Crystal structure of (+)-N-[(1R,5S,6S,9S)-5-hydroxymethyl-3,3,9-trimethyl-8-oxo-2,4,7-trioxabicyclo[4.3.0]nonan-9-yl]acetamide

In the title compound, the 1,3-dioxane ring is in a chair-like conformation, while the fused oxolane ring adopts an envelope form. In the crystal, classical O—H⋯O and N—H⋯O hydrogen bonds link the molecules into a sheet structure.


Chemical context
Sphingofungin F [systematic name: (2S,3R,4R,5S,E)-2amino-3,4,5-trihydroxy-2-methyl-14-oxoicos-6-enoic acid] was isolated from the fermentation broth of Paecilomyces variotii by Horn et al. (1992). It shows antifungal activity by inhibition of the serine palmitoyltransferase to suppress the early step of biosynthesis of the sphingosines (Zweerink et al., 1992). The structure of sphingofungin F features a hydrophilic ,-disubstituted -amino acid moiety possessing four contiguous stereocenters, connected to a hydrophobic carbon chain by E-olefin. The title compound, which is equivalent to the hydrophilic part with correct stereochemistry, was provided in the total synthesis of sphingofungin F (Tsuzaki et al., 2015).

Figure 2
A partial packing diagram, viewed down the b axis, showing the chain structure running along the c axis. Yellow lines indicate the intermolecular O-HÁ Á ÁO hydrogen bonds. Black dashed lines indicate weak intermolecular C-HÁ Á ÁO interactions. Only H atoms involved in the hydrogen bonds are shown for clarity. [Symmetry codes: (i) x, y, z + 1; (iv) x, y, z À 1.]

Figure 4
A packing diagram, viewed down the a axis, showing the hydrogen bonds in the sheet structure parallel to (100 hydrogen bonds enclose an R 4 4 (24) graph-set motif, and the other weak C-HÁ Á ÁO interactions add to the stability of the network (Fig. 4).

Synthesis and crystallization
The title compound was afforded in the total synthesis of sphingofungin F from a d-ribose derivative (Tsuzaki et al., 2015). Purification was carried out by silica gel column chromatography, and colorless crystals were obtained from an ethyl acetate solution under a hexane-saturated atmosphere, by slow evaporation at ambient temperature.

(+)-N-[(1R,5S,6S,9S)-5-Hydroxymethyl-3,3,9-trimethyl-8-oxo-2,4,7-trioxabicyclo[4.3.0]nonan-9-yl]acetamide
Crystal data 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 > 2σ(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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 )
x y z U iso */U eq C1 0.9761 (