Femtosecond responses of hydrated DNA irradiated by ionizing rays focus on the sugar-phosphate part

Abstract

In this article we investigate the mechanisms of DNA ionization upon irradiation by 0.5 MeV alpha particles. We focus on the sugar-phosphate group and its hydration shell. In radiation chemistry, the term quasi-direct effect refers the physical and chemical responses taking place after irradiation of solvent molecules pertaining to the solvation shells of solutes. The molecular mechanisms accounting for the quasi-direct effect are actually largely elusive, especially for those prevailing in the early time scales (<10 -12 s). We report Real-Time-Time-Dependent Auxiliary Density Functional Theory simulations carried out within the framework of hybrid QM/MM scheme (Quantum Mechanics/Molecular Mechanics) with polarizable and non-polarizable embedding. Ten water molecules from the solvation shell of DNA backbone are independently irradiated. We find that during the first femtoseconds after irradiation, the holes formed on the irradiated water remains at their sites of formation. Electrostatic induction within the environment doesn't significantly impact charge migrations. We address the hypothesis that charge migration driven by electron correlation is responsible for an ultrafast H2O + -to-DNA charge transfers, which would account for a quasi-direct effect. We find that pure charge migration at fixed nuclear positions is not responsible for the quasi-direct effect when considering sugar-phosphate solvation shells.

Irradiation of Plutonium Tributyl Phosphate Complexes by Ionizing Alpha Particles: A Computational Study

“…The application of complex boundary conditions was extended to the Schrödinger equation, , and then to the time-dependent Schrödinger equation applied on molecular systems to deal with diffuse reactions such as collisions between atoms. , In this context, CAP have been introduced as an alternative to mask functions . By adding a complex component to the system’s Hamiltonian, the electron density is gradually absorbed beyond a threshold distance. ,,− CAPs have been shown to be very effective when coupled with various electronic structures methods such as multiconfigurational methods, − coupled-cluster methods, − Lanczos-based approach, and Electron Attachment Algebraic-Diagrammatic Construction (EA-ADC) method in the study of metastable resonance states for anionic molecular systems. Its applications are extended in the generation of high harmonic generation (HHG) spectra with RT-TD-DFT, other Time-Dependent methods (TD-CIS, TD-SE, TD-CI), − or in non-Hermitian exceptional point (EPs) degeneracies .…”

“…Collision would thus result in the formation of a superposition of a large number of quantum states and can be difficult to reproduce for molecules with more than ten atoms using wave function methods, considering the final active space size. Despite possible shortcomings of RT-TD-DFT to describe matter under strong field irradiation, ,, which are related to approximation in exchange-correlation functional approximations, RT-TD-DFT remains a very appealing methodology enabling the study of large system as compared to time-dependent wave function methods.…”