Ethyl 4,6-O-benzyl­idene-2-de­oxy-N-phthalimido-1-thio-β-d-glucopyran­oside

Christoffer Hamark; Jens Landström; Lars Eriksson; Göran Widmalm

doi:10.1107/S1600536810047070

. 2010 Nov 20;66(Pt 12):o3249. doi: 10.1107/S1600536810047070

Ethyl 4,6-O-benzylidene-2-deoxy-N-phthalimido-1-thio-β-d-glucopyranoside

Christoffer Hamark ^a, Jens Landström ^a, Lars Eriksson ^b,^*, Göran Widmalm ^a

PMCID: PMC3011798 PMID: 21589535

Abstract

In the title compound, C₂₃H₂₃NO₆S, the plane of the N-phthalimido group makes a dihedral angle of 67.4 (1)° with the least square plane of the sugar ring defined by the C2, C3, C5 and O5 atoms using standard glucose nomenclature. The thioethyl group has the exo-anomeric conformation. In the crystal, intermolecular hydrogen bonds involving the hydroxy groups and the carbonyl O atoms of adjacent N-phthalimido groups form chains parallel to the b axis. The chains are further stabilized by C—H⋯π interactions.

Related literature

For the chemistry and applications of N-acetyl-β-d-glucosamine derivatives, see: Tan et al. (2009 ▶); Werz et al. (2007 ▶). For the conformation of related compounds, see: Lemieux & Koto (1974 ▶); Färnbäck et al. (2007 ▶). For the synthesis of the title compound, see: Lönn (1985 ▶). For puckering parameters, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C₂₃H₂₃NO₆S
M _r = 441.48
Orthorhombic,
a = 8.6728 (6) Å
b = 9.7583 (10) Å
c = 25.3102 (15) Å
V = 2142.0 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.19 mm⁻¹
T = 293 K
0.30 × 0.12 × 0.05 mm

Data collection

Stoe IPDS diffractometer
Absorption correction: numerical (X-RED; Stoe & Cie, 1997) ▶ T _min = 0.730, T _max = 0.933
12985 measured reflections
5120 independent reflections
2352 reflections with I > 2σ(I)
R _int = 0.110

Refinement

R[F ² > 2σ(F ²)] = 0.036
wR(F ²) = 0.110
S = 0.83
5120 reflections
281 parameters
H-atom parameters constrained
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.27 e Å⁻³
Absolute structure: Flack (1983 ▶), 1544 Friedel pairs
Flack parameter: −0.07 (10)

Data collection: EXPOSE (Stoe & Cie, 1997) ▶; cell refinement: CELL (Stoe & Cie, 1997) ▶; data reduction: INTEGRATE (Stoe & Cie, 1997) ▶; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 1999 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810047070/rz2504sup1.cif

e-66-o3249-sup1.cif^{(23.5KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810047070/rz2504Isup2.hkl

e-66-o3249-Isup2.hkl^{(250.8KB, hkl)}

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

Cg is the centroid of the C23—C28 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H3A⋯O30ⁱ	0.82	2.27	3.014 (3)	150
C14—H14⋯Cgⁱ	0.93	2.98	3.613 (3)	126

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Symmetry code: (i) Inline graphic .

Acknowledgments

This work was supported by a grant from the Swedish Research Council and by the Faculty of Natural Sciences at Stockholm University

supplementary crystallographic information

Comment

N-acetyl-D-glucosamine (D-GlcNAc) is found in nature in bacteria, crustaceans as well as in mammals. In glycoproteins the β-D-GlcNAc is present in N-linked oligosaccharides and it is of great importance to have access to a large arsenal of different suitably protected synthetic precursors in order to carry out synthesis of a variety of different oligosaccharides (Werz et al. 2007). These can be used as probes in microarray applications or to synthesize N-linked glycoproteins (Tan et al. 2009). In the structure shown in Fig. 1 the least square plane of the N-phthaloyl group makes a dihedral angle of 67.4 (1)° to the sugar ring plane defined by the four atoms (C2,C3,C5,O5).

In glycosides the φ torsion angle (H1—C1—S1—C7) is of particular interest and is for the title compound in agreement with the exo-anomeric effect (Lemieux & Koto, 1974). It is, however sligthly shifted away from a staggered conformation, to 25.4°. The Cremer & Pople (1975) parameters for the different rings are for (O5—C5): Q=0.585 (3) Å, θ=8.4 (3)° and φ=329 (2)°, for (O4,C4,C5,C6,O6,C9): Q=0.575 (3) Å, θ=3.4 (3)° and φ=126 (4)°. These Q-values are similar to total puckering amplitudes for previously described pyranosides (Färnbäck et al., 2007).

Intermolecular hydrogen bonding from the hydroxy group is present (Table 1) where one of the carbonyl O atoms in the N-phthaloyl group act as acceptor, making up chains along the [010] direction shown in Fig. 2. In addition to this conventional hydrogen bond the intermolecular packing is stabilized due to interactions between substituents of the sugar rings. There is a salient C—H···π interaction between the center of gravity (Cg) of the ring C23—C28 of the N-phthaloyl group and the meta position (C14) of the phenyl group (C10—C15). Furthermore there are three more π···π interactions present with d(Cg—Cg) < 4.8 Å with dihedral angles between the interacting π systems in the vicinity of 60° indicating a herringbone packing pattern.

Experimental

The synthesis of the title compound has been described previously (Lönn, 1985). Colourless crystals of the title compound were grown from diethyl ether/pentane (1:1 v/v) at ambient temperature.