Abstract
Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the Nimino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C–Br…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).
Highlights
Natural or chemical modified nucleobases represent an important class of molecules with considerable properties as constituents of DNA and RNA
We report the crystal structure analysis for all the investigated systems accompanied by the computational QTAIMS analysis aimed at quantitatively describe the localized hydrogen bond (HB) and XBs
In addition to X-ray analyses, the topological analysis based on the QM and subsequent QTAIMS calculations have confirmed that all the experimentally identified short-range interactions correspond to bond CP at which interaction energies are sensibly larger, and in some cases much larger, than the thermal energies
Summary
Natural or chemical modified nucleobases represent an important class of molecules with considerable properties as constituents of DNA and RNA. These modified nucleobases are profitable to originate new nucleic acid structures, to identify binding sites, and to broaden the suitability of nucleic acids in the field of diagnostics, therapeutics, biomolecular engineering, and nanotechnology [1,2]. It is not surprising that in the past couple of decades, considerable attention has been attracted by the role played by noncovalent interactions flanking hydrogen bond (HB) and engaging halogen atoms in the molecular recognition and supramolecular assembly of halo (halogen)-modified nucleobases. As the strength of an XB depends on the size and polarizability of the halogen atom, which both increase with the halogen atomic number, F atom rarely forms halogen bonds, and typically Cl, Br, and I atoms are considered in biologically relevant compounds [5]
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