i-Motif DNA in isolated hemiprotonated cytosine dimers, studied using IR spectroscopy and theoretical calculations.

This study provides a comprehensive investigation of the structural and vibrational properties of protonated cytosine monomers and dimers. Experimental IRPD spectroscopy, combined with theoretical calculations, revealed distinct behaviors for monomers and dimers. We find that protonated cytosine monomers predominantly adopt the enol form in the gas phase, with a contribution from the keto form between 25% and 33%. For dimers, our computations predict a keto-enol configuration to be more stable than the keto-keto form by 1.5 kcal mol-1. However, experimentally, the keto-keto form emerged as the dominant structure. The theoretically most stable keto-enol configuration undergoes a structural reorganization in MD simulations with explicit methanol, forming the dynamically unstable neutral-keto-protonated-keto complex. This reorganization highlights the role of environmental factors in modulating tautomer populations.