Hydrogen-Bonding between Pyrimidine and Water:  A Vibrational Spectroscopic Analysis

Abstract

We present an experimental and a theoretical study on hydrogen-bonding between pyrimidine and water as the H-donor. The degree of hydrogen-bonding in this binary system varies with mixture composition. This was monitored experimentally by polarization-resolved linear Raman spectroscopy with the pyrimidine ring breathing mode nu1 as a marker band. A subsequent quantitative line shape analysis of the isotropic Raman intensity for 24 pyrimidine/water mixtures clearly revealed a splitting into three spectral components upon dilution with water. The two additional peaks have been assigned to distinct groups of hydrogen-bonded species that differ in the number of pyrimidine nitrogen atoms (N) involved in hydrogen-bonding to water hydrogen atoms (H). From the integrated Raman intensities for "free" and "hydrogen-bonded" pyrimidine, a concentration profile for these species was established. Our assignments and interpretations are supported by quantum mechanical calculations of structures and by vibrational spectra for pyrimidine and 10 pyrimidine/water complexes with increasing water content. Also, accurate structure-spectra correlations for different cluster subgroups have been determined; within each particular cluster subgroup the water content varies, and a perfect negative correlation between NH hydrogen-bond distances and nu1 wavenumbers was observed.

Effect of pressure on heterocyclic compounds: Pyrimidine and s-triazine

“…32 Considering many nucleic acids, including uracil, cytosine, and thymine are derivatives of pyrimidine ring, pyrimidine can be considered as a prototype representation among N-containing heterocycles. 33 Pyrimidine is a two nitrogencontaining ring (Figure 1(a)), and crystallizes into Pna2 1 space group below 294 K at atmospheric pressure. 34 Several works concerning the vibrational spectra have been conducted.…”

A combined experimental and theoretical approach to the study of hydrogen bond interaction in the binary mixture of N-methylimidazole with water

“…Especially, in respective processes these substances often interact with aqueous media, and their solutions in water exhibit particularly complex structures and often also peculiar behavior. Although different experimental and theoretical investigations have been undertaken for these mixtures [20][21][22][23][24][25][26][27][28][29][30][31][32], it still remains a challenging task to explore their physicochemical properties of aqueous solutions and the nature of interactions between N-heterocyclic molecules with water. To date, except for the work of Dohnal and coworkers [32], no report is available in the literature on the thermodynamic properties of N-methylimidazole (MeIm) used as precursor for the synthesis of ionic liquids in aqueous solutions at different temperatures.…”

Spectroscopic and computational insight into weak noncovalent interactions in crystalline pyrimidine

“…This approach has been successfully used elsewhere to compute small vibrational shifts in pyrimidine induced by complexation with water and produces results remarkably consistent with those from second-order Møller-Plesset perturbation theory (MP2) [5,15].…”