Electron-induced hydrogen loss in uracil in a water cluster environment

Smyth, Maeve; Kohanoff, Jorge; Fabrikant, I. I.

doi:10.1063/1.4874841

Cited by 44 publications

(52 citation statements)

References 57 publications

(102 reference statements)

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“…[16,17] Figure 2a shows the ion yield of the dimer anion as afunction of the incident electron energy.Reflecting the mass spectrum of Figure 1, an abundant zero eV peak is visible, which is located at this energy owing to as tabilizing interaction between the TNI and surrounding molecules in the cluster. [18] In addition to the low-energy feature,asignal arises at higher electron energies from about 4u pt o1 5eV. Thef irst peak at about 5.4 eV is above the three mentioned p*r esonances and must thus be ascribed to ac ore-excited resonance.…”

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confidence: 90%

The Effect of Solvation on Electron Attachment to Pure and Hydrated Pyrimidine Clusters

et al. 2015

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The interaction of low‐energy electrons with biomolecules plays an important role in the radiation‐induced alteration of biological tissue at the molecular level. At electron energies below 15 eV, dissociative electron attachment is one of the most important processes in terms of the chemical transformation of molecules. So far, a common approach to study processes at the molecular level has been to carry out investigations with single biomolecular building blocks like pyrimidine as model molecules. Electron attachment to single pyrimidine, as well as to pure clusters and hydrated clusters, was investigated in this study. In striking contrast to the situation with isolated molecules and hydrated clusters, where no anionic monomer is detectable, we were able to observe the molecular anion for the pure clusters. Furthermore, there is evidence that solvation effectively prevents the ring fragmentation of pyrimidine after electron capture.

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confidence: 90%

The Effect of Solvation on Electron Attachment to Pure and Hydrated Pyrimidine Clusters

et al. 2015

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“…In order to start answering this question, Smyth et al extended the previous work by supplementing Rmatrix calculations with multiple scattering theory to take the effect of microsolvation, i.e. the presence of a small number of water molecules hydrogen-bonded to Uracil, on the DEA process into account [63]. A first finding was that the N1-H resonance shifted towards lower energies due to the stabilising role of the environment.…”

Section: Dissociative Electron Attachment (Dea) In Nucleobasesmentioning

confidence: 99%

“…Full scattering R-Matrix calculations have been performed for systems as large as single DNA nucleobases in vacuum [74,75], and microsolvated by up 5 water molecules [76]. This is practically the state-of-the-art for the calculation of electronic resonance cross-sections, while for DEA probably the largest system studied is the one in [63]. Theoretical and experimental progress in DEA has been reviewed very recently [77].…”

Section: Dissociative Electron Attachment (Dea) In Nucleobasesmentioning

confidence: 99%

“…The microsolvated system consists of a Thymine base surrounded by five explicit water molecules (See Figure 13). These water molecules make hydrogen bonds with the Thymine at all possible positions involving N and Oatoms (C-atoms do not make significant hydrogen bonds), and were taken from previous studies [63,91]. The water molecules in this system provide a representation for the first solvation shell of Thymine.…”

Section: 12mentioning

confidence: 99%

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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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“…As for the fragmentation itself, less literature is available. The first attemptt os tudy the effect of microhydration on the reactivity of NBs was the theoretical work by Smyth et al, [23] who were ablet os how that the presence of water enhanced the fragmentation of uracil anion. This prediction was strongly contradicted by the experimental work of Kočišek et al [24] on uracil and thymine, for which as tabilising effect of water related to the suppressiono ft he dissociative channels of uracil and thymine was pointed out.…”

Section: Introductionmentioning

confidence: 99%

Ab Initio Study of the Stepwise versus Concerted Fragmentation Pathways in Microhydrated Thymine Radical Cations

Semmeq

Monari

Badawi

et al. 2019

Chemistry A European J

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Thymine radiation-induced fragmentation is characterised by ring openinga nd the loss of HNCO/NCO.T hese pathways have been investigated using DFT calculations in the presence of zero, one and two water molecules. In addition to the already characterised stepwise fragmentation mechanism, we propose an ovel concerted pathway reported here for the first time. We show that both the stepwise and concerted mechanismsa re competitive with activation energies of 2.05 eV and 2.00 eV,r espectively,i nt he gas phase. The effect of microhydration on these mechanisms are examinedb ased on the most stable conformations found by an exploration of the potentiale nergy surfacep erformed by using DFT-based ab initio molecular dynamics. Microhydration is also accompanied by an increase in the activation energies, with respect to gas phase, amounting to 0.47 eV-an increase that is associated to as tabilisinge ffect of water in agreement with recente xperimental studies. However, we also point out that this effect is greatlyd ependent on the specific water arrangement aroundt hymine and could be limited to only 0.13 eV for some configurations.

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Electron-induced hydrogen loss in uracil in a water cluster environment

Cited by 44 publications

References 57 publications

The Effect of Solvation on Electron Attachment to Pure and Hydrated Pyrimidine Clusters

The Effect of Solvation on Electron Attachment to Pure and Hydrated Pyrimidine Clusters

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

Ab Initio Study of the Stepwise versus Concerted Fragmentation Pathways in Microhydrated Thymine Radical Cations

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