First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation

Abstract

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.

Following the density evolution using real time density functional theory and density based indexes: Application to model push–pull molecules

“…RT‐TDDFT has been largely used to model electron dynamics in molecular systems, to simulate the electron density reorganization or to analyze excited states evolution in time 8,9 . Furthermore, by applying a strong electric field, it also possible to simulate nonlinear optical phenomena such as ionization of molecules 10 . Simulations may be carried out for molecules in the gas phase, but it is eventually possible to simulate the environment explicitly for example by means of the coupling between RT‐TDDFT and polarizable force fields 11 …”

“…8,9 Furthermore, by applying a strong electric field, it also possible to simulate nonlinear optical phenomena such as ionization of molecules. 10 Simulations may be carried out for molecules in the gas phase, but it is eventually possible to simulate the environment explicitly for example by means of the coupling between RT-TDDFT and polarizable force fields. 11 Nonetheless, whatever of these two formalisms is chosen, the drawbacks related to the underlying DFT approach impact the reliability of the results.…”

Multiscale molecular modelling: from electronic structure to dynamics of nanosystems and beyond

“…The work has been extended to include the effects of retardation, 105 Ehrenfest dynamics 64 and a variety of applications on the effects of ionizing radiation. 106,107…”

Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides

“…Detailed models such as real-time time-dependent density functional theory (RT-TDDFT) can be used for such cases. [20][21][22][23] If needed, corrections can then be applied to the experimentally obtained model. Using a combination of damage modeling and experimental data to correct structures is indeed feasible.…”