Probing the selectivity of theophylline toward cytosine and adenine: Insights from gas-phase complexes and DFT calculations

The high specificity of the interaction between theophylline and its aptamer has long been recognized. Here, we explored whether the observed preference for cytosine over adenine could be related to the respective affinity between these two binding sections, similar to the “Lock PINS” and corresponding “Key Cuts” intheophylline. Gas-phase complexes between theophylline and cytosine (THEOP·C) or adenine (THEOP·A) were generated by supersonic expansion combined with laser ablation, enabling their isolation and allowing the intrinsic binding interactions to be probed without solvent or matrix perturbations. Mass-resolved IR and UV spectroscopy, together with DFT calculations, enabled the identification of two stable conformations for each dimer, stabilized by strong NH···N and NH···OC double hydrogen bonds. For the dimers in the aptamer, despite their similar hydrogen-bonding motifs, theoretical analysis shows that THEOP·C is around 20 kJ/mol more stable than THEOP·A. This highlights that, in addition to other crucial effects, the binding strength between the pairs is also a significant factor contributing to this preference. • Role of strong intermolecular interactions independently of bulk effects. • Assessing ligand–binding pocket stability through binding energy. • Binding strength shown as key factor in aptamer selectivity.