Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy

Autores
Foglia, Nicolás Oscar; González Lebrero, Mariano Camilo; Biekofsky, Rodolfo R.; Estrin, Dario Ariel
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The calculation of potential energy and free-energy profiles along complex chemical reactions or rare event processes is of great interest because of their importance for many areas in chemistry, molecular biology, and material science. One typical way to generate these profiles is to add a bias potential to modify the energy surface, which can act on a selected degree of freedom in the system. However, in these cases, the quality of the result is strongly dependent on the selection of the degree of freedom over which this bias potential acts. The present work introduces a simple method for the analysis of the degree of freedom selected to describe a chemical process. The proposed methodology is based on the decomposition of contributions to the potential energy profiles by the integration of forces along a reaction path, which allows evaluating the different contributions to the energy change. This could be useful for discriminating the contributions to the energy arising from different regions of the system, which is particularly useful in systems with complex environments that must be represented using hybrid quantum mechanics/molecular mechanics schemes. Furthermore, this methodology allows in generating a quick and simple analysis of the degree of freedom which is used to describe the potential energy profile associated with the reactive process. This is computationally more accessible than the corresponding free-energy profile and can therefore be used as a simple estimator of reaction coordinate adequacy.
Fil: Foglia, Nicolás Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
Fil: González Lebrero, Mariano Camilo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
Fil: Biekofsky, Rodolfo R.. Moebius Research Ltd.; Reino Unido
Fil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
Materia
elastric band
energy profile
restraint optimization
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/142359
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/142359
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacyFoglia, Nicolás OscarGonzález Lebrero, Mariano CamiloBiekofsky, Rodolfo R.Estrin, Dario Arielelastric bandenergy profilerestraint optimizationhttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1The calculation of potential energy and free-energy profiles along complex chemical reactions or rare event processes is of great interest because of their importance for many areas in chemistry, molecular biology, and material science. One typical way to generate these profiles is to add a bias potential to modify the energy surface, which can act on a selected degree of freedom in the system. However, in these cases, the quality of the result is strongly dependent on the selection of the degree of freedom over which this bias potential acts. The present work introduces a simple method for the analysis of the degree of freedom selected to describe a chemical process. The proposed methodology is based on the decomposition of contributions to the potential energy profiles by the integration of forces along a reaction path, which allows evaluating the different contributions to the energy change. This could be useful for discriminating the contributions to the energy arising from different regions of the system, which is particularly useful in systems with complex environments that must be represented using hybrid quantum mechanics/molecular mechanics schemes. Furthermore, this methodology allows in generating a quick and simple analysis of the degree of freedom which is used to describe the potential energy profile associated with the reactive process. This is computationally more accessible than the corresponding free-energy profile and can therefore be used as a simple estimator of reaction coordinate adequacy.Fil: Foglia, Nicolás Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: González Lebrero, Mariano Camilo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Biekofsky, Rodolfo R.. Moebius Research Ltd.; Reino UnidoFil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaAmerican Chemical Society2020-01-30info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/142359Foglia, Nicolás Oscar; González Lebrero, Mariano Camilo; Biekofsky, Rodolfo R.; Estrin, Dario Ariel; Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy; American Chemical Society; Journal of Chemical Theory and Computation; 16; 3; 30-1-2020; 1618-16291549-9618CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jctc.9b01081info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.9b01081info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:27:25Zoai:ri.conicet.gov.ar:11336/142359instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 14:27:26.207CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy
title Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy
spellingShingle Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy
Foglia, Nicolás Oscar
elastric band
energy profile
restraint optimization
title_short Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy
title_full Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy
title_fullStr Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy
title_full_unstemmed Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy
title_sort Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy
dc.creator.none.fl_str_mv Foglia, Nicolás Oscar
González Lebrero, Mariano Camilo
Biekofsky, Rodolfo R.
Estrin, Dario Ariel
author Foglia, Nicolás Oscar
author_facet Foglia, Nicolás Oscar
González Lebrero, Mariano Camilo
Biekofsky, Rodolfo R.
Estrin, Dario Ariel
author_role author
author2 González Lebrero, Mariano Camilo
Biekofsky, Rodolfo R.
Estrin, Dario Ariel
author2_role author
author
author
dc.subject.none.fl_str_mv elastric band
energy profile
restraint optimization
topic elastric band
energy profile
restraint optimization
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The calculation of potential energy and free-energy profiles along complex chemical reactions or rare event processes is of great interest because of their importance for many areas in chemistry, molecular biology, and material science. One typical way to generate these profiles is to add a bias potential to modify the energy surface, which can act on a selected degree of freedom in the system. However, in these cases, the quality of the result is strongly dependent on the selection of the degree of freedom over which this bias potential acts. The present work introduces a simple method for the analysis of the degree of freedom selected to describe a chemical process. The proposed methodology is based on the decomposition of contributions to the potential energy profiles by the integration of forces along a reaction path, which allows evaluating the different contributions to the energy change. This could be useful for discriminating the contributions to the energy arising from different regions of the system, which is particularly useful in systems with complex environments that must be represented using hybrid quantum mechanics/molecular mechanics schemes. Furthermore, this methodology allows in generating a quick and simple analysis of the degree of freedom which is used to describe the potential energy profile associated with the reactive process. This is computationally more accessible than the corresponding free-energy profile and can therefore be used as a simple estimator of reaction coordinate adequacy.
Fil: Foglia, Nicolás Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
Fil: González Lebrero, Mariano Camilo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
Fil: Biekofsky, Rodolfo R.. Moebius Research Ltd.; Reino Unido
Fil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
description The calculation of potential energy and free-energy profiles along complex chemical reactions or rare event processes is of great interest because of their importance for many areas in chemistry, molecular biology, and material science. One typical way to generate these profiles is to add a bias potential to modify the energy surface, which can act on a selected degree of freedom in the system. However, in these cases, the quality of the result is strongly dependent on the selection of the degree of freedom over which this bias potential acts. The present work introduces a simple method for the analysis of the degree of freedom selected to describe a chemical process. The proposed methodology is based on the decomposition of contributions to the potential energy profiles by the integration of forces along a reaction path, which allows evaluating the different contributions to the energy change. This could be useful for discriminating the contributions to the energy arising from different regions of the system, which is particularly useful in systems with complex environments that must be represented using hybrid quantum mechanics/molecular mechanics schemes. Furthermore, this methodology allows in generating a quick and simple analysis of the degree of freedom which is used to describe the potential energy profile associated with the reactive process. This is computationally more accessible than the corresponding free-energy profile and can therefore be used as a simple estimator of reaction coordinate adequacy.
publishDate 2020
dc.date.none.fl_str_mv 2020-01-30
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/142359
Foglia, Nicolás Oscar; González Lebrero, Mariano Camilo; Biekofsky, Rodolfo R.; Estrin, Dario Ariel; Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy; American Chemical Society; Journal of Chemical Theory and Computation; 16; 3; 30-1-2020; 1618-1629
1549-9618
CONICET Digital
CONICET
url http://hdl.handle.net/11336/142359
identifier_str_mv Foglia, Nicolás Oscar; González Lebrero, Mariano Camilo; Biekofsky, Rodolfo R.; Estrin, Dario Ariel; Reaction path analysis from potential energy contributions using forces: An accessible estimator of reaction coordinate adequacy; American Chemical Society; Journal of Chemical Theory and Computation; 16; 3; 30-1-2020; 1618-1629
1549-9618
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jctc.9b01081
info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.9b01081
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.22299

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