Solvation effect on the vertical ionization energy of adenine‐thymine base pair: From microhydration to bulk

Mukherjee, Madhubani; Haldar, Soumi; Dutta, Achintya Kumar

doi:10.1002/qua.26127

Cited by 5 publications

(4 citation statements)

References 42 publications

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“…The first 55 snapshots are selected out of the original 400 snapshots using an energy-based prescreening scheme. 59,60 The instantaneous average VDE of these 55 snapshots is 8.29 eV, which is in good agreement with the original instantaneous average VDE of 8.24 eV. In the next step, we increased the number of water molecules included in the EA-EOM-DLPNO- CCSD-based QM/MM calculations in a shellwise manner for these 55 snapshots.…”

Section: Computational Detailssupporting

confidence: 70%

“…To further understand the distance dependence of the stabilizing effect provided by water, we have studied the effect of the size of the water environment on the calculated VDE values. First 55 snapshots are selected out of the original 400 snapshots using an energy-based pre-screening scheme 59,60 . The average VDE of these 55 snapshots is 8.29 eV, which is in good agreement with the original average value of 8.24 eV.…”

Section: Bulk-solvationmentioning

confidence: 99%

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Electron Attachment to Cytosine: The Role of Water

2021

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We present an EOM-CCSD based QM/MM study on the electron attachment process to cytosine, solvated in water. The microhydration studies cannot capture the effect of bulk water environment on the electron attachment process and one need to include large number of water molecules in the calculation to get converged results. The electron attachment in the bulk solvated cytosine happened through a doorway mechanism, where the initial electron is localized on water. The electron subsequently gets transferred to cytosine by mixing of electronic and nuclear degrees of freedom which happens at an ultrafast time scale. The bulk water environment stabilizes the cytosine bound anion by an extensive hydrogen-bonding network and enhances the electron transfer rate by manifold from that observed in the gas phase. The predicted adiabatic electron affinity and electron transfer rate obtained from our QM/MM calculations are consistent with the available experimental results.

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Section: Computational Detailssupporting

confidence: 70%

Section: Bulk-solvationmentioning

confidence: 99%

Electron Attachment to Cytosine: The Role of Water

2021

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“…To have a quantitative understanding of the dependence of VDE values on the number of water molecules, we have checked the convergence of the VDE with respect to the number of solvation shells. We have first prescreened 42 snapshots using energy‐based criteria . We have chosen only those snapshots whose VDE values are within 0.65 eV of the average VDE of the original 400 snapshots.…”

Section: Resultsmentioning

confidence: 99%

Interactions of Solvated Electrons with Nucleobases: The Effect of Base Pairing

2020

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We have investigated the effect of base pairing on the electron attachment to nucleobases in bulk water, taking the guanineÀ cytosine (GC) base pair as a test case. The presence of the complementary base reinforces the stabilization effect provided by water and preferentially stabilizes the anion by hydrogen bonding. The electron attachment in bulk-solvated GC happens through a doorway mechanism, where the initial electron attached state is water bound, and it subsequently gets converted to a GC bound state. The additional electron in the final GC bound state is localized on the cytosine, similar to that in the gas phase. The transfer of the electron from the initial water-bound state to the final GC bound state happens due to the mixing of electronic and nuclear degrees of freedom and takes place at a picosecond time scale.[a] Dr.

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“…Biased Sampling Using the VDE as the Parameter. Previous studies 35,86 on the ionization potential of solvated molecules have shown that biased sampling can be used as a handy tool to reduce the computational cost and time. In this study, a biased sampling was performed on the 400 snapshots generated in the previous step from the QM/MM dynamics.…”

Section: Calculation Of Electron Affinitymentioning

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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Solvation effect on the vertical ionization energy of adenine‐thymine base pair: From microhydration to bulk

Cited by 5 publications

References 42 publications

Electron Attachment to Cytosine: The Role of Water

Electron Attachment to Cytosine: The Role of Water

Interactions of Solvated Electrons with Nucleobases: The Effect of Base Pairing

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

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