Crystal and Molecular Structure of 3,N⁴-Ethenocytidine Hydrochloride. A Study of the Dimensions and Molecular Interactions of the Fluorescent ε-Cytidine System

The crystal structure of 3,N⁴-ethenocytidine hydrochloride (1, ∊-Cyd-HCl) has been determined to provide the molecular dimensions of this fluorescent analogue of a cytosine nucleoside and to probe its capability for molecular interaction. The crystals of 1 are monoclinic, with a = 6.330 (1), b = 16.968 (2), c = 6.695 (1) Å, and β = 115° 22 (1)′, and there are two C₁₁H₁₄N₃O₅⁺Cl^- entities in the space group P2₁. The structure has been refined to an R factor of 0.045 on 1675 nonzero reflections (Mo Kα). The ∊-cytosine moiety is slightly nonplanar with a maximum deviation of 0.037 Å from the best plane through the ten nonhydrogen atoms; there are some minor differences in bond lengths and angles from those found in protonated unbridged cytosine derivatives. The arrangement about the glycosyl bond is anti (x_C-N = 42.6°) and the ribose ring exists in the C(2′)-endo or the C(2′)-endo-C-(3′)-exo conformation. The C(4′)-C(5′) exocyclic bond is in a gauche-gauche arrangement. There appears to be a C(6)-H(6)-O(5′) intramolecular hydrogen bond. The N-H bond in the base and the three hydroxyl groups in the sugar are involved in an intermolecular hydrogen bonding arrangement in which the chloride anion acts as an acceptor for three hydrogen bonds. Translationally equivalent ∊-cytosine bases crystallize such that a chloride anion lies between them in the plane of the rings in a fashion similar to that observed for other unbridged cytosine salts. This arrangement results in some short H-Cl^- and H-O contacts. This packing also results in another Cl^- lying 3.21 Å above the plane of the ∊-cytosine cation. This latter type of “ion pair” interaction is quite common in anhydrous halide salts of nucleic acid bases and nucleosides. There is no base-base overlap.