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Acta Crystallogr Sect E Struct Rep Online. 2008 April 1; 64(Pt 4): o731.
Published online 2008 March 20. doi:  10.1107/S1600536808007290
PMCID: PMC2960992

1,3-Bis(chloro­meth­yl)-2-methyl-5-nitro­benzene

Abstract

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 π–π 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 Cl(...)Cl contacts of 3.462 (1) Å.

Related literature

For related literature, see: McBee (1951 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o731-scheme1.jpg

Experimental

Crystal data

  • C9H9Cl2NO2
  • M r = 234.07
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o731-efi2.jpg
  • a = 8.921 (3) Å
  • b = 16.141 (6) Å
  • c = 7.511 (3) Å
  • β = 111.929 (6)°
  • V = 1003.3 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.62 mm−1
  • T = 273 (2) K
  • 0.47 × 0.38 × 0.18 mm

Data collection

  • Bruker SMART CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.760, T max = 0.897
  • 2900 measured reflections
  • 1113 independent reflections
  • 976 reflections with I > 2σ(I)
  • R int = 0.017

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.106
  • S = 1.06
  • 1102 reflections
  • 66 parameters
  • H-atom parameters constrained
  • Δρmax = 0.34 e Å−3
  • Δρmin = −0.39 e Å−3

Data collection: SMART (Bruker, 1997 [triangle]); cell refinement: SAINT (Bruker, 2001 [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 global, I. DOI: 10.1107/S1600536808007290/bi2284sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808007290/bi2284Isup2.hkl

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

Acknowledgments

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.

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

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).

Figures

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.
Fig. 2.
View of the packing along the normal to the bc-plane.

Crystal data

C9H9Cl2NO2F000 = 480
Mr = 234.07Dx = 1.550 Mg m3
Monoclinic, C2/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 711 reflections
a = 8.921 (3) Åθ = 2.5–27.1º
b = 16.141 (6) ŵ = 0.62 mm1
c = 7.511 (3) ÅT = 273 (2) K
β = 111.929 (6)ºBlock, colourless
V = 1003.3 (6) Å30.47 × 0.38 × 0.18 mm
Z = 4

Data collection

Bruker SMART CCD diffractometer1113 independent reflections
Radiation source: fine-focus sealed tube976 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.017
T = 273(2) Kθmax = 27.1º
[var phi] and ω scansθmin = 2.5º
Absorption correction: multi-scan(SADABS; Bruker, 2001)h = −11→9
Tmin = 0.760, Tmax = 0.897k = −20→19
2900 measured reflectionsl = −9→9

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.035H-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 reflectionsΔρmax = 0.34 e Å3
66 parametersΔρmin = −0.39 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

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*/UeqOcc. (<1)
Cl10.58497 (5)0.11383 (3)−0.00170 (7)0.0545 (2)
N11.0000−0.17528 (13)0.25000.0507 (5)
C30.86254 (17)−0.04274 (9)0.2433 (2)0.0347 (3)
H3A0.7713−0.07210.23790.042*
C11.00000.08774 (13)0.25000.0332 (4)
C20.86253 (17)0.04352 (9)0.2446 (2)0.0328 (3)
C41.0000−0.08388 (13)0.25000.0347 (5)
O10.8703 (2)−0.21053 (9)0.2040 (3)0.0840 (6)
C51.00000.18142 (15)0.25000.0528 (6)
H5A0.89740.20120.24610.079*0.50
H5B1.01860.20120.13950.079*0.50
H5C1.08400.20120.36440.079*0.50
C60.71110 (19)0.08572 (12)0.2402 (2)0.0438 (4)
H6A0.73930.13510.31950.053*
H6B0.65200.04890.29250.053*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0409 (3)0.0665 (4)0.0483 (3)0.01565 (19)0.0076 (2)0.00775 (19)
N10.0643 (14)0.0341 (10)0.0476 (12)0.0000.0139 (10)0.000
C30.0296 (7)0.0409 (8)0.0314 (7)−0.0052 (6)0.0088 (6)0.0017 (6)
C10.0345 (10)0.0339 (10)0.0289 (10)0.0000.0092 (8)0.000
C20.0292 (7)0.0403 (8)0.0276 (7)0.0035 (6)0.0091 (6)0.0004 (5)
C40.0394 (11)0.0311 (10)0.0300 (10)0.0000.0087 (8)0.000
O10.0821 (12)0.0432 (8)0.1149 (15)−0.0220 (8)0.0233 (11)−0.0013 (9)
C50.0587 (16)0.0335 (12)0.0644 (17)0.0000.0209 (13)0.000
C60.0346 (8)0.0570 (10)0.0398 (8)0.0109 (7)0.0139 (7)0.0025 (7)

Geometric parameters (Å, °)

Cl1—C61.8017 (18)C1—C51.512 (3)
N1—O11.2178 (19)C2—C61.502 (2)
N1—C41.475 (3)C5—H5A0.960
C3—C41.3787 (19)C5—H5B0.960
C3—C21.392 (2)C5—H5C0.960
C3—H3A0.930C6—H6A0.970
C1—C21.4064 (18)C6—H6B0.970
O1—N1—O1i124.3 (2)C3—C4—N1118.79 (10)
O1—N1—C4117.85 (12)C1—C5—H5A109.5
O1i—N1—C4117.85 (12)C1—C5—H5B109.5
C4—C3—C2118.94 (14)H5A—C5—H5B109.5
C4—C3—H3A120.5C1—C5—H5C109.5
C2—C3—H3A120.5H5A—C5—H5C109.5
C2—C1—C2i119.01 (19)H5B—C5—H5C109.5
C2—C1—C5120.50 (10)C2—C6—Cl1110.75 (11)
C2i—C1—C5120.50 (10)C2—C6—H6A109.5
C3—C2—C1120.34 (13)Cl1—C6—H6A109.5
C3—C2—C6117.12 (14)C2—C6—H6B109.5
C1—C2—C6122.53 (15)Cl1—C6—H6B109.5
C3i—C4—C3122.4 (2)H6A—C6—H6B108.1
C3i—C4—N1118.79 (10)
C4—C3—C2—C10.91 (19)C2—C3—C4—N1179.54 (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—C3i15.08 (14)
C5—C1—C2—C3179.54 (10)O1—N1—C4—C315.08 (14)
C2i—C1—C2—C6179.53 (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—Cl184.18 (15)

Symmetry codes: (i) −x+2, y, −z+1/2.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C6—H6A···O1ii0.972.663.427 (3)136

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BI2284).

References

  • 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. [PubMed]

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