Low-Energy Electron-Induced Single Strand Breaks in 2′-Deoxycytidine-3′-monophosphate Using the Local Complex Potential Based Time-Dependent Wave Packet Approach

Abstract

Recent experimental and theoretical investigations on resonant electron scattering off DNA and DNA fragments using low-energy electrons (LEEs), to propose the mechanism for single strand breaks (SSBs) and double strand breaks (DSBs), have received considerable attention. It is our purpose here to understand theoretically the comprehensive route to SSB in a selected DNA fragment, namely, 2'-deoxycytidine-3'-monophosphate (3'-dCMPH), induced by LEE (0-3 eV) scattering using the local complex potential based time-dependent wave packet (LCP-TDWP) approach. To the best of our knowledge, there is no time-dependent quantum mechanical study that has been reported in the literature for this DNA fragment to date. Initial results obtained from our calculation in the gas phase provide a good agreement with experimental observation and show the plausibility of SSB at 0.75 eV, which is very close to the highest SSB yield reported from the experimental measurement (0.8 eV) on plasmid DNA in the condensed phase.

Effect of quantum tunneling on single strand breaks in a modeled gas phase cytidine nucleotide induced by low energy electron: A theoretical approach

“…Though, we have used different width function [ A − (R)] in the present and previous studies, the life time of the metastable anion still lies within 18-20 fs range which falls under the expected shape resonance life time (10-100 fs) for the anionic 3 -dCMPH molecule. The amplitude of the vibrational wave-function moves towards the right turning point of the E A − (R) right from the beginning in the time evolution plots, thereby justifying an impulse model 36 resonance process and support our similar findings in earlier investigations 32,33 for this system.…”

“…The fragmented products at R C-O = 5.67 a 0 (3.00 Å) of Fig. 3(e) are seen as the highly stable phosphate anion and the nucleoside radical with the extra electron is located on the phosphate group in analogy to that we found in our HF investigation 32 but differ from that of our DFT-B3LYP based investigation 33 where the extra electron was seen over the deoxyribose ring. The electron transfer originates from the base π * to the 3 C-O σ * orbital as proposed in our earlier HF 32 and DFT-B3LYP 33 based studies is once again show comforting confirmation from the present investigation.…”

“…(b) If the LEE attaches to the base below 1 eV, the favorable pathway for transferring the excess charge in the gas phase is exclusively via "charge induced dissociation" which resembles a S N 2 type process 26,32,33 and the time taken for such a process is found to be within 18-20 fs. (c) If the LEE attaches to the base above 1 eV, i.e., at higher vibrational levels, the prominent decay channel follows quantum mechanical tunneling which may have a substantial role during DNA damage.…”

“…5(a), we have plotted the auto-correlation function χ 0 (R)|ψ 0 (R, t) obtained from present and previous 32 Fig. 5(b) along with those calculated from HF, 32 DFT-B3LYP 33 methods, and experimental result. 22 The calculated σ 0←0 (E) fragmentation profile of Fig.…”

“…In our recent attempts, we have demonstrated single strand breaks in a modeled DNA fragment 3 -dCMPH in gas phase from the ab initio Hartree Fock (HF) 32 and later the correlated density functional theory (DFT) -Becke, 3-parameter, Lee-Yang-Parr (B3LYP) methods 33 and local complex potential based time dependent wave packet (LCP-TDWP) approach. The starting point for our time dependent calculations (TDCs) was the neutral and anionic potential energy (PE) curves of the 3 -dCMPH moiety and the decay function resulting from the electron attachment to the target (3 -dCMPH) molecule.…”