Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav A.; Landau, Arie; Ahmed, Musahid; Krylov, Anna I.

doi:10.1021/jp1063726

Cited by 102 publications

(216 citation statements)

References 75 publications

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“…These effects are discussed in details in a forthcoming paper on ionization of individual DNA bases. 63 The AIE and the ten lowest VIEs for the dimers are presented in Table 4 and the corresponding molecular orbitals are shown in Figs. 7-9.…”

Section: E Ies Of Cytosine Monomer and Dimersmentioning

confidence: 99%

Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

Kostko

Bravaya

Krylov

et al. 2010

Phys. Chem. Chem. Phys.

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124

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Photoionization of the cytosine dimer 2 SummaryWe report a combined theoretical and experimental study of ionization of cytosine monomers and dimers.Gas-phase molecules are generated by thermal vaporization of cytosine followed by expansion of the vapor in a continuous supersonic jet seeded in Ar. The resulting species are investigated by single photon ionization with tunable vacuum-ultraviolet (VUV) synchrotron radiation and mass analyzed using reflectron mass spectrometry. Energy onsets for the measured photoionization efficiency (PIE) spectra are 8.60±0.05 eV and 7.6±0.1 eV for the monomer and the dimer, respectively, and provide an estimate for the adiabatic ionization energies (AIE). The first AIE and the ten lowest vertical ionization energies (VIEs) for selected isomers of cytosine dimer computed using equation-of-motion coupled-cluster (EOM-IP-CCSD) method are reported. The comparison of the computed VIEs with the derivative of the PIE spectra, suggests that multiple isomers of the cytosine dimer are present in the molecular beam. The calculations reveal that the large red shift (0.7 eV) of the first IE of the lowest-energy cytosine dimer is due to strong inter-fragment electrostatic interactions, i.e., the hole localized on one of the fragments is stabilized by the dipole moment of the other. A sharp rise in the CH + signal at 9.20±0.05 eV is ascribed to the formation of protonated cytosine by dissociation of the ionized dimers. The dominant role of this channel is supported by the computed energy thresholds for the CH + appearance and the barrierless or nearly barrierless ionization-induced proton transfer observed for five isomers of the dimer.3

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Section: E Ies Of Cytosine Monomer and Dimersmentioning

confidence: 99%

Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

Kostko

Bravaya

Krylov

et al. 2010

Phys. Chem. Chem. Phys.

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124

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“…This self-consistent GW method increases the G 0 W 0 VIPs of the HOMO levels by 0.32, 0.32, 0.52, 0.41, and 0.44 eV and decreases the G 0 W 0 VEAs of the LUMO levels by 0.54, 0.50, 0.46, 0.53, and 0.53 eV for G, A, C, T, and U, respectively. Results from advanced quantum chemistry methods are also listed in Table I, including complete active space with second-order perturbation theory (CASPT2) 13,14 , coupled-cluster with singles, doubles, and perturbative triple excitations (CCSD(T)) 13,14 , and equation of motion ionization potential coupled-cluster (EOM-IP-CCSD) 15 . VIPs from CASPT2, CCSD(T), and EOM-IP-CCSD for the HOMO levels are very similar, and close to the experimental mean values within 0.07, 0.07, and 0.05 eV, respectively.…”

Section: Convergence Benchmarkmentioning

confidence: 99%

Photoelectron properties of DNA and RNA bases from many-body perturbation theory

2011

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The photoelectron properties of DNA and RNA bases are studied using many-body perturbation theory within the GW approximation, together with a recently developed Lanczos-chain approach. Calculated vertical ionization potentials, electron affinities, and total density of states are in good agreement with experimental values and photoemission spectra. Convergence benchmark demonstrates the importance of using an optimal polarizability basis in the GW calculations. A detailed analysis of the role of exchange and correlation in both many-body and density-functional theory calculations shows that while self-energy corrections are strongly orbital-dependent, they nevertheless remain almost constant for states that share the same bonding character. Finally, we report on the inverse lifetimes of DNA and RNA bases, that are found to depend linearly on quasi-particle energies for all deep valence states. In general, our G0W0-Lanczos approach provides an efficient yet accurate and fully-converged description of quasiparticle properties of five DNA and RNA bases.

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“…In bare NABs the relaxation energy is 0.2-0.4 eV, whereas in the dimers the difference between adiabatic and vertical IEs is larger. To quantify the effect of structural relaxation on photoionization efficiency (PIE) curves, we computed Franck-Condon factors (FCFs) for the lowest-energy tautomers of NABs [9]. In all cases, we observed that the 0←0 transitions have non-negligible FCFs and that the onsets of the PIE curves indeed represent AIEs.…”

Section: Introductionmentioning

confidence: 99%

The effect of microhydration on ionization energies of thymine

et al. 2011

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A combined theoretical and experimental study of the effect of microhydration on ionization energies (IEs) of thymine is presented. The experimental IEs are derived from photoionization efficiency curves recorded using tunable synchrotron For the ionized states that are localized on thymine the dominant contribution to the IE reduction is the electrostatic interaction between the delocalized positive charge on thymine and the dipole moment of the water molecule.

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Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

Cited by 102 publications

References 75 publications

Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

Photoelectron properties of DNA and RNA bases from many-body perturbation theory

The effect of microhydration on ionization energies of thymine

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