Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso

Autores
Lund, Albert M.; Orendt, Anita M.; Pagola, Gabriel Ignacio; Ferraro, Marta Beatriz; Facelli, Julio C.
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Previously, it was shown that crystal structure prediction based on genetic algorithms (MGAC program) coupled with force field methods could consistently find experimental structures of crystals. However, inaccuracies in the force field potentials often resulted in poor energetic ranking of the experimental structure, limiting the usefulness of the method. In this work, dispersion-corrected density functional theory is employed to improve the accuracy of the energy rankings, using the software package Quantum Espresso. The best choices of running parameters for this application were determined, followed by completion of crystal optimizations on a test set of archetypical pharmaceutical molecules. It is shown here that the variable cell optimization of experimental structures reproduces the experimental structure with high accuracy (RMS < 0.5 Å) for this test set. It is also shown that the use of electronic structure theory based methods greatly improves the energetic ranking of structures produced by MGAC when used with a force field method, such that the experimental match is found with a high degree of accuracy.
Fil: Lund, Albert M.. University of Utah; Estados Unidos
Fil: Orendt, Anita M.. University of Utah; Estados Unidos
Fil: Pagola, Gabriel Ignacio. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires; Argentina
Fil: Ferraro, Marta Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina
Fil: Facelli, Julio C.. University of Utah; Estados Unidos
Materia
Prediction
Crystal
Pharmaceutical
Quantum
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:11336/2512
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum EspressoLund, Albert M.Orendt, Anita M.Pagola, Gabriel IgnacioFerraro, Marta BeatrizFacelli, Julio C.PredictionCrystalPharmaceuticalQuantumhttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1Previously, it was shown that crystal structure prediction based on genetic algorithms (MGAC program) coupled with force field methods could consistently find experimental structures of crystals. However, inaccuracies in the force field potentials often resulted in poor energetic ranking of the experimental structure, limiting the usefulness of the method. In this work, dispersion-corrected density functional theory is employed to improve the accuracy of the energy rankings, using the software package Quantum Espresso. The best choices of running parameters for this application were determined, followed by completion of crystal optimizations on a test set of archetypical pharmaceutical molecules. It is shown here that the variable cell optimization of experimental structures reproduces the experimental structure with high accuracy (RMS < 0.5 Å) for this test set. It is also shown that the use of electronic structure theory based methods greatly improves the energetic ranking of structures produced by MGAC when used with a force field method, such that the experimental match is found with a high degree of accuracy.Fil: Lund, Albert M.. University of Utah; Estados UnidosFil: Orendt, Anita M.. University of Utah; Estados UnidosFil: Pagola, Gabriel Ignacio. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires; ArgentinaFil: Ferraro, Marta Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; ArgentinaFil: Facelli, Julio C.. University of Utah; Estados UnidosAmerican Chemical Society2013-03-20info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/2512Lund, Albert M.; Orendt, Anita M.; Pagola, Gabriel Ignacio; Ferraro, Marta Beatriz; Facelli, Julio C.; Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso; American Chemical Society; Crystal Growth & Design; 13; 5; 20-3-2013; 2181-21891528-7483enginfo:eu-repo/semantics/altIdentifier/url/http://pubs.acs.org/doi/abs/10.1021/cg4002797info:eu-repo/semantics/altIdentifier/doi/10.1021/cg4002797info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:44:20Zoai:ri.conicet.gov.ar:11336/2512instacron: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 09:44:20.466CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso
title Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso
spellingShingle Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso
Lund, Albert M.
Prediction
Crystal
Pharmaceutical
Quantum
title_short Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso
title_full Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso
title_fullStr Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso
title_full_unstemmed Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso
title_sort Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso
dc.creator.none.fl_str_mv Lund, Albert M.
Orendt, Anita M.
Pagola, Gabriel Ignacio
Ferraro, Marta Beatriz
Facelli, Julio C.
author Lund, Albert M.
author_facet Lund, Albert M.
Orendt, Anita M.
Pagola, Gabriel Ignacio
Ferraro, Marta Beatriz
Facelli, Julio C.
author_role author
author2 Orendt, Anita M.
Pagola, Gabriel Ignacio
Ferraro, Marta Beatriz
Facelli, Julio C.
author2_role author
author
author
author
dc.subject.none.fl_str_mv Prediction
Crystal
Pharmaceutical
Quantum
topic Prediction
Crystal
Pharmaceutical
Quantum
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.3
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Previously, it was shown that crystal structure prediction based on genetic algorithms (MGAC program) coupled with force field methods could consistently find experimental structures of crystals. However, inaccuracies in the force field potentials often resulted in poor energetic ranking of the experimental structure, limiting the usefulness of the method. In this work, dispersion-corrected density functional theory is employed to improve the accuracy of the energy rankings, using the software package Quantum Espresso. The best choices of running parameters for this application were determined, followed by completion of crystal optimizations on a test set of archetypical pharmaceutical molecules. It is shown here that the variable cell optimization of experimental structures reproduces the experimental structure with high accuracy (RMS < 0.5 Å) for this test set. It is also shown that the use of electronic structure theory based methods greatly improves the energetic ranking of structures produced by MGAC when used with a force field method, such that the experimental match is found with a high degree of accuracy.
Fil: Lund, Albert M.. University of Utah; Estados Unidos
Fil: Orendt, Anita M.. University of Utah; Estados Unidos
Fil: Pagola, Gabriel Ignacio. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires; Argentina
Fil: Ferraro, Marta Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina
Fil: Facelli, Julio C.. University of Utah; Estados Unidos
description Previously, it was shown that crystal structure prediction based on genetic algorithms (MGAC program) coupled with force field methods could consistently find experimental structures of crystals. However, inaccuracies in the force field potentials often resulted in poor energetic ranking of the experimental structure, limiting the usefulness of the method. In this work, dispersion-corrected density functional theory is employed to improve the accuracy of the energy rankings, using the software package Quantum Espresso. The best choices of running parameters for this application were determined, followed by completion of crystal optimizations on a test set of archetypical pharmaceutical molecules. It is shown here that the variable cell optimization of experimental structures reproduces the experimental structure with high accuracy (RMS < 0.5 Å) for this test set. It is also shown that the use of electronic structure theory based methods greatly improves the energetic ranking of structures produced by MGAC when used with a force field method, such that the experimental match is found with a high degree of accuracy.
publishDate 2013
dc.date.none.fl_str_mv 2013-03-20
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/11336/2512
Lund, Albert M.; Orendt, Anita M.; Pagola, Gabriel Ignacio; Ferraro, Marta Beatriz; Facelli, Julio C.; Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso; American Chemical Society; Crystal Growth & Design; 13; 5; 20-3-2013; 2181-2189
1528-7483
url http://hdl.handle.net/11336/2512
identifier_str_mv Lund, Albert M.; Orendt, Anita M.; Pagola, Gabriel Ignacio; Ferraro, Marta Beatriz; Facelli, Julio C.; Optimization of Crystal Structures of Archetypical Pharmaceutical Compounds: A Plane-Wave DFT‐D Study Using Quantum Espresso; American Chemical Society; Crystal Growth & Design; 13; 5; 20-3-2013; 2181-2189
1528-7483
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://pubs.acs.org/doi/abs/10.1021/cg4002797
info:eu-repo/semantics/altIdentifier/doi/10.1021/cg4002797
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 13.069144

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