Effects of protonation on proton transfer processes in Watson–Crick adenine–thymine base pair

Intermolecular proton transfer processes in the Watson and Crick adenine–thymine neutral and protonated base pairs have been studied using the density functional theory (DFT) with the non-local hybrid B3LYP density functional. Protonated systems subject to study are those resulting from protonation at the main basic sites of the base pair model, namely N₇ and N₃ of adenine and O₂^′ and O₄^′ of thymine. Protonation of adenine induces a strengthening by about 4–5 kcal/mol of the base pair and does not significantly modify the double proton transfer energy profile obtained for the unprotonated system. On the other hand, protonation at the O₄^′ and O₂^′ thymine moiety causes thymine’s N₃ proton to spontaneously transfer to adenine while non-transferred minima disappear at this level of theory. The different behaviour between protonated adenine– thymine and protonated guanine–cytosine is discussed. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Contribution to the Fernando Bernardi Memorial Issue.