Microhydration of ionized building blocks of DNA/RNA: infrared spectra of pyrimidine^{+}-(hbox {H}_{2}hbox {O})_{text {1-3}} clusters

Abstract

Hydration of biomolecules is an important physiological process that governs their structure, stability, and function. Herein, we probe the microhydration structure of cationic pyrimidine (Pym), a common building block of DNA/RNA bases, by infrared photodissociation spectroscopy (IRPD) of mass-selected microhydrated clusters, hbox {Pym}^{+}-hbox {W}_{n} (W=hbox {H}_{2}hbox {O}), in the size range n=1–3. The IRPD spectra recorded in the OH and CH stretch range are sensitive to the evolution of the hydration network. Analysis with density functional theory calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level provides a consistent picture of the most stable structures and their energetic and vibrational properties. The global minima of hbox {Pym}^{+}-hbox {W}_{n} predicted by the calculations are characterized by H-bonded structures, in which the H-bonded hbox {W}_{n} solvent cluster is attached to the most acidic C4–H proton of hbox {Pym}^{+} via a single CH...O ionic H-bond. These isomers are identified as predominant carrier of the IRPD spectra, although less stable local minima provide minor contributions. In general, the formation of the H-bonded solvent network (exterior ion solvation) is energetically preferred to less stable structures with interior ion solvation because of cooperative nonadditive three-body polarization effects. Progressive hydration activates the C4–H bond, along with increasing charge transfer from hbox {Pym}^{+} to hbox {W}_{n}, although no proton transfer is observed in the size range nleqslant 3. The solvation with protic, dipolar, and hydrophilic W ligands is qualitative different from solvation with aprotic, quadrupolar, and hydrophobic hbox {N}_{2} ligands, which strongly prefer interior ion solvation by uppi stacking interactions. Comparison of hbox {Pym}^{+}-W with Pym-W and hbox {H}^{+}Pym-W reveals the drastic effect of ionization and protonation on the Pym...W interaction.Graphic