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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/5743
Ver los metadatos del registro completo
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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 Técnicas2025-09-29T09:47:00Zoai: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:34982025-09-29 09:47:00.916CONICET 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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13.070432 |