organic compounds
(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
The 8H9NO3, is characterized by a complex three-dimensional hydrogen-bond network in which every molecule is connected to six symmetry-related neighbours.
of the title compound, CRelated literature
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
Crystal data
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Data collection
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Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell CAD-4 Software; 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.
Supporting information
10.1107/S1600536812035313/nc2287sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812035313/nc2287Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812035313/nc2287Isup3.cml
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
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.All hydrogen atoms were located from a difference Fourier map and refined with isotropic displacement parameters. The
was determined on the basis of 705 Friedel pairs.Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell
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).Fig. 1. Crystal structure of the title compound with labelling and displacement ellipsoids drawn at the 50% probability level. Fig. 2. 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. |
C8H9NO3 | F(000) = 176 |
Mr = 167.16 | Dx = 1.380 Mg m−3 |
Monoclinic, P21 | Cu Kα radiation, λ = 1.54178 Å |
Hall symbol: P 2yb | Cell parameters from 25 reflections |
a = 4.8159 (5) Å | θ = 35–46° |
b = 10.2482 (5) Å | µ = 0.90 mm−1 |
c = 8.3573 (9) Å | T = 193 K |
β = 102.842 (4)° | Needle, colourless |
V = 402.15 (6) Å3 | 0.60 × 0.06 × 0.06 mm |
Z = 2 |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.021 |
Radiation source: rotating anode | θmax = 70.0°, θmin = 5.4° |
Graphite monochromator | h = −5→5 |
ω/2θ scans | k = −12→12 |
2174 measured reflections | l = −10→10 |
1514 independent reflections | 3 standard reflections every 60 min |
1501 reflections with I > 2σ(I) | intensity decay: 5% |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | All 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 = 1.08 | Δρmax = 0.21 e Å−3 |
1514 reflections | Δρmin = −0.12 e Å−3 |
146 parameters | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
1 restraint | Extinction coefficient: 0.018 (3) |
Primary atom site location: structure-invariant direct methods | Absolute structure: Flack, (1983) |
Secondary atom site location: difference Fourier map | Absolute structure parameter: −0.04 (16) |
C8H9NO3 | V = 402.15 (6) Å3 |
Mr = 167.16 | Z = 2 |
Monoclinic, P21 | Cu Kα radiation |
a = 4.8159 (5) Å | µ = 0.90 mm−1 |
b = 10.2482 (5) Å | T = 193 K |
c = 8.3573 (9) Å | 0.60 × 0.06 × 0.06 mm |
β = 102.842 (4)° |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.021 |
2174 measured reflections | 3 standard reflections every 60 min |
1514 independent reflections | intensity decay: 5% |
1501 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.026 | All H-atom parameters refined |
wR(F2) = 0.071 | Δρmax = 0.21 e Å−3 |
S = 1.08 | Δρmin = −0.12 e Å−3 |
1514 reflections | Absolute structure: Flack, (1983) |
146 parameters | Absolute structure parameter: −0.04 (16) |
1 restraint |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.4167 (3) | 0.60278 (13) | 0.16499 (15) | 0.0204 (3) | |
C2 | 0.6543 (3) | 0.54538 (12) | 0.29376 (15) | 0.0193 (3) | |
H2 | 0.822 (3) | 0.5471 (15) | 0.2490 (18) | 0.014 (3)* | |
C3 | 0.7220 (3) | 0.63193 (13) | 0.44623 (15) | 0.0195 (3) | |
H3 | 0.881 (4) | 0.5923 (17) | 0.525 (2) | 0.023 (4)* | |
C4 | 0.8147 (3) | 0.76563 (13) | 0.39626 (17) | 0.0244 (3) | |
H4 | 0.992 (4) | 0.7516 (17) | 0.364 (2) | 0.023 (4)* | |
C5 | 0.6001 (3) | 0.81945 (14) | 0.2530 (2) | 0.0291 (3) | |
H5 | 0.591 (4) | 0.911 (2) | 0.238 (2) | 0.041 (5)* | |
C6 | 0.4214 (3) | 0.74407 (14) | 0.14727 (17) | 0.0277 (3) | |
H6 | 0.289 (4) | 0.7814 (18) | 0.059 (2) | 0.023 (4)* | |
O7 | 0.5884 (2) | 0.41531 (9) | 0.32843 (12) | 0.0246 (2) | |
H7 | 0.730 (5) | 0.381 (2) | 0.375 (2) | 0.038 (5)* | |
O8 | 0.47685 (18) | 0.64281 (10) | 0.51340 (11) | 0.0221 (2) | |
H8 | 0.530 (4) | 0.644 (2) | 0.607 (3) | 0.031 (5)* | |
O9 | 0.8700 (2) | 0.85292 (10) | 0.53125 (14) | 0.0320 (3) | |
H9 | 0.730 (5) | 0.870 (2) | 0.559 (3) | 0.045 (6)* | |
C10 | 0.2197 (3) | 0.52459 (15) | 0.07211 (16) | 0.0252 (3) | |
H10 | 0.220 (4) | 0.431 (2) | 0.0850 (19) | 0.024 (4)* | |
C11 | −0.0065 (3) | 0.57476 (17) | −0.05275 (17) | 0.0316 (3) | |
N12 | −0.1938 (3) | 0.61195 (18) | −0.15135 (17) | 0.0451 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0145 (6) | 0.0289 (7) | 0.0186 (5) | 0.0032 (5) | 0.0053 (4) | 0.0007 (5) |
C2 | 0.0106 (6) | 0.0241 (6) | 0.0233 (6) | 0.0012 (5) | 0.0043 (5) | 0.0010 (5) |
C3 | 0.0086 (5) | 0.0255 (6) | 0.0227 (5) | 0.0031 (4) | −0.0001 (4) | 0.0005 (5) |
C4 | 0.0128 (6) | 0.0260 (7) | 0.0344 (7) | −0.0030 (5) | 0.0054 (5) | −0.0046 (5) |
C5 | 0.0271 (8) | 0.0222 (7) | 0.0391 (8) | −0.0003 (5) | 0.0098 (6) | 0.0065 (5) |
C6 | 0.0229 (7) | 0.0318 (8) | 0.0273 (6) | 0.0039 (6) | 0.0034 (5) | 0.0097 (6) |
O7 | 0.0167 (5) | 0.0204 (5) | 0.0340 (5) | 0.0034 (4) | −0.0001 (4) | 0.0022 (4) |
O8 | 0.0134 (4) | 0.0328 (5) | 0.0197 (4) | 0.0006 (4) | 0.0030 (3) | −0.0018 (4) |
O9 | 0.0135 (5) | 0.0332 (6) | 0.0489 (6) | −0.0054 (4) | 0.0060 (4) | −0.0162 (5) |
C10 | 0.0186 (6) | 0.0354 (7) | 0.0212 (6) | 0.0016 (5) | 0.0034 (5) | −0.0014 (5) |
C11 | 0.0250 (7) | 0.0477 (9) | 0.0208 (6) | −0.0052 (6) | 0.0024 (6) | −0.0037 (6) |
N12 | 0.0319 (7) | 0.0705 (11) | 0.0269 (6) | 0.0011 (7) | −0.0064 (5) | 0.0055 (6) |
C1—C10 | 1.3479 (19) | C4—H4 | 0.963 (18) |
C1—C6 | 1.4563 (19) | C5—C6 | 1.334 (2) |
C1—C2 | 1.5054 (16) | C5—H5 | 0.94 (2) |
C2—O7 | 1.4151 (15) | C6—H6 | 0.943 (18) |
C2—C3 | 1.5272 (17) | O7—H7 | 0.79 (2) |
C2—H2 | 0.962 (16) | O8—H8 | 0.77 (2) |
C3—O8 | 1.4200 (16) | O9—H9 | 0.78 (3) |
C3—C4 | 1.5277 (18) | C10—C11 | 1.426 (2) |
C3—H3 | 0.981 (17) | C10—H10 | 0.96 (2) |
C4—O9 | 1.4178 (17) | C11—N12 | 1.144 (2) |
C4—C5 | 1.5019 (19) | ||
C10—C1—C6 | 123.87 (12) | C5—C4—C3 | 110.86 (10) |
C10—C1—C2 | 120.34 (12) | O9—C4—H4 | 107.3 (10) |
C6—C1—C2 | 115.77 (11) | C5—C4—H4 | 109.1 (10) |
O7—C2—C1 | 110.18 (11) | C3—C4—H4 | 105.9 (10) |
O7—C2—C3 | 113.10 (10) | C6—C5—C4 | 122.94 (13) |
C1—C2—C3 | 110.92 (10) | C6—C5—H5 | 119.0 (12) |
O7—C2—H2 | 110.0 (10) | C4—C5—H5 | 118.1 (12) |
C1—C2—H2 | 106.6 (9) | C5—C6—C1 | 122.05 (12) |
C3—C2—H2 | 105.8 (9) | C5—C6—H6 | 120.6 (11) |
O8—C3—C2 | 109.47 (10) | C1—C6—H6 | 117.4 (11) |
O8—C3—C4 | 110.90 (11) | C2—O7—H7 | 108.3 (16) |
C2—C3—C4 | 108.30 (10) | C3—O8—H8 | 106.5 (14) |
O8—C3—H3 | 111.0 (10) | C4—O9—H9 | 111.1 (17) |
C2—C3—H3 | 108.2 (10) | C1—C10—C11 | 122.16 (14) |
C4—C3—H3 | 108.9 (10) | C1—C10—H10 | 123.0 (10) |
O9—C4—C5 | 112.14 (12) | C11—C10—H10 | 114.9 (10) |
O9—C4—C3 | 111.28 (11) | N12—C11—C10 | 177.70 (18) |
C10—C1—C2—O7 | −16.29 (16) | O8—C3—C4—C5 | −68.05 (13) |
C6—C1—C2—O7 | 165.07 (11) | C2—C3—C4—C5 | 52.09 (14) |
C10—C1—C2—C3 | −142.30 (13) | O9—C4—C5—C6 | −149.07 (14) |
C6—C1—C2—C3 | 39.06 (15) | C3—C4—C5—C6 | −24.01 (19) |
O7—C2—C3—O8 | −63.88 (13) | C4—C5—C6—C1 | 1.4 (2) |
C1—C2—C3—O8 | 60.49 (13) | C10—C1—C6—C5 | 172.38 (14) |
O7—C2—C3—C4 | 175.09 (9) | C2—C1—C6—C5 | −9.0 (2) |
C1—C2—C3—C4 | −60.54 (13) | C6—C1—C10—C11 | −0.6 (2) |
O8—C3—C4—O9 | 57.48 (13) | C2—C1—C10—C11 | −179.10 (12) |
C2—C3—C4—O9 | 177.62 (10) | C1—C10—C11—N12 | −141 (4) |
D—H···A | D—H | H···A | D···A | 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−1/2, −z+1; (ii) x+1, y, z+1; (iii) −x+1, y+1/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C8H9NO3 |
Mr | 167.16 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 193 |
a, b, c (Å) | 4.8159 (5), 10.2482 (5), 8.3573 (9) |
β (°) | 102.842 (4) |
V (Å3) | 402.15 (6) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 0.90 |
Crystal size (mm) | 0.60 × 0.06 × 0.06 |
Data collection | |
Diffractometer | Enraf–Nonius CAD-4 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2174, 1514, 1501 |
Rint | 0.021 |
(sin θ/λ)max (Å−1) | 0.609 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.026, 0.071, 1.08 |
No. of reflections | 1514 |
No. of parameters | 146 |
No. of restraints | 1 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.21, −0.12 |
Absolute structure | Flack, (1983) |
Absolute structure parameter | −0.04 (16) |
Computer programs: CAD-4 Software (Enraf–Nonius, 1989), CORINC (Dräger & Gattow, 1971), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | 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−1/2, −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
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).