Theoretical determination of electron affinity and ionization potential of DNA and RNA bases

Russo, Nino; Toscano, Marirosa; Grand, André

doi:10.1002/1096-987x(20001115)21:14<1243::aid-jcc3>3.0.co;2-m

Cited by 142 publications

(27 citation statements)

References 46 publications

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“…Ionization (electron detachment) and electron attachment processes precede electron transfer. Hence, it is crucial to understand and predict ionization and electron affinity (EA) of biomolecular systems, such as DNA, fluorescent proteins, and melanin . Ionization plays a significant role in DNA damage and unfolding of its helical structures in the presence of ultraviolet radiation .…”

Section: Introductionmentioning

confidence: 99%

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

Bose

Ghosh

2017

J Comput Chem

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We introduce a computationally efficient approach for calculating spectroscopic properties, such as ionization energies (IEs) in the condensed phase. Discrete quantum mechanical/molecular mechanical (QM/MM) approaches for spectroscopic properties in a dynamic system, such as aqueous solution, need a large sample space to obtain converged estimates, especially for the cases where particle (electron) number is not conserved, such as IEs or electron affinities (EAs). We devise a biased sampling technique based on an approximate estimate of interaction energy between the solute and solvent, that accelerates the convergence and therefore, reduces the computational cost significantly. The approximate interaction energy also provides a good measure of the spectral width of the chromophores in the condensed phase. This technique has been tested and benchmarked for (i) phenol, (ii) HBDI anion (hydroxybenzylidene dimethyl imidazolinone), and (iii) thymine in water. © 2017 Wiley Periodicals, Inc.

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Section: Introductionmentioning

confidence: 99%

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

Bose

Ghosh

2017

J Comput Chem

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“…[25][26][27][28] At that level of methodology, the AEA values of cytosine and guanine VB anions were predicted to be around zero [26][27][28] and significantly negative for adenine (in the range of −0.35 eV to −0.17 eV). [26][27][28] The most accurate RI-MP2-R12/CCSD(T) value of 0.04 eV for the VB anion of uracil was calculated by Bachorz et al 29 Nevertheless, the vertical electron affinities (VEAs) of all the nucleobases seem to be negative. 25,26,28 The experimental and computational results concerning the electrophilic properties of nucleobases are summarized in several excellent reviews.…”

Section: Introductionmentioning

confidence: 98%

“…[26][27][28] The most accurate RI-MP2-R12/CCSD(T) value of 0.04 eV for the VB anion of uracil was calculated by Bachorz et al 29 Nevertheless, the vertical electron affinities (VEAs) of all the nucleobases seem to be negative. 25,26,28 The experimental and computational results concerning the electrophilic properties of nucleobases are summarized in several excellent reviews. [30][31][32] The well-established fact that the parent valence anions of nucleobases exist in the condensed phase 33 suggests that interactions with the environment support their covalent anionic form.…”

Section: Introductionmentioning

confidence: 99%

Photoelectron spectroscopy and density functional theory studies on the uridine homodimer radical anions

Storoniak

Wang

et al. 2012

The Journal of Chemical Physics

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We report the photoelectron spectrum (PES) of the homogeneous dimer anion radical of uridine, (rU)(2)(●-). It features a broad band consisting of an onset of ∼1.2 eV and a maximum at the electron binding energy (EBE) ranging from 2.0 to 2.5 eV. Calculations performed at the B3LYP∕6-31++G∗∗ level of theory suggest that the PES is dominated by dimeric radical anions in which one uridine nucleoside, hosting the excess charge on the base moiety, forms hydrogen bonds via its O8 atom with hydroxyl of the other neutral nucleoside's ribose. The calculated adiabatic electron affinities (AEAGs) and vertical detachment energies (VDEs) of the most stable homodimers show an excellent agreement with the experimental values. The anionic complexes consisting of two intermolecular uracil-uracil hydrogen bonds appeared to be substantially less stable than the uracil-ribose dimers. Despite the fact that uracil-uracil anionic homodimers are additionally stabilized by barrier-free electron-induced proton transfer, their relative thermodynamic stabilities and the calculated VDEs suggest that they do not contribute to the experimental PES spectrum of (rU)(2)(●-).

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“…Due to its biological relevance, the light induced ionization processes in NABs have been studied extensively, both theoretically and experimentally . Among the four NABs, guanine has the lowest ionization energy (IE) and is, therefore, the site where the migrating hole gets trapped .…”

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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Theoretical determination of electron affinity and ionization potential of DNA and RNA bases

Cited by 142 publications

References 46 publications

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

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

Photoelectron spectroscopy and density functional theory studies on the uridine homodimer radical anions

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

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