Crystallographic evidence of Watson–Crick connectivity in the base pair of anionic adenine with thymine

Utilizing an ionic liquid strategy, we report crystal structures of salts of free anionic nucleobases and base pairs previously studied only computationally and in the gas phase. Reaction of tetrabutylammonium ([N(4444)](+)) or tetrabutylphosphonium ([P(4444)](+)) hydroxide with adenine (HAd) and thymine (HThy) led to hydrated salts of deprotonated adenine, [N(4444)][Ad]·2H(2)O, and thymine, [P(4444)][Thy]·2H(2)O, as well as the double salt cocrystal, [P(4444)](2)[Ad][Thy]·3H(2)O·2HThy. The cocrystal includes the anionic [Ad(−)(HThy)] base pair which is a stable formation in the solid state that has previously not even been suggested. It exhibits Watson–Crick connectivity as found in DNA but which is unusual for the free neutral base pairs. The stability of the observed anionic bases and their supramolecular formations and hydrates has also been examined by electronic structure calculations, contributing to more insight into how base pairs can bind when a proton is removed and highlighting mechanisms of stabilization or chemical transformation in the DNA chains.