5-Fluorocytosine/Isocytosine Monohydrate. The First Example of Isomorphic and Isostructural Co-Crystal of Pyrimidine Nucleobases

Abstract

To date, despite the crucial role played by cytosine, uracil, and thymine in the DNA/RNA replication process, no examples showing isomorphic and isostructural behavior among binary co-crystals of natural or modified pyrimidine nucleobases have been so far reported in the literature. In view of the relevance of biochemical and pharmaceutical compounds such as pyrimidine nucleobases and their 5-fluoroderivatives, co-crystals of the molecular complex formed by 5-fluorocytosine and isocytosine monohydrate, C4H4FN3O·C4H5N3O·H2O, have been synthesized by a reaction between 5-fluorocytosine and isocytosine. They represent the first example of isomorphic and isostructural binary co-crystals of pyrimidine nucleobases, as X-ray diffraction analysis shows structural similarities in the solid-state organization of molecules with that of the (1:1) 5-fluorocytosine/5-fluoroisocytosine monohydrate molecular complex, which differs solely in the H/F substitution at the C5 position of isocytosine. Molecules of 5-fluorocytosine and isocytosine are present in the crystal as 1H and 3H-ketoamino tautomers, respectively. They form almost coplanar WC base pairs through nucleobase-to-nucleobase DAA/ADD hydrogen bonding interactions, demonstrating that complementary binding enables the crystallization of specific tautomers. Additional peripheral hydrogen bonds involving all available H atom donor and acceptor sites of the water molecule give a three-dimensional polymeric structure. In the absence of H⋯F hydrogen-bonding interactions, the robustness of the supramolecular architectures based on three-point recognition synthons is responsible for the existence of isostructurality between the two molecular complexes.

Keywords

• nucleobases
• 5-halonucleobases
• cytosine
• 5-fluorocytosine
• base pairs
• hydrogen bond