2-({3-[(2R,4S,5R)-4-Hydroxy-5-hydroxymethyl-2,3,4,5-tetrahydrofuran-2-yl]-5-methyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-1-yl}methyl)isoindoline-1,3-dione

The title compound, C19H19N3O7, is a thymidine derivative and serves as an intermediate in the synthesis of a 99mTc radiolabeled nucleoside analog. Intermolecular O—H⋯O hydrogen bonding is observed between the hydroxy functionalities of the ribose unit themselves as well as between a hydroxy group and an O atom of the phthalimide group of an adjacent molecule. The molecules are stacked on top of each other in the direction of the a axis. The crystal packing is further stabilized by weak intra- and intermolecular C—H⋯O hydrogen bonds. The absolute configuration of the compound is known from the synthesis.

The title compound, C 19 H 19 N 3 O 7 , is a thymidine derivative and serves as an intermediate in the synthesis of a 99m Tc radiolabeled nucleoside analog. Intermolecular O-HÁ Á ÁO hydrogen bonding is observed between the hydroxy functionalities of the ribose unit themselves as well as between a hydroxy group and an O atom of the phthalimide group of an adjacent molecule. The molecules are stacked on top of each other in the direction of the a axis. The crystal packing is further stabilized by weak intra-and intermolecular C-HÁ Á ÁO hydrogen bonds. The absolute configuration of the compound is known from the synthesis.

Refinement
All the H atoms were discernible in the difference electron density map. However, with exception of the hydroxyl hydrogens whose coordinates were refined freely they were situated into the idealized positions and refined by the riding model. The applied constraints: C-H aryl = 0.95; C-H methine = 1.00; C-H methylene = 0.99 and C-H methyl = 0.98Å, respectively, and included in the riding-model approximation with U iso (H) = 1.2U eq (C) or 1.5U eq (C/O) for methyl and hydroxyl H atoms.
The Friedel pairs were not merged and the Flack absolute structure parameter converged to an indeterminate value (Flack, 1983) with a large standard uncertainty (0.3 (9)). The absolute structure has been derived by the known structure of the precursors used in the synthesis. Fig. 1. View of the title structure, with the atom numbering scheme and the displacement ellipsoids drawn at 50% probability level.

Special details
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2sigma(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.