Structure and conformation of 5′-chloro-5′-deoxyarabinosylcytosine: X-ray, 1H and 13C nmr analyses

Abstract

Crystals of 5′-chloroarabinosylcytosine, an inhibitor of nucleic acid synthesis, belong to the orthorhombic space group P212121, and the cell dimensions are a = 6.801(1), b = 9.698(2) and c = 16.497(3) Å. X-ray intensity data were measured on a diffractometer and the structure was determined by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.032 for 1251 observed reflections. The conformation about the glycosyl bond is anti, the furanose ring adopts a C3′ endo/C4′ exo pucker and the conformation of the side chain is gauche+, stabilized by an intramolecular [Formula: see text] hydrogen bond. 1H and 13C nmr spectra confirm the anti conformation about the glycosyl bond. In D2O solution there is an approximately equal population of N- and S-type conformers of the furanose ring and a trans > gauche+ > gauche− distribution of the 5′-CH2Cl side chain rotamers.