Crystal Structure of Methyl 4-Acetamido-4-cyano-4,6-dideoxy-2,3-O-isopropylidene-ß-D-allopyranoside

The detailed structure of methyl


Introduction
With respect to biological and medicinal importance, amino sugars represent a significant group of organic compounds.To understand the mechanism of their biological activity, a lot of suitable synthetically prepared model compounds with well established structure are needed.
Since the crystal and molecular structure determination of 4 by NMR and X-ray methods has already been published [1], we now wish to present the X-ray analysis of acetylated amino nitrile 5.

Structure Elucidation
The title compound 5 was fully characterized by 1 H and 13 C NMR, EIMS, CIMS, [α] D , TLC, mp and elemental analysis data [1].The coupling constants J 1,2 of 6.9 Hz and J 2,3 of 5.2 Hz (in comparison with J 1,2 of 0 Hz and J 2,3 of 6.3 Hz reported for 1 C 4 conformation of 4) suggested an inversion of a 1 C 4 to a 4 C 1 conformation with an equatorial glycosidic methoxyl group and H-3, an axial H-5 and H-2 and favoured 2,3-cis stereochemistry for the isopropylidene group (similar base-catalyzed isomerizations with inversion at C-5 and unchanged configuration at C-3 were observed previously [2,3]) indicating the possibility of either β-D-allo or β-D-gulo configuration.Because the data obtained from NMR measurements were unsufficient, X-ray analysis was used to determine unambiguously correct actual configuration and simultaneously, conformation of the pyranose ring.

X-ray Analysis
The suitable crystals were obtained by slow crystallization from a mixture of ethyl acetate-hexane (1:2, v/v) at room temperature.The relevant crystallographic data and structure refinement are given in Table 1.The bond lengths and bond angles are listed in Table 2.A list of selected torsion angles is given in Table 3.The final positional parameters are summarized in Table 4. Perspective view and the numbering of the atoms is depicted in Figure 2. The hydrogen atoms were refined isotropically in idealized positions riding on the atom to which they are attached.The analysis of ring conformation by calculating puckering parameters [Q = 0.544(4) Å, = 22.9 (5)°, 3 = 326.9(13)°]according to Cremer and Pople [4] has shown that pyranose ring in 5 adopt a 4 C 1 conformation which is slightly distorted into the direction of 0 H 5 [5,6], thus indicating a flattening at C-1 and C-4.

General
The relevant data of synthetic and analytical methods as well as instruments and materials used for the preparation and characterization of the title compound are presented in ref. [1].Analytical sample of 5 was used for generation of suitable crystals.

X-ray Analysis
Crystal and experimental data for compound 5 are given in Table 1.The structure was solved by direct methods and refined by anisotropic full-matrix least-squares technique.The choice of space group and hence the absolute configuration of the compound (1-R, 2-R, 3-R, 4-R, 5-R) was based on the fact that configuration on positions 1, 2, 3 and 5 of pyranose ring is known and could not change.The crystallographic computations were performed with Bruker SHELXTL [8].The ZORTEP program [9] was used for the molecular graphics drawing.
Crystallographic data for the structure reported in this paper have been deposited with the Cambridge Crystallographic Data Centre.The corresponding deposition number is CCDC 140110.Copies of the data can be obtained free of charge on request to The Director, CCDC, 12 Union Road, Cambridge CB2 1EZ, UK (Tel.: +44-1223-336408, Fax: +44-1223 336-033).

Table 3 .
Selected torsion angles [in °] for compound 5 a .a Standard deviations in parentheses.

Table 1 .
Crystal and experimental data for compound 5 a .

Table 2 .
Selected bond lengths [in Å] and bond angles [in °] for compound 5 a .
a Standard deviations in parentheses.