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Acta Crystallogr Sect E Struct Rep Online. 2009 February 1; 65(Pt 2): o242.
Published online 2009 January 8. doi:  10.1107/S1600536808043833
PMCID: PMC2968307

1-(2,3,4,6-Tetra-O-acetyl-β-d-gluco­pyranos­yl)-3-thio­ureidothio­urea monohydrate

Abstract

In the title compound, C16H24N4O9S2·H2O, the hexopyranosyl ring adopts a chair conformation (4 C 1), and the five substituents are in equatorial positions. In the crystal structure, extensive O—H(...)O, N—H(...)S and N—H(...)O hydrogen bonding leads to the formation of a three-dimensional network.

Related literature

For cyclo­addition and nucleophilic addition, see: Pearson et al. (2003 [triangle]); Reitz et al. (1989 [triangle]). For the crystal structure of glycosyl isothio­syanate, see: Jiang et al. (2003 [triangle]). For the crystal structures of glycosyl isothio­syanate methanol and ethanol derivatives, see: Zhang et al. (2001 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0o242-scheme1.jpg

Experimental

Crystal data

  • C16H24N4O9S2·H2O
  • M r = 498.53
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o242-efi1.jpg
  • a = 22.286 (2) Å
  • b = 7.2005 (7) Å
  • c = 15.8772 (17) Å
  • β = 110.119 (2)°
  • V = 2392.3 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.28 mm−1
  • T = 293 (2) K
  • 0.45 × 0.22 × 0.22 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: none
  • 6322 measured reflections
  • 3525 independent reflections
  • 3021 reflections with I > 2σ(I)
  • R int = 0.036

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.141
  • S = 1.07
  • 3525 reflections
  • 289 parameters
  • 7 restraints
  • H-atom parameters constrained
  • Δρmax = 0.42 e Å−3
  • Δρmin = −0.27 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1229 Friedel pairs
  • Flack parameter: −0.16 (12)

Data collection: SMART (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808043833/su2088sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808043833/su2088Isup2.hkl

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

Acknowledgments

The project was supported by the National Natural Science Foundation of China (No. 30701041) and the Scientific Research Project of Inner Mongolia Autonomous Region Colleges and Universities (No. NJZY08149).

supplementary crystallographic information

Comment

Over the past decade, many organic chemists have been engaged in the synthesis of glycosyl isothiosyanates and its derivatives. These compound are versatile reagents in organic synthesis and easily undergo many important reactions, such as cycloaddition (Pearson et al., 2003) and nucleophilic addition (Reitz et al., 1989). Recently, the crystal structures of glycosyl isothiosyanate (Jiang et al., 2003) and the methanol and ethanol derivatives (Zhang et al., 2001) have been reported. However, other derivatives of glycosyl isothiosyanate are still rare. Here we report on the synthesis of a new thiosemicarbazide derivative of glycosyl isothiosyanate, 2,3,4,6-tetra-O-acetyl- β-D-glucopyranosyl dithiourea, (I).

The molecular structure of compound (I) is illustrated in Fig. 1. The hexopyranosyl ring adopts a chair conformation (4C1), and the four substituents are in equatorial positions.

In the crystal extensive O—H···O, N—H···S and N—H···O hydrogen bonding (Table 1) leads to the formation of a three-dimensional network.

Experimental

Compound (I) was prepared by refluxing together equimolar amounts of β-D-2,3,4,6-tetra-O- acetyl-glucopyranosyl isothiocyanate and thiosemicarbazide. After cooling to room temperature, water was added to the mixture and compound (I) was isolated as a white solid. Crystals, suitable for X-ray analysis, were grown from an ethyl acetate and acetonitrile (1:1 / v:v) solution by slow evaporation at room temperature.

Refinement

The compound has a known chiral center [the Flack parameter is -0.16 (12) (Flack, 1983)], and for this reason the Friedel pairs were not merged. The water H-atoms were located in the difference Fourier maps and refined with distance restraintes, O-H = 0.87 (2) Å. The N- and C-bound H-atoms were placed in calculated positions and treated as riding atoms: N—H = 0.86 Å, C—H = 0.96 - 0.98 Å, with Uiso(H) = 1.2 or 1.5Ueq(parent N- or C-atom).

Figures

Fig. 1.
A view of the molecular structure of compound (I), showing the atom-labelling scheme and displacement ellipsoids drawn at the 50% probability level.

Crystal data

C16H24N4O9S2·H2OF(000) = 1048
Mr = 498.53Dx = 1.384 Mg m3
Monoclinic, C2Melting point: not measured K
Hall symbol: C 2yMo Kα radiation, λ = 0.71073 Å
a = 22.286 (2) ÅCell parameters from 7141 reflections
b = 7.2005 (7) Åθ = 1.4–27.7°
c = 15.8772 (17) ŵ = 0.28 mm1
β = 110.119 (2)°T = 293 K
V = 2392.3 (4) Å3Block, colorless
Z = 40.45 × 0.22 × 0.22 mm

Data collection

Bruker SMART CCD area-detector diffractometer3021 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.036
graphiteθmax = 25.0°, θmin = 1.4°
[var phi] scans, and ω scansh = −25→26
6322 measured reflectionsk = −8→8
3525 independent reflectionsl = −18→11

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.055H-atom parameters constrained
wR(F2) = 0.141w = 1/[σ2(Fo2) + (0.0808P)2] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
3525 reflectionsΔρmax = 0.42 e Å3
289 parametersΔρmin = −0.27 e Å3
7 restraintsAbsolute structure: Flack (1983), 1229 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: −0.16 (12)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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
O1W0.0457 (4)0.2431 (10)0.3624 (6)0.193 (3)
H100.06960.20680.33240.232*
H200.00810.19890.33260.232*
S11.01347 (6)0.9344 (2)0.17559 (9)0.0605 (4)
S21.09337 (7)0.5527 (2)0.56716 (9)0.0720 (5)
O10.87014 (12)0.9697 (4)0.28332 (19)0.0433 (7)
O20.79211 (13)1.1140 (5)0.37749 (19)0.0493 (8)
O30.69458 (16)1.2284 (7)0.3502 (3)0.0796 (12)
O40.69663 (12)0.9277 (5)0.18084 (19)0.0467 (7)
O50.67103 (18)0.7887 (8)0.2901 (3)0.0880 (14)
O60.73828 (13)0.5785 (4)0.14481 (18)0.0455 (7)
O70.71021 (18)0.5906 (6)−0.0050 (2)0.0732 (11)
O80.86480 (13)0.5944 (4)0.12682 (18)0.0464 (7)
O90.9131 (2)0.3601 (6)0.2159 (3)0.0902 (14)
N10.95480 (15)0.7892 (5)0.2819 (2)0.0427 (9)
H1A0.95810.72390.32870.051*
N21.06247 (16)0.7629 (6)0.3289 (2)0.0490 (10)
H2A1.09870.79610.32560.059*
N31.06233 (17)0.6483 (6)0.3986 (2)0.0496 (10)
H3A1.05100.53420.38740.060*
N41.0852 (2)0.8905 (7)0.4975 (3)0.0695 (13)
H4B1.07790.96450.45260.083*
H4C1.09600.93450.55100.083*
C10.89174 (18)0.8500 (6)0.2278 (3)0.0396 (10)
H1B0.89400.91950.17590.047*
C20.84790 (19)0.6840 (6)0.1959 (3)0.0387 (10)
H2B0.85380.59770.24590.046*
C30.77758 (18)0.7409 (6)0.1562 (3)0.0387 (10)
H3B0.76930.80280.09830.046*
C40.76213 (18)0.8694 (6)0.2203 (3)0.0396 (10)
H4A0.76810.80440.27680.047*
C50.8067 (2)1.0374 (6)0.2378 (3)0.0423 (10)
H5A0.80481.09020.18000.051*
C60.7926 (2)1.1884 (7)0.2936 (3)0.0487 (11)
H6A0.82491.28480.30500.058*
H6B0.75141.24360.26120.058*
C70.7401 (3)1.1452 (8)0.3977 (4)0.0586 (13)
C80.7464 (4)1.0653 (12)0.4877 (5)0.102 (2)
H8A0.70801.08910.50040.153*
H8B0.78201.12200.53310.153*
H8C0.75320.93370.48720.153*
C90.6553 (2)0.8752 (8)0.2213 (4)0.0534 (12)
C100.5887 (2)0.9374 (11)0.1689 (4)0.0745 (16)
H10A0.56010.89550.19840.112*
H10B0.57580.88590.10960.112*
H10C0.58741.07050.16530.112*
C110.7051 (2)0.5239 (7)0.0609 (3)0.0499 (12)
C120.6616 (3)0.3661 (9)0.0615 (4)0.0735 (17)
H12A0.63890.32730.00110.110*
H12B0.63160.40540.08920.110*
H12C0.68640.26420.09480.110*
C130.8985 (2)0.4365 (7)0.1448 (3)0.0495 (11)
C140.9150 (2)0.3741 (8)0.0673 (4)0.0643 (14)
H14A0.93870.26020.08190.096*
H14B0.94050.46720.05230.096*
H14C0.87650.35430.01700.096*
C151.00857 (19)0.8254 (6)0.2658 (3)0.0418 (10)
C161.0796 (2)0.7105 (7)0.4844 (3)0.0495 (12)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O1W0.265 (7)0.099 (4)0.166 (5)0.007 (5)0.012 (5)−0.014 (4)
S10.0520 (7)0.0731 (9)0.0629 (8)0.0127 (7)0.0280 (6)0.0215 (7)
S20.0840 (10)0.0872 (11)0.0403 (7)0.0242 (8)0.0154 (6)0.0036 (7)
O10.0333 (14)0.0484 (18)0.0460 (17)−0.0008 (13)0.0109 (13)−0.0055 (14)
O20.0468 (17)0.053 (2)0.0451 (18)0.0115 (15)0.0115 (14)−0.0022 (15)
O30.050 (2)0.104 (3)0.088 (3)0.024 (2)0.029 (2)0.003 (3)
O40.0344 (14)0.0564 (19)0.0471 (17)0.0005 (15)0.0112 (13)−0.0011 (16)
O50.062 (2)0.121 (4)0.089 (3)−0.011 (2)0.036 (2)0.022 (3)
O60.0445 (16)0.0522 (19)0.0344 (15)−0.0082 (15)0.0066 (13)−0.0036 (14)
O70.092 (3)0.079 (3)0.0369 (19)−0.017 (2)0.0069 (18)−0.0039 (19)
O80.0526 (17)0.0488 (18)0.0352 (15)0.0105 (16)0.0118 (13)−0.0008 (14)
O90.132 (4)0.073 (3)0.081 (3)0.047 (3)0.056 (3)0.023 (2)
N10.0352 (18)0.051 (2)0.041 (2)0.0027 (17)0.0117 (15)0.0089 (17)
N20.0342 (19)0.069 (3)0.044 (2)0.0034 (18)0.0148 (17)0.008 (2)
N30.046 (2)0.052 (2)0.040 (2)0.0041 (18)0.0019 (17)−0.0040 (18)
N40.079 (3)0.073 (3)0.051 (3)−0.007 (2)0.016 (2)−0.015 (2)
C10.038 (2)0.042 (2)0.039 (2)0.0045 (19)0.0128 (18)0.0030 (19)
C20.041 (2)0.047 (2)0.028 (2)0.0074 (19)0.0111 (18)0.0022 (18)
C30.036 (2)0.044 (2)0.033 (2)−0.001 (2)0.0078 (17)0.0021 (19)
C40.031 (2)0.051 (3)0.035 (2)0.0046 (19)0.0101 (17)0.0036 (19)
C50.042 (2)0.042 (2)0.041 (2)0.001 (2)0.0108 (19)0.000 (2)
C60.049 (3)0.041 (3)0.056 (3)−0.004 (2)0.017 (2)−0.002 (2)
C70.059 (3)0.057 (3)0.065 (3)0.003 (3)0.028 (3)−0.008 (3)
C80.145 (6)0.096 (5)0.087 (5)0.033 (5)0.068 (4)0.017 (4)
C90.044 (3)0.060 (3)0.059 (3)−0.012 (2)0.021 (2)−0.012 (3)
C100.041 (3)0.103 (5)0.080 (4)−0.006 (3)0.022 (3)−0.016 (4)
C110.046 (3)0.052 (3)0.045 (3)0.003 (2)0.007 (2)−0.009 (2)
C120.068 (3)0.075 (4)0.062 (3)−0.022 (3)0.003 (3)−0.018 (3)
C130.054 (3)0.046 (3)0.047 (3)0.006 (2)0.016 (2)0.006 (3)
C140.062 (3)0.067 (4)0.070 (3)0.014 (3)0.031 (3)−0.008 (3)
C150.037 (2)0.045 (3)0.043 (2)0.007 (2)0.0136 (19)−0.005 (2)
C160.034 (2)0.066 (3)0.045 (3)0.009 (2)0.010 (2)−0.011 (2)

Geometric parameters (Å, °)

O1W—H100.868 (10)C1—C21.516 (6)
O1W—H200.867 (8)C1—H1B0.9800
S1—C151.669 (5)C2—C31.530 (5)
S2—C161.684 (5)C2—H2B0.9800
O1—C11.430 (5)C3—C41.501 (6)
O1—C51.434 (5)C3—H3B0.9800
O2—C71.324 (6)C4—C51.528 (6)
O2—C61.439 (6)C4—H4A0.9800
O3—C71.196 (6)C5—C61.503 (6)
O4—C91.345 (6)C5—H5A0.9800
O4—C41.439 (5)C6—H6A0.9700
O5—C91.200 (6)C6—H6B0.9700
O6—C111.342 (5)C7—C81.501 (9)
O6—C31.435 (5)C8—H8A0.9600
O7—C111.192 (6)C8—H8B0.9600
O8—C131.338 (6)C8—H8C0.9600
O8—C21.430 (5)C9—C101.500 (7)
O9—C131.195 (6)C10—H10A0.9600
N1—C151.335 (5)C10—H10B0.9600
N1—C11.440 (5)C10—H10C0.9600
N1—H1A0.8600C11—C121.496 (8)
N2—C151.349 (5)C12—H12A0.9600
N2—N31.382 (5)C12—H12B0.9600
N2—H2A0.8600C12—H12C0.9600
N3—C161.358 (6)C13—C141.471 (7)
N3—H3A0.8600C14—H14A0.9600
N4—C161.312 (7)C14—H14B0.9600
N4—H4B0.8600C14—H14C0.9600
N4—H4C0.8600
H10—O1W—H20104.6 (8)O2—C6—C5110.3 (4)
C1—O1—C5112.1 (3)O2—C6—H6A109.6
C7—O2—C6116.6 (4)C5—C6—H6A109.6
C9—O4—C4117.9 (4)O2—C6—H6B109.6
C11—O6—C3117.9 (3)C5—C6—H6B109.6
C13—O8—C2119.8 (3)H6A—C6—H6B108.1
C15—N1—C1125.6 (4)O3—C7—O2123.8 (5)
C15—N1—H1A117.2O3—C7—C8124.9 (5)
C1—N1—H1A117.2O2—C7—C8111.3 (5)
C15—N2—N3123.2 (4)C7—C8—H8A109.5
C15—N2—H2A118.4C7—C8—H8B109.5
N3—N2—H2A118.4H8A—C8—H8B109.5
C16—N3—N2121.9 (4)C7—C8—H8C109.5
C16—N3—H3A119.0H8A—C8—H8C109.5
N2—N3—H3A119.0H8B—C8—H8C109.5
C16—N4—H4B120.0O5—C9—O4123.2 (5)
C16—N4—H4C120.0O5—C9—C10125.6 (5)
H4B—N4—H4C120.0O4—C9—C10111.2 (5)
O1—C1—N1106.4 (3)C9—C10—H10A109.5
O1—C1—C2111.5 (3)C9—C10—H10B109.5
N1—C1—C2110.1 (4)H10A—C10—H10B109.5
O1—C1—H1B109.6C9—C10—H10C109.5
N1—C1—H1B109.6H10A—C10—H10C109.5
C2—C1—H1B109.6H10B—C10—H10C109.5
O8—C2—C1107.6 (3)O7—C11—O6124.5 (4)
O8—C2—C3107.9 (3)O7—C11—C12124.8 (5)
C1—C2—C3112.2 (3)O6—C11—C12110.7 (4)
O8—C2—H2B109.7C11—C12—H12A109.5
C1—C2—H2B109.7C11—C12—H12B109.5
C3—C2—H2B109.7H12A—C12—H12B109.5
O6—C3—C4108.4 (3)C11—C12—H12C109.5
O6—C3—C2109.1 (3)H12A—C12—H12C109.5
C4—C3—C2109.1 (3)H12B—C12—H12C109.5
O6—C3—H3B110.1O9—C13—O8122.9 (4)
C4—C3—H3B110.1O9—C13—C14125.8 (5)
C2—C3—H3B110.1O8—C13—C14111.4 (4)
O4—C4—C3108.7 (3)C13—C14—H14A109.5
O4—C4—C5110.3 (3)C13—C14—H14B109.5
C3—C4—C5109.0 (3)H14A—C14—H14B109.5
O4—C4—H4A109.7C13—C14—H14C109.5
C3—C4—H4A109.7H14A—C14—H14C109.5
C5—C4—H4A109.7H14B—C14—H14C109.5
O1—C5—C6108.5 (3)N1—C15—N2114.9 (4)
O1—C5—C4106.8 (3)N1—C15—S1125.8 (3)
C6—C5—C4115.2 (4)N2—C15—S1119.3 (3)
O1—C5—H5A108.7N4—C16—N3117.6 (5)
C6—C5—H5A108.7N4—C16—S2124.1 (4)
C4—C5—H5A108.7N3—C16—S2118.2 (4)
C15—N2—N3—C16−107.9 (5)C1—O1—C5—C6−169.4 (3)
C5—O1—C1—N1−178.7 (3)C1—O1—C5—C465.9 (4)
C5—O1—C1—C2−58.6 (4)O4—C4—C5—O1175.5 (3)
C15—N1—C1—O1−116.8 (4)C3—C4—C5—O1−65.3 (4)
C15—N1—C1—C2122.3 (5)O4—C4—C5—C654.9 (5)
C13—O8—C2—C1103.9 (4)C3—C4—C5—C6174.1 (4)
C13—O8—C2—C3−134.9 (4)C7—O2—C6—C5−125.6 (4)
O1—C1—C2—O8168.0 (3)O1—C5—C6—O2−64.5 (4)
N1—C1—C2—O8−74.2 (4)C4—C5—C6—O255.1 (5)
O1—C1—C2—C349.5 (4)C6—O2—C7—O30.8 (7)
N1—C1—C2—C3167.3 (3)C6—O2—C7—C8−178.4 (5)
C11—O6—C3—C4129.2 (4)C4—O4—C9—O52.9 (7)
C11—O6—C3—C2−112.1 (4)C4—O4—C9—C10−176.6 (4)
O8—C2—C3—O673.5 (4)C3—O6—C11—O77.1 (7)
C1—C2—C3—O6−168.1 (3)C3—O6—C11—C12−173.9 (4)
O8—C2—C3—C4−168.2 (3)C2—O8—C13—O93.6 (7)
C1—C2—C3—C4−49.9 (4)C2—O8—C13—C14−175.8 (4)
C9—O4—C4—C3115.1 (4)C1—N1—C15—N2176.3 (4)
C9—O4—C4—C5−125.6 (4)C1—N1—C15—S1−5.0 (7)
O6—C3—C4—O4−63.5 (4)N3—N2—C15—N18.6 (6)
C2—C3—C4—O4177.8 (3)N3—N2—C15—S1−170.2 (3)
O6—C3—C4—C5176.4 (3)N2—N3—C16—N412.4 (7)
C2—C3—C4—C557.7 (4)N2—N3—C16—S2−166.9 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1W—H10···O5i0.868 (10)2.637 (4)3.382 (11)144.5 (5)
O1W—H20···O9ii0.867 (8)2.563 (4)3.181 (9)129.1 (5)
N1—H1A···S2iii0.862.623.400 (4)151
N2—H2A···O3iv0.862.092.856 (5)147
N3—H3A···O1Wv0.862.132.973 (9)167
N4—H4B···O1Wvi0.862.433.244 (9)159
N4—H4C···O1iii0.862.493.323 (5)164

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SU2088).

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