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 ▶).

Experimental

Crystal data

• C₉H₉Cl₂NO₂

• M _r = 234.07

• Monoclinic,

• a = 8.921 (3) Å

• b = 16.141 (6) Å

• c = 7.511 (3) Å

• β = 111.929 (6)°

• V = 1003.3 (6) ų

• 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[F ² > 2σ(F ²)] = 0.035

• wR(F ²) = 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

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.

Supplementary Material

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

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) .

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 U_iso(H) = 1.2U_eq(CH) or 1.5U_eq(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

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

Data collection

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

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

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 (Ų)

	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*

Atomic displacement parameters (Ų)

	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, °)

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.

Hydrogen-bond geometry (Å, °)

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.