The α-d-anomer of 2′-de­oxy­cyti­dine: crystal structure, nucleo­side conformation and Hirshfeld surface analysis

β-2′-De­oxy­ribo­nucleo­sides are the constituents of nucleic acids, whereas their anomeric α-analogues are rarely found in nature. Moreover, not much infor­mation is available on the structural and conformational parameters of α-2′-de­oxy­ribo­nucleo­sides. This study reports on the single-crystal X-ray structure of α-2′-de­oxy­cyti­dine, C(9)H(13)N(3)O(4) (1), and the conformational param­eters characterizing 1 were determined. The conformation at the glycosylic bond is anti, with χ = 173.4 (2)°, and the sugar residue adopts an almost symmetrical C2′-endo-C3′-exo twist ([Image: see text]; S-type), with P = 179.7°. Both values lie outside the conformational range usually preferred by α-nucleo­sides. In addition, the amino group at the nucleobase shows partial double-bond character. This is supported by two separated signals for the amino protons in the (1)H NMR spectrum, indicating a hindered rotation around the C4—N4 bond and a relatively short C—N bond in the solid state. Crystal packing is controlled by N—H⋯O and O—H⋯O contacts between the nucleobase and sugar moieties. Moreover, two weak C—H⋯N contacts (C1′—H1′ and C3′—H3′A) are observed. A Hirshfeld surface analysis was carried out and the results support the inter­molecular inter­actions observed by the X-ray analysis.