The effect of sequence on the ionization of guanine in DNA

Chakraborty, Rahul; Ghosh, Debashree

doi:10.1039/c5cp07804k

Cited by 25 publications

(23 citation statements)

References 67 publications

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“…A plot of ωB97X-D3 values vs IP-EOM-DLPNO-CCSD values ( Figure 6) for the first ionized states gives an almost perfectly straight line fit. So, as observed in the previous studies by Ghosh and co-workers, [42] the DFT/ωB97X-D3 method can be a good alternative for the EOM-CCSD methods. However, the Δ-based nature of calculation restricts it only to the first IP values.…”

Section: Ionization Energysupporting

confidence: 71%

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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Section: Ionization Energysupporting

confidence: 71%

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 Figure 2a, the first main VIE (VIE #1) computed by the GFCCSD approach in this work is reduced from ∼7.02 eV in [G−C] 1 to ∼6.64 eV in [G−C] 3 , showing same tendency as the gas phase B3LYP results based on the same geometries and base set. 11 Further comparison shows the B3LYP result is ∼0.2 eV higher than the GFCCSD result for [G−C] 1 , which is close to the deviation reported in another work 10 where the gas phase EOM-IP-CCSD result of a similar G−C single base pair was ∼0.15 eV lower than the DFT result using ωB97x-D density functional. As the system expands to [G−C] 2 and [G−C] 3 , the B3LYP results then become consistently ∼0.2 eV lower than the GFCCSD results.…”

Section: Resultssupporting

confidence: 84%

Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments

Kowalski

Panyala

Krishnamoorthy

2020

The Journal of Chemical Physics

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Accurate description of the ionization process in DNA is crucial to the understanding of the DNA damage under exposure to ionizing radiation, and the exploration of the potential application of DNA strands in nano-electronics. In this work, by employing our recently developed Green's function coupled-cluster (GFCC) library on supercomputing facilities, we have studied the spectral functions of several guanine−cytosine (G−C) base pair structures ([G−C] n , n = 1−3) for the first time in a relatively broad near-valence regime ([-25.0,-5.0] eV) in the coupled-cluster with singles and doubles (CCSD) level. Our focus is to give a preliminary manybody coupled-cluster understanding and guideline of the vertical ionization energy (VIE), spectral profile, and ionization feature changes of these systems as the system size expands in this near-valence regime. The results show that, as the system size expands, even though the lowest VIEs keep decreasing, the changes of spectral function profile and the relative peak positions get unexpectedly smaller. Further analysis of the ionized states associated with the most intensive peak in the spectral functions reveals non-negligible |2h, 1p 's in the ionized wave functions of the considered G−C base pair systems. The leading |2h, 1p 's associated with the main ionizations from the cytosine part of the G−C base pairs feature a transition from the intra-base-pair cytosine π → π * excitation to the inter-base-pair electron excitation as the size of G−C base pairs expands, which also indicates the minimum quantum region in the many-body calculations of DNA systems.

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“…[26][27][28][29] In our earlier work, we have studied the effect of sequence on the vertical ionization energies (VIEs) of NABs, especially guanine. [30] We have shown that stacking can reduce the VIEs considerably, especially when there is a long -GGG-sequence. We have also shown the length scale of the interactions with neighboring NABs that affect the VIEs.…”

Section: Introductionmentioning

confidence: 80%

“…The electron detachment from the NABs in DNA depends on factors such as hydrogen bonding, sequence of DNA, solvent interactions as well as thermal fluctuations . In our earlier work, we have studied the effect of sequence on the vertical ionization energies (VIEs) of NABs, especially guanine . We have shown that stacking can reduce the VIEs considerably, especially when there is a long –GGG– sequence.…”

Section: Introductionmentioning

confidence: 99%

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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The effect of sequence on the ionization of guanine in DNA

Cited by 25 publications

References 67 publications

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

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

Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments

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

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