Are accurate computations of the 13C' shielding feasible at the DFT level of theory?

Autores
Vila, Jorge Alberto; Arnautova, Yelena A.; Martín, Osvaldo Antonio; Scheraga, Harold A.
Año de publicación
2014
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The goal of this study is twofold. First, to investigate the relative influence of the main structural factors affecting the computation of the 13C0 shielding, namely, the conformation of the residue itself and the next nearest-neighbor effects. Second, to determine whether calculation of the 13C0 shielding at the density functional level of theory (DFT), with an accuracy similar to that of the 13Ca shielding, is feasible with the existing computational resources. The DFT calculations, carried out for a large number of possible conformations of the tripeptide Ac-GXY-NMe, with different combinations of X and Y residues, enable us to conclude that the accurate computation of the 13C0 shielding for a given residue X depends on the: (i) (/,w) backbone torsional angles of X; (ii) side-chain conformation of X; (iii) (/,w) torsional angles of Y; and (iv) identity of residue Y. Consequently, DFT-based quantum mechanical calculations of the 13C0 shielding, with all these factors taken into account, are two orders of magnitude more CPU demanding than the computation, with similar accuracy, of the 13Ca shielding. Despite not considering the effect of the possible hydrogen bond interaction of the carbonyl oxygen, this work contributes to our general understanding of the main structural factors affecting the accurate computation of the 13C0 shielding in proteins and may spur significant progress in effort to develop new validation methods for protein structures.
Fil: Vila, Jorge Alberto. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis ; Argentina
Fil: Arnautova, Yelena A.. Molsoft L.L.C.; Estados Unidos
Fil: Martín, Osvaldo Antonio. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis ; Argentina
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
Materia
Dft-Computation of Shielding
Protein Validation
Protein Determination
Factors Affecting Shielding Computation
Heavy Nuclei Shielding
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:11336/31301
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Are accurate computations of the 13C' shielding feasible at the DFT level of theory?Vila, Jorge AlbertoArnautova, Yelena A.Martín, Osvaldo AntonioScheraga, Harold A.Dft-Computation of ShieldingProtein ValidationProtein DeterminationFactors Affecting Shielding ComputationHeavy Nuclei Shieldinghttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The goal of this study is twofold. First, to investigate the relative influence of the main structural factors affecting the computation of the 13C0 shielding, namely, the conformation of the residue itself and the next nearest-neighbor effects. Second, to determine whether calculation of the 13C0 shielding at the density functional level of theory (DFT), with an accuracy similar to that of the 13Ca shielding, is feasible with the existing computational resources. The DFT calculations, carried out for a large number of possible conformations of the tripeptide Ac-GXY-NMe, with different combinations of X and Y residues, enable us to conclude that the accurate computation of the 13C0 shielding for a given residue X depends on the: (i) (/,w) backbone torsional angles of X; (ii) side-chain conformation of X; (iii) (/,w) torsional angles of Y; and (iv) identity of residue Y. Consequently, DFT-based quantum mechanical calculations of the 13C0 shielding, with all these factors taken into account, are two orders of magnitude more CPU demanding than the computation, with similar accuracy, of the 13Ca shielding. Despite not considering the effect of the possible hydrogen bond interaction of the carbonyl oxygen, this work contributes to our general understanding of the main structural factors affecting the accurate computation of the 13C0 shielding in proteins and may spur significant progress in effort to develop new validation methods for protein structures.Fil: Vila, Jorge Alberto. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis ; ArgentinaFil: Arnautova, Yelena A.. Molsoft L.L.C.; Estados UnidosFil: Martín, Osvaldo Antonio. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis ; ArgentinaFil: Scheraga, Harold A.. Cornell University; Estados UnidosWiley2014-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/31301Vila, Jorge Alberto; Arnautova, Yelena A.; Martín, Osvaldo Antonio; Scheraga, Harold A.; Are accurate computations of the 13C' shielding feasible at the DFT level of theory?; Wiley; Journal Of Computational Chemistry; 35; 4; 2-2014; 309-3120192-8651CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://onlinelibrary.wiley.com/doi/10.1002/jcc.23499/abstractinfo:eu-repo/semantics/altIdentifier/doi/10.1002/jcc.23499info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:58:00Zoai:ri.conicet.gov.ar:11336/31301instacron: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 09:58:00.533CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Are accurate computations of the 13C' shielding feasible at the DFT level of theory?
title Are accurate computations of the 13C' shielding feasible at the DFT level of theory?
spellingShingle Are accurate computations of the 13C' shielding feasible at the DFT level of theory?
Vila, Jorge Alberto
Dft-Computation of Shielding
Protein Validation
Protein Determination
Factors Affecting Shielding Computation
Heavy Nuclei Shielding
title_short Are accurate computations of the 13C' shielding feasible at the DFT level of theory?
title_full Are accurate computations of the 13C' shielding feasible at the DFT level of theory?
title_fullStr Are accurate computations of the 13C' shielding feasible at the DFT level of theory?
title_full_unstemmed Are accurate computations of the 13C' shielding feasible at the DFT level of theory?
title_sort Are accurate computations of the 13C' shielding feasible at the DFT level of theory?
dc.creator.none.fl_str_mv Vila, Jorge Alberto
Arnautova, Yelena A.
Martín, Osvaldo Antonio
Scheraga, Harold A.
author Vila, Jorge Alberto
author_facet Vila, Jorge Alberto
Arnautova, Yelena A.
Martín, Osvaldo Antonio
Scheraga, Harold A.
author_role author
author2 Arnautova, Yelena A.
Martín, Osvaldo Antonio
Scheraga, Harold A.
author2_role author
author
author
dc.subject.none.fl_str_mv Dft-Computation of Shielding
Protein Validation
Protein Determination
Factors Affecting Shielding Computation
Heavy Nuclei Shielding
topic Dft-Computation of Shielding
Protein Validation
Protein Determination
Factors Affecting Shielding Computation
Heavy Nuclei Shielding
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The goal of this study is twofold. First, to investigate the relative influence of the main structural factors affecting the computation of the 13C0 shielding, namely, the conformation of the residue itself and the next nearest-neighbor effects. Second, to determine whether calculation of the 13C0 shielding at the density functional level of theory (DFT), with an accuracy similar to that of the 13Ca shielding, is feasible with the existing computational resources. The DFT calculations, carried out for a large number of possible conformations of the tripeptide Ac-GXY-NMe, with different combinations of X and Y residues, enable us to conclude that the accurate computation of the 13C0 shielding for a given residue X depends on the: (i) (/,w) backbone torsional angles of X; (ii) side-chain conformation of X; (iii) (/,w) torsional angles of Y; and (iv) identity of residue Y. Consequently, DFT-based quantum mechanical calculations of the 13C0 shielding, with all these factors taken into account, are two orders of magnitude more CPU demanding than the computation, with similar accuracy, of the 13Ca shielding. Despite not considering the effect of the possible hydrogen bond interaction of the carbonyl oxygen, this work contributes to our general understanding of the main structural factors affecting the accurate computation of the 13C0 shielding in proteins and may spur significant progress in effort to develop new validation methods for protein structures.
Fil: Vila, Jorge Alberto. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis ; Argentina
Fil: Arnautova, Yelena A.. Molsoft L.L.C.; Estados Unidos
Fil: Martín, Osvaldo Antonio. Cornell University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis ; Argentina
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
description The goal of this study is twofold. First, to investigate the relative influence of the main structural factors affecting the computation of the 13C0 shielding, namely, the conformation of the residue itself and the next nearest-neighbor effects. Second, to determine whether calculation of the 13C0 shielding at the density functional level of theory (DFT), with an accuracy similar to that of the 13Ca shielding, is feasible with the existing computational resources. The DFT calculations, carried out for a large number of possible conformations of the tripeptide Ac-GXY-NMe, with different combinations of X and Y residues, enable us to conclude that the accurate computation of the 13C0 shielding for a given residue X depends on the: (i) (/,w) backbone torsional angles of X; (ii) side-chain conformation of X; (iii) (/,w) torsional angles of Y; and (iv) identity of residue Y. Consequently, DFT-based quantum mechanical calculations of the 13C0 shielding, with all these factors taken into account, are two orders of magnitude more CPU demanding than the computation, with similar accuracy, of the 13Ca shielding. Despite not considering the effect of the possible hydrogen bond interaction of the carbonyl oxygen, this work contributes to our general understanding of the main structural factors affecting the accurate computation of the 13C0 shielding in proteins and may spur significant progress in effort to develop new validation methods for protein structures.
publishDate 2014
dc.date.none.fl_str_mv 2014-02
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/11336/31301
Vila, Jorge Alberto; Arnautova, Yelena A.; Martín, Osvaldo Antonio; Scheraga, Harold A.; Are accurate computations of the 13C' shielding feasible at the DFT level of theory?; Wiley; Journal Of Computational Chemistry; 35; 4; 2-2014; 309-312
0192-8651
CONICET Digital
CONICET
url http://hdl.handle.net/11336/31301
identifier_str_mv Vila, Jorge Alberto; Arnautova, Yelena A.; Martín, Osvaldo Antonio; Scheraga, Harold A.; Are accurate computations of the 13C' shielding feasible at the DFT level of theory?; Wiley; Journal Of Computational Chemistry; 35; 4; 2-2014; 309-312
0192-8651
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://onlinelibrary.wiley.com/doi/10.1002/jcc.23499/abstract
info:eu-repo/semantics/altIdentifier/doi/10.1002/jcc.23499
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
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
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 13.070432

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