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Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches

[Image: see text] The determination of the redox properties of nucleobases is of paramount importance to get insight into the charge-transfer processes in which they are involved, such as those occurring in DNA-inspired biosensors. Although many theoretical and experimental studies have been conduct...

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Autores principales: Lucia-Tamudo, Jesús, Cárdenas, Gustavo, Anguita-Ortiz, Nuria, Díaz-Tendero, Sergio, Nogueira, Juan J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2022
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326891/
https://www.ncbi.nlm.nih.gov/pubmed/35771991
http://dx.doi.org/10.1021/acs.jcim.2c00234
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author Lucia-Tamudo, Jesús
Cárdenas, Gustavo
Anguita-Ortiz, Nuria
Díaz-Tendero, Sergio
Nogueira, Juan J.
author_facet Lucia-Tamudo, Jesús
Cárdenas, Gustavo
Anguita-Ortiz, Nuria
Díaz-Tendero, Sergio
Nogueira, Juan J.
author_sort Lucia-Tamudo, Jesús
collection PubMed
description [Image: see text] The determination of the redox properties of nucleobases is of paramount importance to get insight into the charge-transfer processes in which they are involved, such as those occurring in DNA-inspired biosensors. Although many theoretical and experimental studies have been conducted, the value of the one-electron oxidation potentials of nucleobases is not well-defined. Moreover, the most appropriate theoretical protocol to model the redox properties has not been established yet. In this work, we have implemented and evaluated different static and dynamic approaches to compute the one-electron oxidation potentials of solvated nucleobases. In the static framework, two thermodynamic cycles have been tested to assess their accuracy against the direct determination of oxidation potentials from the adiabatic ionization energies. Then, the introduction of vibrational sampling, the effect of implicit and explicit solvation models, and the application of the Marcus theory have been analyzed through dynamic methods. The results revealed that the static direct determination provides more accurate results than thermodynamic cycles. Moreover, the effect of sampling has not shown to be relevant, and the results are improved within the dynamic framework when the Marcus theory is applied, especially in explicit solvent, with respect to the direct approach. Finally, the presence of different tautomers in water does not affect significantly the one-electron oxidation potentials.
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spelling pubmed-93268912022-07-28 Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches Lucia-Tamudo, Jesús Cárdenas, Gustavo Anguita-Ortiz, Nuria Díaz-Tendero, Sergio Nogueira, Juan J. J Chem Inf Model [Image: see text] The determination of the redox properties of nucleobases is of paramount importance to get insight into the charge-transfer processes in which they are involved, such as those occurring in DNA-inspired biosensors. Although many theoretical and experimental studies have been conducted, the value of the one-electron oxidation potentials of nucleobases is not well-defined. Moreover, the most appropriate theoretical protocol to model the redox properties has not been established yet. In this work, we have implemented and evaluated different static and dynamic approaches to compute the one-electron oxidation potentials of solvated nucleobases. In the static framework, two thermodynamic cycles have been tested to assess their accuracy against the direct determination of oxidation potentials from the adiabatic ionization energies. Then, the introduction of vibrational sampling, the effect of implicit and explicit solvation models, and the application of the Marcus theory have been analyzed through dynamic methods. The results revealed that the static direct determination provides more accurate results than thermodynamic cycles. Moreover, the effect of sampling has not shown to be relevant, and the results are improved within the dynamic framework when the Marcus theory is applied, especially in explicit solvent, with respect to the direct approach. Finally, the presence of different tautomers in water does not affect significantly the one-electron oxidation potentials. American Chemical Society 2022-06-30 2022-07-25 /pmc/articles/PMC9326891/ /pubmed/35771991 http://dx.doi.org/10.1021/acs.jcim.2c00234 Text en © 2022 The Authors. Published by 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 Lucia-Tamudo, Jesús
Cárdenas, Gustavo
Anguita-Ortiz, Nuria
Díaz-Tendero, Sergio
Nogueira, Juan J.
Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches
title Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches
title_full Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches
title_fullStr Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches
title_full_unstemmed Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches
title_short Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches
title_sort computation of oxidation potentials of solvated nucleobases by static and dynamic multilayer approaches
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326891/
https://www.ncbi.nlm.nih.gov/pubmed/35771991
http://dx.doi.org/10.1021/acs.jcim.2c00234
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