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1. Comment un électron induit un dommage oxydatif dans l’ADN

   Ma, Jun ; Denisov, Sergey ; Adhikary, Amitava A ; Mostafavi, Mehran ( January 2020 , Les Actualités chimiques)

   null (Ed.)

   How can an electron induce oxidative damage in DNA DNA damage caused by the dissociative electron attachment (DEA) has been well-studied in the gas and solid phases. However, understanding of this process at the fundamental level in solution is still a challenge. The electrons, after losing their kinetic energy via ionization and excitation events, are thermalized and undergo a multistep hydration process with a time constant of ca. ≤ 1 ps, to becoming fully trapped as a hydrated or solvated electron (esol- or eaq-). Prior to the formation of esol-, the electron exists in its presolvated (or prehydrated) state (epre-) with no kinetic energy. We used picosecond pulse radiolysis to generate electrons in water or in liquid diethylene glycol (DEG) to observe the dynamics of capture of these electrons by DNA/RNA bases, nucleosides, and nucleotides. In diethylene glycol, we demonstrate that unlike esol- and epre-, eqf- effectively attaches itself to the RNA-nucleoside, ribothymidine, forming the excited state of the anion that undergoes the N1-C1 ́ glycosidic bond dissociation. Thanks to DEA, this process induced in fact by eqf- leads to an oxidation of the parent molecule similar to the hydroxyl radical (•OH), leading to the same glycosidic bond (N1-C1 ́) cleavage. 

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2. Reaction mechanism and dynamics for C8-hydroxylation of 9-methylguanine radical cation by water molecules

   https://doi.org/10.1039/d1cp03884b  

   Zhou, Wenjing ; Liu, Jianbo ( November 2021 , Physical Chemistry Chemical Physics)

   In contrast to their spontaneous deprotonation in aqueous solution, reactions of guanine and guanosine radical cations with water in the gas phase are exclusively initiated by hydration of the radical cations as reported in recent work (Y. Sun et al. , Phys. Chem. Chem. Phys. , 2018, 20 , 27510). As gas-phase hydration reactions closely mimic the actual scenario for guanine radical cations in double-stranded DNA, exploration of subsequent reactions within their water complexes can provide an insight into the resulting oxidative damage to nucleosides. Herein guided-ion beam mass spectrometry experiment and direct dynamics trajectory simulations were carried out to examine prototype complexes of the 9-methylguanine radical cation with one and two water ligands ( i.e. , 9MG˙ + ·(H 2 O) 1–2 ) in the gas phase, wherein the complexes were activated by collisional activation in the experiment and by thermal excitation at high temperatures in the simulations. Guided by mass spectroscopic measurements, trajectory results and reaction potential energy surface, three reaction pathways were identified. The first two reaction pathways start with H-atom abstraction from water by the O6 and N7 atoms in 9MG˙ + and are referred to as HA O6 and HA N7 , respectively. The primary products of HA O6 and HA N7 reactions, including [9MG + H O6 ] + /[9MG + H N7 ] + and ˙OH, react further to either form [8OH-9MG + H O6 ]˙ + and [8OH-9MG + H N7 ]˙ + via C8-hydroxylation or form radical cations of 6- enol -guanine (6- enol -G˙ + ) and 7H-guanine (7HG˙ + ) via S N 2-type methanol elimination. The third reaction pathway corresponds to the formation of 8OH-9MG + by H elimination from the complex, referred to as HE. Among these product channels, [8OH-9MG + H N7 ]˙ + has the most favorable formation probability, especially in the presence of additional water molecules. This product may serve as a preceding structure to the 8-oxo-7,8-dihydroguanine lesion in DNA and has implications for health effects of radiation exposure and radiation therapy. 

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3. One-electron oxidation of ds(5′-GGG-3′) and ds(5′-G(8OG)G-3′) and the nature of hole distribution: a density functional theory (DFT) study

   https://doi.org/10.1039/c9cp06244k  

   Kumar, Anil ; Adhikary, Amitava ; Sevilla, Michael D. ; Close, David M. ( March 2020 , Physical Chemistry Chemical Physics)

   null (Ed.)

   Of particular interest in radiation-induced charge transfer processes in DNA is the extent of hole localization immediately after ionization and subsequent relaxation. To address this, we considered double stranded oligomers containing guanine (G) and 8-oxoguanine (8OG), i.e. , ds(5′-GGG-3′) and ds(5′-G8OGG-3′) in B-DNA conformation. Using DFT, we calculated a variety of properties, viz. , vertical and adiabatic ionization potentials, spin density distributions in oxidized stacks, solvent and solute reorganization energies and one-electron oxidation potential ( E 0 ) in the aqueous phase. Calculations for the vertical state of the -GGG- cation radical showed that the spin was found mainly (67%) on the middle G. However, upon relaxation to the adiabatic -GGG- cation radical, the spin localized (96%) on the 5′-G, as observed in experiments. Hole localizations on the middle G and 3′-G were higher in energy by 0.5 kcal mol −1 and 0.4 kcal mol −1 , respectively, than that of 5′-G. In the -G8OGG- cation radical, the spin localized only on the 8OG in both vertical and adiabatic states. The calculated vertical ionization potentials of -GGG- and -G8OGG- stacks were found to be lower than that of the vertical ionization potential of a single G in DNA. The calculated E 0 values of -GGG- and -G8OGG- stacks are 1.15 and 0.90 V, respectively, which owing to stacking effects are substantially lower than the corresponding experimental E 0 values of their monomers (1.49 and 1.18 V, respectively). SOMO to HOMO level switching is observed in these oxidized stacks. Consequently, our calculations predict that local double oxidations in DNA will form triplet diradical states, which are especially significant for high LET radiations. 

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4. Effects of Intra‐Base Pair Proton Transfer on Dissociation and Singlet Oxygenation of 9‐Methyl‐8‐Oxoguanine−1‐Methyl‐Cytosine Base‐Pair Radical Cations

   https://doi.org/10.1002/cphc.202300511  

   Moe, May Myat ; Tsai, Midas ; Liu, Jianbo ( October 2023 , ChemPhysChem)

   8‐Oxoguanosine is the most common oxidatively generated base damage and pairs with complementary cytidine within duplex DNA. The 8‐oxoguanosine−cytidine lesion, if not recognized and removed, not only leads to G‐to‐T transversion mutations but renders the base pair being more vulnerable to the ionizing radiation and singlet oxygen (¹O₂) damage. Herein, reaction dynamics of a prototype Watson−Crick base pair [9MOG ⋅ 1MC]⋅⁺, consisting of 9‐methyl‐8‐oxoguanine radical cation (9MOG⋅⁺) and 1‐methylcystosine (1MC), was examined using mass spectrometry coupled with electrospray ionization. We first detected base‐pair dissociation in collisions with the Xe gas, which provided insight into intra‐base pair proton transfer of 9MOG⋅⁺ ⋅ 1MC[9MOG − H_N1]⋅ ⋅ [1MC+H_N3′]⁺and subsequent non‐statistical base‐pair separation. We then measured the reaction of [9MOG ⋅ 1MC]⋅⁺with¹O₂, revealing the two most probable pathways, C5‐O₂addition and H_N7‐abstraction at 9MOG. Reactions were entangled with the two forms of 9MOG radicals and base‐pair structures as well as multi‐configurations between open‐shell radicals and¹O₂(that has a mixed singlet/triplet character). These were disentangled by utilizing approximately spin‐projected density functional theory, coupled‐cluster theory and multi‐referential electronic structure modeling. The work delineated base‐pair structural context effects and determined relative reactivity toward¹O₂as [9MOG − H]⋅>9MOG⋅⁺>[9MOG − H_N1]⋅ ⋅ [1MC+H_N3′]⁺≥9MOG⋅⁺ ⋅ 1MC.

    

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5. Extreme Ultraviolet Reflection-Absorption (XUV-RA) Spectroscopy: Probing Dynamics at Surfaces from a Molecular Perspective

   https://doi.org/https://doi.org/10.1021/acs.accounts.1c00765  

   Biswas, Somnath ; Baker, L. Robert ( March 2022 , Accounts of chemical research)

   Extreme ultraviolet (XUV) light sources based on high harmonic generation are enabling the development of novel spectroscopic methods to help advance the frontiers of ultrafast science and technology. In this account we discuss the development of XUV-RA spectroscopy at near grazing incident reflection geometry and highlight recent applications of this method to study ultrafast electron dynamics at surfaces. Measuring core-to-valence transitions with broadband, femtosecond pulses of XUV light extends the benefits of x-ray absorption spectroscopy to a laboratory tabletop by providing a chemical fingerprint of materials, including the ability to resolve individual elements with sensitivity to oxidation state, spin state, carrier polarity, and coordination geometry. Combining this chemical state sensitivity with femtosecond time resolution provides new insight into the material properties that govern charge carrier dynamics in complex materials. It is well known that surface dynamics differ significantly from equivalent processes in bulk materials, and that charge separation, trapping, transport, and recombination occurring uniquely at surfaces governs the efficiency of numerous technologically relevant processes spanning photocatalysis, photovoltaics, and information storage and processing. Importantly, XUV-RA spectroscopy at near grazing angle is also surface sensitive with a probe depth of 3 nm, providing a new window into electronic and structural dynamics at surfaces and interfaces. Here we highlight the unique capabilities and recent applications of XUVRA spectroscopy to study photo-induced surface dynamics in metal oxide semiconductors, including photocatalytic oxides (Fe2O3, Co3O4 NiO, and CuFeO2) as well as photoswitchable magnetic oxide (CoFe2O4). We first compare the ultrafast electron self-trapping rates via small polaron formation at the surface and bulk of Fe2O3 where we note that the energetics and kinetics of this process differ significantly at the surface. Additionally, we demonstrate the ability to systematically tune this kinetics by molecular functionalization, thereby, providing a route to control carrier transport at surfaces. We also measure the spectral signatures of charge transfer excitons with site specific localization of both electrons and holes in a series of transition metal oxide semiconductors (Fe2O3, NiO, Co3O4). The presence of valence band holes probed at the oxygen L1-edge confirms a direct relationship between the metal-oxygen bond covalency and water oxidation efficiency. For a mixed metal oxide CuFeO2 in the layered delafossite structure, XUV-RA reveals that the sub-picosecond hole thermalization from O 2p to Cu 3d states of CuFeO2 leads to the spatial separation of electrons and holes, resulting in exceptional photocatalytic performance for H2 evolution and CO2 reduction of this material. Finally, we provide an example to show the ability of XUV-RA to probe spin state specific dynamics in a the photo-switchable ferrimagnet, cobalt ferrite (CoFe2O4). This study provides a detailed understating of ultrafast spin switching in a complex magnetic material with site-specific resolution. In summary, the applications of XUV-RA spectroscopy demonstrated here illustrate the current abilities and future promise of this method to extend molecule-level understanding from well-defined photochemical complexes to complex materials so that charge and spin dynamics at surfaces can be tuned with the precision of molecular photochemistry. 

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