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Acta Crystallogr Sect E Struct Rep Online. 2010 February 1; 66(Pt 2): o321.
Published online 2010 January 9. doi:  10.1107/S1600536809055664
PMCID: PMC2979748

1-[4-(β-d-Allopyranos­yloxy)benzyl­idene]semicarbazide hemihydrate

Abstract

The mol­ecule of the title compound, C14H19N3O7·0.5H2O, exhibits an E conformation about the C=N double bond. The water mol­ecule possesses crystallographically imposed twofold symmetry. In the crystal structure, the mol­ecules are connected by inter­molecular O—H(...)O and N—H(...)O hydrogen bonds into a three-dimensional network.

Related literature

For the properties of helicid (systematic name: 4-formyl­phenl-β-d-allopyran­oside), see: Chen et al. (1981 [triangle]); Sha & Mao (1987 [triangle]). For the synthesis of the title compound, see: Zhu et al. (2008 [triangle]). For related structures, see: Fan et al. (2007 [triangle]); Yang et al. (2008 [triangle])

An external file that holds a picture, illustration, etc.
Object name is e-66-0o321-scheme1.jpg

Experimental

Crystal data

  • C14H19N3O7·0.5H2O
  • M r = 350.33
  • Trigonal, An external file that holds a picture, illustration, etc.
Object name is e-66-0o321-efi1.jpg
  • a = 8.6373 (12) Å
  • c = 37.021 (7) Å
  • V = 2391.8 (7) Å3
  • Z = 6
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 113 K
  • 0.28 × 0.25 × 0.21 mm

Data collection

  • Rigaku Saturn CCD area-detector diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005 [triangle]) T min = 0.967, T max = 0.975
  • 15783 measured reflections
  • 2242 independent reflections
  • 2161 reflections with I > 2σ(I)
  • R int = 0.038

Refinement

  • R[F 2 > 2σ(F 2)] = 0.033
  • wR(F 2) = 0.085
  • S = 1.09
  • 2242 reflections
  • 235 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.45 e Å−3
  • Δρmin = −0.18 e Å−3

Data collection: CrystalClear (Rigaku/MSC, 2005 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809055664/rz2403sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809055664/rz2403Isup2.hkl

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

Acknowledgments

The authors thank Mr Zhi-Hua Mao of the Analytical & Testing Center of Sichuan University for the X-ray data collection.

supplementary crystallographic information

Comment

The natural product helicid, 4-formylphenl-β-D-allopyranoside, which is a major active ingredient of herbal medicine, is extracted from the fruit of Helicia nilagirica Beed growing at the Yunnan mountain of China (Chen et al., 1981). It has showed great biological effects on the central nervous system with low toxicity (Sha & Mao, 1987), and has been used to treating ache and insomnia for a long time. Some derivatives of this compound have been reported with good pharmacological activity (Fan et al., 2007; Yang et al., 2008). The title compound has been synthetized via condensation reaction of helicid and semicarbazide hydrochloride in ethanol (Zhu et al., 2008).

In this title compound (Fig. 1), the pyranoside ring adopts a stable chair conformation with the hydroxyl group at C3 in axial position and the other substituents at C1, C2 and C4 in equatorial position. The N1═C13 double bond in the molecule exhibits an E conformation, as indicated by the values of the C(13)–N(1)–N(2)–C(14) and C(11)–C(10)–C(13)–N(1) torsion angles of 176.28(0.19) and -160.45 (1/5)°, respectively. The average C–C bond lengths in the pyranoside ring is 1.52 (3) Å. The average C(sp3)–O and C(sp2)–O bond lengths are 1.426 (2) and 1.319 (2)Å, respectively. Intermolecular O—H···.O and N—H···.O hydrogen bonds (Table 1) are present in the crystal structure, generating a three-dimensional network.

Experimental

Sodium acetate was added to a solution of semicarbazide hydrochloride (3.52 mmol) in water (5 ml) until pH 5–6. The solution was added to a solution of helicid (3.52 mmol) in ethanol (40 ml), then some drops of glacial acetic acid were added and the mixture was refluxed for 5 h. The reaction mixture was then cooled at room temperature. The colourless solid obtained was filtered, washed with water and recrystallized from ethanol/water (Zhu et al., 2008). Colourless crystals suitable for X-ray analysis were obtained by slow evaporation of an ethanol/water (5:1 v/v) solution at room temperature.

Refinement

The independent water H atom and the H atom bound to N2 were located in a difference Fourier map and refined freely. All other H atoms are positioned geometrically and refined in riding mode, with C—H = 0.95–1.00 Å, O—H = 0.84 Å and N—H = 0.88 Å, and with Uiso(H) = 1.2 Ueq (C, N, O). In the absence of significant anomalous dispersion effects, Friedel pairs were merged. The choice of space group P3121 rather than P3221 is arbitrary.

Figures

Fig. 1.
The molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level. The water H atoms are related by the symmetry operation 1+x-y, 2-y, 5/3-z.

Crystal data

C14H19N3O7·0.5H2ODx = 1.459 Mg m3
Mr = 350.33Mo Kα radiation, λ = 0.71073 Å
Trigonal, P3121Cell parameters from 6972 reflections
Hall symbol: P 31 2"θ = 2.7–27.9°
a = 8.6373 (12) ŵ = 0.12 mm1
c = 37.021 (7) ÅT = 113 K
V = 2391.8 (7) Å3Block, colourless
Z = 60.28 × 0.25 × 0.21 mm
F(000) = 1110

Data collection

Rigaku Saturn CCD area-detector diffractometer2242 independent reflections
Radiation source: rotating anode2161 reflections with I > 2σ(I)
confocalRint = 0.038
Detector resolution: 7.31 pixels mm-1θmax = 27.9°, θmin = 2.7°
ω and [var phi] scansh = −8→11
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005)k = −11→8
Tmin = 0.967, Tmax = 0.975l = −46→47
15783 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.033H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.085w = 1/[σ2(Fo2) + (0.034P)2 + 1.0221P] where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.001
2242 reflectionsΔρmax = 0.45 e Å3
235 parametersΔρmin = −0.18 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008)
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0188 (16)

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
O10.61554 (18)0.67753 (19)0.64253 (3)0.0159 (3)
O20.35880 (19)0.6142 (2)0.59033 (4)0.0214 (3)
H20.30610.58260.57030.032*
O30.6592 (2)0.4735 (2)0.55878 (3)0.0198 (3)
H30.58110.47040.54480.030*
O40.90103 (18)0.5337 (2)0.61006 (3)0.0172 (3)
H40.96430.53450.62740.026*
O50.79887 (18)0.41000 (19)0.68003 (3)0.0174 (3)
H50.74740.35990.69940.026*
O60.67202 (18)0.64621 (18)0.70151 (3)0.0168 (3)
O71.4664 (2)1.6732 (2)0.85781 (4)0.0209 (3)
O80.5415 (3)1.00000.83330.0238 (5)
N11.1795 (2)1.3137 (2)0.80203 (4)0.0184 (4)
N21.2921 (3)1.4869 (2)0.81373 (5)0.0223 (4)
C60.5446 (3)0.7359 (3)0.58453 (5)0.0186 (4)
H6A0.57490.85670.59290.022*
H6B0.57160.74290.55840.022*
N31.3533 (2)1.3743 (2)0.86433 (5)0.0221 (4)
H3A1.40481.38790.88550.027*
H3B1.28771.26660.85520.027*
C10.6556 (3)0.6741 (3)0.60486 (5)0.0151 (4)
H10.78540.75920.60050.018*
C20.6120 (3)0.4842 (3)0.59529 (5)0.0157 (4)
H2A0.48110.40040.59870.019*
C30.7162 (3)0.4258 (3)0.61925 (5)0.0154 (4)
H3C0.67660.29750.61430.018*
C40.6833 (3)0.4471 (3)0.65893 (5)0.0147 (4)
H4A0.55610.36030.66520.018*
C50.7213 (3)0.6362 (3)0.66559 (5)0.0148 (4)
H5A0.85110.72350.66180.018*
C70.7687 (2)0.8103 (3)0.71830 (5)0.0152 (4)
C80.7913 (3)0.8084 (3)0.75549 (5)0.0192 (4)
H80.73540.69860.76840.023*
C90.8963 (3)0.9682 (3)0.77356 (5)0.0194 (4)
H90.91220.96720.79890.023*
C100.9789 (3)1.1305 (3)0.75499 (5)0.0173 (4)
C110.9447 (3)1.1300 (3)0.71811 (5)0.0179 (4)
H110.99301.24030.70550.021*
C120.8411 (3)0.9710 (3)0.69954 (5)0.0172 (4)
H120.82000.97210.67440.021*
C131.1015 (3)1.3027 (3)0.77191 (5)0.0182 (4)
H131.12401.40970.76010.022*
C141.3745 (3)1.5160 (3)0.84621 (5)0.0167 (4)
H8O0.555 (5)0.913 (5)0.8381 (10)0.070 (12)*
H2N1.304 (4)1.579 (4)0.8014 (7)0.031 (7)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0173 (7)0.0204 (7)0.0126 (6)0.0114 (6)−0.0008 (5)−0.0020 (5)
O20.0171 (7)0.0322 (9)0.0146 (6)0.0122 (7)−0.0017 (5)−0.0015 (6)
O30.0229 (8)0.0301 (8)0.0120 (6)0.0174 (7)−0.0025 (6)−0.0048 (6)
O40.0149 (7)0.0242 (7)0.0132 (6)0.0103 (6)0.0006 (5)0.0007 (5)
O50.0170 (7)0.0209 (7)0.0148 (6)0.0099 (6)0.0021 (5)0.0046 (5)
O60.0170 (7)0.0178 (7)0.0123 (6)0.0063 (6)0.0014 (5)−0.0022 (5)
O70.0250 (8)0.0192 (7)0.0170 (6)0.0100 (6)−0.0016 (6)−0.0026 (6)
O80.0316 (10)0.0150 (10)0.0194 (10)0.0075 (5)−0.0008 (4)−0.0016 (8)
N10.0222 (9)0.0152 (8)0.0181 (8)0.0095 (7)−0.0023 (7)−0.0023 (6)
N20.0326 (10)0.0155 (9)0.0187 (8)0.0121 (8)−0.0074 (8)−0.0017 (7)
C60.0200 (9)0.0194 (10)0.0165 (9)0.0099 (8)0.0015 (8)0.0010 (8)
N30.0242 (9)0.0194 (9)0.0207 (8)0.0093 (7)−0.0056 (7)0.0018 (7)
C10.0155 (9)0.0172 (9)0.0120 (8)0.0077 (8)0.0014 (7)−0.0001 (7)
C20.0152 (9)0.0177 (9)0.0129 (8)0.0072 (7)0.0010 (7)−0.0016 (7)
C30.0154 (9)0.0152 (9)0.0152 (8)0.0072 (7)0.0009 (7)0.0001 (7)
C40.0126 (9)0.0153 (9)0.0140 (8)0.0054 (7)−0.0001 (7)0.0005 (7)
C50.0137 (8)0.0181 (9)0.0119 (8)0.0074 (7)0.0010 (7)−0.0003 (7)
C70.0137 (8)0.0167 (9)0.0158 (8)0.0081 (7)−0.0009 (7)−0.0025 (7)
C80.0234 (10)0.0182 (9)0.0162 (9)0.0106 (8)0.0002 (7)0.0020 (7)
C90.0258 (10)0.0218 (10)0.0126 (8)0.0133 (9)−0.0012 (8)0.0005 (7)
C100.0196 (10)0.0179 (9)0.0179 (9)0.0121 (8)−0.0016 (7)−0.0020 (7)
C110.0204 (10)0.0174 (9)0.0175 (9)0.0106 (8)−0.0002 (8)0.0007 (7)
C120.0194 (9)0.0210 (10)0.0127 (8)0.0113 (8)0.0001 (7)0.0003 (7)
C130.0237 (10)0.0178 (9)0.0155 (9)0.0123 (8)−0.0008 (8)−0.0001 (7)
C140.0183 (9)0.0185 (10)0.0148 (8)0.0104 (8)0.0006 (7)−0.0001 (7)

Geometric parameters (Å, °)

O1—C51.419 (2)N3—H3B0.8800
O1—C11.441 (2)C1—C21.530 (3)
O2—C61.428 (2)C1—H11.0000
O2—H20.8400C2—C31.518 (3)
O3—C21.428 (2)C2—H2A1.0000
O3—H30.8400C3—C41.524 (2)
O4—C31.430 (2)C3—H3C1.0000
O4—H40.8400C4—C51.517 (3)
O5—C41.424 (2)C4—H4A1.0000
O5—H50.8400C5—H5A1.0000
O6—C71.381 (2)C7—C121.390 (3)
O6—C51.412 (2)C7—C81.392 (2)
O7—C141.257 (2)C8—C91.387 (3)
O8—H8O0.84 (3)C8—H80.9500
N1—C131.281 (2)C9—C101.395 (3)
N1—N21.385 (2)C9—H90.9500
N2—C141.355 (2)C10—C111.397 (3)
N2—H2N0.88 (3)C10—C131.466 (3)
C6—C11.511 (3)C11—C121.390 (3)
C6—H6A0.9900C11—H110.9500
C6—H6B0.9900C12—H120.9500
N3—C141.326 (3)C13—H130.9500
N3—H3A0.8800
C5—O1—C1112.67 (14)O5—C4—C5110.79 (15)
C6—O2—H2109.5O5—C4—C3107.90 (15)
C2—O3—H3109.5C5—C4—C3109.50 (15)
C3—O4—H4109.5O5—C4—H4A109.5
C4—O5—H5109.5C5—C4—H4A109.5
C7—O6—C5116.12 (15)C3—C4—H4A109.5
C13—N1—N2114.29 (17)O6—C5—O1107.44 (14)
C14—N2—N1119.87 (16)O6—C5—C4108.02 (15)
C14—N2—H2N118.8 (18)O1—C5—C4110.68 (15)
N1—N2—H2N121.1 (18)O6—C5—H5A110.2
O2—C6—C1110.08 (16)O1—C5—H5A110.2
O2—C6—H6A109.6C4—C5—H5A110.2
C1—C6—H6A109.6O6—C7—C12122.61 (16)
O2—C6—H6B109.6O6—C7—C8116.71 (17)
C1—C6—H6B109.6C12—C7—C8120.69 (18)
H6A—C6—H6B108.2C9—C8—C7119.40 (19)
C14—N3—H3A120.0C9—C8—H8120.3
C14—N3—H3B120.0C7—C8—H8120.3
H3A—N3—H3B120.0C8—C9—C10120.94 (17)
O1—C1—C6105.85 (14)C8—C9—H9119.5
O1—C1—C2108.28 (15)C10—C9—H9119.5
C6—C1—C2113.83 (16)C9—C10—C11118.51 (18)
O1—C1—H1109.6C9—C10—C13123.76 (17)
C6—C1—H1109.6C11—C10—C13117.73 (18)
C2—C1—H1109.6C12—C11—C10121.15 (18)
O3—C2—C3107.20 (15)C12—C11—H11119.4
O3—C2—C1111.32 (15)C10—C11—H11119.4
C3—C2—C1110.59 (15)C11—C12—C7119.07 (17)
O3—C2—H2A109.2C11—C12—H12120.5
C3—C2—H2A109.2C7—C12—H12120.5
C1—C2—H2A109.2N1—C13—C10122.22 (18)
O4—C3—C2107.37 (15)N1—C13—H13118.9
O4—C3—C4111.43 (15)C10—C13—H13118.9
C2—C3—C4110.23 (15)O7—C14—N3123.06 (18)
O4—C3—H3C109.3O7—C14—N2119.55 (17)
C2—C3—H3C109.3N3—C14—N2117.39 (18)
C4—C3—H3C109.3
C13—N1—N2—C14176.28 (19)O5—C4—C5—O6−67.07 (19)
C5—O1—C1—C6−175.23 (15)C3—C4—C5—O6174.03 (15)
C5—O1—C1—C262.35 (19)O5—C4—C5—O1175.56 (14)
O2—C6—C1—O1−62.49 (19)C3—C4—C5—O156.7 (2)
O2—C6—C1—C256.3 (2)C5—O6—C7—C1231.4 (3)
O1—C1—C2—O3−176.33 (15)C5—O6—C7—C8−148.63 (17)
C6—C1—C2—O366.3 (2)O6—C7—C8—C9176.08 (18)
O1—C1—C2—C3−57.27 (19)C12—C7—C8—C9−3.9 (3)
C6—C1—C2—C3−174.68 (15)C7—C8—C9—C100.2 (3)
O3—C2—C3—O454.20 (19)C8—C9—C10—C114.0 (3)
C1—C2—C3—O4−67.32 (18)C8—C9—C10—C13−175.52 (19)
O3—C2—C3—C4175.75 (15)C9—C10—C11—C12−4.5 (3)
C1—C2—C3—C454.2 (2)C13—C10—C11—C12174.99 (19)
O4—C3—C4—O5−54.48 (19)C10—C11—C12—C70.9 (3)
C2—C3—C4—O5−173.59 (15)O6—C7—C12—C11−176.63 (17)
O4—C3—C4—C566.18 (19)C8—C7—C12—C113.4 (3)
C2—C3—C4—C5−52.9 (2)N2—N1—C13—C10179.26 (18)
C7—O6—C5—O1−91.06 (18)C9—C10—C13—N119.1 (3)
C7—O6—C5—C4149.50 (15)C11—C10—C13—N1−160.4 (2)
C1—O1—C5—O6179.21 (14)N1—N2—C14—O7−174.97 (17)
C1—O1—C5—C4−63.07 (19)N1—N2—C14—N35.1 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H2···O7i0.841.852.6905 (19)175
O3—H3···O8ii0.841.942.7447 (16)159
O4—H4···O5iii0.842.052.8277 (19)154
O4—H4···O50.842.342.7725 (19)113
O5—H5···O2iv0.841.852.693 (2)178
N3—H3A···O4v0.882.243.096 (2)165
N3—H3A···O3v0.882.462.896 (2)111
O8—H8O···O7vi0.84 (3)1.95 (3)2.7163 (17)151 (4)
N2—H2N···O3vii0.88 (3)2.14 (3)3.014 (2)176 (2)

Symmetry codes: (i) −x+y, −x+2, z−1/3; (ii) −x+y, −x+1, z−1/3; (iii) −x+2, −x+y+1, −z+4/3; (iv) −x+1, −x+y, −z+4/3; (v) −y+2, xy+1, z+1/3; (vi) x−1, y−1, z; (vii) −x+2, −x+y+2, −z+4/3.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RZ2403).

References

  • Chen, W. S., Lu, S. D. & Eberhard, B. (1981). Liebigs Ann. Chem.10, 1893–1897.
  • Fan, B., Li, J. L., Li, Y. & Yin, S. F. (2007). Chin. J. Org. Chem.27, 1150–1154.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Rigaku/MSC (2005). CrystalClear Rigaku/MSC, The Woodlands, Texas, USA.
  • Sha, J. Z. & Mao, H. K. (1987). Chin. Pharm. Bull.22, 21–27.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Yang, H. J., Hu, C., Li, Y. & Yin, S. F. (2008). Chin. J. Org. Chem.28, 899–902.
  • Zhu, Q. L., Li, Y., Li, J., Tang, Q., Guo, C. H. & Yin, S. F. (2008). West Chin. J. Pharm. Sci.23, 12–16.

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