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

Shao, C.-L.; Li, C.; Liu, Z.; Wei, M.-Y.; Wang, C.-Y.

doi:10.1107/S1600536808007290

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 64| Part 4| April 2008| Page o731

doi:10.1107/S1600536808007290

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

Chang-Lun Shao,^a ^* Chunyuan Li,^b Zhen Liu,^c Mei-Yan Wei ^d and Chang-Yun Wang ^a

^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 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 ).

Experimental

Crystal data

C₉H₉Cl₂NO₂
M_r = 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 ) 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[F² > 2σ(F²)] = 0.035
wR(F²) = 0.106
S = 1.06
1102 reflections
66 parameters
H-atom parameters constrained
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.39 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; 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.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808007290/bi2284sup1.cif

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

checkCIF report

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.

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

	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.

11,3-Bis(chloromethyl)-2-methyl-5-nitrobenzene top

Crystal data top

C₉H₉Cl₂NO₂	F(000) = 480
M_r = 234.07	D_x = 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 = 2.5–27.1°
b = 16.141 (6) Å	µ = 0.62 mm⁻¹
c = 7.511 (3) Å	T = 273 K
β = 111.929 (6)°	Block, colourless
V = 1003.3 (6) Å³	0.47 × 0.38 × 0.18 mm
Z = 4

Data collection top

Bruker SMART CCD diffractometer	1113 independent reflections
Radiation source: fine-focus sealed tube	976 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.017
ϕ and ω scans	θ_max = 27.1°, θ_min = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −11→9
T_min = 0.760, T_max = 0.897	k = −20→19
2900 measured reflections	l = −9→9

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.106	H-atom parameters constrained
S = 1.06	w = 1/[σ²(F_o²) + (0.0614P)² + 0.6055P] where P = (F_o² + 2F_c²)/3
1102 reflections	(Δ/σ)_max < 0.001
66 parameters	Δρ_max = 0.34 e Å⁻³
0 restraints	Δρ_min = −0.39 e Å⁻³

Crystal data top

C₉H₉Cl₂NO₂	V = 1003.3 (6) Å³
M_r = 234.07	Z = 4
Monoclinic, C2/c	Mo Kα radiation
a = 8.921 (3) Å	µ = 0.62 mm⁻¹
b = 16.141 (6) Å	T = 273 K
c = 7.511 (3) Å	0.47 × 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)
T_min = 0.760, T_max = 0.897	R_int = 0.017
2900 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.035	0 restraints
wR(F²) = 0.106	H-atom parameters constrained
S = 1.06	Δρ_max = 0.34 e Å⁻³
1102 reflections	Δρ_min = −0.39 e Å⁻³
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

	x	y	z	U_iso*/U_eq	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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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 code: (i) −x+2, y, −z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C6—H6A···O1ⁱⁱ	0.97	2.66	3.427 (3)	136

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

Experimental details

Crystal data
Chemical formula	C₉H₉Cl₂NO₂
M_r	234.07
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	273
a, b, c (Å)	8.921 (3), 16.141 (6), 7.511 (3)
β (°)	111.929 (6)
V (Å³)	1003.3 (6)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.62
Crystal size (mm)	0.47 × 0.38 × 0.18

Data collection
Diffractometer	Bruker SMART CCD diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2001)
T_min, T_max	0.760, 0.897
No. of measured, independent and observed [I > 2σ(I)] reflections	2900, 1113, 976
R_int	0.017
(sin θ/λ)_max (Å⁻¹)	0.641

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.035, 0.106, 1.06
No. of reflections	1102
No. of parameters	66
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	D—H···A
C6—H6A···O1ⁱ	0.97	2.66	3.427 (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

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