https://doi.org/10.1140/epjd/s10053-021-00065-z
Regular Article - Clusters and Nanostructures
Microhydration of ionized building blocks of DNA/RNA: infrared spectra of pyrimidine
-
clusters
Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623, Berlin, Germany
Received:
28
September
2020
Accepted:
9
December
2020
Published online:
2
March
2021
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, 
-
(W=
), in the size range 
–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 - predicted by the calculations are characterized by H-bonded structures, in which the H-bonded solvent cluster is attached to the most acidic C4–H proton of 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 to , although no proton transfer is observed in the size range 
3. The solvation with protic, dipolar, and hydrophilic W ligands is qualitative different from solvation with aprotic, quadrupolar, and hydrophobic 
ligands, which strongly prefer interior ion solvation by 
stacking interactions. Comparison of -W with Pym-W and 
Pym-W reveals the drastic effect of ionization and protonation on the Pym...W interaction.
Supplementary Information The online version of this article https://doi.org/10.1140/epjd/s10053-021-00065-z.
© The Author(s) 2021
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