Microhydration of protonated biomolecular building blocks: protonated pyrimidine

Abstract

Protonation and hydration of biomolecules govern their structure, conformation, and function. Herein, we explore the microhydration structure in mass-selected protonated pyrimidine–water clusters (H⁺Pym–W_n, n = 1–4) by a combination of infrared photodissociation spectroscopy (IRPD) between 2450 and 3900 cm⁻¹ and density functional theory (DFT) calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level. We further present the IR spectrum of H⁺Pym–N₂ to evaluate the effect of solvent polarity on the intrinsic molecular parameters of H⁺Pym. Our combined spectroscopic and computational approach unequivocally shows that protonation of Pym occurs at one of the two equivalent basic ring N atoms and that the ligands in H⁺Pym–L (L = N₂ or W) preferentially form linear H-bonds to the resulting acidic NH group. Successive addition of water ligands results in the formation of a H-bonded solvent network which increasingly weakens the NH group. Despite substantial activation of the N–H bond upon microhydration, no intracluster proton transfer occurs up to n = 4 because of the balance of relative proton affinities of Pym and W_n and the involved solvation energies. Comparison to neutral Pym–W_n clusters reveals the drastic effects of protonation on microhydration with respect to both structure and interaction strength.