Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies

Autores
Álvarez, Hugo Ariel; Llerena Suster, Carlos Rafael; McCarthy, Andrés Norman
Año de publicación
2014
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Acetonitrile is widely utilized in scientific research, presenting an ideal solvent media for a large number of organic reactions. Its use at the industrial scale ranges from the production of molecules of pharmaceutical interest to photographic films. Additionally, certain enzyme based catalytic processes show great functionality in Acetonitrile media. Furthermore, numerous enzymes continue to act as efficient biocatalyzers in acetonitrile solution, showing in some cases significant changes in their original specificity and selectivity. Consequently, the study of the behavior of such proteins in this solvent by means of potent computational methods such as Molecular Dynamics results of great interest. Many molecular models for Acetonitrile have been developed for use in Molecular Dynamic studies. Nevertheless, all acetonitrile models developed up to date are only capable of performing reasonably when used with integration time-steps no greater than 2 femtoseconds (fs). We present two molecular models for acetonitrile which perform both efficiently and reliably with integration time steps of up to 4 fs. Furthermore, the optimization procedure used has enabled to achieve this performance improvement at no cost as regards the agreement between the experimental macroscopic data for Acetonitrile and the corresponding properties evaluated for the models here presented.
Facultad de Ciencias Exactas
Materia
Ciencias Exactas
Acetonitrilos
Simulación de Dinámica Molecular
Acetonitrile; Three-site Models; Molecular Dynamics; Integration Time-step Scalability
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-nd/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/72322

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network_name_str SEDICI (UNLP)
spelling Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics StudiesÁlvarez, Hugo ArielLlerena Suster, Carlos RafaelMcCarthy, Andrés NormanCiencias ExactasAcetonitrilosSimulación de Dinámica MolecularAcetonitrile; Three-site Models; Molecular Dynamics; Integration Time-step ScalabilityAcetonitrile is widely utilized in scientific research, presenting an ideal solvent media for a large number of organic reactions. Its use at the industrial scale ranges from the production of molecules of pharmaceutical interest to photographic films. Additionally, certain enzyme based catalytic processes show great functionality in Acetonitrile media. Furthermore, numerous enzymes continue to act as efficient biocatalyzers in acetonitrile solution, showing in some cases significant changes in their original specificity and selectivity. Consequently, the study of the behavior of such proteins in this solvent by means of potent computational methods such as Molecular Dynamics results of great interest. Many molecular models for Acetonitrile have been developed for use in Molecular Dynamic studies. Nevertheless, all acetonitrile models developed up to date are only capable of performing reasonably when used with integration time-steps no greater than 2 femtoseconds (fs). We present two molecular models for acetonitrile which perform both efficiently and reliably with integration time steps of up to 4 fs. Furthermore, the optimization procedure used has enabled to achieve this performance improvement at no cost as regards the agreement between the experimental macroscopic data for Acetonitrile and the corresponding properties evaluated for the models here presented.Facultad de Ciencias Exactas2014-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdf49-62http://sedici.unlp.edu.ar/handle/10915/72322enginfo:eu-repo/semantics/altIdentifier/url/https://www.ajouronline.com/index.php/AJCIS/article/view/637info:eu-repo/semantics/altIdentifier/issn/2321-5658info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-nd/4.0/Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:11:53Zoai:sedici.unlp.edu.ar:10915/72322Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:11:53.946SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies
title Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies
spellingShingle Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies
Álvarez, Hugo Ariel
Ciencias Exactas
Acetonitrilos
Simulación de Dinámica Molecular
Acetonitrile; Three-site Models; Molecular Dynamics; Integration Time-step Scalability
title_short Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies
title_full Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies
title_fullStr Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies
title_full_unstemmed Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies
title_sort Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies
dc.creator.none.fl_str_mv Álvarez, Hugo Ariel
Llerena Suster, Carlos Rafael
McCarthy, Andrés Norman
author Álvarez, Hugo Ariel
author_facet Álvarez, Hugo Ariel
Llerena Suster, Carlos Rafael
McCarthy, Andrés Norman
author_role author
author2 Llerena Suster, Carlos Rafael
McCarthy, Andrés Norman
author2_role author
author
dc.subject.none.fl_str_mv Ciencias Exactas
Acetonitrilos
Simulación de Dinámica Molecular
Acetonitrile; Three-site Models; Molecular Dynamics; Integration Time-step Scalability
topic Ciencias Exactas
Acetonitrilos
Simulación de Dinámica Molecular
Acetonitrile; Three-site Models; Molecular Dynamics; Integration Time-step Scalability
dc.description.none.fl_txt_mv Acetonitrile is widely utilized in scientific research, presenting an ideal solvent media for a large number of organic reactions. Its use at the industrial scale ranges from the production of molecules of pharmaceutical interest to photographic films. Additionally, certain enzyme based catalytic processes show great functionality in Acetonitrile media. Furthermore, numerous enzymes continue to act as efficient biocatalyzers in acetonitrile solution, showing in some cases significant changes in their original specificity and selectivity. Consequently, the study of the behavior of such proteins in this solvent by means of potent computational methods such as Molecular Dynamics results of great interest. Many molecular models for Acetonitrile have been developed for use in Molecular Dynamic studies. Nevertheless, all acetonitrile models developed up to date are only capable of performing reasonably when used with integration time-steps no greater than 2 femtoseconds (fs). We present two molecular models for acetonitrile which perform both efficiently and reliably with integration time steps of up to 4 fs. Furthermore, the optimization procedure used has enabled to achieve this performance improvement at no cost as regards the agreement between the experimental macroscopic data for Acetonitrile and the corresponding properties evaluated for the models here presented.
Facultad de Ciencias Exactas
description Acetonitrile is widely utilized in scientific research, presenting an ideal solvent media for a large number of organic reactions. Its use at the industrial scale ranges from the production of molecules of pharmaceutical interest to photographic films. Additionally, certain enzyme based catalytic processes show great functionality in Acetonitrile media. Furthermore, numerous enzymes continue to act as efficient biocatalyzers in acetonitrile solution, showing in some cases significant changes in their original specificity and selectivity. Consequently, the study of the behavior of such proteins in this solvent by means of potent computational methods such as Molecular Dynamics results of great interest. Many molecular models for Acetonitrile have been developed for use in Molecular Dynamic studies. Nevertheless, all acetonitrile models developed up to date are only capable of performing reasonably when used with integration time-steps no greater than 2 femtoseconds (fs). We present two molecular models for acetonitrile which perform both efficiently and reliably with integration time steps of up to 4 fs. Furthermore, the optimization procedure used has enabled to achieve this performance improvement at no cost as regards the agreement between the experimental macroscopic data for Acetonitrile and the corresponding properties evaluated for the models here presented.
publishDate 2014
dc.date.none.fl_str_mv 2014-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
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info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/72322
url http://sedici.unlp.edu.ar/handle/10915/72322
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.ajouronline.com/index.php/AJCIS/article/view/637
info:eu-repo/semantics/altIdentifier/issn/2321-5658
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-nd/4.0/
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
dc.format.none.fl_str_mv application/pdf
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repository.mail.fl_str_mv alira@sedici.unlp.edu.ar
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