organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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(2E,4R,5R,6S)-2-(4,5,6-Trihy­dr­oxy­cyclo­hex-2-en-1-yl­­idene)aceto­nitrile

aDepartment of Organic Chemistry, University of Yaounde I, PO Box 812 Yaounde, Cameroon, and bUniversity Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
*Correspondence e-mail: ngadjuibt@yahoo.fr

(Received 11 July 2012; accepted 9 August 2012; online 23 August 2012)

The crystal structure of the title compound, C8H9NO3, is characterized by a complex three-dimensional hydrogen-bond network in which every mol­ecule is connected to six symmetry-related neighbours.

Related literature

For the isolation of this natural product, see: Hua et al. (2004[Hua, Z., Zhi-Xin, L. & Jian-Min, Y. (2004). Chin. J. Chem. 22, 1200-1203.]). For previous phytochemical and biological studies of the stem bark of Thecacoris annobonae, see: Kuete et al. (2010[Kuete, V., Poumale Poumale, H. M., Guedem, A. N., Shiono, Y., Randrianasolo, R. & Ngadjui, B. T. (2010). S. Afr. J. Bot. 76, 536-542.]).

[Scheme 1]

Experimental

Crystal data
  • C8H9NO3

  • Mr = 167.16

  • Monoclinic, P 21

  • a = 4.8159 (5) Å

  • b = 10.2482 (5) Å

  • c = 8.3573 (9) Å

  • β = 102.842 (4)°

  • V = 402.15 (6) Å3

  • Z = 2

  • Cu Kα radiation

  • μ = 0.90 mm−1

  • T = 193 K

  • 0.60 × 0.06 × 0.06 mm

Data collection
  • Enraf–Nonius CAD-4 diffractometer

  • 2174 measured reflections

  • 1514 independent reflections

  • 1501 reflections with I > 2σ(I)

  • Rint = 0.021

  • 3 standard reflections every 60 min intensity decay: 5%

Refinement
  • R[F2 > 2σ(F2)] = 0.026

  • wR(F2) = 0.071

  • S = 1.08

  • 1514 reflections

  • 146 parameters

  • 1 restraint

  • All H-atom parameters refined

  • Δρmax = 0.21 e Å−3

  • Δρmin = −0.12 e Å−3

  • Absolute structure: Flack, (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.])

  • Flack parameter: −0.04 (16)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O7—H7⋯O9i 0.79 (2) 1.93 (2) 2.6885 (14) 160 (2)
O8—H8⋯N12ii 0.77 (2) 2.18 (2) 2.9138 (16) 160 (2)
O9—H9⋯O7iii 0.78 (3) 2.02 (2) 2.7944 (15) 170 (2)
Symmetry codes: (i) [-x+2, y-{\script{1\over 2}}, -z+1]; (ii) x+1, y, z+1; (iii) [-x+1, y+{\script{1\over 2}}, -z+1].

Data collection: CAD-4 Software (Enraf–Nonius, 1989[Enraf-Nonius (1989). CAD-4 Software. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 Software; data reduction: CORINC (Dräger & Gattow, 1971[Dräger, M. & Gattow, G. (1971). Acta Chem. Scand. 25, 761-762.]); program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: PLATON.

Supporting information


Comment top

Previous phytochemical and biological studies of the stem bark of Thecacoris annobonae (Euphorbiaceae) led to several bioactive secondary metabolites: Kuete et al. (2010). In the continuation of this investigation, the title compound was isolated from the leaves of the same plant using chromatographic methods and characterized by single crystal X-ray diffraction. It should be noted that this natural product was previously obtained from the root of Semiaquilegia adoxoides (Ranunculaceae): Hua et al. (2004).

In the crystal structure of the title compound the six membered ring adopts an envelope conformation in which C(3) is 0.678 (1) Å below the ring plane (Fig. 1). The acrylonitrile group is nearly coplanar to the least square plane of the ring system. The packing is characterized by a complex three-dimensional network formed by hydrogen bonds. Every molecule interacts by hydrogen bonds with six symmetry related molecules. While the hydroxyl groups O7 and O9 are both donor and acceptor of hydrogen bonds, O8 only interacts with N12 via hydrogen bonding (Fig. 2 and Table 1).

Related literature top

For the isolation of this natural product, see: Hua et al. (2004). For previous phytochemical and biological studies of the stem bark of Thecacoris annobonae, see: Kuete et al. (2010).

Experimental top

Air-dried powder of leaves of Thecacoris annobonae (1.37 kg) was successively macerated with hexane, ethyl acetate and methanol for two days each. Three fractions H (30 g), E (45 g), and M (61 g) were collected. The Methanol fraction M was subjected to a silica gel column chromatography eluted with CH2Cl2 to MeOH gradient yielding 7 mg of this secondary metabolite. It crystallized as needles in three of the fractions eluted with the mixture CH2Cl2/MeOH in a ratio of 97:3.

Refinement top

All hydrogen atoms were located from a difference Fourier map and refined with isotropic displacement parameters. The absolute structure was determined on the basis of 705 Friedel pairs.

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell refinement: CAD-4 Software (Enraf–Nonius, 1989); data reduction: CORINC (Dräger & Gattow, 1971); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
Fig. 1. Crystal structure of the title compound with labelling and displacement ellipsoids drawn at the 50% probability level.

Fig. 2. Crystal structure of the title compound with view along the a-axis. For calrity only H-atoms involved in hydrogen bonds are shown. Intermolecular hydrogen bonding is represented as dashed lines.
(2E,4R,5R,6S)-2-(4,5,6-Trihydroxycyclohex-2-en-1- ylidene)acetonitrile top
Crystal data top
C8H9NO3F(000) = 176
Mr = 167.16Dx = 1.380 Mg m3
Monoclinic, P21Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ybCell parameters from 25 reflections
a = 4.8159 (5) Åθ = 35–46°
b = 10.2482 (5) ŵ = 0.90 mm1
c = 8.3573 (9) ÅT = 193 K
β = 102.842 (4)°Needle, colourless
V = 402.15 (6) Å30.60 × 0.06 × 0.06 mm
Z = 2
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.021
Radiation source: rotating anodeθmax = 70.0°, θmin = 5.4°
Graphite monochromatorh = 55
ω/2θ scansk = 1212
2174 measured reflectionsl = 1010
1514 independent reflections3 standard reflections every 60 min
1501 reflections with I > 2σ(I) intensity decay: 5%
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullAll H-atom parameters refined
R[F2 > 2σ(F2)] = 0.026 w = 1/[σ2(Fo2) + (0.0474P)2 + 0.0306P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.071(Δ/σ)max < 0.001
S = 1.08Δρmax = 0.21 e Å3
1514 reflectionsΔρmin = 0.12 e Å3
146 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
1 restraintExtinction coefficient: 0.018 (3)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack, (1983)
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.04 (16)
Crystal data top
C8H9NO3V = 402.15 (6) Å3
Mr = 167.16Z = 2
Monoclinic, P21Cu Kα radiation
a = 4.8159 (5) ŵ = 0.90 mm1
b = 10.2482 (5) ÅT = 193 K
c = 8.3573 (9) Å0.60 × 0.06 × 0.06 mm
β = 102.842 (4)°
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.021
2174 measured reflections3 standard reflections every 60 min
1514 independent reflections intensity decay: 5%
1501 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.026All H-atom parameters refined
wR(F2) = 0.071Δρmax = 0.21 e Å3
S = 1.08Δρmin = 0.12 e Å3
1514 reflectionsAbsolute structure: Flack, (1983)
146 parametersAbsolute structure parameter: 0.04 (16)
1 restraint
Special details top

Experimental. 1H–, 13C– and two-dimensional-NMR spectra were recorded on Bruker AVANCE II-400 MHz s pectrometer equipped with a 5 mm observe probe and a z-gradient coil using standard pulse sequences. HR-ESI-MS was carried out on a Waters Q-TOF Ultima III mass spectrometer. HR-ESI-MS m/z 190.0470 (calcd. for [C8H9NO3+Na]+ 190.0475); NMR (1H-NMR, 400 MHz, acetone-d6): 6.55 (1H, dd, J = 2.5, 10.1 Hz, H-2), 6.04 (1H, dd, J = 1.8, 10.1 Hz, H-3), 4.11–4.16 (1H, m, H-4), 4.40–4.44 (1H, m, H-5), 4.44–4.50 (1H, m, H-6), 5.63 (1H, s, H-7), 4.60 (1H, d, J = 7.9 Hz, OH-5), 4.16–4.18 (2H, m, OH-4 and 6); (13C-NMR, 100 MHz, acetone-d6): 159.7 (C-1), 124.0 (C-2), 139.6 (C-3), 74.5 (C-4), 69.6 (C-5), 71.9 (C-6),93.7 (C-7), 117.6 (C-8).

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) top
xyzUiso*/Ueq
C10.4167 (3)0.60278 (13)0.16499 (15)0.0204 (3)
C20.6543 (3)0.54538 (12)0.29376 (15)0.0193 (3)
H20.822 (3)0.5471 (15)0.2490 (18)0.014 (3)*
C30.7220 (3)0.63193 (13)0.44623 (15)0.0195 (3)
H30.881 (4)0.5923 (17)0.525 (2)0.023 (4)*
C40.8147 (3)0.76563 (13)0.39626 (17)0.0244 (3)
H40.992 (4)0.7516 (17)0.364 (2)0.023 (4)*
C50.6001 (3)0.81945 (14)0.2530 (2)0.0291 (3)
H50.591 (4)0.911 (2)0.238 (2)0.041 (5)*
C60.4214 (3)0.74407 (14)0.14727 (17)0.0277 (3)
H60.289 (4)0.7814 (18)0.059 (2)0.023 (4)*
O70.5884 (2)0.41531 (9)0.32843 (12)0.0246 (2)
H70.730 (5)0.381 (2)0.375 (2)0.038 (5)*
O80.47685 (18)0.64281 (10)0.51340 (11)0.0221 (2)
H80.530 (4)0.644 (2)0.607 (3)0.031 (5)*
O90.8700 (2)0.85292 (10)0.53125 (14)0.0320 (3)
H90.730 (5)0.870 (2)0.559 (3)0.045 (6)*
C100.2197 (3)0.52459 (15)0.07211 (16)0.0252 (3)
H100.220 (4)0.431 (2)0.0850 (19)0.024 (4)*
C110.0065 (3)0.57476 (17)0.05275 (17)0.0316 (3)
N120.1938 (3)0.61195 (18)0.15135 (17)0.0451 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0145 (6)0.0289 (7)0.0186 (5)0.0032 (5)0.0053 (4)0.0007 (5)
C20.0106 (6)0.0241 (6)0.0233 (6)0.0012 (5)0.0043 (5)0.0010 (5)
C30.0086 (5)0.0255 (6)0.0227 (5)0.0031 (4)0.0001 (4)0.0005 (5)
C40.0128 (6)0.0260 (7)0.0344 (7)0.0030 (5)0.0054 (5)0.0046 (5)
C50.0271 (8)0.0222 (7)0.0391 (8)0.0003 (5)0.0098 (6)0.0065 (5)
C60.0229 (7)0.0318 (8)0.0273 (6)0.0039 (6)0.0034 (5)0.0097 (6)
O70.0167 (5)0.0204 (5)0.0340 (5)0.0034 (4)0.0001 (4)0.0022 (4)
O80.0134 (4)0.0328 (5)0.0197 (4)0.0006 (4)0.0030 (3)0.0018 (4)
O90.0135 (5)0.0332 (6)0.0489 (6)0.0054 (4)0.0060 (4)0.0162 (5)
C100.0186 (6)0.0354 (7)0.0212 (6)0.0016 (5)0.0034 (5)0.0014 (5)
C110.0250 (7)0.0477 (9)0.0208 (6)0.0052 (6)0.0024 (6)0.0037 (6)
N120.0319 (7)0.0705 (11)0.0269 (6)0.0011 (7)0.0064 (5)0.0055 (6)
Geometric parameters (Å, º) top
C1—C101.3479 (19)C4—H40.963 (18)
C1—C61.4563 (19)C5—C61.334 (2)
C1—C21.5054 (16)C5—H50.94 (2)
C2—O71.4151 (15)C6—H60.943 (18)
C2—C31.5272 (17)O7—H70.79 (2)
C2—H20.962 (16)O8—H80.77 (2)
C3—O81.4200 (16)O9—H90.78 (3)
C3—C41.5277 (18)C10—C111.426 (2)
C3—H30.981 (17)C10—H100.96 (2)
C4—O91.4178 (17)C11—N121.144 (2)
C4—C51.5019 (19)
C10—C1—C6123.87 (12)C5—C4—C3110.86 (10)
C10—C1—C2120.34 (12)O9—C4—H4107.3 (10)
C6—C1—C2115.77 (11)C5—C4—H4109.1 (10)
O7—C2—C1110.18 (11)C3—C4—H4105.9 (10)
O7—C2—C3113.10 (10)C6—C5—C4122.94 (13)
C1—C2—C3110.92 (10)C6—C5—H5119.0 (12)
O7—C2—H2110.0 (10)C4—C5—H5118.1 (12)
C1—C2—H2106.6 (9)C5—C6—C1122.05 (12)
C3—C2—H2105.8 (9)C5—C6—H6120.6 (11)
O8—C3—C2109.47 (10)C1—C6—H6117.4 (11)
O8—C3—C4110.90 (11)C2—O7—H7108.3 (16)
C2—C3—C4108.30 (10)C3—O8—H8106.5 (14)
O8—C3—H3111.0 (10)C4—O9—H9111.1 (17)
C2—C3—H3108.2 (10)C1—C10—C11122.16 (14)
C4—C3—H3108.9 (10)C1—C10—H10123.0 (10)
O9—C4—C5112.14 (12)C11—C10—H10114.9 (10)
O9—C4—C3111.28 (11)N12—C11—C10177.70 (18)
C10—C1—C2—O716.29 (16)O8—C3—C4—C568.05 (13)
C6—C1—C2—O7165.07 (11)C2—C3—C4—C552.09 (14)
C10—C1—C2—C3142.30 (13)O9—C4—C5—C6149.07 (14)
C6—C1—C2—C339.06 (15)C3—C4—C5—C624.01 (19)
O7—C2—C3—O863.88 (13)C4—C5—C6—C11.4 (2)
C1—C2—C3—O860.49 (13)C10—C1—C6—C5172.38 (14)
O7—C2—C3—C4175.09 (9)C2—C1—C6—C59.0 (2)
C1—C2—C3—C460.54 (13)C6—C1—C10—C110.6 (2)
O8—C3—C4—O957.48 (13)C2—C1—C10—C11179.10 (12)
C2—C3—C4—O9177.62 (10)C1—C10—C11—N12141 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O7—H7···O9i0.79 (2)1.93 (2)2.6885 (14)160 (2)
O8—H8···N12ii0.77 (2)2.18 (2)2.9138 (16)160 (2)
O9—H9···O7iii0.78 (3)2.02 (2)2.7944 (15)170 (2)
Symmetry codes: (i) x+2, y1/2, z+1; (ii) x+1, y, z+1; (iii) x+1, y+1/2, z+1.

Experimental details

Crystal data
Chemical formulaC8H9NO3
Mr167.16
Crystal system, space groupMonoclinic, P21
Temperature (K)193
a, b, c (Å)4.8159 (5), 10.2482 (5), 8.3573 (9)
β (°) 102.842 (4)
V3)402.15 (6)
Z2
Radiation typeCu Kα
µ (mm1)0.90
Crystal size (mm)0.60 × 0.06 × 0.06
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
2174, 1514, 1501
Rint0.021
(sin θ/λ)max1)0.609
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.026, 0.071, 1.08
No. of reflections1514
No. of parameters146
No. of restraints1
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.21, 0.12
Absolute structureFlack, (1983)
Absolute structure parameter0.04 (16)

Computer programs: CAD-4 Software (Enraf–Nonius, 1989), CORINC (Dräger & Gattow, 1971), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O7—H7···O9i0.79 (2)1.93 (2)2.6885 (14)160 (2)
O8—H8···N12ii0.77 (2)2.18 (2)2.9138 (16)160 (2)
O9—H9···O7iii0.78 (3)2.02 (2)2.7944 (15)170 (2)
Symmetry codes: (i) x+2, y1/2, z+1; (ii) x+1, y, z+1; (iii) x+1, y+1/2, z+1.
 

Acknowledgements

We thank Dr J. C. Liermann (Mainz) for performing the NMR spectroscopy.

References

First citationAltomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119.  Web of Science CrossRef CAS IUCr Journals
First citationDräger, M. & Gattow, G. (1971). Acta Chem. Scand. 25, 761–762.
First citationEnraf–Nonius (1989). CAD-4 Software. Enraf–Nonius, Delft, The Netherlands.
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals
First citationHua, Z., Zhi-Xin, L. & Jian-Min, Y. (2004). Chin. J. Chem. 22, 1200–1203.
First citationKuete, V., Poumale Poumale, H. M., Guedem, A. N., Shiono, Y., Randrianasolo, R. & Ngadjui, B. T. (2010). S. Afr. J. Bot. 76, 536–542.  Web of Science CrossRef CAS
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals

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ISSN: 2056-9890
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