Cargando…
Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree method...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8003674/ https://www.ncbi.nlm.nih.gov/pubmed/33804640 http://dx.doi.org/10.3390/molecules26061743 |
_version_ | 1783671745329233920 |
---|---|
author | Green, James A. Jouybari, Martha Yaghoubi Aranda, Daniel Improta, Roberto Santoro, Fabrizio |
author_facet | Green, James A. Jouybari, Martha Yaghoubi Aranda, Daniel Improta, Roberto Santoro, Fabrizio |
author_sort | Green, James A. |
collection | PubMed |
description | We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2–3 bright states and all the close by dark states, for a total of 6–9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications. |
format | Online Article Text |
id | pubmed-8003674 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-80036742021-03-28 Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases Green, James A. Jouybari, Martha Yaghoubi Aranda, Daniel Improta, Roberto Santoro, Fabrizio Molecules Article We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2–3 bright states and all the close by dark states, for a total of 6–9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications. MDPI 2021-03-20 /pmc/articles/PMC8003674/ /pubmed/33804640 http://dx.doi.org/10.3390/molecules26061743 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Green, James A. Jouybari, Martha Yaghoubi Aranda, Daniel Improta, Roberto Santoro, Fabrizio Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases |
title | Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases |
title_full | Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases |
title_fullStr | Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases |
title_full_unstemmed | Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases |
title_short | Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases |
title_sort | nonadiabatic absorption spectra and ultrafast dynamics of dna and rna photoexcited nucleobases |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8003674/ https://www.ncbi.nlm.nih.gov/pubmed/33804640 http://dx.doi.org/10.3390/molecules26061743 |
work_keys_str_mv | AT greenjamesa nonadiabaticabsorptionspectraandultrafastdynamicsofdnaandrnaphotoexcitednucleobases AT jouybarimarthayaghoubi nonadiabaticabsorptionspectraandultrafastdynamicsofdnaandrnaphotoexcitednucleobases AT arandadaniel nonadiabaticabsorptionspectraandultrafastdynamicsofdnaandrnaphotoexcitednucleobases AT improtaroberto nonadiabaticabsorptionspectraandultrafastdynamicsofdnaandrnaphotoexcitednucleobases AT santorofabrizio nonadiabaticabsorptionspectraandultrafastdynamicsofdnaandrnaphotoexcitednucleobases |