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

Abstract

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 O 2 ′ and O 4 ′ 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 O 4 ′ and O 2 ′ 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.