Acta Cryst. (2008). E64, o731 [ doi:10.1107/S1600536808007290 ]
The title compound, C9H9Cl2NO2, is a natural product isolated from the endophytic fungus No. B77 of the mangrove tree from the South China Sea coast. In the crystal structure, the molecules lie on twofold axes and form offset stacks through face-to-face ![[pi]](/logos/entities/pi_rmgif.gif)
- interactions. Adjacent molecules in each stack are related by a centre of inversion and have an interplanar separation of 3.53 (1) Å, with a centroid-centroid distance of 3.76 (1) Å. Between stacks, there are C-H
O interactions to the nitro groups and ClCl contacts of 3.462 (1) Å.
A strain of fungus (No. B77) was deposited in the Department of Applied Chemistry, Zhongshan University, Guangzhou, P. R. China. Culture conditions: GYT medium (glucose 10 g/L, peptone 2 g/L, yeast extract 1 g/L, NaCl 2.5 g/L) incubated at 298 K for 30 d. For the extraction and separation of the metabolite, the cultures (130 L) were filtered through cheesecloth, the filtrate was concentrated to 3 L below 323 K, then extracted three times by shaking with an equal volume of ethyl acetate. The extract was evaporated under reduced pressure and the combined organic extracts were subjected to silica-gel column chromatography, eluting with petroleum ether/ethyl acetate. Crystals of the title compound were obtained by evaporation of a methanol solution.
H atoms were positioned geometrically and treated as riding, with C—H = 0.93 (aromatic CH), 0.96 (methyl CH3) or 0.97 Å (methylene CH2), and with Uiso(H) = 1.2Ueq(CH) or 1.5Ueq(CH3, CH2).
Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
![[Figure 1]](./bi2284fig1thm.gif)
| Fig. 1. The molecular structure with displacement ellipsoids at 30% probability for non-H atoms. Primed atoms are generated by the symmetry operator: -x + 2, y, -z + 1/2. |
![[Figure 2]](./bi2284fig2thm.gif)
| Fig. 2. View of the packing along the normal to the bc-plane. |
| C9H9Cl2NO2 | F000 = 480 |
| Mr = 234.07 | Dx = 1.550 Mg m−3 |
| Monoclinic, C2/c | Mo Kα radiation λ = 0.71073 Å |
| Hall symbol: -C 2yc | Cell parameters from 711 reflections |
| a = 8.921 (3) Å | θ = 2.5–27.1º |
| b = 16.141 (6) Å | µ = 0.62 mm−1 |
| c = 7.511 (3) Å | T = 273 (2) K |
| β = 111.929 (6)º | Block, colourless |
| V = 1003.3 (6) Å3 | 0.47 × 0.38 × 0.18 mm |
| Z = 4 |
| Bruker SMART CCD diffractometer | 1113 independent reflections |
| Radiation source: fine-focus sealed tube | 976 reflections with I > 2σ(I) |
| Monochromator: graphite | Rint = 0.017 |
| T = 273(2) K | θmax = 27.1º |
| φ and ω scans | θmin = 2.5º |
| Absorption correction: multi-scan (SADABS; Bruker, 2001) | h = −11→9 |
| Tmin = 0.760, Tmax = 0.897 | k = −20→19 |
| 2900 measured reflections | l = −9→9 |
| Refinement on F2 | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| R[F2 > 2σ(F2)] = 0.035 | H-atom parameters constrained |
| wR(F2) = 0.106 | w = 1/[σ2(Fo2) + (0.0614P)2 + 0.6055P] where P = (Fo2 + 2Fc2)/3 |
| S = 1.06 | (Δ/σ)max < 0.001 |
| 1102 reflections | Δρmax = 0.34 e Å−3 |
| 66 parameters | Δρmin = −0.39 e Å−3 |
| Primary atom site location: structure-invariant direct methods | Extinction correction: none |
| C9H9Cl2NO2 | V = 1003.3 (6) Å3 |
| Mr = 234.07 | Z = 4 |
| Monoclinic, C2/c | Mo Kα |
| a = 8.921 (3) Å | µ = 0.62 mm−1 |
| b = 16.141 (6) Å | T = 273 (2) K |
| c = 7.511 (3) Å | 0.47 × 0.38 × 0.18 mm |
| β = 111.929 (6)º |
| Bruker SMART CCD diffractometer | 1113 independent reflections |
| Absorption correction: multi-scan (SADABS; Bruker, 2001) | 976 reflections with I > 2σ(I) |
| Tmin = 0.760, Tmax = 0.897 | Rint = 0.017 |
| 2900 measured reflections |
| R[F2 > 2σ(F2)] = 0.035 | 66 parameters |
| wR(F2) = 0.106 | H-atom parameters constrained |
| S = 1.06 | Δρmax = 0.34 e Å−3 |
| 1102 reflections | Δρmin = −0.39 e Å−3 |
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 | Occ. (<1) | |
| Cl1 | 0.58497 (5) | 0.11383 (3) | −0.00170 (7) | 0.0545 (2) | |
| N1 | 1.0000 | −0.17528 (13) | 0.2500 | 0.0507 (5) | |
| C3 | 0.86254 (17) | −0.04274 (9) | 0.2433 (2) | 0.0347 (3) | |
| H3A | 0.7713 | −0.0721 | 0.2379 | 0.042* | |
| C1 | 1.0000 | 0.08774 (13) | 0.2500 | 0.0332 (4) | |
| C2 | 0.86253 (17) | 0.04352 (9) | 0.2446 (2) | 0.0328 (3) | |
| C4 | 1.0000 | −0.08388 (13) | 0.2500 | 0.0347 (5) | |
| O1 | 0.8703 (2) | −0.21053 (9) | 0.2040 (3) | 0.0840 (6) | |
| C5 | 1.0000 | 0.18142 (15) | 0.2500 | 0.0528 (6) | |
| H5A | 0.8974 | 0.2012 | 0.2461 | 0.079* | 0.50 |
| H5B | 1.0186 | 0.2012 | 0.1395 | 0.079* | 0.50 |
| H5C | 1.0840 | 0.2012 | 0.3644 | 0.079* | 0.50 |
| C6 | 0.71110 (19) | 0.08572 (12) | 0.2402 (2) | 0.0438 (4) | |
| H6A | 0.7393 | 0.1351 | 0.3195 | 0.053* | |
| H6B | 0.6520 | 0.0489 | 0.2925 | 0.053* |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Cl1 | 0.0409 (3) | 0.0665 (4) | 0.0483 (3) | 0.01565 (19) | 0.0076 (2) | 0.00775 (19) |
| N1 | 0.0643 (14) | 0.0341 (10) | 0.0476 (12) | 0.000 | 0.0139 (10) | 0.000 |
| C3 | 0.0296 (7) | 0.0409 (8) | 0.0314 (7) | −0.0052 (6) | 0.0088 (6) | 0.0017 (6) |
| C1 | 0.0345 (10) | 0.0339 (10) | 0.0289 (10) | 0.000 | 0.0092 (8) | 0.000 |
| C2 | 0.0292 (7) | 0.0403 (8) | 0.0276 (7) | 0.0035 (6) | 0.0091 (6) | 0.0004 (5) |
| C4 | 0.0394 (11) | 0.0311 (10) | 0.0300 (10) | 0.000 | 0.0087 (8) | 0.000 |
| O1 | 0.0821 (12) | 0.0432 (8) | 0.1149 (15) | −0.0220 (8) | 0.0233 (11) | −0.0013 (9) |
| C5 | 0.0587 (16) | 0.0335 (12) | 0.0644 (17) | 0.000 | 0.0209 (13) | 0.000 |
| C6 | 0.0346 (8) | 0.0570 (10) | 0.0398 (8) | 0.0109 (7) | 0.0139 (7) | 0.0025 (7) |
| Cl1—C6 | 1.8017 (18) | C1—C5 | 1.512 (3) |
| N1—O1 | 1.2178 (19) | C2—C6 | 1.502 (2) |
| N1—C4 | 1.475 (3) | C5—H5A | 0.960 |
| C3—C4 | 1.3787 (19) | C5—H5B | 0.960 |
| C3—C2 | 1.392 (2) | C5—H5C | 0.960 |
| C3—H3A | 0.930 | C6—H6A | 0.970 |
| C1—C2 | 1.4064 (18) | C6—H6B | 0.970 |
| O1—N1—O1i | 124.3 (2) | C3—C4—N1 | 118.79 (10) |
| O1—N1—C4 | 117.85 (12) | C1—C5—H5A | 109.5 |
| O1i—N1—C4 | 117.85 (12) | C1—C5—H5B | 109.5 |
| C4—C3—C2 | 118.94 (14) | H5A—C5—H5B | 109.5 |
| C4—C3—H3A | 120.5 | C1—C5—H5C | 109.5 |
| C2—C3—H3A | 120.5 | H5A—C5—H5C | 109.5 |
| C2—C1—C2i | 119.01 (19) | H5B—C5—H5C | 109.5 |
| C2—C1—C5 | 120.50 (10) | C2—C6—Cl1 | 110.75 (11) |
| C2i—C1—C5 | 120.50 (10) | C2—C6—H6A | 109.5 |
| C3—C2—C1 | 120.34 (13) | Cl1—C6—H6A | 109.5 |
| C3—C2—C6 | 117.12 (14) | C2—C6—H6B | 109.5 |
| C1—C2—C6 | 122.53 (15) | Cl1—C6—H6B | 109.5 |
| C3i—C4—C3 | 122.4 (2) | H6A—C6—H6B | 108.1 |
| C3i—C4—N1 | 118.79 (10) | ||
| C4—C3—C2—C1 | 0.91 (19) | C2—C3—C4—N1 | 179.54 (9) |
| C4—C3—C2—C6 | −179.08 (11) | O1—N1—C4—C3i | −164.92 (14) |
| C2i—C1—C2—C3 | −0.46 (10) | O1i—N1—C4—C3i | 15.08 (14) |
| C5—C1—C2—C3 | 179.54 (10) | O1—N1—C4—C3 | 15.08 (14) |
| C2i—C1—C2—C6 | 179.53 (15) | O1i—N1—C4—C3 | −164.92 (14) |
| C5—C1—C2—C6 | −0.47 (15) | C3—C2—C6—Cl1 | −95.84 (15) |
| C2—C3—C4—C3i | −0.46 (9) | C1—C2—C6—Cl1 | 84.18 (15) |
| Symmetry codes: (i) −x+2, y, −z+1/2. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| C6—H6A···O1ii | 0.97 | 2.66 | 3.427 (3) | 136 |
| Symmetry codes: (ii) −x+3/2, y+1/2, −z+1/2. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| C6—H6A···O1i | 0.97 | 2.66 | 3.427 (3) | 136 |
| Symmetry codes: (i) −x+3/2, y+1/2, −z+1/2. |
Financial support is acknowledged from the National Natural Science Foundation of China (Nos. 40776073, 20072058), the Cultivation Fund of the Key Scientific and Technical Innovation Project, Ministry of Education of China (No. 706038), the Program for New Century Excellent Talents in Universities, Ministry of Education of China (No. NCET-05–0600), Post-Doctoral Start-up Fund of Ocean University of China (No. 1404–82421036) and Syngenta Limited, UK.
Bruker (1997). SMART. Bruker AXS Inc., Madison, Wisconsin, USA.
Bruker (2001). SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
Mcbee, E. T. (1951). J. Am. Chem. Soc. 73, 3932–3934.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.
The title compound was isolated from the endophytic fungus No.B77 from the mangrove tree from the South China Sea coast. As far as we know, this compound has not been reported previously as a natural product, but only as a synthetic compound (Mcbee, 1951). The molecules lie on crystallographic twofold axes (Fig. 1) and form offset π···π stacks (Fig. 2).