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Acta Crystallogr Sect E Struct Rep Online. 2010 October 1; 66(Pt 10): o2561.
Published online 2010 September 15. doi:  10.1107/S1600536810036238
PMCID: PMC2983228

6-Methyl-2-pyridyl N-acetyl-1-thio-β-d-glucosa­minide methanol monosolvate

Abstract

In the title compound, C14H20N2O5S·CH4O, the pyran­ose and pyridine rings are linked through an S atom. The pyran­ose ring has a normal chair conformation. An intra­molecular O—H(...)N hydrogen bond occurs. Inter­molecular O—H(...)O, N—H(...)O, O—H(...)N and weak C—H(...)O hydrogen bonding is present in the crystal structure.

Related literature

For applications of glucopyran­osides, see: Ashry et al. (2006 [triangle]). For the structure of an α-d-glucosa­minide, see: Harrison et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2561-scheme1.jpg

Experimental

Crystal data

  • C14H20N2O5S·CH4O
  • M r = 360.42
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2561-efi1.jpg
  • a = 7.3841 (15) Å
  • b = 14.041 (3) Å
  • c = 17.038 (4) Å
  • V = 1766.5 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.22 mm−1
  • T = 296 K
  • 0.51 × 0.27 × 0.2 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.932, T max = 0.950
  • 12687 measured reflections
  • 3173 independent reflections
  • 2997 reflections with I > 2σ(I)
  • R int = 0.161

Refinement

  • R[F 2 > 2σ(F 2)] = 0.066
  • wR(F 2) = 0.170
  • S = 1.05
  • 3173 reflections
  • 222 parameters
  • H-atom parameters constrained
  • Δρmax = 0.56 e Å−3
  • Δρmin = −0.70 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1334 Fiedel pairs
  • Flack parameter: 0.01 (12)

Data collection: SMART (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810036238/xu5024sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810036238/xu5024Isup2.hkl

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

Acknowledgments

This project was sponsored by the Cultivation Program of Young and Middle-aged Academic Leaders in Zhejiang Higher Education Institutions, the Natural Science Foundation of Ningbo City (Nos. 2009 A610047 and 2010 A610027) and the K. C. Wong Magna Fund of Ningbo University. We thank Professor X. Li for help with the structural analysis.

supplementary crystallographic information

Comment

Thioglycosides are widely employed as biological inhibitors, glycosyl donors and enzyme resistant ligands for affinity chromatography (Ashry et al., 2006). Here we report the crystal structure of the title compound (Scheme 1). The title compound crystallizes exclusively as the β anomer. The molecule contains a pyranose ring and a pyridine ring linked by a sulfur atom. The pyranose ring has a normal chair conformation, similar to that found in an α-D-glucosaminide (Harrison et al. 2007). The extensive hydrogen bonding network is present in the crystal structure, involving O—H···O, O—H···N and N—H···O hydrogen bonding (Table 1). Weak intermolecular C—H···O hydrogen bonding is also present in the crystal structure.

Experimental

6'-Methyl-2'-pyridyl-2,3,4,6-tetraacetyl-1-thio-β-D-glucosaminide (1.5 g, 3.3 mmol) was dissolved in MeOH (10 ml) and one equivalent MeONa was added. The process of deacetylation was monitored by 1H NMR. After removal of the solvent, the solid residue was washed with ethanol and ether, and then crystallized from H2O/MeOH to give the title compound (0.23 g) as colorless crystals.

Refinement

H atoms were placed in calculated positions and treated using a riding-model, C–H = 0.93–0.98 Å with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(C), N–H = 0.86 with Uiso(H) = 1.2Ueq(N), O—H = 0.82 Å with Uiso(H) = 1.5Ueq(O).

Figures

Fig. 1.
A view of (I) showing the labeling of the non-H atoms and 50% probability ellipsoids. Dashed line indicates the hydrogen bonding.

Crystal data

C14H20N2O5S·CH4OF(000) = 768
Mr = 360.42Dx = 1.355 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 12040 reflections
a = 7.3841 (15) Åθ = 1.9–24.5°
b = 14.041 (3) ŵ = 0.22 mm1
c = 17.038 (4) ÅT = 296 K
V = 1766.5 (6) Å3Block, colourless
Z = 40.51 × 0.27 × 0.2 mm

Data collection

Bruker SMART CCD area-detector diffractometer3173 independent reflections
Radiation source: fine-focus sealed tube2997 reflections with I > 2σ(I)
graphiteRint = 0.161
Detector resolution: 0 pixels mm-1θmax = 25.2°, θmin = 1.9°
[var phi] and ω scansh = −8→8
Absorption correction: multi-scan (SADABS; Bruker, 2001)k = −16→16
Tmin = 0.932, Tmax = 0.950l = −20→20
12687 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.066H-atom parameters constrained
wR(F2) = 0.170w = 1/[σ2(Fo2) + (0.1077P)2 + 0.760P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.003
3173 reflectionsΔρmax = 0.56 e Å3
222 parametersΔρmin = −0.70 e Å3
0 restraintsAbsolute structure: Flack (1983), 1334 Fiedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.01 (12)

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 F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 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 (Å2)

xyzUiso*/Ueq
S10.80502 (12)0.14422 (6)0.34312 (4)0.0246 (2)
O10.6461 (3)0.24215 (17)0.23124 (11)0.0209 (5)
O20.3258 (3)0.26631 (17)0.13049 (12)0.0238 (5)
H2A0.30870.26600.08290.036*
O30.7290 (3)0.28865 (18)0.02141 (12)0.0243 (5)
H3A0.63760.32040.01350.036*
O40.9501 (3)0.12909 (17)0.04864 (13)0.0237 (5)
H4A0.86950.09060.03920.036*
O51.0621 (4)−0.03011 (17)0.24234 (16)0.0327 (6)
O60.8051 (4)−0.00609 (19)0.51072 (18)0.0449 (8)
H60.79820.05170.50480.067*
N11.0936 (4)0.1246 (2)0.20602 (15)0.0221 (6)
H1A1.16890.17110.20240.027*
N20.8034 (4)0.1914 (2)0.49004 (14)0.0232 (6)
C10.8218 (5)0.2112 (2)0.25267 (16)0.0205 (6)
H1B0.90100.26650.26040.025*
C20.9047 (4)0.1441 (2)0.19007 (17)0.0191 (6)
H2C0.83690.08410.18910.023*
C30.8913 (4)0.1928 (2)0.10900 (16)0.0179 (6)
H3B0.97730.24600.10960.021*
C40.7073 (4)0.2349 (2)0.09201 (15)0.0186 (6)
H4B0.61900.18370.08370.022*
C50.6461 (4)0.2985 (2)0.15999 (16)0.0189 (6)
H5A0.73110.35160.16580.023*
C60.4550 (4)0.3376 (2)0.14950 (17)0.0211 (7)
H6A0.41810.36900.19760.025*
H6B0.45620.38500.10810.025*
C70.8079 (5)0.2318 (2)0.41830 (17)0.0220 (7)
C80.8187 (5)0.3293 (2)0.40626 (18)0.0272 (7)
H8A0.81970.35490.35590.033*
C90.8281 (6)0.3875 (3)0.4726 (2)0.0360 (9)
H9A0.83830.45320.46710.043*
C100.8221 (5)0.3470 (3)0.5465 (2)0.0343 (8)
H10A0.82650.38530.59100.041*
C110.8095 (5)0.2491 (3)0.55384 (17)0.0268 (7)
C120.8040 (6)0.2002 (3)0.63295 (18)0.0342 (8)
H12A0.79560.13260.62550.051*
H12B0.70050.22210.66190.051*
H12C0.91230.21490.66160.051*
C131.1595 (5)0.0380 (2)0.22624 (18)0.0258 (8)
C141.3633 (5)0.0325 (3)0.2284 (2)0.0370 (9)
H14A1.3997−0.03070.24310.055*
H14B1.40890.07730.26610.055*
H14C1.41110.04730.17750.055*
C150.9488 (6)−0.0426 (3)0.4639 (3)0.0419 (10)
H15A1.03110.00800.45110.063*
H15B0.9002−0.06910.41640.063*
H15C1.0120−0.09120.49250.063*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0396 (5)0.0254 (4)0.0087 (4)−0.0002 (4)−0.0009 (3)0.0015 (3)
O10.0240 (12)0.0320 (12)0.0068 (9)0.0013 (9)0.0010 (8)0.0021 (9)
O20.0240 (11)0.0350 (12)0.0124 (10)−0.0047 (10)−0.0019 (9)0.0012 (9)
O30.0243 (12)0.0387 (14)0.0100 (10)0.0057 (11)0.0008 (8)0.0050 (9)
O40.0247 (11)0.0313 (12)0.0150 (10)0.0001 (10)0.0048 (9)−0.0054 (9)
O50.0398 (15)0.0250 (13)0.0333 (14)0.0013 (11)0.0009 (12)0.0023 (11)
O60.0568 (19)0.0269 (13)0.0509 (17)0.0004 (15)0.0235 (16)0.0076 (12)
N10.0221 (14)0.0258 (14)0.0184 (13)−0.0009 (11)−0.0029 (11)0.0024 (11)
N20.0258 (14)0.0322 (15)0.0117 (12)0.0010 (13)−0.0009 (11)0.0008 (10)
C10.0252 (15)0.0290 (16)0.0073 (12)0.0010 (14)0.0000 (12)−0.0004 (12)
C20.0237 (15)0.0215 (15)0.0120 (13)−0.0002 (13)0.0007 (11)0.0014 (12)
C30.0224 (15)0.0246 (16)0.0068 (13)−0.0012 (12)0.0020 (12)−0.0024 (12)
C40.0223 (16)0.0270 (16)0.0064 (13)−0.0029 (13)0.0026 (11)−0.0002 (11)
C50.0271 (16)0.0219 (14)0.0078 (13)−0.0031 (13)0.0002 (11)0.0009 (12)
C60.0238 (16)0.0288 (16)0.0107 (13)−0.0020 (13)−0.0010 (12)−0.0013 (12)
C70.0218 (15)0.0331 (17)0.0111 (13)0.0014 (15)0.0003 (12)−0.0026 (12)
C80.0349 (18)0.0301 (17)0.0167 (15)0.0039 (15)0.0015 (15)0.0009 (12)
C90.045 (2)0.0299 (18)0.0335 (19)0.0033 (17)0.0035 (18)−0.0029 (15)
C100.0397 (19)0.041 (2)0.0221 (16)0.0042 (18)0.0008 (16)−0.0115 (15)
C110.0231 (15)0.045 (2)0.0124 (14)0.0043 (15)−0.0010 (13)−0.0036 (14)
C120.042 (2)0.052 (2)0.0090 (14)0.0022 (19)−0.0021 (15)−0.0020 (14)
C130.039 (2)0.0228 (16)0.0155 (14)0.0028 (15)−0.0014 (14)−0.0017 (12)
C140.036 (2)0.034 (2)0.041 (2)0.0059 (16)−0.0039 (17)0.0026 (16)
C150.035 (2)0.037 (2)0.054 (3)0.0018 (18)0.009 (2)0.0094 (19)

Geometric parameters (Å, °)

S1—C71.776 (3)C4—C51.531 (4)
S1—C11.810 (3)C4—H4B0.9800
O1—C11.416 (4)C5—C61.524 (4)
O1—C51.449 (3)C5—H5A0.9800
O2—C61.420 (4)C6—H6A0.9700
O2—H2A0.8200C6—H6B0.9700
O3—C41.429 (3)C7—C81.386 (5)
O3—H3A0.8200C8—C91.397 (5)
O4—C31.431 (4)C8—H8A0.9300
O4—H4A0.8200C9—C101.382 (5)
O5—C131.227 (4)C9—H9A0.9300
O6—C151.423 (5)C10—C111.383 (5)
O6—H60.8200C10—H10A0.9300
N1—C131.355 (4)C11—C121.513 (4)
N1—C21.447 (4)C12—H12A0.9600
N1—H1A0.8600C12—H12B0.9600
N2—C71.348 (4)C12—H12C0.9600
N2—C111.357 (4)C13—C141.507 (6)
C1—C21.550 (4)C14—H14A0.9600
C1—H1B0.9800C14—H14B0.9600
C2—C31.545 (4)C14—H14C0.9600
C2—H2C0.9800C15—H15A0.9600
C3—C41.510 (5)C15—H15B0.9600
C3—H3B0.9800C15—H15C0.9600
C7—S1—C1104.68 (15)O2—C6—H6A108.9
C1—O1—C5112.5 (2)C5—C6—H6A108.9
C6—O2—H2A109.5O2—C6—H6B108.9
C4—O3—H3A109.5C5—C6—H6B108.9
C3—O4—H4A109.5H6A—C6—H6B107.7
C15—O6—H6109.5N2—C7—C8123.4 (3)
C13—N1—C2124.3 (3)N2—C7—S1111.3 (2)
C13—N1—H1A117.9C8—C7—S1125.3 (2)
C2—N1—H1A117.9C7—C8—C9117.5 (3)
C7—N2—C11118.3 (3)C7—C8—H8A121.3
O1—C1—C2111.8 (2)C9—C8—H8A121.3
O1—C1—S1108.4 (2)C10—C9—C8119.6 (3)
C2—C1—S1107.3 (2)C10—C9—H9A120.2
O1—C1—H1B109.8C8—C9—H9A120.2
C2—C1—H1B109.8C9—C10—C11119.5 (3)
S1—C1—H1B109.8C9—C10—H10A120.2
N1—C2—C3108.2 (2)C11—C10—H10A120.2
N1—C2—C1111.5 (3)N2—C11—C10121.6 (3)
C3—C2—C1108.7 (2)N2—C11—C12116.2 (3)
N1—C2—H2C109.5C10—C11—C12122.2 (3)
C3—C2—H2C109.5C11—C12—H12A109.5
C1—C2—H2C109.5C11—C12—H12B109.5
O4—C3—C4112.3 (2)H12A—C12—H12B109.5
O4—C3—C2110.2 (2)C11—C12—H12C109.5
C4—C3—C2113.7 (2)H12A—C12—H12C109.5
O4—C3—H3B106.7H12B—C12—H12C109.5
C4—C3—H3B106.7O5—C13—N1123.1 (3)
C2—C3—H3B106.7O5—C13—C14122.6 (3)
O3—C4—C3105.5 (2)N1—C13—C14114.3 (3)
O3—C4—C5111.2 (2)C13—C14—H14A109.5
C3—C4—C5110.4 (2)C13—C14—H14B109.5
O3—C4—H4B109.9H14A—C14—H14B109.5
C3—C4—H4B109.9C13—C14—H14C109.5
C5—C4—H4B109.9H14A—C14—H14C109.5
O1—C5—C6107.1 (2)H14B—C14—H14C109.5
O1—C5—C4108.3 (2)O6—C15—H15A109.5
C6—C5—C4113.2 (3)O6—C15—H15B109.5
O1—C5—H5A109.3H15A—C15—H15B109.5
C6—C5—H5A109.3O6—C15—H15C109.5
C4—C5—H5A109.3H15A—C15—H15C109.5
O2—C6—C5113.3 (3)H15B—C15—H15C109.5

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···O2i0.862.152.925 (4)149
O2—H2A···O3ii0.822.022.794 (3)156
O3—H3A···O4ii0.821.882.646 (3)155
O4—H4A···O6iii0.821.822.637 (4)176
O6—H6···N20.821.982.795 (4)175
C8—H8A···O5iv0.932.483.329 (4)151
C12—H12C···O1v0.962.583.520 (4)165
C15—H15C···O3vi0.962.563.367 (5)142

Symmetry codes: (i) x+1, y, z; (ii) x−1/2, −y+1/2, −z; (iii) −x+3/2, −y, z−1/2; (iv) −x+2, y+1/2, −z+1/2; (v) x+1/2, −y+1/2, −z+1; (vi) −x+2, y−1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU5024).

References

  • Ashry, E. S. H., Awad, L. F. & Atta, A. I. (2006). Tetrahedron, 62, 2943–2998.
  • Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2007). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Harrison, W. T. A., Yathirajan, H. S., Narayana, B., Sreevidya, T. V. & Sarojini, B. K. (2007). Acta Cryst. E63, o3248.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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