OpenMechanochem: A Python module for mechanochemical simulations

The interest in mechanochemical research has dramatically increased in recent years with the advent of computational chemistry tools where detailed reaction thermodynamics, and kinetics can be studied. However, most chemistry software packages do not address mechanochemical phenomena and computation...

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Autores principales:	Danjo De Chavez, Jun-ya Hasegawa
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Mechanochemistry Molecular simulations Quantum chemistry Atomic simulation environment Potential energy surface Computer software QA76.75-76.765
Acceso en línea:	https://doaj.org/article/83a78cfbf78b4c18aceb6b473c01753b
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id	oai:doaj.org-article:83a78cfbf78b4c18aceb6b473c01753b
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spelling	oai:doaj.org-article:83a78cfbf78b4c18aceb6b473c01753b2021-11-18T04:50:22ZOpenMechanochem: A Python module for mechanochemical simulations2352-711010.1016/j.softx.2021.100879https://doaj.org/article/83a78cfbf78b4c18aceb6b473c01753b2021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2352711021001436https://doaj.org/toc/2352-7110The interest in mechanochemical research has dramatically increased in recent years with the advent of computational chemistry tools where detailed reaction thermodynamics, and kinetics can be studied. However, most chemistry software packages do not address mechanochemical phenomena and computational chemists need to modify a quantum chemical software to perform specialized simulations. Current implementation includes Force Modified Potential Energy Surface (FMPES), External Force Explicitly Included (EFEI), and Enforce Geometry Optimizations (EGO) formalisms. This also includes a wall potential based function to simulate mechanical grinding. In this work, a Python module that allows inclusion of external forces during molecular geometry optimizations and molecular dynamics simulations while virtually employing any quantum chemical or molecular mechanical software is presented. It is expected that OpenMechanochem will facilitate mechanochemical reaction simulations that will explain the interplay of external forces to a chemical system.Danjo De ChavezJun-ya HasegawaElsevierarticleMechanochemistryMolecular simulationsQuantum chemistryAtomic simulation environmentPotential energy surfaceComputer softwareQA76.75-76.765ENSoftwareX, Vol 16, Iss , Pp 100879- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Mechanochemistry Molecular simulations Quantum chemistry Atomic simulation environment Potential energy surface Computer software QA76.75-76.765
spellingShingle	Mechanochemistry Molecular simulations Quantum chemistry Atomic simulation environment Potential energy surface Computer software QA76.75-76.765 Danjo De Chavez Jun-ya Hasegawa OpenMechanochem: A Python module for mechanochemical simulations
description	The interest in mechanochemical research has dramatically increased in recent years with the advent of computational chemistry tools where detailed reaction thermodynamics, and kinetics can be studied. However, most chemistry software packages do not address mechanochemical phenomena and computational chemists need to modify a quantum chemical software to perform specialized simulations. Current implementation includes Force Modified Potential Energy Surface (FMPES), External Force Explicitly Included (EFEI), and Enforce Geometry Optimizations (EGO) formalisms. This also includes a wall potential based function to simulate mechanical grinding. In this work, a Python module that allows inclusion of external forces during molecular geometry optimizations and molecular dynamics simulations while virtually employing any quantum chemical or molecular mechanical software is presented. It is expected that OpenMechanochem will facilitate mechanochemical reaction simulations that will explain the interplay of external forces to a chemical system.
format	article
author	Danjo De Chavez Jun-ya Hasegawa
author_facet	Danjo De Chavez Jun-ya Hasegawa
author_sort	Danjo De Chavez
title	OpenMechanochem: A Python module for mechanochemical simulations
title_short	OpenMechanochem: A Python module for mechanochemical simulations
title_full	OpenMechanochem: A Python module for mechanochemical simulations
title_fullStr	OpenMechanochem: A Python module for mechanochemical simulations
title_full_unstemmed	OpenMechanochem: A Python module for mechanochemical simulations
title_sort	openmechanochem: a python module for mechanochemical simulations
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/83a78cfbf78b4c18aceb6b473c01753b
work_keys_str_mv	AT danjodechavez openmechanochemapythonmoduleformechanochemicalsimulations AT junyahasegawa openmechanochemapythonmoduleformechanochemicalsimulations
_version_	1718424985962283008

OpenMechanochem: A Python module for mechanochemical simulations

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