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

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ISSN: 2056-9890

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

aSchool of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China, bCollege of Science, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China, cCollege of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang, Henan 471022, People's Republic of China, and dSchool of Pharmacy, Guangdong Medical College, Dongguan, Guangdong 523808, People's Republic of China
*Correspondence e-mail: shaochanglun@ouc.edu.cn

(Received 24 February 2008; accepted 17 March 2008; online 20 March 2008)

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 ππ 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[McBee, E. T. (1951). J. Am. Chem. Soc. 73, 3932-3934.]).

[Scheme 1]

Experimental

Crystal data
  • C9H9Cl2NO2

  • Mr = 234.07

  • Monoclinic, C 2/c

  • 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[Bruker (2001). SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.760, Tmax = 0.897

  • 2900 measured reflections

  • 1113 independent reflections

  • 976 reflections with I > 2σ(I)

  • Rint = 0.017

Refinement
  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C6—H6A⋯O1i 0.97 2.66 3.427 (3) 136
Symmetry code: (i) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: SMART (Bruker, 1997[Bruker (1997). SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2001[Bruker (2001). SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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).

Related literature top

For related literature, see: Mcbee (1951).

Experimental top

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 top

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).

Computing details top

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).

Figures top
[Figure 1] 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] Fig. 2. View of the packing along the normal to the bc-plane.
11,3-Bis(chloromethyl)-2-methyl-5-nitrobenzene top
Crystal data top
C9H9Cl2NO2F(000) = 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 = 2.5–27.1°
b = 16.141 (6) ŵ = 0.62 mm1
c = 7.511 (3) ÅT = 273 K
β = 111.929 (6)°Block, colourless
V = 1003.3 (6) Å30.47 × 0.38 × 0.18 mm
Z = 4
Data collection top
Bruker SMART CCD
diffractometer
1113 independent reflections
Radiation source: fine-focus sealed tube976 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.017
ϕ and ω scansθmax = 27.1°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
h = 119
Tmin = 0.760, Tmax = 0.897k = 2019
2900 measured reflectionsl = 99
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.106H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0614P)2 + 0.6055P]
where P = (Fo2 + 2Fc2)/3
1102 reflections(Δ/σ)max < 0.001
66 parametersΔρmax = 0.34 e Å3
0 restraintsΔρmin = 0.39 e Å3
Crystal data top
C9H9Cl2NO2V = 1003.3 (6) Å3
Mr = 234.07Z = 4
Monoclinic, C2/cMo Kα radiation
a = 8.921 (3) ŵ = 0.62 mm1
b = 16.141 (6) ÅT = 273 K
c = 7.511 (3) Å0.47 × 0.38 × 0.18 mm
β = 111.929 (6)°
Data collection top
Bruker SMART CCD
diffractometer
1113 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
976 reflections with I > 2σ(I)
Tmin = 0.760, Tmax = 0.897Rint = 0.017
2900 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0350 restraints
wR(F2) = 0.106H-atom parameters constrained
S = 1.06Δρmax = 0.34 e Å3
1102 reflectionsΔρmin = 0.39 e Å3
66 parameters
Special details top

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*/UeqOcc. (<1)
Cl10.58497 (5)0.11383 (3)0.00170 (7)0.0545 (2)
N11.00000.17528 (13)0.25000.0507 (5)
C30.86254 (17)0.04274 (9)0.2433 (2)0.0347 (3)
H3A0.77130.07210.23790.042*
C11.00000.08774 (13)0.25000.0332 (4)
C20.86253 (17)0.04352 (9)0.2446 (2)0.0328 (3)
C41.00000.08388 (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) top
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, º) top
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—C6179.08 (11)O1—N1—C4—C3i164.92 (14)
C2i—C1—C2—C30.46 (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—C3164.92 (14)
C5—C1—C2—C60.47 (15)C3—C2—C6—Cl195.84 (15)
C2—C3—C4—C3i0.46 (9)C1—C2—C6—Cl184.18 (15)
Symmetry code: (i) x+2, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C6—H6A···O1ii0.972.663.427 (3)136
Symmetry code: (ii) x+3/2, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC9H9Cl2NO2
Mr234.07
Crystal system, space groupMonoclinic, C2/c
Temperature (K)273
a, b, c (Å)8.921 (3), 16.141 (6), 7.511 (3)
β (°) 111.929 (6)
V3)1003.3 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.62
Crystal size (mm)0.47 × 0.38 × 0.18
Data collection
DiffractometerBruker SMART CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.760, 0.897
No. of measured, independent and
observed [I > 2σ(I)] reflections
2900, 1113, 976
Rint0.017
(sin θ/λ)max1)0.641
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.106, 1.06
No. of reflections1102
No. of parameters66
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.34, 0.39

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C6—H6A···O1i0.972.663.427 (3)136.4
Symmetry code: (i) x+3/2, y+1/2, z+1/2.
 

Acknowledgements

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.

References

First citationBruker (1997). SMART. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBruker (2001). SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationMcBee, E. T. (1951). J. Am. Chem. Soc. 73, 3932–3934.  CrossRef CAS Web of Science Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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.

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COMMUNICATIONS
ISSN: 2056-9890
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