An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase

Bose, Sritama; Ghosh, Debashree

doi:10.1002/jcc.24875

Cited by 11 publications

(16 citation statements)

References 96 publications

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“…We have noticed that solvatochromic shift in VIE (DVIE) is directly proportional to DE int . [70] In the case of guanine, we have noticed similar correlation ( Figure S2(a) in Supporting Information). It is important to mention here that the computation of DE int for a configuration is computationally inexpensive when compared to a hybrid QM/ EFP calculation to predict DVIE.…”

Section: Biased Sampling For Faster Convergencesupporting

confidence: 70%

“…The difference in interaction energy can be expressed as,

Δ E_{int} = \sum_{\begin{matrix} i \in solute \\ j \in solvent \end{matrix}} \frac{Q_{i, es} q_{j}}{r_{i j}} - \sum_{\begin{matrix} i \in solute \\ j \in solvent \end{matrix}} \frac{Q_{i, gs} q_{j}}{r_{i j}},

where

Q_{i, es}

and

Q_{i, gs}

refer to the charge of the i th atom of the solute (QM region) in its excited and ground state, respectively, and q j refers to the charge of the j th atom of the solvent (MM region) and r ij is the distance between these points. We have noticed that solvatochromic shift in VIE (ΔVIE) is directly proportional to Δ E int . In the case of guanine, we have noticed similar correlation (Figure S2(a) in Supporting Information).…”

Section: Computational Detailssupporting

confidence: 68%

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Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study

2017

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Ionization of nucleobases is affected by their biological environment, which includes both the effect of adjacent nucleotides as well as the presence of water around it. Guanine and its nucleotide have the lowest ionization potentials among the various DNA bases. Therefore, the threshold of ionization is dependent on that of guanine and its characterization is crucial to the prediction of interaction of light with DNA. We investigate the effect of solvation on the vertical ionization energies (VIEs) of guanine and its nucleotide. In this work, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) approach with effective fragment potential as the MM method of choice and equation-of-motion coupled-cluster for ionization potential with singles and doubles (EOM-IP-CCSD) as the QM method. The performance of the hybrid scheme with respect to the full QM method shows an accuracy of ≤ 0.02-0.04 eV. The lowest few ionizations of the nucleotide are found to be from different parts of the moiety, that is, the nucleic acid base, phosphate, or sugar, and these ionization energies are very closely spaced giving rise to a very complicated spectrum. Furthermore, microsolvation has large effects on these ionizations and can lead to red or blue shift depending on the position of the water molecule. Even a single water molecule can change the order of ionized states in the nucleotide. The VIEs of the bulk solvated chromophores are predicted and compared to existing experimental spectra. The predominant role of polarization in the solvatochromic shift is noticed. © 2017 Wiley Periodicals, Inc.

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Section: Biased Sampling For Faster Convergencesupporting

confidence: 70%

“…The difference in interaction energy can be expressed as,

Δ E_{int} = \sum_{\begin{matrix} i \in solute \\ j \in solvent \end{matrix}} \frac{Q_{i, es} q_{j}}{r_{i j}} - \sum_{\begin{matrix} i \in solute \\ j \in solvent \end{matrix}} \frac{Q_{i, gs} q_{j}}{r_{i j}},

where

Q_{i, es}

and

Q_{i, gs}

Section: Computational Detailssupporting

confidence: 68%

Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study

2017

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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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“…The microsolvation studies on thymine always show a red-shift in the IP values. [29,41] A careful look at the mono-hydrated and di-hydrated structures shows that the isomers for which the water molecules are exclusively hydrogen bonded to thymine (1B and 2B) show a red-shift of the second IP values. However, the overall trend in microsolvation studies on the AT base pair shows that the presence of one or two water molecules cannot reproduce the behavior of the bulk environment.…”

Section: Ionization Energymentioning

confidence: 99%

“…[11,21] However, the efficiency of the EFP-EOM-CCSD method is limited by the expensive EOM-CCSD calculation on the solute, which can become a bottleneck for base pairs and larger DNA fragments, especially when one needs to run hundreds of snapshots to perform dynamic averaging of the calculation over multiple snapshots. Ghosh and co-workers have recently reported a biased sampling technique, [29] which can reduce the number of snapshots required to get converged IP values. However, to the best of our knowledge, no explicit solvation-based studies have been reported to investigate the effect of bulk solvation on the IP values of base pairs.…”

mentioning

confidence: 99%

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

Mukherjee

Haldar

Dutta

2019

Int J of Quantum Chemistry

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In the present work, we investigate the effect of aqueous environment on the vertical ionization potential (VIP) of adenine-thymine (AT) base pair using a multilayer equation of the motion-coupled cluster method. The microsolvation can cause both blue-shift and red-shit of the IP values. However, the bulk water environment always results in the red-shift of the vertical ionization potential. Our study shows that the correct treatment of the short-range interaction plays an essential role in determining the magnitude of the red-shift. We have developed a biased sampling scheme based on Koopmans' energy, which can significantly speed up the convergence with respect to the number of solvent-solute configurations.

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An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase

Cited by 11 publications

References 96 publications

Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study

Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study

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

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

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