One-electron oxidation and redox potential of nucleobases and deoxyribonucleosides computed by QM/MM simulations

Wang, Jiayue; Yang, Songqiu; Yan, Zhang

doi:10.1016/j.cplett.2019.136948

Cited by 18 publications

(16 citation statements)

References 46 publications

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“…The relative order of the one-electron oxidation potentials previously determined by experiments and theory 1,2,4,5,17,18,26,28,30,31 is successfully reproduced by our calculations using both static and dynamic approaches: G < A < T < C < U. Thus, guanine is the most oxidizable nucleobase followed by adenine, i.e., purine molecules are proner than pyrimidines to transfer an electron to a sacrificial agent present in the environment.…”

Section: Tautomerism Effectssupporting

confidence: 69%

See 1 more Smart Citation

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

Lucia-Tamudo

Cárdenas

Anguita-Ortiz

et al. 2022

Preprint

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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, 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.

show abstract

Section: Tautomerism Effectssupporting

confidence: 69%

“…Table 1: Experimental [3][4][5][17][18][19][20][21][22][23] and theoretical 1,2,[24][25][26][27][28][29][30] ranges provided by the literature for one-electron oxidation potentials of the nucleobases in aqueous solution.…”

Section: Introductionmentioning

confidence: 99%

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

Lucia-Tamudo

Cárdenas

Anguita-Ortiz

et al. 2022

Preprint

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show abstract

“…The experimental estimates of the AEA of bulk solvated nucleobases are mostly based on a one-electron reduction potential measurement. A good number of theoretical studies − are available in the literature on the calculation of redox potentials. However, only a handful of explicit solvation-based studies − on the EA of hydrated nucleobases are available in the literature.…”

Section: Introductionmentioning

confidence: 99%

Efficient EOM-CC-based Protocol for the Calculation of Electron Affinity of Solvated Nucleobases: Uracil as a Case Study

Mukherjee

Tripathi

Brehm

et al. 2020

J. Chem. Theory Comput.

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We present an explicit solvation protocol for the calculation of electron affinity values of the solvated nucleobases. The protocol uses a quantum mechanics/molecular mechanics (QM/MM) approach based on the newly implemented domainbased pair natural orbital EOM-CCSD (equation-of-motion coupled-cluster single−double) method. The stability of the solvated nucleobase anion is sensitive to the local distribution of the water molecules around the nucleobase, and the calculated electron affinity values converge slowly with respect to the number of snapshots and the size of the water box. The use of nonpolarizable water molecules leads to an overestimation of the electron affinity and makes the result sensitive to the size of the QM region in the QM/MM calculation. The electron affinity values, although sensitive to the size of the basis set, lead to an almost constant blue shift of the electron affinity upon the increase in the basis set. The present protocol allows for a controllable description of the various parameters affecting the electron affinity value, and the calculated adiabatic electron affinity values are in excellent agreement with experimental results.

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“…The relative order of the one-electron oxidation potentials previously determined by experiments and theory 1 , 2 , 4 , 5 , 17 , 18 , 26 , 28 , 30 , 32 is successfully reproduced by our calculations using both static and dynamic approaches: G < A < T < C < U. Thus, guanine is the most oxidizable nucleobase followed by adenine, that is, purine molecules are more prone than pyrimidines to transfer an electron to a sacrificial agent present in the environment.…”

Section: Resultsmentioning

confidence: 99%

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

Lucia-Tamudo

Cárdenas

Anguita-Ortiz

et al. 2022

J. Chem. Inf. Model.

View full text Add to dashboard Cite

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.

show abstract

One-electron oxidation and redox potential of nucleobases and deoxyribonucleosides computed by QM/MM simulations

Cited by 18 publications

References 46 publications

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

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

Efficient EOM-CC-based Protocol for the Calculation of Electron Affinity of Solvated Nucleobases: Uracil as a Case Study

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

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