Consistent acetonitrile molecular models for both standard and computationally efficient molecular dynamics studies

Autores
Alvarez, 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.
Fil: Alvarez, Hugo Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Física de Líquidos y Sistemas Biológicos (i); Argentina. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biologicas; Argentina
Fil: Llerena Suster, Carlos Rafael. Universidad Nacional de la Plata. Facultad de Cs.exactas. Departamento de Cs.biologicas. Laboratorio de Invest.de Proteinas Vegetales; Argentina
Fil: Mccarthy, Andrés Norman. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Física de Líquidos y Sistemas Biológicos (i); Argentina. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biologicas; Argentina
Materia
Acetonitrile
Three-site models
Molecular dynamics
Integration tme-step scalability
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:11336/5743
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/5743
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Consistent acetonitrile molecular models for both standard and computationally efficient molecular dynamics studiesAlvarez, Hugo ArielLlerena Suster, Carlos RafaelMccarthy, Andrés NormanAcetonitrileThree-site modelsMolecular dynamicsIntegration tme-step scalabilityhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Acetonitrile 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.Fil: Alvarez, Hugo Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Física de Líquidos y Sistemas Biológicos (i); Argentina. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biologicas; ArgentinaFil: Llerena Suster, Carlos Rafael. Universidad Nacional de la Plata. Facultad de Cs.exactas. Departamento de Cs.biologicas. Laboratorio de Invest.de Proteinas Vegetales; ArgentinaFil: Mccarthy, Andrés Norman. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Física de Líquidos y Sistemas Biológicos (i); Argentina. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biologicas; ArgentinaAsian Online Journals2014-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/5743Alvarez, Hugo Ariel; Llerena Suster, Carlos Rafael; Mccarthy, Andrés Norman; Consistent acetonitrile molecular models for both standard and computationally efficient molecular dynamics studies; Asian Online Journals; Asian Journal of Computer and Information Systems; 2; 3; 6-2014; 49-622321-5658enginfo:eu-repo/semantics/altIdentifier/url/http://www.ajouronline.com/index.php?journal=AJCIS&page=article&op=view&path%5B%5D=637&path%5B%5D=747info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:15:52Zoai:ri.conicet.gov.ar:11336/5743instacron: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:34982025-10-22 11:15:52.881CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
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
Alvarez, Hugo Ariel
Acetonitrile
Three-site models
Molecular dynamics
Integration tme-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 Alvarez, Hugo Ariel
Llerena Suster, Carlos Rafael
Mccarthy, Andrés Norman
author Alvarez, Hugo Ariel
author_facet Alvarez, 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 Acetonitrile
Three-site models
Molecular dynamics
Integration tme-step scalability
topic Acetonitrile
Three-site models
Molecular dynamics
Integration tme-step scalability
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
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.
Fil: Alvarez, Hugo Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Física de Líquidos y Sistemas Biológicos (i); Argentina. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biologicas; Argentina
Fil: Llerena Suster, Carlos Rafael. Universidad Nacional de la Plata. Facultad de Cs.exactas. Departamento de Cs.biologicas. Laboratorio de Invest.de Proteinas Vegetales; Argentina
Fil: Mccarthy, Andrés Norman. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Física de Líquidos y Sistemas Biológicos (i); Argentina. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Departamento de Ciencias Biologicas; Argentina
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
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/11336/5743
Alvarez, Hugo Ariel; Llerena Suster, Carlos Rafael; Mccarthy, Andrés Norman; Consistent acetonitrile molecular models for both standard and computationally efficient molecular dynamics studies; Asian Online Journals; Asian Journal of Computer and Information Systems; 2; 3; 6-2014; 49-62
2321-5658
url http://hdl.handle.net/11336/5743
identifier_str_mv Alvarez, Hugo Ariel; Llerena Suster, Carlos Rafael; Mccarthy, Andrés Norman; Consistent acetonitrile molecular models for both standard and computationally efficient molecular dynamics studies; Asian Online Journals; Asian Journal of Computer and Information Systems; 2; 3; 6-2014; 49-62
2321-5658
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.ajouronline.com/index.php?journal=AJCIS&page=article&op=view&path%5B%5D=637&path%5B%5D=747
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
application/pdf
dc.publisher.none.fl_str_mv Asian Online Journals
publisher.none.fl_str_mv Asian Online Journals
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 12.982451

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