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, $$\hbox {Pym}^{+}$$ 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

Microhydration of the Pyrrole Cation (Py+) Revealed by IR Spectroscopy: Ionization-Induced Rearrangement of the Hydrogen-Bonded Network of Py+(H2O)2

“…Quantum chemical calculations are carried out at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level to determine the structural, energetic, vibrational, and electronic properties of the investigated clusters . This level has provided reliable results in our previous studies of related microhydrated aromatic cluster ions. ,,− Harmonic vibrational frequencies are scaled by factors of 0.9619 for NH and CH stretching vibrations and 0.9631 for OH stretching vibrations to optimize the agreement with the measured frequencies of bare Py and H 2 O, ν NH = 3531 cm –1 and ν 1/3 = 3657/3756 cm –1 , respectively . Total binding energies ( D 0 ), relative energies ( E 0 ), and dissociation energies of the most-weakly bonded ligand ( E diss ) are corrected for zero-point vibrational energy (ZPE).…”

“…This study is motivated by two aspects. The first one considers the evolution of the hydration network around Py + , in particular the competition between noncooperative interior ion hydration and cooperative formation of a H-bonded solvent network. ,,,,,,− , Noncooperative three-body effects arise in clusters, in which H 2 O molecules successively solvate an interior cation, from increasing delocalization of the positive charge over the whole cluster, leading to reduced electrostatic and inductive forces of the central cation to the individual ligands. On the other hand, cooperative three-body effects are observed in clusters, in which H 2 O molecules successively form a H-bonded solvent network, because the positive charge induces additional multipoles in the nearby ligand (via polarization) which in turn strengthen the H-bonds to further ligands.…”

Measurement of the effect of 5-Fluorouracil as an anticancer drug on the nitric oxide levels on HepG2 cell line

“…It is critical to understand that 5-FU is a pyrimidine antagonist [21]. This distinction indicates any specific natural material with which it interferes: in this case, pyrimidines consider the building blocks of DNA [22]. Moreover, 5-fluorouracil acts as a radiosensitizer, an immunosuppressive agent, and a xenobiotic [23].…”