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
Highlights
The structure, stability, and function of almost all biomolecules are strongly governed by their hydration environment, and without hydration these macromolecules often remain inactive [1]
The infrared photodissociation spectroscopy (IRPD) spectra recorded in the OH and CH stretch range are sensitive to the evolution of the hydration network
We recently reported IR photodissociation (IRPD) spectra of microhydrated structures of protonated Pym, H+Pym-Wn 4 (W=H2O), which confirmed the exclusive N-protonation of neutral Pym and the preference of polar W for forming NH· · · O type linear ionic hydrogen bonds (H-bonds) [43]
Summary
The structure, stability, and function of almost all biomolecules are strongly governed by their hydration environment, and without hydration these macromolecules often remain inactive [1]. The surface water molecules attached to these large biochemical architectures, which are popularly known as biological or interfacial water, are key to their function [2,3,4,5,6,7,8,9,10]. Such surface water molecules actively participate in charge transport [3,8,10,11,12,13,14] and are crucial for recognition of proteins and drugs through balancing enthalpic and entropic contributions to the overall free energy [15,16,17].
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