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 N-7 and N-3 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 N-3 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.