Effect of hydrogen bond site on proton irradiation of guanine–cytosine base pair: A real-time first-principles study

Ion beam irradiation is widely used in radiotherapy and radiation protection. Investigating hydrogen bond site effects on DNA ionization under proton irradiation is crucial for understanding DNA damage mechanisms. We use real-time time-dependent density functional theory (rt-TDDFT) to establish guanine–cytosine (GC) base pair models and investigate their ionization damage processes under proton irradiation with different hydrogen bond positions in this study. By tracking the deposition energy, electronic stopping power (ESP), atomic forces, charge density, and excited electrons, we explore the impact of hydrogen bond positions on GC base pair ionization damage. The analysis indicates that, compared with the configurations of hydrogen bonds, the hydrogen bond donor (cytosine for LHB, guanine for MHB and RHB) cannot be ignored. Our findings offer important insights into the ionization mechanism and damage processes of DNA molecules during ion beam irradiation, which can guide applications in radiotherapy and radiation protection.