Anion spectroscopy of uracil, thymine and the amino-oxo and amino-hydroxy tautomers of cytosine and their water clusters

Schiedt, J.; Weinkauf, R.; Neumark, Daniel M.; Schlag, E. W.

doi:10.1016/s0301-0104(98)00361-9

Cited by 298 publications

(491 citation statements)

References 61 publications

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“…This supposition is based on the electron affinities of isolated nucleobases. Indeed, the adiabatic gas-phase electron affinities of the valence anions of canonical tautomers of nucleic bases, calculated at the B3LYP/DZP++ level, diminish in the following sequence [81]: U>T>C>G>A, and for pyrimidines compare very well with the values extrapolated from photoelectron spectra of nucleobase•(H 2 O) n clusters [82]. This AEA sequence therefore suggests that thymine and cytosine molecules are primary targets for the formation of nucleic base anions in DNA.…”

Section: Interactions Of Dna With Proteins and Proton Transfer Inducementioning

confidence: 55%

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

Rak

Mazurkiewicz

Kobyłecka

et al. 2008

Challenges and Advances in Computational Chemistry and Physics

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Abstract:The last decade has witnessed immense advances in our understanding of the effects of ionizing radiation on biological systems. As the genetic information carrier in biological systems, DNA is the most important species which is prone to damage by high energy photons. Ionizing radiations destroy DNA indirectly by forming low energy electrons (LEEs) as secondary products of the interaction between ionizing radiation and water. An understanding of the mechanism that leads to the formation of single and double strand breaks may be important in guiding the further development of anticancer radiation therapy. In this article we demonstrate the likely involvement of stable nucleobases anions in the formation of DNA strand breaks -a concept which the radiation research community has not focused on so far. In Section 21.1 we discuss the current status of studies related to the interaction between DNA and LEEs. The next section is devoted to the description of proton transfer induced by electron attachment to the complexes between nucleobases and various proton donorsa process leading to the strong stabilization of nucleobases anions. Then, we review our results concerning the anionic binary complexes of nucleobases with particular emphasize on the GC and AT systems. Next, the possible consequences of interactions between DNA and proteins in the context of electron attachment are briefly discussed. Further, we focus on existing proposal of single strand break formation in DNA. Ultimately, open questions as well perspectives of studies on electron induced DNA damage are discussed

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Section: Interactions Of Dna With Proteins and Proton Transfer Inducementioning

confidence: 55%

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

Rak

Mazurkiewicz

Kobyłecka

et al. 2008

Challenges and Advances in Computational Chemistry and Physics

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“…The most accurate molecular orbital approach, however, is CASPT2. [117] It is important to remember that these methods are very sensitive to the choice and the size of the basis set that is used to represent the molecular orbitals, especially for calculating EA. Anions are frequently loosely bound and require diffuse basis orbitals and large basis sets.…”

Section: Electron Affinitiesmentioning

confidence: 99%

“…The BLYP affinity is fortuitously close to the PS experimental value. [36] Experimental Reference PS 0.15 ± 0.12 [117] More accurate functionals are constructed by combining GGAs with HF (exact) exchange in an appropriate proportion. This is the case for the hybrid B3LYP functional [124,125], which has proved itself to be particularly reliable for predicting AEAs of DNA components [122].…”

Section: Electron Affinitiesmentioning

confidence: 99%

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

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Abstract. DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts from the interaction of radiation -either photons or swift ions -with the biological medium. Such interactions cause electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, in particular strand breaks in plasmid DNA [1]. These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage.In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.

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“…The important of nonperturbative triples for the dipole bound anions of HCN and HNC has been discussed by Peterson and Gutowski. 32 The realization that CCSD(T) or CCSDT methods together with large flexible basis sets are required to describe accurately dipole bound anions is disconcerting as such calculations are computationally prohibitive for the large molecule or cluster systems currently being studied experimentally and theoretically 42,45,[71][72][73] For these systems, it has often been necessary to compromise on the theoretical method employed.…”

Section: Ab Initio Treatment Of Dipole-bound Anionsmentioning

confidence: 99%

A Drude-model approach to dispersion interactions in dipole-bound anions

Wang¹,

Jordan²

2001

The Journal of Chemical Physics

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A one-electron model potential for calculating the binding energy of an excess electron interacting with polar molecules and their clusters is described. The unique feature of this potential is the treatment of polarization and dispersion effects by means of a Drude model. The approach is tested by calculating the energies for binding an excess electron to HCN, (HCN)2, HNC, and (HNC)2. The model potential results are found to be in good agreement with the predictions of high-level all-electron calculations.

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Anion spectroscopy of uracil, thymine and the amino-oxo and amino-hydroxy tautomers of cytosine and their water clusters

Cited by 298 publications

References 61 publications

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

A Drude-model approach to dispersion interactions in dipole-bound anions

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