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Acta Crystallogr Sect E Struct Rep Online. 2010 December 1; 66(Pt 12): o3263.
Published online 2010 November 20. doi:  10.1107/S1600536810047732
PMCID: PMC3011483

1β,10α:4β,5α-Diep­oxy-7αH-germacran-6β-ol monohydrate

Abstract

In the title compound, C15H26O3·H2O, a sesquiterpenoid mol­ecule with a germacrene backbone that contains two epoxide groups and one hydroxyl group. Inter­molecular O—H(...)O hydrogen bonds between the ep­oxy groups and solvent water mol­ecules give rise to an infinite three-dimensional supra­molecular structure.

Related literature

For the biosystematic and ecological evaluation of the title compound, see: Al Yousuf et al. (1999 [triangle]). For the isolation, see Li et al. (2009 [triangle]). For the determination of its absolute structure, see: Aguilar-Guadarrama & Rios (2004 [triangle]), Moodley et al. (2004 [triangle]). For related structures, see Takahashi et al. (1983 [triangle]), Barrero et al. (1999 [triangle]).

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Object name is e-66-o3263-scheme1.jpg

Experimental

Crystal data

  • C15H26O3·H2O
  • M r = 272.37
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o3263-efi1.jpg
  • a = 8.087 (2) Å
  • b = 11.380 (3) Å
  • c = 16.943 (5) Å
  • V = 1559.2 (8) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 293 K
  • 0.31 × 0.13 × 0.07 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2000 [triangle]) T min = 0.757, T max = 1.000
  • 8291 measured reflections
  • 1759 independent reflections
  • 1281 reflections with I > 2σ(I)
  • R int = 0.080

Refinement

  • R[F 2 > 2σ(F 2)] = 0.062
  • wR(F 2) = 0.148
  • S = 1.06
  • 1759 reflections
  • 186 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.16 e Å−3
  • Δρmin = −0.15 e Å−3

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 I, global. DOI: 10.1107/S1600536810047732/jj2065sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810047732/jj2065Isup2.hkl

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

Acknowledgments

This work was supported financially by a grant from the Guangdong Pharmaceutical University Foundation for Young Teachers.

supplementary crystallographic information

Comment

Terpenoids are large naturally-occuring organic molecules derived from five-carbon isoprene units assembled and modified in numerous ways. A sesquiterpenoid is a 15-carbon modified multicyclic terpenoid hydrocarbon molecule that differs from one another in its functional groups. The title compound, C15H26O3, H2O, is a sesquiterpenoid molecule with a germacrene backbone that contains two epoxide groups at the 1–10 and 4–5 ring positions and one alcohol group at the C6 position, respectively (Fig. 1). Crystal packing hss been stabilized as a result of a single water molecule that has crystallized in the unit cell giving rise to O—H···O intermolecular hydrogen bonds between the epoxy groups and the adjacent water molecules (Table 1). This forms an infinite 3-D supramolecular structure (Fig. 2).

Experimental

The title compound was synthesized by the method of Li et al. (2009). It was purified by repeated column chromatography over silica gel, ODS, and sephadex LH-20. It was then dissolved in a mixed solution of chloroform and methanol (ca 5:1). Colorless needle-like crystals were formed by slow evaporation of the solution in air.

Refinement

All the H atoms were placed in idealized positions and constrained to ride on their parent atoms, with C—H (methine) distances of 0.98 Å, C—H (methylene) 0.97 Å, C—H (methyl) 0.96Å, and an O—H distance of 0.82 Å, with Uiso(H) set at 1.2Ueq(C) and 1.5Ueq(O). A rotating group model was used for the OH group.

Figures

Fig. 1.
The molecular structure of the title compound, showing 30% displacement ellipsoids.
Fig. 2.
Packing diagram of the title compound viewed down the a axis. Dashed lines indicate O—H—O hydrogen bonds.

Crystal data

C15H26O3·H2OF(000) = 600
Mr = 272.37Dx = 1.160 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1361 reflections
a = 8.087 (2) Åθ = 4.8–39.9°
b = 11.380 (3) ŵ = 0.08 mm1
c = 16.943 (5) ÅT = 293 K
V = 1559.2 (8) Å3Prismatic, colorless
Z = 40.31 × 0.13 × 0.07 mm

Data collection

Bruker SMART CCD area-detector diffractometer1759 independent reflections
Radiation source: fine-focus sealed tube1281 reflections with I > 2σ(I)
graphiteRint = 0.080
[var phi] and ω scansθmax = 26.0°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 2000)h = −9→9
Tmin = 0.757, Tmax = 1.000k = −14→11
8291 measured reflectionsl = −20→20

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.062H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.148w = 1/[σ2(Fo2) + (0.0727P)2] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.005
1759 reflectionsΔρmax = 0.16 e Å3
186 parametersΔρmin = −0.15 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.010 (3)

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
O10.3976 (4)1.2287 (2)0.77838 (15)0.0499 (8)
O20.3551 (4)1.2022 (2)0.59240 (17)0.0540 (9)
H30.40811.20050.55120.081*
O30.1549 (4)0.7702 (2)0.79520 (15)0.0519 (8)
O4−0.0212 (5)0.7428 (3)0.9509 (2)0.0686 (11)
C10.2708 (6)0.8691 (3)0.7992 (2)0.0402 (10)
H10.37810.85460.77420.048*
C20.2798 (6)0.9355 (3)0.8767 (2)0.0505 (12)
H2A0.37500.90790.90630.061*
H2B0.18180.91800.90750.061*
C30.2933 (6)1.0692 (3)0.8662 (2)0.0527 (12)
H3A0.18441.10060.85450.063*
H3B0.33031.10380.91540.063*
C40.4113 (6)1.1048 (3)0.8008 (2)0.0420 (10)
C50.3410 (5)1.1380 (3)0.7247 (2)0.0396 (10)
H50.22041.13040.72200.048*
C60.4256 (5)1.1207 (3)0.64782 (19)0.0402 (10)
H60.54331.13860.65420.048*
C70.4075 (5)0.9917 (3)0.6206 (2)0.0432 (11)
H70.45110.94300.66350.052*
C80.2216 (5)0.9560 (4)0.6100 (2)0.0482 (11)
H8A0.15341.02300.62400.058*
H8B0.20260.93930.55460.058*
C90.1633 (7)0.8502 (4)0.6583 (2)0.0534 (12)
H9A0.06300.81980.63440.064*
H9B0.24670.78920.65470.064*
C100.1297 (5)0.8741 (3)0.7439 (2)0.0427 (10)
C110.5160 (6)0.9655 (4)0.5473 (2)0.0539 (12)
H110.47101.01090.50310.065*
C120.6958 (6)1.0003 (6)0.5569 (3)0.090 (2)
H12A0.74040.96320.60310.134*
H12B0.70361.08410.56250.134*
H12C0.75720.97580.51140.134*
C130.5033 (9)0.8344 (4)0.5254 (3)0.088 (2)
H13A0.39150.81620.51080.133*
H13B0.53480.78740.57000.133*
H13C0.57560.81790.48190.133*
C14−0.0276 (6)0.9371 (4)0.7621 (3)0.0664 (14)
H14A−0.03421.00730.73090.100*
H14B−0.02990.95750.81710.100*
H14C−0.11980.88700.75020.100*
C150.5860 (6)1.0613 (4)0.8082 (2)0.0536 (12)
H15A0.62881.08230.85920.080*
H15B0.65301.09650.76790.080*
H15C0.58780.97740.80240.080*
H4−0.133 (8)0.744 (5)0.935 (3)0.09 (2)*
H4C0.024 (6)0.740 (4)0.900 (3)0.069 (15)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.065 (2)0.0368 (15)0.0480 (15)−0.0061 (14)0.0068 (15)−0.0068 (13)
O20.061 (2)0.0475 (18)0.0531 (17)0.0085 (16)0.0069 (16)0.0150 (14)
O30.065 (2)0.0356 (15)0.0556 (16)−0.0072 (14)0.0096 (16)0.0006 (14)
O40.059 (3)0.089 (3)0.058 (2)−0.023 (2)0.0027 (19)−0.021 (2)
C10.049 (3)0.033 (2)0.039 (2)−0.0066 (19)0.010 (2)−0.0017 (18)
C20.068 (3)0.046 (3)0.038 (2)−0.009 (2)0.013 (2)−0.0009 (19)
C30.068 (3)0.049 (3)0.042 (2)−0.009 (2)0.017 (2)−0.011 (2)
C40.055 (3)0.034 (2)0.037 (2)−0.003 (2)0.006 (2)−0.0017 (17)
C50.039 (2)0.038 (2)0.042 (2)−0.0011 (18)0.0045 (19)−0.0060 (18)
C60.040 (3)0.043 (2)0.038 (2)0.006 (2)0.0017 (19)0.0019 (18)
C70.058 (3)0.042 (2)0.0298 (17)0.015 (2)−0.0041 (19)0.0029 (17)
C80.066 (3)0.042 (2)0.037 (2)0.007 (2)−0.014 (2)−0.0026 (18)
C90.067 (3)0.041 (3)0.052 (3)−0.002 (2)−0.006 (2)−0.002 (2)
C100.045 (3)0.035 (2)0.048 (2)−0.0069 (19)0.004 (2)−0.0018 (18)
C110.071 (3)0.058 (3)0.033 (2)0.020 (3)−0.003 (2)0.000 (2)
C120.058 (4)0.138 (5)0.073 (3)0.026 (4)0.018 (3)−0.015 (4)
C130.147 (6)0.067 (3)0.051 (3)0.042 (4)0.007 (4)−0.013 (2)
C140.046 (3)0.056 (3)0.097 (3)−0.003 (2)0.007 (3)0.002 (3)
C150.055 (3)0.060 (3)0.046 (2)−0.011 (2)−0.006 (2)−0.002 (2)

Geometric parameters (Å, °)

O1—C51.450 (4)C7—C81.568 (6)
O1—C41.464 (4)C7—H70.9800
O2—C61.438 (4)C8—C91.529 (5)
O2—H30.8200C8—H8A0.9700
O3—C11.467 (5)C8—H8B0.9700
O3—C101.481 (4)C9—C101.501 (5)
O4—H40.94 (6)C9—H9A0.9700
O4—H4C0.93 (4)C9—H9B0.9700
C1—C101.477 (6)C10—C141.492 (6)
C1—C21.517 (5)C11—C121.516 (7)
C1—H10.9800C11—C131.541 (6)
C2—C31.536 (5)C11—H110.9800
C2—H2A0.9700C12—H12A0.9600
C2—H2B0.9700C12—H12B0.9600
C3—C41.518 (5)C12—H12C0.9600
C3—H3A0.9700C13—H13A0.9600
C3—H3B0.9700C13—H13B0.9600
C4—C51.459 (5)C13—H13C0.9600
C4—C151.502 (6)C14—H14A0.9600
C5—C61.484 (5)C14—H14B0.9600
C5—H50.9800C14—H14C0.9600
C6—C71.545 (5)C15—H15A0.9600
C6—H60.9800C15—H15B0.9600
C7—C111.550 (6)C15—H15C0.9600
C5—O1—C460.1 (2)C9—C8—C7116.0 (3)
C6—O2—H3109.5C9—C8—H8A108.3
C1—O3—C1060.1 (2)C7—C8—H8A108.3
C1—O3—H4C114.1 (12)C9—C8—H8B108.3
C10—O3—H4C124.0 (13)C7—C8—H8B108.3
H4—O4—H4C96 (4)H8A—C8—H8B107.4
O3—C1—C1060.4 (2)C10—C9—C8115.4 (3)
O3—C1—C2116.9 (3)C10—C9—H9A108.4
C10—C1—C2124.6 (4)C8—C9—H9A108.4
O3—C1—H1114.6C10—C9—H9B108.4
C10—C1—H1114.6C8—C9—H9B108.4
C2—C1—H1114.6H9A—C9—H9B107.5
C1—C2—C3113.3 (3)C1—C10—O359.4 (2)
C1—C2—H2A108.9C1—C10—C14123.1 (3)
C3—C2—H2A108.9O3—C10—C14112.3 (3)
C1—C2—H2B108.9C1—C10—C9117.8 (4)
C3—C2—H2B108.9O3—C10—C9113.4 (3)
H2A—C2—H2B107.7C14—C10—C9116.2 (4)
C4—C3—C2113.2 (3)C12—C11—C13110.1 (5)
C4—C3—H3A108.9C12—C11—C7114.0 (4)
C2—C3—H3A108.9C13—C11—C7110.0 (4)
C4—C3—H3B108.9C12—C11—H11107.5
C2—C3—H3B108.9C13—C11—H11107.5
H3A—C3—H3B107.7C7—C11—H11107.5
C5—C4—O159.5 (2)C11—C12—H12A109.5
C5—C4—C15121.8 (3)C11—C12—H12B109.5
O1—C4—C15114.2 (4)H12A—C12—H12B109.5
C5—C4—C3118.0 (4)C11—C12—H12C109.5
O1—C4—C3113.5 (3)H12A—C12—H12C109.5
C15—C4—C3116.2 (4)H12B—C12—H12C109.5
O1—C5—C460.5 (2)C11—C13—H13A109.5
O1—C5—C6120.0 (3)C11—C13—H13B109.5
C4—C5—C6124.1 (4)H13A—C13—H13B109.5
O1—C5—H5114.0C11—C13—H13C109.5
C4—C5—H5114.0H13A—C13—H13C109.5
C6—C5—H5114.0H13B—C13—H13C109.5
O2—C6—C5107.7 (3)C10—C14—H14A109.5
O2—C6—C7112.4 (3)C10—C14—H14B109.5
C5—C6—C7110.2 (3)H14A—C14—H14B109.5
O2—C6—H6108.8C10—C14—H14C109.5
C5—C6—H6108.8H14A—C14—H14C109.5
C7—C6—H6108.8H14B—C14—H14C109.5
C6—C7—C11111.6 (3)C4—C15—H15A109.5
C6—C7—C8111.8 (3)C4—C15—H15B109.5
C11—C7—C8113.7 (3)H15A—C15—H15B109.5
C6—C7—H7106.4C4—C15—H15C109.5
C11—C7—H7106.4H15A—C15—H15C109.5
C8—C7—H7106.4H15B—C15—H15C109.5
H4C—O3—C1—C10−116.7 (14)O2—C6—C7—C8−60.0 (4)
C10—O3—C1—C2116.3 (4)C5—C6—C7—C860.0 (4)
H4C—O3—C1—C2−0.4 (14)C6—C7—C8—C9−123.0 (3)
O3—C1—C2—C3−139.3 (4)C11—C7—C8—C9109.5 (4)
C10—C1—C2—C3−68.2 (5)C7—C8—C9—C1077.7 (5)
C1—C2—C3—C4−42.3 (6)C2—C1—C10—O3−104.0 (4)
C5—O1—C4—C15113.9 (4)O3—C1—C10—C1498.1 (4)
C5—O1—C4—C3−109.7 (4)C2—C1—C10—C14−5.8 (6)
C2—C3—C4—C5100.5 (5)O3—C1—C10—C9−102.2 (4)
C2—C3—C4—O1167.1 (4)C2—C1—C10—C9153.9 (4)
C2—C3—C4—C15−57.4 (5)H4C—O3—C10—C1100.5 (15)
C4—O1—C5—C6−114.7 (4)C1—O3—C10—C14−116.3 (4)
C15—C4—C5—O1−101.2 (4)H4C—O3—C10—C14−15.8 (15)
C3—C4—C5—O1102.2 (4)C1—O3—C10—C9109.5 (4)
O1—C4—C5—C6108.0 (4)H4C—O3—C10—C9−150.0 (15)
C15—C4—C5—C66.8 (6)C8—C9—C10—C1−85.0 (5)
C3—C4—C5—C6−149.8 (4)C8—C9—C10—O3−151.5 (4)
O1—C5—C6—O2−84.7 (4)C8—C9—C10—C1476.1 (5)
C4—C5—C6—O2−157.4 (3)C6—C7—C11—C1252.2 (5)
O1—C5—C6—C7152.4 (3)C8—C7—C11—C12179.8 (4)
C4—C5—C6—C779.7 (5)C6—C7—C11—C13176.3 (4)
O2—C6—C7—C1168.5 (4)C8—C7—C11—C13−56.2 (5)
C5—C6—C7—C11−171.4 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H3···O4i0.822.032.819 (4)160
O4—H4···O2ii0.94 (6)1.92 (6)2.836 (5)164 (5)
O4—H4C···O30.93 (4)2.10 (5)3.013 (4)166 (4)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: JJ2065).

References

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  • Al Yousuf, M. H., Bashir, A. K., Crabb, T. A., Blunden, G. & Yang, M.-H. (1999). Biochem. System. Ecol.27, 107–109.
  • Barrero, A. F., Herrador, M. M., Quilez, J. F., Alvarez-Manzaneda, R., Portal, D., Gavin, J. A., Gravalos, D. G., Simmonds, M. S. J. & Blaney, W. M. (1999). Phytochemistry, 51, 529–541. [PubMed]
  • Bruker (2007). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Li, S. M., Yang, X. W., Li, Y. L., Shen, Y. H., Feng, L., Wang, Y. H., Zeng, H. W., Liu, X. H., Zhang, C. S., Long, C. L. & Zhang, W. D. (2009). Planta Med.75, 1591–1596. [PubMed]
  • Moodley, N., Mulholland, D. A. & Crouch, N. R. (2004). J. Nat. Prod.67, 918–920. [PubMed]
  • Sheldrick, G. M. (2000). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Takahashi, T., Nemoto, H., Tsuji, J. & Miura, I. (1983). Tetrahedron Lett.24, 3485–3488.

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