Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software
The open‐source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high‐pressure limit reaction rate coefficients, and pressure‐dependent rate coefficient over multi‐well...
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| Veröffentlicht in: | International journal of chemical kinetics 2023-06, Vol.55 (6), p.300-323 |
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| creator | Dana, Alon Grinberg Johnson, Matthew S. Allen, Joshua W. Sharma, Sandeep Raman, Sumathy Liu, Mengjie Gao, Connie W. Grambow, Colin A. Goldman, Mark J. Ranasinghe, Duminda S. Gillis, Ryan J. Payne, A. Mark Li, Yi‐Pei Dong, Xiaorui Spiekermann, Kevin A. Wu, Haoyang Dames, Enoch E. Buras, Zachary J. Vandewiele, Nick M. Yee, Nathan W. Merchant, Shamel S. Buesser, Beat Class, Caleb A. Goldsmith, Franklin West, Richard H. Green, William H. |
| description | The open‐source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high‐pressure limit reaction rate coefficients, and pressure‐dependent rate coefficient over multi‐well molecular potential energy surfaces (PES) including the effects of collisional energy transfer on phenomenological kinetics. Arkane can use estimates to fill in information for molecules or reactions where quantum chemistry information is missing. The software solves the internal energy master equation for complex unimolecular reaction systems. Inputs to the software include converged electronic structure computations performed by the user using a variety of supported software packages (Gaussian, Molpro, Orca, TeraChem, Q‐Chem, Psi4). The software outputs high‐pressure limit rate coefficients and pressure‐dependent phenomenological rate coefficients, as well as computed thermodynamic properties (enthalpy, entropy, and constant pressure heat capacity) with added energy corrections. Some of the key features of Arkane include treatment of 1D, 2D or ND hindered internal rotation modes, treatment of free internal rotation modes, quantum tunneling effect consideration, transition state theory (TST) and Rice‐Ramsperger‐Kassel‐Marcus (RRKM) rate coefficient computations, master equation solution with four implemented methods, inverse‐Laplace transform of high‐pressure limit rate coefficients into the energy domain, energy corrections based on bond‐additivity or isodesmic reactions, automated and efficient PES exploration, and PES sensitivity analysis. The present work describes the design of Arkane, how it should be used, and refers to the theory that it employs. Arkane is distributed via the RMG‐Py software suite (https://github.com/ReactionMechanismGenerator/RMG‐Py). |
| doi_str_mv | 10.1002/kin.21637 |
| format | Article |
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Mark ; Li, Yi‐Pei ; Dong, Xiaorui ; Spiekermann, Kevin A. ; Wu, Haoyang ; Dames, Enoch E. ; Buras, Zachary J. ; Vandewiele, Nick M. ; Yee, Nathan W. ; Merchant, Shamel S. ; Buesser, Beat ; Class, Caleb A. ; Goldsmith, Franklin ; West, Richard H. ; Green, William H.</creator><creatorcontrib>Dana, Alon Grinberg ; Johnson, Matthew S. ; Allen, Joshua W. ; Sharma, Sandeep ; Raman, Sumathy ; Liu, Mengjie ; Gao, Connie W. ; Grambow, Colin A. ; Goldman, Mark J. ; Ranasinghe, Duminda S. ; Gillis, Ryan J. ; Payne, A. Mark ; Li, Yi‐Pei ; Dong, Xiaorui ; Spiekermann, Kevin A. ; Wu, Haoyang ; Dames, Enoch E. ; Buras, Zachary J. ; Vandewiele, Nick M. ; Yee, Nathan W. ; Merchant, Shamel S. ; Buesser, Beat ; Class, Caleb A. ; Goldsmith, Franklin ; West, Richard H. ; Green, William H. ; Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)</creatorcontrib><description>The open‐source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high‐pressure limit reaction rate coefficients, and pressure‐dependent rate coefficient over multi‐well molecular potential energy surfaces (PES) including the effects of collisional energy transfer on phenomenological kinetics. Arkane can use estimates to fill in information for molecules or reactions where quantum chemistry information is missing. The software solves the internal energy master equation for complex unimolecular reaction systems. Inputs to the software include converged electronic structure computations performed by the user using a variety of supported software packages (Gaussian, Molpro, Orca, TeraChem, Q‐Chem, Psi4). The software outputs high‐pressure limit rate coefficients and pressure‐dependent phenomenological rate coefficients, as well as computed thermodynamic properties (enthalpy, entropy, and constant pressure heat capacity) with added energy corrections. Some of the key features of Arkane include treatment of 1D, 2D or ND hindered internal rotation modes, treatment of free internal rotation modes, quantum tunneling effect consideration, transition state theory (TST) and Rice‐Ramsperger‐Kassel‐Marcus (RRKM) rate coefficient computations, master equation solution with four implemented methods, inverse‐Laplace transform of high‐pressure limit rate coefficients into the energy domain, energy corrections based on bond‐additivity or isodesmic reactions, automated and efficient PES exploration, and PES sensitivity analysis. The present work describes the design of Arkane, how it should be used, and refers to the theory that it employs. Arkane is distributed via the RMG‐Py software suite (https://github.com/ReactionMechanismGenerator/RMG‐Py).</description><identifier>ISSN: 0538-8066</identifier><identifier>EISSN: 1097-4601</identifier><identifier>DOI: 10.1002/kin.21637</identifier><language>eng</language><publisher>Hoboken: Wiley Subscription Services, Inc</publisher><subject>Automation ; chemical kinetics ; Chemistry ; Coefficients ; Electronic structure ; Energy ; Energy transfer ; Enthalpy ; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY ; Internal energy ; Laplace transforms ; Potential energy ; potential energy surface ; Pressure dependence ; pressure‐dependent reactions ; Quantum chemistry ; Quantum tunnelling ; Reaction kinetics ; reaction mechanism generator ; Rotation ; Sensitivity analysis ; Software packages ; Statistical mechanics ; Thermodynamic properties ; Thermodynamics</subject><ispartof>International journal of chemical kinetics, 2023-06, Vol.55 (6), p.300-323</ispartof><rights>2023 The Authors. published by Wiley Periodicals LLC</rights><rights>2023. This article is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). 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Mark</creatorcontrib><creatorcontrib>Li, Yi‐Pei</creatorcontrib><creatorcontrib>Dong, Xiaorui</creatorcontrib><creatorcontrib>Spiekermann, Kevin A.</creatorcontrib><creatorcontrib>Wu, Haoyang</creatorcontrib><creatorcontrib>Dames, Enoch E.</creatorcontrib><creatorcontrib>Buras, Zachary J.</creatorcontrib><creatorcontrib>Vandewiele, Nick M.</creatorcontrib><creatorcontrib>Yee, Nathan W.</creatorcontrib><creatorcontrib>Merchant, Shamel S.</creatorcontrib><creatorcontrib>Buesser, Beat</creatorcontrib><creatorcontrib>Class, Caleb A.</creatorcontrib><creatorcontrib>Goldsmith, Franklin</creatorcontrib><creatorcontrib>West, Richard H.</creatorcontrib><creatorcontrib>Green, William H.</creatorcontrib><creatorcontrib>Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)</creatorcontrib><title>Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software</title><title>International journal of chemical kinetics</title><description>The open‐source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high‐pressure limit reaction rate coefficients, and pressure‐dependent rate coefficient over multi‐well molecular potential energy surfaces (PES) including the effects of collisional energy transfer on phenomenological kinetics. Arkane can use estimates to fill in information for molecules or reactions where quantum chemistry information is missing. The software solves the internal energy master equation for complex unimolecular reaction systems. Inputs to the software include converged electronic structure computations performed by the user using a variety of supported software packages (Gaussian, Molpro, Orca, TeraChem, Q‐Chem, Psi4). The software outputs high‐pressure limit rate coefficients and pressure‐dependent phenomenological rate coefficients, as well as computed thermodynamic properties (enthalpy, entropy, and constant pressure heat capacity) with added energy corrections. Some of the key features of Arkane include treatment of 1D, 2D or ND hindered internal rotation modes, treatment of free internal rotation modes, quantum tunneling effect consideration, transition state theory (TST) and Rice‐Ramsperger‐Kassel‐Marcus (RRKM) rate coefficient computations, master equation solution with four implemented methods, inverse‐Laplace transform of high‐pressure limit rate coefficients into the energy domain, energy corrections based on bond‐additivity or isodesmic reactions, automated and efficient PES exploration, and PES sensitivity analysis. The present work describes the design of Arkane, how it should be used, and refers to the theory that it employs. 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Mark ; Li, Yi‐Pei ; Dong, Xiaorui ; Spiekermann, Kevin A. ; Wu, Haoyang ; Dames, Enoch E. ; Buras, Zachary J. ; Vandewiele, Nick M. ; Yee, Nathan W. ; Merchant, Shamel S. ; Buesser, Beat ; Class, Caleb A. ; Goldsmith, Franklin ; West, Richard H. ; Green, William H.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3597-ed1d434f29d19c308b7468d5b265228668aa406b3010879883c31629d5402aef3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Automation</topic><topic>chemical kinetics</topic><topic>Chemistry</topic><topic>Coefficients</topic><topic>Electronic structure</topic><topic>Energy</topic><topic>Energy transfer</topic><topic>Enthalpy</topic><topic>INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY</topic><topic>Internal energy</topic><topic>Laplace transforms</topic><topic>Potential energy</topic><topic>potential energy surface</topic><topic>Pressure dependence</topic><topic>pressure‐dependent reactions</topic><topic>Quantum chemistry</topic><topic>Quantum tunnelling</topic><topic>Reaction kinetics</topic><topic>reaction mechanism generator</topic><topic>Rotation</topic><topic>Sensitivity analysis</topic><topic>Software packages</topic><topic>Statistical mechanics</topic><topic>Thermodynamic properties</topic><topic>Thermodynamics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dana, Alon Grinberg</creatorcontrib><creatorcontrib>Johnson, Matthew S.</creatorcontrib><creatorcontrib>Allen, Joshua W.</creatorcontrib><creatorcontrib>Sharma, Sandeep</creatorcontrib><creatorcontrib>Raman, Sumathy</creatorcontrib><creatorcontrib>Liu, Mengjie</creatorcontrib><creatorcontrib>Gao, Connie W.</creatorcontrib><creatorcontrib>Grambow, Colin A.</creatorcontrib><creatorcontrib>Goldman, Mark J.</creatorcontrib><creatorcontrib>Ranasinghe, Duminda S.</creatorcontrib><creatorcontrib>Gillis, Ryan J.</creatorcontrib><creatorcontrib>Payne, A. 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Mark</au><au>Li, Yi‐Pei</au><au>Dong, Xiaorui</au><au>Spiekermann, Kevin A.</au><au>Wu, Haoyang</au><au>Dames, Enoch E.</au><au>Buras, Zachary J.</au><au>Vandewiele, Nick M.</au><au>Yee, Nathan W.</au><au>Merchant, Shamel S.</au><au>Buesser, Beat</au><au>Class, Caleb A.</au><au>Goldsmith, Franklin</au><au>West, Richard H.</au><au>Green, William H.</au><aucorp>Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software</atitle><jtitle>International journal of chemical kinetics</jtitle><date>2023-06</date><risdate>2023</risdate><volume>55</volume><issue>6</issue><spage>300</spage><epage>323</epage><pages>300-323</pages><issn>0538-8066</issn><eissn>1097-4601</eissn><abstract>The open‐source statistical mechanics software described here, Arkane–Automated Reaction Kinetics and Network Exploration–facilitates computations of thermodynamic properties of chemical species, high‐pressure limit reaction rate coefficients, and pressure‐dependent rate coefficient over multi‐well molecular potential energy surfaces (PES) including the effects of collisional energy transfer on phenomenological kinetics. Arkane can use estimates to fill in information for molecules or reactions where quantum chemistry information is missing. The software solves the internal energy master equation for complex unimolecular reaction systems. Inputs to the software include converged electronic structure computations performed by the user using a variety of supported software packages (Gaussian, Molpro, Orca, TeraChem, Q‐Chem, Psi4). The software outputs high‐pressure limit rate coefficients and pressure‐dependent phenomenological rate coefficients, as well as computed thermodynamic properties (enthalpy, entropy, and constant pressure heat capacity) with added energy corrections. Some of the key features of Arkane include treatment of 1D, 2D or ND hindered internal rotation modes, treatment of free internal rotation modes, quantum tunneling effect consideration, transition state theory (TST) and Rice‐Ramsperger‐Kassel‐Marcus (RRKM) rate coefficient computations, master equation solution with four implemented methods, inverse‐Laplace transform of high‐pressure limit rate coefficients into the energy domain, energy corrections based on bond‐additivity or isodesmic reactions, automated and efficient PES exploration, and PES sensitivity analysis. The present work describes the design of Arkane, how it should be used, and refers to the theory that it employs. 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| fulltext | fulltext |
| identifier | ISSN: 0538-8066 |
| ispartof | International journal of chemical kinetics, 2023-06, Vol.55 (6), p.300-323 |
| issn | 0538-8066 1097-4601 |
| language | eng |
| recordid | cdi_osti_scitechconnect_1968115 |
| source | Wiley Online Library Journals Frontfile Complete |
| subjects | Automation chemical kinetics Chemistry Coefficients Electronic structure Energy Energy transfer Enthalpy INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY Internal energy Laplace transforms Potential energy potential energy surface Pressure dependence pressure‐dependent reactions Quantum chemistry Quantum tunnelling Reaction kinetics reaction mechanism generator Rotation Sensitivity analysis Software packages Statistical mechanics Thermodynamic properties Thermodynamics |
| title | Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-13T05%3A31%3A11IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_osti_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Automated%20reaction%20kinetics%20and%20network%20exploration%20(Arkane):%20A%20statistical%20mechanics,%20thermodynamics,%20transition%20state%20theory,%20and%20master%20equation%C2%A0software&rft.jtitle=International%20journal%20of%20chemical%20kinetics&rft.au=Dana,%20Alon%20Grinberg&rft.aucorp=Massachusetts%20Inst.%20of%20Technology%20(MIT),%20Cambridge,%20MA%20(United%20States)&rft.date=2023-06&rft.volume=55&rft.issue=6&rft.spage=300&rft.epage=323&rft.pages=300-323&rft.issn=0538-8066&rft.eissn=1097-4601&rft_id=info:doi/10.1002/kin.21637&rft_dat=%3Cproquest_osti_%3E2803947353%3C/proquest_osti_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2803947353&rft_id=info:pmid/&rfr_iscdi=true |