) catalysts: Influence of support on the hydrogen production
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Thermochemistry Prediction and Automatic Reaction Mechanism Generation for Oxygenated Sulfur Systems: A Case Study of Dimethyl Sulfide Oxidation
journal, February 2020

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms
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The predictive capability of an automatically generated combustion chemistry mechanism: Chemical structures of premixed iso-butanol flames
journal, November 2013

Capturing pressure-dependence in automated mechanism generation: Reactions through cycloalkyl intermediates
journal, January 2003

Computer-Generated Kinetics for Coupled Heterogeneous/Homogeneous Systems: A Case Study in Catalytic Combustion of Methane on Platinum
journal, August 2019

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journal, January 2015

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Reaction: System for Modeling Chemical Reactions
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Automated Reaction Mechanism Generation Including Nitrogen as a Heteroatom: AUTOMATED REACTION MECHANISM GENERATION INCLUDING NITROGEN AS A HETEROATOM
journal, February 2018

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