1-(1-Carboxymethyl-1,4-anhydro-2,3-O-isopropylidene-α-d-erythrofuranosyl)thymine

X-Ray crystallography unequivocally determined the stereochemistry of the thymine base in the title compound, C14H18N2O7. The absolute stereochemistry was determined from the use of d-ribose as the starting material. There are two independent molecules in the asymmetric unit (Z′ = 2) which exist as N—H⋯O hydrogen-bonded pairs in the crystal structure.

X-Ray crystallography unequivocally determined the stereochemistry of the thymine base in the title compound, C 14 H 18 N 2 O 7 . The absolute stereochemistry was determined from the use of d-ribose as the starting material. There are two independent molecules in the asymmetric unit (Z 0 = 2) which exist as N-HÁ Á ÁO hydrogen-bonded pairs in the crystal structure.

Comment
Nucleosides are a powerful class of anti-viral and anti-bacterial agents. Psicofuranine 1 (Fig. 1) is a naturally occurring nucleoside with a branch at the anomeric position of the sugar (Schroeder & Hoeksema, 1959). It has potent anti-bacterial and anti-tumour activity but is cardiotoxic in man (Smith et al., 1973). Psicofuranine is also unstable in acidic and basic conditions with the N-glycosidic bond readily undergoing hydrolytic cleavage (Garrett, 1960). During studies on the synthesis of the 5-carbon analogue of psicofuranine 2 the ester 4 was synthesized. Anomeric radical bromination (Smith et al., 1999) gave rise to a single isolable bromide 5 (Probert et al., 2005) which on displacement with silylated thymine gave a single nucleoside product. The stereochemistry at the anomeric position of the sugar was firmly established by X-ray crystallography and the structure was confirmed as 6 in which the thymine is in the α rather than the desired β position.
There are two crystallographically distinct molecules in the asymmetric unit which are related by a pseudo 2-fold rotation axis (Fig 2). When the two molecules are mapped they show good overlap ( Fig. 3) with RMS deviations of 0.1055 on the positions, 0.082 for the bonds and 3.8892 for the torsion angles. These two molecules form hydrogen bonded pairs in the crystal structure (Fig. 4, Fig. 5). In both cases the central nitrogen (N3, N26) between the two carbonyls of the thymine acts as the donor but hydrogen bonds are formed to different carbonyls of the two thymine rings. The absolute stereochemistry was determined from the use of D-ribose as the starting material. Only classical hydrogen bonding was considered.

Refinement
In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from the use of D-ribose as the starting material.
The H atoms were all located in a difference map, but those attached to carbon atoms were repositioned geometrically.
The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (