Ultrafast dynamics and spectroscopy of DNA/RNA nucleobases and analogues

One goal of the proposed research is to provide a complete understanding of the ultrafast photorelaxation dynamics of DNA/RNA nucleobases and analogues taking into account non-adiabatic and spin-orbit couplings on the same footing. This will deliver for the first time a dynamical picture which describes internal conversion and intersystem crossing processes in a balanced way. A second goal is to develop a general theoretical framework that allows the direct comparison of observables calculated theoretically with the results obtained by ultrafast time-resolved pump- probe femtosecond spectroscopies. Although both goals are intended to support the rapidly developing field of DNA/RNA photodynamics, the methodological developments devised here are completely general and will allow for realistic simulations of general photochemical and photobiological processes. To achieve the goals outlined above we will employ a combination of accurate electronic structure calculations and a recently developed ab initio surface hopping molecular dynamics theory able to include simultaneously non-adiabatic and spin-orbit couplings. Furthermore, we will extend the capabilities of our existing ab initio molecular dynamics code to include ionization yields, which are the observables measured in the corresponding experiments. Strong synergy between theory and experiment will be enhanced by collaborating with the experimental group of C. E. Crespo-Hernndez, who is a leading worldwide expert in the field of femtosecond spectroscopy applied to DNA/RNA systems and analogues. The specific systems under study will be targeted to understand two opposite problems: i) the photostability of DNA/RNA nucleobases, and ii) the origin of light-induced damage in DNA. Internal conversion is usually invoked as responsible for the ultrafast relaxation which prevents DNA photodamage in the electronically excited state, and therefore, explains the remarkable photostability of DNA/RNA nucleobases. The role of triplet states created by intersystem crossing is neglected in dynamical studies because the rate of internal conversion is commonly believed to be much larger than that of intersystem crossing in organic molecules. In a recent study performed by the applicant on cytosine [J. Phys. Chem. Lett. 3, 30903095 (2012)], we demonstrate, however, that population of triplet states via intersystem crossing takes place in a femtosecond time scale, directly competing with internal conversion. One milestone of the present proposal is then to extend such study to the rest of DNA/RNA nucleobases. Furthermore, it is experimentally demonstrated that specific chemical substitutions can strongly increase the rate of intersystem crossing making DNA analogues especially attractive for therapeutic and pharmacological applications due to their potential to damage DNA. A second related milestone of this proposal is thus to investigate specific DNA analogues and rationalize their different behavior. Ionization yields will be calculated in selected systems, according to the interest awaked by the parallel experiments.

This project employed computational simulations to investigate the mechanisms responsible for ultrafast photorelaxation dynamics of DNA/RNA nucleobases and to rationalize the impact of substitution effects. Nucleobases are the principal building blocks of DNA and RNA, which store all genetic information of all life forms. This information can be harmed by ultraviolet (UV) light by electronically exciting the nucleobases, which can then undergo deleterious photoreactions. Similar light-induced side reactions can occur in nucleobase analogues, which, given their similarity to nucleobases, are widely used as "Trojan horses" in medicine and molecular biology. In this project we developed a general theoretical framework to perform excited-state nonadiabatic dynamics simulations including spin changes. The method, coined SHARC (Surface Hopping including ARbitrary Couplings), has been extended to include i) the computation of ionization yields to deliver similar observables as in some gas phase experiments, and ii) a number of new implementations that allow an efficient use of diverse electronic structure methods. The dynamics simulations showed that after UV irradiation the canonical nucleobases cytosine, uracil, and thymine sometimes follow minor reaction paths involving a spin change, which could lead to photoinduced damage of DNA. Alterations of the chemical structure of the nucleobases are sufficient to enhance these minor reaction paths to become the main reaction. Three classes of modified nucleobases were studied: thiobases (where oxygen is replaced by sulphur), azabases (which have additional nitrogen atoms in their aromatic ring), and halobases (which possess a halogen atom). We rationalized why thiobases undergo extremely efficient spin change processes, rendering them interesting as photosensitizers. The studied azabase, 5-azacytosine, a molecule actively used in cancer therapy, was found to not undergo spin changes. In the halobase 5-bromouracil, carbon-halogen bond dissociation leading to highly reactive radicals was found to be unlikely, but formation of triplet states is possible. These findings are useful in the study and design of new drugs and biochemical research tools.