The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study

Quantum mechanical calculations show that an easily accessible non-radiative deactivation route to the ground electronic state exists for photoexcited cytidine, protonated at acidic pH, also when hydrogen bonded to a “neutral” cytidine, forming the building blocks of DNA adopting an I-motif structure. AbstractWe here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time-dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady-state infrared and absorption spectra of a protonated cytidine (CH+), and predict that an easily accessible non-radiative deactivation route exists for the spectroscopic state, explaining its sub-ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out-of-plane motion of the hydrogen substituents of the CC double bond, the so-called ethylenic conical intersection typical of cytidine and other pyrimidine bases. This deactivation route is operative for the two bases forming an hemiprotonated cytidine base pair, [CH ·C]+, the building blocks of I-motif secondary structures, whereas interbase processes play a minor role. N3 protonation disfavors instead the n π* transitions, associated with t...

Source: Photochemistry and Photobiology - July 7, 2023 Category: Science Authors: Lara Martinez ‐Fernandez, Roberto Improta Tags: SPECIAL ISSUE RESEARCH ARTICLE Source Type: research