TDDFT-Based Study on the Proton–DNA Collision

Time-Dependent Density-Functional Theory for Determining the Electron-Capture Cross Section for Protons Impacting on Atoms and Molecules

The use of the Time-Dependent Density-Functional Theory (TDDFT) has increased in the atomic collision field. Calculating the electron-capture cross section (ECCS) for protons is an important question in hadrontherapy and plasma physics, among other areas. In previous studies, it was shown that the approach based on the Local Density Approximation (LDA) fails in the 1-50 keV region, requiring the use of the Optimized Effective Potential (OEP) method. In this work, the ECCS values for 1-50 keV protons impacting on isolated hydrogen, carbon, nitrogen, oxygen, and nitrogenous atoms were determined using the TDDFT. It is shown that adding the Self Interaction Correction to the LDA (LDA-Sic) allows obtaining results close to those provided by the OEP and experiments, with the advantage that the LDA-Sic consumes less computational time. In addition, it was demonstrated that it is imperative to include the spin correction for the specific helium and oxygen cases, in order to get good results for the ECCS using the TDDFT. Theoretical results obtained in this work show excellent agreement with experimental values.

A TD-DFT-Based Study on the Attack of the OH· Radical on a Guanine Nucleotide

Heavy charged particles induce severe damage in DNA, which is a radiobiological advantage when treating radioresistant tumors. However, these particles can also induce cancer in humans exposed to them, such as astronauts in space missions. This damage can be directly induced by the radiation or indirectly by the attack of free radicals mainly produced by water radiolysis. We previously studied the impact of a proton on a DNA base pair, using the Time Dependent-Density Functional Theory (TD-DFT). In this work, we go a step further and study the attack of the OH· radical on the Guanine nucleotide to unveil how this molecule subsequently dissociates. The OH· attack on the H1', H2', H3', and H5' atoms in the guanine was investigated using the Ehrenfest dynamics within the TD-DFT framework. In all cases, the hydrogen abstraction succeeded, and the subsequent base pair dissociation was observed. The DNA dissociates in three major fragments: the phosphate group, the deoxyribose sugar, and the nitrogenous base, with slight differences, no matter which hydrogen atom was attacked. Hydrogen abstraction occurs at about 6 fs, and the nucleotide dissociation at about 100 fs, which agrees with our previous result for the direct proton impact on the DNA. These calculations may be a reference for adjusting reactive force fields so that more complex DNA structures can be studied using classical molecular dynamics, including both direct and indirect DNA damage.

Proton Collision on Deoxyribose Originating from Doubly Ionized Water Molecule Dissociation

In this work, we studied the fragmentation dynamics of 2-deoxy-d-ribose (DR) in solution that arises from the double ionization of a water molecule in its primary hydration shell. This process was modeled in the framework of ab initio molecular dynamics. The charge unbalanced in the solvent molecules produces a Coulomb explosion with the consequent release of protons with kinetic energy in the few electronvolts range, which collide with the surrounding molecules in solution inducing further chemical reactions. In particular, we observe proton collisions with the solute molecule DR, which leads to a complete ring opening. In DNA, damage to the DR moiety may lead to DNA strand breaking. This mechanism can be understood as one of the possible steps in the radiation-induced fragmentation of DNA chains.