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

Abstract

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, $$\hbox {Pym}^{+}$$ Pym + -$$\hbox {W}_{n}$$ W n (W=$$\hbox {H}_{2}\hbox {O}$$ H 2 O ), in the size range $$n=1$$ 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 $$\hbox {Pym}^{+}$$ Pym + -$$\hbox {W}_{n}$$ W n predicted by the calculations are characterized by H-bonded structures, in which the H-bonded $$\hbox {W}_{n}$$ W n solvent cluster is attached to the most acidic C4–H proton of $$\hbox {Pym}^{+}$$ 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 $$\hbox {Pym}^{+}$$ Pym + to $$\hbox {W}_{n}$$ W n , although no proton transfer is observed in the size range $$n\leqslant $$ n ⩽ 3. The solvation with protic, dipolar, and hydrophilic W ligands is qualitative different from solvation with aprotic, quadrupolar, and hydrophobic $$\hbox {N}_{2}$$ N 2 ligands, which strongly prefer interior ion solvation by $$\uppi $$ π stacking interactions. Comparison of $$\hbox {Pym}^{+}$$ Pym + -W with Pym-W and $$\hbox {H}^{+}$$ H + Pym-W reveals the drastic effect of ionization and protonation on the Pym...W interaction. Graphic Abstract