On the Quantum Description of Irradiation Dynamics in Systems of Biological Relevance

Dinh, Phuong Mai; Bourg, Lila Bouëssel du; Gao, Cong-Zhang; Gu, Bing-Lin; Lacombe, Lionel; McAllister, Maeve; Smyth, Maeve; Tribello, Gareth A.; Vincendon, M.; Kohanoff, Jorge; Reinhard, P.‐G.; Sanche, Léon; Suraud, E.

doi:10.1007/978-3-319-43030-0_8

Cited by 6 publications

(3 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Before cleavage the excess electron, whose probability distribution is represented here by a blue surface, is located at one of the end bases, in this case thymine (middle panel). When the C-O bond is stretched, the excess electron transfers to the phosphate involved in this bond (right panel) [110]. Related experimental work was carried out earlier for GCAT tetranucleotides in which G or A had been removed [111].…”

Section: Larger Dna Models: Polynucleotides and Double Strandsmentioning

confidence: 91%

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

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Larger Dna Models: Polynucleotides and Double Strandsmentioning

confidence: 91%

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

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

Self Cite

View full text Add to dashboard Cite

show abstract

“…Theory and computer modeling have been mobilized for many years to assist in the interpretation of experimental data, and excellent reviews have been published (34)(35)(36)(37)(38). The great variety of methodologies developed in the field cannot be summarized here.…”

Section: Introductionmentioning

confidence: 99%

First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation

Omar

Hasnaoui

Lande

2021

Annu. Rev. Phys. Chem.

View full text Add to dashboard Cite

Ionizing rays cause damage to genomes, proteins, and signaling pathways that normally regulate cell activity, with harmful consequences such as accelerated aging, tumors, and cancers but also with beneficial effects in the context of radiotherapies. While the great pace of research in the twentieth century led to the identification of the molecular mechanisms for chemical lesions on the building blocks of biomacromolecules, the last two decades have brought renewed questions, for example, regarding the formation of clustered damage or the rich chemistry involving the secondary electrons produced by radiolysis. Radiation chemistry is now meeting attosecond science, providing extraordinary opportunities to unravel the very first stages of biological matter radiolysis. This review provides an overview of the recent progress made in this direction, focusing mainly on the atto- to femto- to picosecond timescales. We review promising applications of time-dependent density functional theory in this context.

show abstract

“…For bulk solid materials, one way is direct elastic knock-off of the nucleus from its crystal position 14 . However, for small organic molecules, a more efficient method is ionization of the molecule by knocking out a deep electron from the molecule [15][16][17] . The initial ionization process is followed by hot carrier cooling, which can empty the bonding electronic state and transfer the hot carrier electron energy to the nucleus, hence causing bond breakage 18,19 .…”

mentioning

confidence: 99%

The cage effect of electron beam irradiation damage in cryo-electron microscopy

Li,

Kang,

Dai

et al. 2024

npj Comput Mater

View full text Add to dashboard Cite

Electron beam irradiation can cause damage to biological and organic samples, as determined via transmission electron microscopy (TEM). Cryo-electron microscopy (cryo-EM) significantly reduces such damage by quickly freezing the environmental water around organic molecules. However, there are multiple hypotheses about the mechanism of cryo-protection in cryo-EM. A lower temperature can cause less molecular dissociation in the first stage, or frozen water can have a “cage” effect by preventing the dissociated fragments from flying away. In this work, we use real-time time-dependent density functional theory molecular dynamics(rt-TDDFT-MD) simulations to study the related dynamics. We use our recently developed natural orbital branching (NOB) algorithm to describe the molecular dissociation process after the molecule is ionized. We find that despite the difference in surrounding water molecules at different temperatures, the initial dissociation process is similar. On the other hand, the dissociated fragments fly away at room temperature, while they remain in the same cage when frozen water is used. Our results provide direct support for the cage effect mechanism.

show abstract

On the Quantum Description of Irradiation Dynamics in Systems of Biological Relevance

Cited by 6 publications

References 79 publications

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

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

First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation

The cage effect of electron beam irradiation damage in cryo-electron microscopy

Contact Info

Product

Resources

About