Attosecond dynamics simulations of glycine irradiated by α-particle: Comment on "A never-ending story in the sky: The secrets of chemical evolution" by C. Puzzarini and V. Barone

Shape Resonances in DNA: Nucleobase Release, Reduction, and Dideoxynucleoside Products Induced by 1.3 to 2.3 eV Electrons

Understanding the details of DNA damage caused by high-energy particles or photons is complicated by the multitude of reactive species, arising from the ionization and dissociation of H₂O, DNA, and protein. In this work, oligonucleotides (ODNs) are irradiated with a beam of low-energy electrons of 1.3 to 2.3 eV, which can only induce damage via the decay of shape resonances into various dissociative electron attachment channels. Using LC-MS/MS analysis, the major products are the release of nonmodified nucleobases (NB; Cyt ≫ Thy ∼ Ade > Gua). Additional damage includes 5,6-dihydropyrimidines (dHT > dHU) and eight nucleosides with modified sugar moieties consisting of 2',3'- and 2',5'-dideoxynucleosides (ddG > ddA ∼ ddC > ddT). The distribution of products is remarkably different in a 16-mer ODN compared to that observed previously with thymidylyl-(3'-5')-thymidine. This difference is explained by electron delocalization occurring within a sufficiently long strand, the DEA theory of O'Malley, and recent time-dependent density functional theory calculations.

Nucleic Acids under Stress: Understanding and Simulating Nucleobase Fragmentation Pathways

The effects of radiations on nucleic acids and their constituents is widely studied across several research fields using different experimental and theoretical protocols. While a large number of studies were performed in this context, many fundamental physical and chemical effects are still being investigated, particularly involving the effect of the biological environment. As an example, the interpretation of experimental nucleic acid bases mass spectra, and hence inferring their reactivity in complex environment still poses great challenge. This Minireview summarizes recent theoretical advancements aiming to predict and interpret the reactivity of nucleic acid bases. We focus not only on the understanding of the inherent fragmentation pathways of isolated nucleobases but also on the modeling of a realistic nano-environments highlighting the importance of molecular dynamics simulations and the non-innocent role of the environment and also the possibility to open novel fragmentation pathways.

The physical stage of radiolysis of solvated DNA by high-energy-transfer particles: insights from new first principles simulations

Electron dynamics simulations based on density functional theory are carried out on nanometric molecular systems to decipher the primary processes following irradiation of bio-macromolecules by high energy transfer charged particles.