Low-Lying π* Resonances of Standard and Rare DNA and RNA Bases Studied by the Projected CAP/SAC–CI Method

Kanazawa, Yuki; Ehara, Masahiro; Sommerfeld, Thomas

doi:10.1021/acs.jpca.5b12190

Cited by 42 publications

(38 citation statements)

References 71 publications

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“…Finally, we note that the calculations performed in this work suggest that strong * and * coupling may exist in the cluster excited states. This situation should certainly be investigated using more rigorous theoretical treatments, [56][57][58] to provide a further understanding of the extent of orbital coupling and its impact on the excited state photophysics.…”

Section: On the Mechanism Of Photofragment Productionmentioning

confidence: 99%

Photoexcitation of iodide ion-pyrimidine clusters above the electron detachment threshold: Intracluster electron transfer versus nucleobase-centred excitations

Matthews

Cercola

Mensa-Bonsu

et al. 2018

The Journal of Chemical Physics

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Laser photodissociation spectroscopy of the I·thymine (I·T) and I·cytosine (I·C) nucleobase clusters has been conducted for the first time across the regions above the electron detachment thresholds to explore the excited states and photodissociation channels. Although photodepletion is strong, only weak ionic photofragment signals are observed, indicating that the clusters decay predominantly by electron detachment. The photodepletion spectra of the I·T and I·C clusters display a prominent dipole-bound excited state (I) in the vicinity of the vertical detachment energy (∼4.0 eV). Like the previously studied I·uracil (I·U) cluster [W. L. Li et al., J. Chem. Phys. 145, 044319 (2016)], the I·T cluster also displays a second excited state (II) centred at 4.8 eV, which we similarly assign to a π-π* nucleobase-localized transition. However, no distinct higher-energy absorption bands are evident in the spectra of the I·C. Time-dependent density functional theory (TDDFT) calculations are presented, showing that while each of the I·T and I·U clusters displays a single dominant π-π* nucleobase-localized transition, the corresponding π-π* nucleobase transitions for I·C are split across three separate weaker electronic excitations. I and deprotonated nucleobase anion photofragments are observed upon photoexcitation of both I·U and I·T, with the action spectra showing bands (at 4.0 and 4.8 eV) for both the I and deprotonated nucleobase anion production. The photofragmentation behaviour of the I·C cluster is distinctive as its I photofragment displays a relatively flat profile above the expected vertical detachment energy. We discuss the observed photofragmentation profiles of the I·pyrimidine clusters, in the context of the previous time-resolved measurements, and conclude that the observed photoexcitations are primarily consistent with intracluster electron transfer dominating in the near-threshold region, while nucleobase-centred excitations dominate close to 4.8 eV. TDDFT calculations suggest that charge-transfer transitions [Iodide n (5p) → Uracil σ*] may contribute to the cluster absorption profile across the scanned spectral region, and the possible role of these states is also discussed.

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Section: On the Mechanism Of Photofragment Productionmentioning

confidence: 99%

Photoexcitation of iodide ion-pyrimidine clusters above the electron detachment threshold: Intracluster electron transfer versus nucleobase-centred excitations

Matthews

Cercola

Mensa-Bonsu

et al. 2018

The Journal of Chemical Physics

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“…TASs can be characterized by several different computational approaches, such as SM, complex scaling and complex absorbing potential techniques, and scattering calculations . SM has many variants .…”

Section: Methodsmentioning

confidence: 99%

Shape and core‐excited resonances of thionucleobases

Cheng

Lin

2018

Int J of Quantum Chemistry

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Thionucleobases can be used in chemoradiation therapy of cancer. Shape resonances (SRs) and core-excited resonances (CERs) can lead to fragmentation and eventually result in strand breaks of DNA. In particular, the more energetic CERs are believed to cause double-strand breaks that can hardly be repaired. In this work, both the SRs and CERs of exemplary 2-thiouracil, 4-thiouracil, 2thiothymine, 4-thiothymine, and 6-aza-2-thiothymine are investigated using stabilization method in conjunction with long range corrected time-dependent density functional theory. Results indicate that the energies of (1) p* 1 and p* 2 SRs, (2) n-p* CERs, and (3) mixed resonances of p-p* CERs with p* SRs can be significantly stabilized due to thionation of uracil or thymine. It is noteworthy that the resonant cases of (2) and (3) can be accessed by electrons even at energies below 4 eV.Consequently, the increased decay of temporary anions can enhance strand breaks of DNA.chemoradiation therapy, density functional theory, shape and core-excited resonances, stabilization method, thionucleobases

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“…Recent work demonstrates the ability of adapted quantum chemistry methods to describe resonances in biomolecules and provide information on their energy and lifetime. For example, the complex absorbing potential (CAP)/symmetry adapted cluster-configuration interaction (SACCI) method reproduce the ETS position of the low π * resonances for DNA bases (calculations for substituted forms are also presented, Kanazawa et al 2016). Other groups have applied similar stabilization techniques to halopyrimidines (Cheng et al 2016) to study shape and core-excited resonances using the polarized continuum method (PCM) to model the effect of water when the molecules are in solution.…”

Section: Dissociative Electron Attachment and Resonance Parametersmentioning

confidence: 99%

Electron scattering from molecules and molecular aggregates of biological relevance

Gorfinkiel

Ptasińska

2017

J. Phys. B: At. Mol. Opt. Phys.

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In this Topical Review we survey the current state of the art in the study of low energy electron collisions with biologically relevant molecules and molecular clusters. We briefly describe the methods and techniques used in the investigation of these processes and summarise the results obtained so far for DNA constituents and their model compounds, amino acids, peptide and other biomolecules. The applications of the data obtained is briefly described as well as future required developments.

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Low-Lying π* Resonances of Standard and Rare DNA and RNA Bases Studied by the Projected CAP/SAC–CI Method

Cited by 42 publications

References 71 publications

Photoexcitation of iodide ion-pyrimidine clusters above the electron detachment threshold: Intracluster electron transfer versus nucleobase-centred excitations

Photoexcitation of iodide ion-pyrimidine clusters above the electron detachment threshold: Intracluster electron transfer versus nucleobase-centred excitations

Shape and core‐excited resonances of thionucleobases

Electron scattering from molecules and molecular aggregates of biological relevance

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