Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory

ABSTRACT: We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be suffici...

Full description

Autores:
López Acevedo, Olga Lucía
Makkonen, Esko
Rinke, Patricio
Chen, Xi
Tipo de recurso:
Article of investigation
Fecha de publicación:
2018
Institución:
Universidad de Antioquia
Repositorio:
Repositorio UdeA
Idioma:
eng
OAI Identifier:
oai:bibliotecadigital.udea.edu.co:10495/30419
Acceso en línea:
https://hdl.handle.net/10495/30419
Palabra clave:
ADN
DNA
Plata - química
Silver - chemistry
Dicroismo Circular
Circular Dichroism
Simulación de Dinámica Molecular
Molecular Dynamics Simulation
Nanoestructuras - química
Nanostructures - chemistry
Teoría cuántica
Quantum Theory
Rights
openAccess
License
http://creativecommons.org/licenses/by/2.5/co/
id UDEA2_2fc1c8f14796837880646b8cd6c59157
oai_identifier_str oai:bibliotecadigital.udea.edu.co:10495/30419
network_acronym_str UDEA2
network_name_str Repositorio UdeA
repository_id_str
dc.title.spa.fl_str_mv Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory
title Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory
spellingShingle Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory
ADN
DNA
Plata - química
Silver - chemistry
Dicroismo Circular
Circular Dichroism
Simulación de Dinámica Molecular
Molecular Dynamics Simulation
Nanoestructuras - química
Nanostructures - chemistry
Teoría cuántica
Quantum Theory
title_short Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory
title_full Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory
title_fullStr Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory
title_full_unstemmed Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory
title_sort Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory
dc.creator.fl_str_mv López Acevedo, Olga Lucía
Makkonen, Esko
Rinke, Patricio
Chen, Xi
dc.contributor.author.none.fl_str_mv López Acevedo, Olga Lucía
Makkonen, Esko
Rinke, Patricio
Chen, Xi
dc.subject.decs.none.fl_str_mv ADN
DNA
Plata - química
Silver - chemistry
Dicroismo Circular
Circular Dichroism
Simulación de Dinámica Molecular
Molecular Dynamics Simulation
Nanoestructuras - química
Nanostructures - chemistry
Teoría cuántica
Quantum Theory
topic ADN
DNA
Plata - química
Silver - chemistry
Dicroismo Circular
Circular Dichroism
Simulación de Dinámica Molecular
Molecular Dynamics Simulation
Nanoestructuras - química
Nanostructures - chemistry
Teoría cuántica
Quantum Theory
description ABSTRACT: We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.
publishDate 2018
dc.date.issued.none.fl_str_mv 2018
dc.date.accessioned.none.fl_str_mv 2022-09-05T20:52:38Z
dc.date.available.none.fl_str_mv 2022-09-05T20:52:38Z
dc.type.spa.fl_str_mv info:eu-repo/semantics/article
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dc.type.local.spa.fl_str_mv Artículo de investigación
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status_str publishedVersion
dc.identifier.citation.spa.fl_str_mv Makkonen, E., Rinke, P., López-Acevedo, O. y Chen, X. (2018). Propiedades ópticas del ADN mediado por plata a partir de la dinámica molecular y la teoría funcional de la densidad dependiente del tiempo. Revista Internacional de Ciencias Moleculares , 19 (8), 2346. MDPI AG. Obtenido de http://dx.doi.org/10.3390/ijms19082346
dc.identifier.issn.none.fl_str_mv 1661-6596
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/10495/30419
dc.identifier.doi.none.fl_str_mv 10.3390/ijms19082346
dc.identifier.eissn.none.fl_str_mv 1422-0067
identifier_str_mv Makkonen, E., Rinke, P., López-Acevedo, O. y Chen, X. (2018). Propiedades ópticas del ADN mediado por plata a partir de la dinámica molecular y la teoría funcional de la densidad dependiente del tiempo. Revista Internacional de Ciencias Moleculares , 19 (8), 2346. MDPI AG. Obtenido de http://dx.doi.org/10.3390/ijms19082346
1661-6596
10.3390/ijms19082346
1422-0067
url https://hdl.handle.net/10495/30419
dc.language.iso.spa.fl_str_mv eng
language eng
dc.relation.ispartofjournalabbrev.spa.fl_str_mv Int. J. Mol. Sci.
dc.rights.spa.fl_str_mv info:eu-repo/semantics/openAccess
dc.rights.uri.*.fl_str_mv http://creativecommons.org/licenses/by/2.5/co/
dc.rights.accessrights.spa.fl_str_mv http://purl.org/coar/access_right/c_abf2
dc.rights.creativecommons.spa.fl_str_mv https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/2.5/co/
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dc.format.extent.spa.fl_str_mv 13
dc.format.mimetype.spa.fl_str_mv application/pdf
dc.publisher.spa.fl_str_mv DMPI
dc.publisher.group.spa.fl_str_mv Grupo de Física Atómica y Molecular
dc.publisher.place.spa.fl_str_mv Basilea, Suiza
institution Universidad de Antioquia
bitstream.url.fl_str_mv https://bibliotecadigital.udea.edu.co/bitstream/10495/30419/1/LopezOlga_2018_OpticalPropertiesSilverMediated.pdf
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repository.name.fl_str_mv Repositorio Institucional Universidad de Antioquia
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spelling López Acevedo, Olga LucíaMakkonen, EskoRinke, PatricioChen, Xi2022-09-05T20:52:38Z2022-09-05T20:52:38Z2018Makkonen, E., Rinke, P., López-Acevedo, O. y Chen, X. (2018). Propiedades ópticas del ADN mediado por plata a partir de la dinámica molecular y la teoría funcional de la densidad dependiente del tiempo. Revista Internacional de Ciencias Moleculares , 19 (8), 2346. MDPI AG. Obtenido de http://dx.doi.org/10.3390/ijms190823461661-6596https://hdl.handle.net/10495/3041910.3390/ijms190823461422-0067ABSTRACT: We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.COL000844113application/pdfengDMPIGrupo de Física Atómica y MolecularBasilea, Suizainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_2df8fbb1https://purl.org/redcol/resource_type/ARTArtículo de investigaciónhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/2.5/co/http://purl.org/coar/access_right/c_abf2https://creativecommons.org/licenses/by/4.0/Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional TheoryADNDNAPlata - químicaSilver - chemistryDicroismo CircularCircular DichroismSimulación de Dinámica MolecularMolecular Dynamics SimulationNanoestructuras - químicaNanostructures - chemistryTeoría cuánticaQuantum TheoryInt. J. Mol. Sci.International Journal of Molecular Sciences23462358198ORIGINALLopezOlga_2018_OpticalPropertiesSilverMediated.pdfLopezOlga_2018_OpticalPropertiesSilverMediated.pdfArtículo de investigaciónapplication/pdf2652306https://bibliotecadigital.udea.edu.co/bitstream/10495/30419/1/LopezOlga_2018_OpticalPropertiesSilverMediated.pdf647fe3994cd58dccbb95041cb65ae14eMD51CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8927https://bibliotecadigital.udea.edu.co/bitstream/10495/30419/2/license_rdf1646d1f6b96dbbbc38035efc9239ac9cMD52LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://bibliotecadigital.udea.edu.co/bitstream/10495/30419/3/license.txt8a4605be74aa9ea9d79846c1fba20a33MD5310495/30419oai:bibliotecadigital.udea.edu.co:10495/304192022-09-05 15:52:39.471Repositorio Institucional Universidad de Antioquiaandres.perez@udea.edu.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