5-Meth­oxy-2-methyl-4-nitro-1-phenyl-1H-imidazole

The title compound, C₁₁H₁₁N₃O₃, contains two planar fragments, viz. the imidazole and phenyl rings. These rings are significantly twisted with respect one to another, with a dihedral angle of 63.99 (8)°. The nitro group is almost coplanar with the imidazole plane, while the meth­oxy group is almost perpendicular to it [the C—C—O—C torsion angle is 65.1 (4)°]. In spite of this, there is a short C(meth­oxy)—H...O(nitro) contact that might be regarded as an intra­molecular hydrogen bond. Weak inter­molecular C—H...N(imidazole) and C—H...O(nitro) hydrogen bonds create quite a complicated network that consists of stacks of imidazole rings strengthened by these hydrogen bonds. The significant twist between the planar fragments is a necessary condition for creating such a packing, which has also been observed in some other 1-aryl-4-nitro­imidazole derivatives.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.034
• wR factor = 0.058
• Data-to-parameter ratio = 9.0

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT432_ALERT_2_B Short Inter X...Y Contact  O5     ..  C51     ..       2.91 Ang.

Alert level C
PLAT230_ALERT_2_C Hirshfeld Test Diff for    O42    -   N4      ..       5.44 su
PLAT390_ALERT_3_C Deviating Methyl C51     X-C-H Bond Angle ......     102.80 Deg.
PLAT391_ALERT_3_C Deviating Methyl C51     H-C-H Bond Angle ......     117.50 Deg.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H16    ..  O41     ..       2.69 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H21A   ..  O5      ..       2.84 Ang.

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           29.26
           From the CIF: _reflns_number_total               1739
           Count of symmetry unique reflns         1821
           Completeness (_total/calc)             95.50%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   5 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

S1. Comment

Nitroimidazoles have been intensively investigated as radiosensitizers of hypoxic tumor cells and as veterinary drugs (Smithen & Hardy, 1982). For some time we have studied weak intermolecular interactions in 4-nitroimidazole derivatives (e.g. Kubicki et al., 2001, 2002).

Similar packing by means of weak C—H···N and C—H···O hydrogen bonds was observed in the crystal structures of (1–4'-methylphenyl)- and (1–4'-methoxyphenyl)-4-nitro-5-methylimidazole (Kubicki, 2004). Interestingly, both these compounds have similar packing modes in spite of crystallizing in different space groups, the former one in the non-centrosymmetric Pna2₁, and the latter in centrosymmetric P2₁/c. The title compound is a third example, in still another space group (P2₁2₁2₁). All three compounds have also similar unit-cell parameters a, b and c. A comparison of the unit-cell parameters of the title compound determined at 100 K with those determined at room temperature [6.800 (1), 7.527 (1), 23.103 (2)] shows that the compression perpendicular to the imidazole ring planes (i.e. along stack axis, a) is the strongest. That might be related to the lack of π-π interactions in this case, the imidazole planes are parallel but shifted.

Related literature

The present work is a part of our study of intermolecular interactions in 4-nitroimidazole derivatives, which started with 1-phenyl-4-nitroimidazole (Kubicki et al., 2001, 2002). A similar packing of 1-aryl-4-nitroimidazoles was described in detail by Kubicki (2004). For related literature, see: Smithen & Hardy (1982).

S2. Experimental

1.2 g of Sodium was dissolved in 50 ml of dry methanol. To the resulting warm solution, 0.52 g (2 mmol) of 5-bromo-2-methyl-4-nitro-1-phenylimidazole was added and the reaction mixture was stirred at room temperature for 24 h. Afterwards the mixture was neutralized by concentrated HCl to pH 7 and the excess of methanol was removed under vacuum. The residue was treated by 20 ml of water and the organic solid was filtered off, dried then recrystallized from hot methanol to give 0.25 g (54%) of the product.

S3. Refinement

Friedel pairs were merged by SORTAV (Blessing, 1989). Hydrogen atoms were freely refined, for hydrogen atoms of each methyl group one common isotropic displacement parameter was used.

Computing details

Data collection: CrysAlis CCD (Oxford Diffraction, 2002); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. Anisotropic displacement ellipsoid representation (at the 50% probability level) of the title compound (Siemens, 1989), together with numbering scheme. The hydrogen atoms are drawn as spheres with arbitrary radii.
	Fig. 2. View of the stacking of molecules with weak hydrogen bonds depicted as dashed lines. The view is approximately along direction [103] and the stacking is parallel to (100). The symmetry codes: (i) x,y,z, (ii): x,-1 + y,z, (iii) -1/2 + x,1/2 - y,-z, (iv) -1/2 + x,-1/2 - y,-z, (v) 1/2 + x,1/2 - y,-z, (vi) 1/2 + x,-1/2 - y,-z, (vii) 1 + x,y,z, (viii) 1 + x,-1 + y, z.

5-Methoxy-2-methyl-4-nitro-1-phenyl-1H-imidazole

Crystal data

C11H11N3O3	F(000) = 488
Mr = 233.23	Dx = 1.356 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 4053 reflections
a = 6.6179 (4) Å	θ = 3–20°
b = 7.4711 (5) Å	µ = 0.10 mm^−1
c = 23.1087 (15) Å	T = 100 K
V = 1142.56 (13) Å^3	Block, colourless
Z = 4	0.2 × 0.2 × 0.05 mm

Data collection

Kuma KM4 CCD four-circle diffractometer	1739 independent reflections
Radiation source: fine-focus sealed tube	1210 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.045
ω scans	θmax = 29.3°, θmin = 3.2°
Absorption correction: multi-scan (SORTAV; Blessing, 1989)	h = −8→8
Tmin = 0.989, Tmax = 0.989	k = −9→9
7520 measured reflections	l = −26→30

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.034	Hydrogen site location: difference Fourier map
wR(F^2) = 0.058	All H-atom parameters refined
S = 1.00	w = 1/[σ^2(Fo^2) + (0.019P)^2] where P = (Fo^2 + 2Fc^2)/3
1739 reflections	(Δ/σ)max < 0.001
194 parameters	Δρmax = 0.15 e Å^−3
0 restraints	Δρmin = −0.24 e Å^−3

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
N1	0.7905 (3)	0.35064 (19)	0.09665 (6)	0.0177 (3)
C11	0.7920 (3)	0.4361 (2)	0.15235 (8)	0.0204 (4)
C12	0.6282 (4)	0.4126 (3)	0.18903 (9)	0.0305 (6)
H12	0.522 (3)	0.343 (2)	0.1755 (8)	0.025 (6)*
C13	0.6299 (4)	0.4964 (4)	0.24273 (10)	0.0394 (6)
H13	0.509 (4)	0.471 (3)	0.2681 (9)	0.056 (8)*
C14	0.7895 (4)	0.6040 (3)	0.25869 (9)	0.0347 (6)
H14	0.788 (3)	0.660 (3)	0.2980 (9)	0.039 (6)*
C15	0.9515 (4)	0.6282 (3)	0.22155 (9)	0.0298 (5)
H15	1.071 (3)	0.715 (3)	0.2320 (8)	0.039 (6)*
C16	0.9536 (4)	0.5429 (3)	0.16797 (9)	0.0242 (5)
H16	1.063 (3)	0.558 (2)	0.1431 (9)	0.031 (6)*
C2	0.7919 (3)	0.1686 (2)	0.08417 (7)	0.0193 (4)
C21	0.7984 (4)	0.0271 (3)	0.12882 (9)	0.0279 (5)
H21A	0.859 (4)	−0.080 (3)	0.1163 (10)	0.053 (5)*
H21B	0.662 (3)	0.001 (3)	0.1402 (10)	0.053 (5)*
H21C	0.862 (3)	0.059 (3)	0.1615 (10)	0.053 (5)*
N3	0.7887 (3)	0.14035 (18)	0.02801 (6)	0.0190 (4)
C4	0.7847 (3)	0.3083 (2)	0.00357 (8)	0.0179 (4)
N4	0.7881 (3)	0.3282 (2)	−0.05751 (6)	0.0230 (4)
O41	0.7858 (2)	0.19203 (18)	−0.08821 (5)	0.0314 (4)
O42	0.7943 (2)	0.48142 (18)	−0.07788 (5)	0.0288 (4)
C5	0.7861 (3)	0.4404 (2)	0.04442 (8)	0.0184 (4)
O5	0.7854 (2)	0.61860 (15)	0.04423 (5)	0.0209 (3)
C51	0.6031 (4)	0.7009 (3)	0.02080 (12)	0.0300 (6)
H51A	0.572 (4)	0.647 (3)	−0.0184 (10)	0.054 (4)*
H51B	0.635 (3)	0.829 (3)	0.0222 (9)	0.054 (4)*
H51C	0.502 (4)	0.678 (3)	0.0476 (10)	0.054 (4)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0194 (8)	0.0163 (8)	0.0173 (8)	−0.0006 (8)	0.0005 (8)	−0.0010 (7)
C11	0.0250 (11)	0.0194 (10)	0.0169 (9)	0.0053 (9)	−0.0023 (11)	−0.0022 (8)
C12	0.0266 (13)	0.0399 (15)	0.0250 (13)	−0.0019 (11)	0.0009 (11)	−0.0061 (11)
C13	0.0331 (14)	0.0573 (17)	0.0277 (13)	0.0048 (14)	0.0067 (11)	−0.0091 (13)
C14	0.0422 (14)	0.0404 (14)	0.0215 (11)	0.0139 (13)	−0.0065 (13)	−0.0107 (10)
C15	0.0379 (14)	0.0237 (12)	0.0277 (12)	0.0033 (12)	−0.0102 (11)	−0.0056 (10)
C16	0.0267 (13)	0.0232 (12)	0.0227 (11)	−0.0018 (10)	−0.0012 (10)	0.0002 (10)
C2	0.0179 (10)	0.0177 (10)	0.0224 (10)	−0.0003 (9)	0.0001 (10)	−0.0015 (8)
C21	0.0374 (14)	0.0232 (12)	0.0231 (11)	−0.0020 (13)	−0.0004 (12)	0.0022 (9)
N3	0.0177 (8)	0.0186 (8)	0.0205 (8)	0.0025 (8)	0.0005 (8)	−0.0007 (7)
C4	0.0156 (10)	0.0221 (10)	0.0162 (9)	−0.0001 (10)	−0.0002 (9)	0.0003 (8)
N4	0.0183 (9)	0.0307 (11)	0.0199 (9)	−0.0010 (9)	−0.0008 (8)	−0.0015 (8)
O41	0.0408 (9)	0.0326 (8)	0.0208 (7)	−0.0001 (8)	0.0004 (8)	−0.0093 (6)
O42	0.0333 (9)	0.0294 (8)	0.0237 (7)	−0.0015 (9)	−0.0024 (7)	0.0078 (6)
C5	0.0156 (10)	0.0187 (10)	0.0210 (10)	−0.0019 (9)	0.0004 (10)	0.0017 (8)
O5	0.0240 (7)	0.0145 (7)	0.0244 (7)	−0.0006 (7)	−0.0045 (7)	0.0013 (5)
C51	0.0241 (13)	0.0229 (12)	0.0430 (15)	0.0035 (10)	−0.0059 (11)	−0.0010 (12)

Geometric parameters (Å, º)

N1—C5	1.381 (2)	C2—C21	1.478 (3)
N1—C2	1.390 (2)	C21—H21A	0.94 (2)
N1—C11	1.437 (2)	C21—H21B	0.96 (2)
C11—C16	1.382 (3)	C21—H21C	0.90 (2)
C11—C12	1.388 (3)	N3—C4	1.376 (2)
C12—C13	1.390 (3)	C4—C5	1.366 (2)
C12—H12	0.93 (2)	C4—N4	1.419 (2)
C13—C14	1.378 (4)	N4—O42	1.2384 (18)
C13—H13	1.01 (2)	N4—O41	1.2404 (18)
C14—C15	1.385 (3)	C5—O5	1.332 (2)
C14—H14	1.00 (2)	O5—C51	1.458 (2)
C15—C16	1.392 (3)	C51—H51A	1.01 (2)
C15—H15	1.05 (2)	C51—H51B	0.98 (2)
C16—H16	0.93 (2)	C51—H51C	0.93 (2)
C2—N3	1.315 (2)
C5—N1—C2	107.08 (14)	C2—C21—H21A	113.9 (14)
C5—N1—C11	124.57 (13)	C2—C21—H21B	107.9 (14)
C2—N1—C11	128.35 (14)	H21A—C21—H21B	108 (2)
C16—C11—C12	121.21 (18)	C2—C21—H21C	114.3 (15)
C16—C11—N1	119.74 (19)	H21A—C21—H21C	106 (2)
C12—C11—N1	119.04 (19)	H21B—C21—H21C	105 (2)
C11—C12—C13	118.8 (2)	C2—N3—C4	105.01 (15)
C11—C12—H12	117.1 (12)	C5—C4—N3	112.03 (15)
C13—C12—H12	124.1 (12)	C5—C4—N4	127.70 (16)
C14—C13—C12	120.5 (2)	N3—C4—N4	120.21 (16)
C14—C13—H13	124.2 (13)	O42—N4—O41	122.75 (14)
C12—C13—H13	115.2 (13)	O42—N4—C4	118.39 (15)
C13—C14—C15	120.2 (2)	O41—N4—C4	118.86 (16)
C13—C14—H14	118.7 (13)	O5—C5—C4	136.08 (17)
C15—C14—H14	121.1 (13)	O5—C5—N1	119.24 (15)
C14—C15—C16	119.9 (2)	C4—C5—N1	104.68 (14)
C14—C15—H15	121.3 (11)	C5—O5—C51	115.18 (17)
C16—C15—H15	118.7 (11)	O5—C51—H51A	109.3 (14)
C11—C16—C15	119.2 (2)	O5—C51—H51B	102.7 (14)
C11—C16—H16	120.5 (12)	H51A—C51—H51B	117.3 (19)
C15—C16—H16	120.2 (13)	O5—C51—H51C	105.8 (15)
N3—C2—N1	111.20 (15)	H51A—C51—H51C	112.2 (19)
N3—C2—C21	125.09 (16)	H51B—C51—H51C	108.4 (19)
N1—C2—C21	123.71 (16)
C5—N1—C11—C16	−63.6 (3)	C21—C2—N3—C4	−179.5 (2)
C2—N1—C11—C16	116.7 (2)	C2—N3—C4—C5	0.2 (3)
C5—N1—C11—C12	114.9 (2)	C2—N3—C4—N4	177.62 (19)
C2—N1—C11—C12	−64.7 (3)	C5—C4—N4—O42	0.4 (4)
C16—C11—C12—C13	−1.1 (3)	N3—C4—N4—O42	−176.55 (18)
N1—C11—C12—C13	−179.62 (19)	C5—C4—N4—O41	−179.9 (2)
C11—C12—C13—C14	1.4 (4)	N3—C4—N4—O41	3.1 (3)
C12—C13—C14—C15	−0.7 (4)	N3—C4—C5—O5	179.4 (2)
C13—C14—C15—C16	−0.3 (3)	N4—C4—C5—O5	2.2 (5)
C12—C11—C16—C15	0.1 (3)	N3—C4—C5—N1	−0.2 (3)
N1—C11—C16—C15	178.63 (17)	N4—C4—C5—N1	−177.4 (2)
C14—C15—C16—C11	0.6 (3)	C2—N1—C5—O5	−179.5 (2)
C5—N1—C2—N3	0.0 (2)	C11—N1—C5—O5	0.8 (3)
C11—N1—C2—N3	179.7 (2)	C2—N1—C5—C4	0.1 (2)
C5—N1—C2—C21	179.4 (2)	C11—N1—C5—C4	−179.6 (2)
C11—N1—C2—C21	−0.9 (4)	C4—C5—O5—C51	65.1 (4)
N1—C2—N3—C4	−0.1 (2)	N1—C5—O5—C51	−115.4 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C51—H51A···O42	1.01 (2)	2.36 (2)	3.081 (3)	127.2 (18)
C12—H12···O41^i	0.93 (2)	2.567 (19)	3.343 (3)	141.6 (15)
C16—H16···O41^ii	0.93 (2)	2.69 (2)	3.363 (3)	129.5 (15)
C21—H21A···O5^iii	0.94 (2)	2.84 (2)	3.626 (3)	141.2 (18)
C51—H51B···N3^iv	0.98 (2)	2.54 (2)	3.510 (3)	168.8 (19)

Symmetry codes: (i) x−1/2, −y+1/2, −z; (ii) x+1/2, −y+1/2, −z; (iii) x, y−1, z; (iv) x, y+1, z.