Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method

Autores
Díaz Mirón, Gonzalo; Lien Medrano, Carlos R.; Banerjee, Debarshi; Morzan, Uriel; Sentef, Michael A.; Gebauer, Ralph; Hassanali, Ali
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Recent experimental findings reveal non-conventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed NonAromatic Fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states, remaining absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remain the primary vibrational mode explaining NAF in these systems. In order to simulate larger model systems taking into account the effects of the surrounding environment, in this work we propose using the density functional tight-binding (DFTB) method in combination with non-adiabatic molecular dynamics (NAMD) and the mixed quantum/molecular mechanics (QM/MM) approach. We investigate the mechanism behind NAF in the crystal structure of Lpyroglutamine-ammonium, comparing it with the related non-fluorescent amino acid L-glutamine. Our results extend our previous findings to more realistic systems, demonstrating the efficiency and robustness of the proposed DFTB method in the context of NAMD in biological systems. Furthemore, due to its inherent low computational cost, this method allows for a better sampling on the non-radiative events at the conical intersection which is crucial for a complete understanding of this phenomenon. Beyond contributing to the ongoing exploration of NAF, this work paves the way for future application of this method in more complex biological systems such as amyloid aggregates, biomaterials and non-aromatic proteins.
Fil: Díaz Mirón, Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; Argentina. The Abdus Salam. International Centre for Theoretical Physics; Italia
Fil: Lien Medrano, Carlos R.. Universitat Bremen; Alemania
Fil: Banerjee, Debarshi. The Abdus Salam. International Centre for Theoretical Physics; Italia. Scuola Internazionale Superiore Di Studi Avanzati (sissa);
Fil: Morzan, Uriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; Argentina
Fil: Sentef, Michael A.. Universitat Bremen; Alemania. Max Planck Institute for the Structure and Dynamics of Matter; Alemania
Fil: Gebauer, Ralph. The Abdus Salam. International Centre for Theoretical Physics; Italia
Fil: Hassanali, Ali. The Abdus Salam. International Centre for Theoretical Physics; Italia
Materia
Time dependent density functional theory
Fluorescence
Oligomers
QMMM
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/261452
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding MethodDíaz Mirón, GonzaloLien Medrano, Carlos R.Banerjee, DebarshiMorzan, UrielSentef, Michael A.Gebauer, RalphHassanali, AliTime dependent density functional theoryFluorescenceOligomersQMMMhttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1Recent experimental findings reveal non-conventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed NonAromatic Fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states, remaining absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remain the primary vibrational mode explaining NAF in these systems. In order to simulate larger model systems taking into account the effects of the surrounding environment, in this work we propose using the density functional tight-binding (DFTB) method in combination with non-adiabatic molecular dynamics (NAMD) and the mixed quantum/molecular mechanics (QM/MM) approach. We investigate the mechanism behind NAF in the crystal structure of Lpyroglutamine-ammonium, comparing it with the related non-fluorescent amino acid L-glutamine. Our results extend our previous findings to more realistic systems, demonstrating the efficiency and robustness of the proposed DFTB method in the context of NAMD in biological systems. Furthemore, due to its inherent low computational cost, this method allows for a better sampling on the non-radiative events at the conical intersection which is crucial for a complete understanding of this phenomenon. Beyond contributing to the ongoing exploration of NAF, this work paves the way for future application of this method in more complex biological systems such as amyloid aggregates, biomaterials and non-aromatic proteins.Fil: Díaz Mirón, Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; Argentina. The Abdus Salam. International Centre for Theoretical Physics; ItaliaFil: Lien Medrano, Carlos R.. Universitat Bremen; AlemaniaFil: Banerjee, Debarshi. The Abdus Salam. International Centre for Theoretical Physics; Italia. Scuola Internazionale Superiore Di Studi Avanzati (sissa);Fil: Morzan, Uriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Sentef, Michael A.. Universitat Bremen; Alemania. Max Planck Institute for the Structure and Dynamics of Matter; AlemaniaFil: Gebauer, Ralph. The Abdus Salam. International Centre for Theoretical Physics; ItaliaFil: Hassanali, Ali. The Abdus Salam. International Centre for Theoretical Physics; ItaliaAmerican Chemical Society2024-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/261452Díaz Mirón, Gonzalo; Lien Medrano, Carlos R.; Banerjee, Debarshi; Morzan, Uriel; Sentef, Michael A.; et al.; Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method; American Chemical Society; Journal of Chemical Theory and Computation; 20; 9; 4-2024; 3864-38781549-9618CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jctc.4c00125info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.4c00125info:eu-repo/semantics/altIdentifier/arxiv/https://arxiv.org/abs/2401.09990info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-02-26T10:32:56Zoai:ri.conicet.gov.ar:11336/261452instacron: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:34982026-02-26 10:32:56.99CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method
title Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method
spellingShingle Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method
Díaz Mirón, Gonzalo
Time dependent density functional theory
Fluorescence
Oligomers
QMMM
title_short Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method
title_full Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method
title_fullStr Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method
title_full_unstemmed Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method
title_sort Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method
dc.creator.none.fl_str_mv Díaz Mirón, Gonzalo
Lien Medrano, Carlos R.
Banerjee, Debarshi
Morzan, Uriel
Sentef, Michael A.
Gebauer, Ralph
Hassanali, Ali
author Díaz Mirón, Gonzalo
author_facet Díaz Mirón, Gonzalo
Lien Medrano, Carlos R.
Banerjee, Debarshi
Morzan, Uriel
Sentef, Michael A.
Gebauer, Ralph
Hassanali, Ali
author_role author
author2 Lien Medrano, Carlos R.
Banerjee, Debarshi
Morzan, Uriel
Sentef, Michael A.
Gebauer, Ralph
Hassanali, Ali
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Time dependent density functional theory
Fluorescence
Oligomers
QMMM
topic Time dependent density functional theory
Fluorescence
Oligomers
QMMM
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Recent experimental findings reveal non-conventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed NonAromatic Fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states, remaining absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remain the primary vibrational mode explaining NAF in these systems. In order to simulate larger model systems taking into account the effects of the surrounding environment, in this work we propose using the density functional tight-binding (DFTB) method in combination with non-adiabatic molecular dynamics (NAMD) and the mixed quantum/molecular mechanics (QM/MM) approach. We investigate the mechanism behind NAF in the crystal structure of Lpyroglutamine-ammonium, comparing it with the related non-fluorescent amino acid L-glutamine. Our results extend our previous findings to more realistic systems, demonstrating the efficiency and robustness of the proposed DFTB method in the context of NAMD in biological systems. Furthemore, due to its inherent low computational cost, this method allows for a better sampling on the non-radiative events at the conical intersection which is crucial for a complete understanding of this phenomenon. Beyond contributing to the ongoing exploration of NAF, this work paves the way for future application of this method in more complex biological systems such as amyloid aggregates, biomaterials and non-aromatic proteins.
Fil: Díaz Mirón, Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; Argentina. The Abdus Salam. International Centre for Theoretical Physics; Italia
Fil: Lien Medrano, Carlos R.. Universitat Bremen; Alemania
Fil: Banerjee, Debarshi. The Abdus Salam. International Centre for Theoretical Physics; Italia. Scuola Internazionale Superiore Di Studi Avanzati (sissa);
Fil: Morzan, Uriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; Argentina
Fil: Sentef, Michael A.. Universitat Bremen; Alemania. Max Planck Institute for the Structure and Dynamics of Matter; Alemania
Fil: Gebauer, Ralph. The Abdus Salam. International Centre for Theoretical Physics; Italia
Fil: Hassanali, Ali. The Abdus Salam. International Centre for Theoretical Physics; Italia
description Recent experimental findings reveal non-conventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed NonAromatic Fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states, remaining absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remain the primary vibrational mode explaining NAF in these systems. In order to simulate larger model systems taking into account the effects of the surrounding environment, in this work we propose using the density functional tight-binding (DFTB) method in combination with non-adiabatic molecular dynamics (NAMD) and the mixed quantum/molecular mechanics (QM/MM) approach. We investigate the mechanism behind NAF in the crystal structure of Lpyroglutamine-ammonium, comparing it with the related non-fluorescent amino acid L-glutamine. Our results extend our previous findings to more realistic systems, demonstrating the efficiency and robustness of the proposed DFTB method in the context of NAMD in biological systems. Furthemore, due to its inherent low computational cost, this method allows for a better sampling on the non-radiative events at the conical intersection which is crucial for a complete understanding of this phenomenon. Beyond contributing to the ongoing exploration of NAF, this work paves the way for future application of this method in more complex biological systems such as amyloid aggregates, biomaterials and non-aromatic proteins.
publishDate 2024
dc.date.none.fl_str_mv 2024-04
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/11336/261452
Díaz Mirón, Gonzalo; Lien Medrano, Carlos R.; Banerjee, Debarshi; Morzan, Uriel; Sentef, Michael A.; et al.; Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method; American Chemical Society; Journal of Chemical Theory and Computation; 20; 9; 4-2024; 3864-3878
1549-9618
CONICET Digital
CONICET
url http://hdl.handle.net/11336/261452
identifier_str_mv Díaz Mirón, Gonzalo; Lien Medrano, Carlos R.; Banerjee, Debarshi; Morzan, Uriel; Sentef, Michael A.; et al.; Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method; American Chemical Society; Journal of Chemical Theory and Computation; 20; 9; 4-2024; 3864-3878
1549-9618
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jctc.4c00125
info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.4c00125
info:eu-repo/semantics/altIdentifier/arxiv/https://arxiv.org/abs/2401.09990
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/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 12.665996

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