Collision site effect on the radiation dynamics of cytosine induced by proton

Abstract

By combing the time-dependent density functional calculations for electrons with molecular dynamics simulations for ions (TDDFT-MD) nonadiabatically in real time, we investigate the microscopic mechanism of collisions between cytosine and low-energy protons with incident energy ranging from 150 eV to 1000 eV. To explore the effects of the collision site and the proton incident energy on irradiation processes of cytosine, two collision sites are specially considered, which are N and O both acting as the proton receptors when forming hydrogen bonds with guanine. Not only the energy loss and the scattering angle of the projectile, but also the electronic and ionic degrees of freedom of the target are identified. It is found that the energy loss of proton increases linearly with the increase of the incident energy in both situations, which are 14.2% and 21.1% of the incident energy respectively. However, the scattering angles show different behaviors in these two situations when the incident kinetic energy increases. When proton collides with O, the scattering angle of proton is larger and the energy lost is more, while proton captures less electrons from O. The calculated fragment mass distribution shows the high counts of the fragment mass of 1, implying the production of H+ fragment ion from cytosine even for proton with the incident energy lower than keV. Furthermore, the calculated results show that N on cytosine is easier to be combined with low-energy protons to form NH bonds than O.

Time-Dependent Density Functional Theory for Atomic Collisions: A Progress Report

“…More can be said about the study of collisions involving molecules. A number of TDDFT calculations, many of them using the Octopus code [66] and combining the TDKS equations with the Ehrenfest dynamics method to account for the motion of the nuclei, have been carried out to date [42,[82][83][84][85][86][87][88][89][90][91][92][93]. The difficulty of addressing the complicated ion-molecule problem with explicit many-body methods, coupled with the many successes of stationary density functional theory in the quantum chemistry realm, makes this area a natural field for TDDFT and simplified TDDFT-inspired approaches.…”

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

“…The use of the TDDFT to study collisions has gained much attention in recent decades. There are works that studied the following colliding systems: proton–helium and α particle–helium, proton–argon, proton–neon, proton–methane, , gold–butane, proton–cytosine, proton–DNA base pair, and proton–beryllium . One of the first works published in this area is that of Avendaño et al, in which the TDDFT was used to calculate the ECCS in the proton–helium collision .…”

Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA

“…The study of the interaction of protons with DNA is also important for space travels since about 88% of the galactic cosmic rays are made up of protons . Many studies have been carried out for investigating the physico-chemical process of the interaction of energetic protons with DNA and/or its components, either experimentally or theoretically. − Seraide et al used the time-dependent density functional theory (TDDFT) in conjunction with the Ehrenfest dynamics to simulate the collision of a proton with a DNA cytosine–guanine base pair (bp), while Wang et al used the TDDFT to simulate the collision of a proton with a cytosine molecule. To the best of our knowledge, these works are among the first to simulate the direct collision of a proton with a DNA component.…”

“…Thus, classical molecular dynamics simulations (MD) become a more efficient option since it would demand much less computing times, as shown in refs 12–14. However, none of the just cited works described the proton-DNA collision processes explicitly, as done in refs and .…”