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The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model
[Image: see text] In this contribution we present a quantum dynamical study of the photoexcited hydrogen bonded base pair adenine–thymine (AT) in a Watson–Crick arrangement. To that end, we parametrize Linear Vibronic Coupling (LVC) models with Time-Dependent Density Functional Theory (TD-DFT) calcu...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9281421/ https://www.ncbi.nlm.nih.gov/pubmed/34609880 http://dx.doi.org/10.1021/acs.jpca.1c08132 |
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author | Jouybari, Martha Yaghoubi Green, James A. Improta, Roberto Santoro, Fabrizio |
author_facet | Jouybari, Martha Yaghoubi Green, James A. Improta, Roberto Santoro, Fabrizio |
author_sort | Jouybari, Martha Yaghoubi |
collection | PubMed |
description | [Image: see text] In this contribution we present a quantum dynamical study of the photoexcited hydrogen bonded base pair adenine–thymine (AT) in a Watson–Crick arrangement. To that end, we parametrize Linear Vibronic Coupling (LVC) models with Time-Dependent Density Functional Theory (TD-DFT) calculations, exploiting a fragment diabatization scheme (FrD) we have developed to define diabatic states on the basis of individual chromophores in a multichromophoric system. Wavepacket propagations were run with the multilayer extension of the Multiconfiguration Time-Dependent Hartree method. We considered excitations to the three lowest bright states, a ππ* state of thymine and two ππ* states (L(a) and L(b)) of adenine, and we found that on the 100 fs time scale the main decay pathways involve intramonomer population transfers toward nπ* states of the same nucleobase. In AT this transfer is less effective than in the isolated nucleobases, because hydrogen bonding destabilizes the nπ* states. The population transfer to the A → T charge transfer state is negligible, making the ultrafast (femtosecond) decay through the proton coupled electron transfer mechanism unlikely, in line with experimental results in apolar solvents. The excitation energy transfer is also very small. We carefully compare the predictions of LVC Hamiltonians obtained with different sets of diabatic states, defined so to match either local states of the two separated monomers or the base pair adiabatic states in the Franck–Condon region. To that end we also extend the flexibility of the FrD-LVC approach, introducing a new strategy to define fragments diabatic states that account for the effect of the rest of the multichromohoric system through a Molecular Mechanics potential. |
format | Online Article Text |
id | pubmed-9281421 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-92814212022-07-15 The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model Jouybari, Martha Yaghoubi Green, James A. Improta, Roberto Santoro, Fabrizio J Phys Chem A [Image: see text] In this contribution we present a quantum dynamical study of the photoexcited hydrogen bonded base pair adenine–thymine (AT) in a Watson–Crick arrangement. To that end, we parametrize Linear Vibronic Coupling (LVC) models with Time-Dependent Density Functional Theory (TD-DFT) calculations, exploiting a fragment diabatization scheme (FrD) we have developed to define diabatic states on the basis of individual chromophores in a multichromophoric system. Wavepacket propagations were run with the multilayer extension of the Multiconfiguration Time-Dependent Hartree method. We considered excitations to the three lowest bright states, a ππ* state of thymine and two ππ* states (L(a) and L(b)) of adenine, and we found that on the 100 fs time scale the main decay pathways involve intramonomer population transfers toward nπ* states of the same nucleobase. In AT this transfer is less effective than in the isolated nucleobases, because hydrogen bonding destabilizes the nπ* states. The population transfer to the A → T charge transfer state is negligible, making the ultrafast (femtosecond) decay through the proton coupled electron transfer mechanism unlikely, in line with experimental results in apolar solvents. The excitation energy transfer is also very small. We carefully compare the predictions of LVC Hamiltonians obtained with different sets of diabatic states, defined so to match either local states of the two separated monomers or the base pair adiabatic states in the Franck–Condon region. To that end we also extend the flexibility of the FrD-LVC approach, introducing a new strategy to define fragments diabatic states that account for the effect of the rest of the multichromohoric system through a Molecular Mechanics potential. American Chemical Society 2021-10-05 2021-10-14 /pmc/articles/PMC9281421/ /pubmed/34609880 http://dx.doi.org/10.1021/acs.jpca.1c08132 Text en © 2021 American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Jouybari, Martha Yaghoubi Green, James A. Improta, Roberto Santoro, Fabrizio The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model |
title | The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine
Basepair Investigated with a Fragment-based Diabatization
and a Linear Vibronic Coupling Model |
title_full | The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine
Basepair Investigated with a Fragment-based Diabatization
and a Linear Vibronic Coupling Model |
title_fullStr | The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine
Basepair Investigated with a Fragment-based Diabatization
and a Linear Vibronic Coupling Model |
title_full_unstemmed | The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine
Basepair Investigated with a Fragment-based Diabatization
and a Linear Vibronic Coupling Model |
title_short | The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine
Basepair Investigated with a Fragment-based Diabatization
and a Linear Vibronic Coupling Model |
title_sort | ultrafast quantum dynamics of photoexcited adenine–thymine
basepair investigated with a fragment-based diabatization
and a linear vibronic coupling model |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9281421/ https://www.ncbi.nlm.nih.gov/pubmed/34609880 http://dx.doi.org/10.1021/acs.jpca.1c08132 |
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