Influence of the local environment on the intrinsic structures of gas-phase cytidine-5′-monophosphates

Gas-phase conformations of the deprotonated disodium cationized 2′-deoxycytidine-5′-monophosphate and cytidine-5′-monophosphate nucleotides, [pdCyd−H+2Na]⁺ and [pCyd−H+2Na]⁺, are studied by infrared multiple photon dissociation (IRMPD) action spectroscopy. Analysis of the experimental results is assisted by complimentary electronic structure calculations of low-energy conformers at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. These calculations provide relative energetics and predicted IR spectra of the calculated conformers for comparison to the measured IRMPD action spectra in the IR fingerprint and hydrogen-stretching regions. Comparisons between the predicted IR and measured IRMPD spectra provide insight into the conformations accessed by [pdCyd−H+2Na]⁺ and [pCyd−H+2Na]⁺ during the experiments. Comparison of these calculations and spectroscopic analysis with those performed in previous studies for cytidine nucleotides representing those present in different local environments allows for elucidation of the impact of the local environment on the intrinsic structure of these nucleotides. Comparison of these results with similar studies of the cytidine nucleosides also helps reveal the impact of the phosphate moiety on structure. Although several conformers of both [pdCyd−H+2Na]⁺ and [pCyd−H+2Na]⁺ are observed experimentally, a common sodium cation binding mode is observed, highlighting the importance of the stabilization it provides to the cytidine nucleotides.