Two 1-substituted 4-nitro­imidazoles

Crystalline 4-nitro-1-phenyl­imidazole, C₉H₇N₃O₂, (I), and 4′-­nitro-1-phenyl-4,1′-bii­imidazole, C₁₂H₉N₅O₂, (II), contain C—H...O and C—H...N hydrogen bonds, connecting the mol­ecules into infinite chains. The aromatic fragments in both compounds are nearly planar. The dihedral angles between the benzene and imidazole rings are 26.78 (5)° in (I) and 29.36 (8)° in (II).

S1. Comment

The imidazole ring is present in a number of biologically active compounds as well as in many natural products (Josephy & Mason, 1985). 1-Substituted 4-nitroimidazoles are generated in excellent yields from the reaction of 1,4-dinitroimidazoles with primary amines (Suwiński & Salwińska, 1990; Suwiński & Wagner, 1997). Here, we present the crystal structures of two compounds of this kind, (I) and (II). \sch

In (I), both benzene and imidazole rings are almost perfectly planar [maximum deviations from the least-squares planes are 0.0070 (9) and 0.0048 (7) Å for benzene and imidazole rings, respectively] and the dihedral angle between these planes is 26.78 (5)°. The nitro group is twisted slightly but significantly [by 6.91 (14)°] with respect to the plane of the five-membered ring. The C2—N3 bond length is shorter than N3—C4 [1.311 (2) and 1.363 (2) Å, respectively]. In (II), all rings are also planar, with maximum deviations from the least-squares planes of 0.0039 (13), 0.0046 (12) and 0.0049 (17) Å for nitroimidazole, imidazole and benzene rings, respectively.

The dihedral angle between benzene and imidazole rings is 29.36 (8)° [similar value was found for (I)] while the angle between two imidazole rings is significantly smaller, 11.28 (13)°. The reason for this can be of a geometrical nature: five-membered rings afford more space around the junction bond than the six-membered one. The twist angle of nitro group is smaller than in (I) [3.3 (3)°].

In compound (I), there is a statistically significant deformation of the endocyclic bond angles pattern in the benzene ring due to the influence of electron-accepting nitroimidazole substituent. These deformations are generally consistent with those described by Domenicano (1988) and are comparable with those found for the cyano group. In (II), these effects are negligible because of weaker electron-accepting properties of imidazole as compared with the nitroimidazole.

In both compounds, there are weak though important hydrogen bonds C—H···O and C—H···N (see Table 3). In (I), two such bonds connect the molecules into infinite chains (Fig. 1). Isolated chains have also been found in the crystal structure of (II); in this case, however, chains are comprised of hydrogen-bonded centrosymmetric dimers. The linearity of these contacts as well as their determinative role in the crystal packing justify the using of the term "hydrogen bonds" in these cases (Desiraju & Steiner, 1999). We have not detected any interplanar interactions, the distance between chains being close to the sums of van der Waals radii. In the nitro group of (I), the N1—O2 bond is significantly shorter than N1—O1. These could be related to the fact that the O2 atom acts as an acceptor in a hydrogen bond, however, no such shortening can be found in 2 and therefore it probably should be labelled as an artefact.

S2. Experimental

The synthesis of the compounds (I) and (II) was described elsewhere (Suwiński & Salwińska, 1990; Suwiński & Wagner, 1997). Crystals appropriate for data collection were obtained by slow evaporation from methanol solution.

Computing details

For both compounds, data collection: CrysAlis CCD (KUMA Diffraction, 1999). Cell refinement: CrysAlis RED (KUMA Diffraction, 1999) for (I); CrysAlis CCD for (II). Data reduction: CrysAlis RED for (I); CrysAlis CCD for (II). For both compounds, program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997). Molecular graphics: Stereochemical Workstation (Siemens, 1989) for (I); Stereochemical workstation (Siemens 1989) for (II). Software used to prepare material for publication: Stereochemical Workstation for (I); Stereochemical workstation for (II).

Figures

	Fig. 1. View of hydrogen-bonded motive of compound (I) (Siemens, 1989) with the atomic labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and the hydrogen atoms are depicted as spheres of arbitrary radii. Symmetry codes: (i) x - 1/2, 1/2 - y, 1 - z; (ii) 1/2 + x, 1/2 - y, 1 - z; (iii) 1 + x, y, z.
	Fig. 2. View of hydrogen-bonded motive of compound (II) (Siemens, 1989) with the atomic labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and the hydrogen atoms are depicted as spheres of arbitrary radii. Symmetry codes: (i) - x, - y, 1 - z; (ii) -x, y - 1/2, 1/2 - z; (iii) x, -1/2 + y, 1/2 + z.

(I) 1-phenyl-4-nitroimidazole

Crystal data

C9H7N3O2	F(000) = 784
Mr = 189.18	Dx = 1.498 Mg m^−3
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 1027 reflections
a = 11.088 (2) Å	θ = 1–50°
b = 6.884 (1) Å	µ = 0.11 mm^−1
c = 21.976 (4) Å	T = 293 K
V = 1677.4 (5) Å^3	Prismatic, colourless
Z = 8	0.5 × 0.2 × 0.2 mm

Data collection

KUMA KM4-CCD diffractometer	1424 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.046
Graphite monochromator	θmax = 27.1°, θmin = 3.6°
ω/2θ scans	h = −14→14
8680 measured reflections	k = −5→8
1846 independent reflections	l = −27→28

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.035	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.096	w = 1/[σ^2(Fo^2) + (0.0573P)^2 + 0.0033P] where P = (Fo^2 + 2Fc^2)/3
S = 1.08	(Δ/σ)max = 0.001
1846 reflections	Δρmax = 0.22 e Å^−3
156 parameters	Δρmin = −0.23 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0045 (13)

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
N2	0.84427 (9)	0.09313 (16)	0.58588 (5)	0.0230 (3)
O2	0.95214 (8)	0.09132 (15)	0.59995 (4)	0.0318 (3)
N3	0.69680 (9)	0.18320 (16)	0.50867 (5)	0.0227 (3)
O1	0.76318 (9)	0.03601 (16)	0.61899 (4)	0.0352 (3)
N1	0.82342 (9)	0.26126 (14)	0.43359 (4)	0.0195 (3)
C5	0.89461 (11)	0.21182 (18)	0.48199 (5)	0.0197 (3)
C6	0.86295 (11)	0.32408 (18)	0.37463 (5)	0.0203 (3)
C11	0.97382 (12)	0.4141 (2)	0.36843 (6)	0.0238 (3)
C8	0.82550 (13)	0.3578 (2)	0.26806 (6)	0.0278 (3)
C2	0.70604 (11)	0.24310 (19)	0.45225 (6)	0.0222 (3)
C9	0.93557 (13)	0.4503 (2)	0.26129 (6)	0.0284 (3)
C4	0.81398 (11)	0.16430 (18)	0.52645 (5)	0.0201 (3)
C7	0.78864 (13)	0.2936 (2)	0.32475 (6)	0.0243 (3)
C10	1.00987 (13)	0.4773 (2)	0.31126 (6)	0.0280 (3)
H111	1.0254 (12)	0.431 (2)	0.4019 (6)	0.027 (4)*
H21	0.6390 (13)	0.270 (2)	0.4265 (6)	0.029 (4)*
H71	0.7102 (13)	0.231 (2)	0.3301 (6)	0.023 (4)*
H81	0.7721 (14)	0.340 (2)	0.2324 (7)	0.031 (4)*
H51	0.9803 (14)	0.214 (2)	0.4802 (6)	0.028 (4)*
H101	1.0879 (14)	0.547 (2)	0.3059 (6)	0.037 (4)*
H91	0.9607 (13)	0.498 (2)	0.2223 (7)	0.032 (4)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N2	0.0208 (6)	0.0288 (6)	0.0195 (6)	−0.0006 (4)	0.0019 (4)	−0.0013 (4)
O2	0.0215 (5)	0.0488 (7)	0.0251 (5)	−0.0014 (4)	−0.0027 (4)	0.0065 (4)
N3	0.0184 (6)	0.0260 (6)	0.0237 (6)	0.0007 (4)	0.0018 (4)	−0.0018 (4)
O1	0.0277 (5)	0.0551 (7)	0.0230 (5)	−0.0045 (5)	0.0069 (4)	0.0072 (5)
N1	0.0195 (5)	0.0210 (6)	0.0180 (5)	0.0000 (4)	−0.0003 (4)	−0.0001 (4)
C5	0.0176 (7)	0.0229 (7)	0.0188 (6)	0.0011 (5)	−0.0012 (4)	−0.0001 (5)
C6	0.0237 (7)	0.0193 (6)	0.0178 (6)	0.0032 (5)	0.0004 (5)	0.0004 (5)
C11	0.0227 (7)	0.0286 (7)	0.0199 (7)	0.0008 (5)	−0.0018 (5)	0.0007 (5)
C8	0.0348 (8)	0.0291 (7)	0.0195 (6)	0.0057 (6)	−0.0052 (5)	−0.0024 (5)
C2	0.0183 (6)	0.0243 (7)	0.0240 (6)	0.0005 (5)	−0.0011 (5)	−0.0019 (5)
C9	0.0350 (8)	0.0305 (8)	0.0196 (7)	0.0074 (6)	0.0045 (5)	0.0033 (6)
C4	0.0201 (6)	0.0210 (6)	0.0192 (6)	0.0002 (5)	0.0002 (5)	−0.0013 (5)
C7	0.0259 (7)	0.0237 (7)	0.0235 (7)	−0.0005 (5)	−0.0034 (5)	−0.0021 (5)
C10	0.0260 (7)	0.0316 (8)	0.0264 (7)	0.0008 (6)	0.0041 (5)	0.0041 (6)

Geometric parameters (Å, º)

N2—O1	1.2216 (13)	C5—C4	1.3641 (17)
N2—O2	1.2355 (13)	C6—C11	1.3833 (17)
N2—C4	1.4348 (16)	C6—C7	1.3872 (17)
N3—C2	1.3106 (17)	C11—C10	1.3883 (17)
N3—C4	1.3631 (16)	C8—C7	1.3837 (19)
N1—C5	1.3677 (15)	C8—C9	1.385 (2)
N1—C2	1.3703 (15)	C9—C10	1.3855 (18)
N1—C6	1.4346 (15)
O1—N2—O2	124.07 (11)	C7—C6—N1	119.11 (11)
O1—N2—C4	118.67 (10)	C6—C11—C10	119.04 (12)
O2—N2—C4	117.25 (10)	C7—C8—C9	120.27 (12)
C2—N3—C4	103.10 (10)	N3—C2—N1	112.71 (11)
C5—N1—C2	107.02 (10)	C8—C9—C10	120.04 (12)
C5—N1—C6	126.95 (10)	N3—C4—C5	113.36 (11)
C2—N1—C6	126.02 (10)	N3—C4—N2	121.11 (11)
C4—C5—N1	103.80 (11)	C5—C4—N2	125.48 (11)
C11—C6—C7	121.18 (11)	C8—C7—C6	119.18 (13)
C11—C6—N1	119.70 (11)	C9—C10—C11	120.27 (14)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H21···O2^i	0.953 (14)	2.353 (14)	3.2466 (16)	156.0 (11)
C5—H51···N3^ii	0.952 (15)	2.514 (15)	3.4338 (18)	162.5 (12)

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

(II) 1-(1-phenyl-4-imidazolyl)-4-nitroimidazole

Crystal data

C12H9N5O2	Dx = 1.498 Mg m^−3
Mr = 255.24	Melting point: 209-211 (methanol) K
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
a = 14.143 (3) Å	Cell parameters from 531 reflections
b = 3.888 (1) Å	θ = 1–50°
c = 20.660 (4) Å	µ = 0.11 mm^−1
β = 94.92 (3)°	T = 293 K
V = 1131.9 (4) Å^3	Plate, colourless
Z = 4	0.4 × 0.2 × 0.02 mm
F(000) = 528

Data collection

KUMA KM4 CCD diffractometer	1046 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.056
Graphite monochromator	θmax = 29.4°, θmin = 3.4°
ω/2θ scans	h = −19→15
6713 measured reflections	k = −5→5
2882 independent reflections	l = −27→28

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.046	All H-atom parameters refined
wR(F^2) = 0.105	w = 1/[σ^2(Fo^2) + (0.0453P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 0.78	(Δ/σ)max < 0.001
2882 reflections	Δρmax = 0.16 e Å^−3
209 parameters	Δρmin = −0.17 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0034 (10)

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
N6	0.23611 (11)	0.0437 (4)	0.39758 (7)	0.0412 (4)
N1	0.01115 (11)	−0.3600 (4)	0.37315 (7)	0.0398 (4)
C4	−0.13052 (14)	−0.5578 (6)	0.36235 (9)	0.0443 (6)
N3	−0.09174 (13)	−0.6482 (4)	0.30671 (8)	0.0490 (5)
C9	0.09675 (15)	−0.1879 (5)	0.39356 (10)	0.0398 (5)
C10	0.16838 (15)	−0.1183 (6)	0.35678 (11)	0.0437 (6)
N8	0.11439 (13)	−0.0749 (5)	0.45543 (8)	0.0536 (5)
N17	−0.22617 (13)	−0.6559 (5)	0.37163 (10)	0.0589 (5)
C11	0.32471 (14)	0.1763 (5)	0.38106 (10)	0.0425 (5)
C5	−0.06947 (15)	−0.3834 (6)	0.40436 (11)	0.0449 (6)
O2	−0.26021 (10)	−0.5573 (5)	0.42069 (8)	0.0794 (6)
C7	0.19943 (18)	0.0634 (6)	0.45584 (11)	0.0556 (7)
C2	−0.00587 (18)	−0.5220 (6)	0.31513 (10)	0.0468 (6)
O1	−0.26964 (12)	−0.8270 (5)	0.32952 (9)	0.0891 (7)
C12	0.33392 (17)	0.2862 (6)	0.31788 (11)	0.0492 (6)
C16	0.40009 (17)	0.1998 (6)	0.42756 (12)	0.0553 (7)
C14	0.49497 (19)	0.4421 (7)	0.34865 (14)	0.0615 (7)
C13	0.41958 (18)	0.4194 (6)	0.30233 (13)	0.0574 (7)
C15	0.48545 (19)	0.3308 (7)	0.41093 (15)	0.0658 (8)
H161	0.3937 (15)	0.111 (5)	0.4708 (11)	0.069 (7)*
H71	0.2321 (13)	0.173 (5)	0.4928 (9)	0.047 (6)*
H101	0.1734 (13)	−0.159 (5)	0.3134 (10)	0.056 (6)*
H51	−0.0762 (13)	−0.283 (5)	0.4459 (10)	0.051 (6)*
H21	0.0414 (14)	−0.534 (5)	0.2846 (9)	0.055 (6)*
H121	0.2758 (15)	0.271 (5)	0.2842 (10)	0.063 (7)*
H141	0.5522 (16)	0.532 (6)	0.3366 (10)	0.070 (7)*
H131	0.4236 (15)	0.500 (6)	0.2571 (11)	0.083 (8)*
H151	0.5351 (16)	0.347 (5)	0.4434 (11)	0.070 (8)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N6	0.0405 (11)	0.0476 (11)	0.0359 (10)	0.0034 (9)	0.0061 (8)	−0.0003 (9)
N1	0.0400 (11)	0.0443 (11)	0.0355 (10)	0.0035 (9)	0.0060 (8)	0.0004 (9)
C4	0.0404 (13)	0.0576 (15)	0.0348 (12)	0.0009 (11)	0.0035 (10)	−0.0001 (11)
N3	0.0540 (12)	0.0551 (12)	0.0379 (10)	0.0022 (10)	0.0030 (9)	−0.0031 (9)
C9	0.0407 (13)	0.0399 (14)	0.0390 (13)	0.0033 (11)	0.0036 (10)	−0.0001 (10)
C10	0.0444 (14)	0.0532 (15)	0.0337 (13)	0.0034 (12)	0.0044 (11)	−0.0031 (12)
N8	0.0536 (13)	0.0694 (14)	0.0386 (11)	−0.0104 (10)	0.0093 (9)	−0.0077 (10)
N17	0.0447 (12)	0.0788 (15)	0.0522 (12)	0.0007 (11)	−0.0015 (11)	−0.0107 (12)
C11	0.0399 (13)	0.0423 (13)	0.0463 (13)	0.0026 (11)	0.0100 (11)	−0.0029 (11)
C5	0.0443 (14)	0.0551 (15)	0.0357 (13)	0.0039 (12)	0.0053 (11)	−0.0018 (12)
O2	0.0547 (11)	0.1269 (16)	0.0585 (11)	−0.0137 (10)	0.0163 (9)	−0.0240 (11)
C7	0.0587 (16)	0.0717 (18)	0.0366 (14)	−0.0082 (14)	0.0057 (12)	−0.0126 (13)
C2	0.0534 (16)	0.0512 (15)	0.0366 (13)	0.0056 (12)	0.0083 (12)	−0.0017 (12)
O1	0.0596 (11)	0.1261 (17)	0.0801 (13)	−0.0193 (11)	−0.0034 (10)	−0.0435 (12)
C12	0.0435 (14)	0.0550 (16)	0.0502 (15)	0.0063 (12)	0.0103 (12)	−0.0002 (12)
C16	0.0522 (16)	0.0619 (17)	0.0514 (15)	−0.0007 (13)	0.0026 (13)	0.0075 (13)
C14	0.0490 (17)	0.0568 (17)	0.081 (2)	−0.0042 (13)	0.0218 (16)	0.0024 (15)
C13	0.0559 (17)	0.0585 (17)	0.0599 (17)	0.0054 (14)	0.0158 (14)	0.0045 (14)
C15	0.0483 (17)	0.074 (2)	0.0729 (19)	−0.0025 (15)	−0.0052 (15)	−0.0012 (16)

Geometric parameters (Å, º)

N6—C7	1.353 (2)	C9—N8	1.354 (2)
N6—C10	1.374 (2)	N8—C7	1.317 (3)
N6—C11	1.423 (2)	N17—O1	1.219 (2)
N1—C2	1.357 (2)	N17—O2	1.220 (2)
N1—C5	1.360 (2)	C11—C16	1.376 (3)
N1—C9	1.415 (2)	C11—C12	1.390 (3)
C4—C5	1.353 (3)	C12—C13	1.381 (3)
C4—N3	1.362 (2)	C16—C15	1.381 (3)
C4—N17	1.434 (3)	C14—C13	1.373 (3)
N3—C2	1.308 (3)	C14—C15	1.375 (3)
C9—C10	1.345 (3)
C7—N6—C10	105.75 (19)	O1—N17—O2	123.6 (2)
C7—N6—C11	127.3 (2)	O1—N17—C4	118.3 (2)
C10—N6—C11	126.94 (17)	O2—N17—C4	118.1 (2)
C2—N1—C5	107.17 (18)	C16—C11—C12	120.4 (2)
C2—N1—C9	124.39 (17)	C16—C11—N6	120.14 (19)
C5—N1—C9	128.37 (17)	C12—C11—N6	119.5 (2)
C5—C4—N3	112.94 (19)	C4—C5—N1	104.14 (19)
C5—C4—N17	127.2 (2)	N8—C7—N6	113.0 (2)
N3—C4—N17	119.8 (2)	N3—C2—N1	112.6 (2)
C2—N3—C4	103.16 (18)	C13—C12—C11	119.2 (2)
C10—C9—N8	112.41 (19)	C11—C16—C15	119.5 (2)
C10—C9—N1	126.39 (18)	C13—C14—C15	120.0 (3)
N8—C9—N1	121.20 (18)	C14—C13—C12	120.4 (2)
C9—C10—N6	105.36 (18)	C14—C15—C16	120.5 (3)
C7—N8—C9	103.46 (18)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C7—H71···O2^i	0.959 (19)	2.34 (2)	3.249 (3)	158.9 (15)
C5—H51···N8^i	0.955 (19)	2.56 (2)	3.505 (3)	168.7 (15)
C2—H21···N3^ii	0.959 (19)	2.56 (2)	3.309 (3)	135.2 (16)
C10—H101···N3^ii	0.919 (19)	2.65 (2)	3.460 (3)	148.0 (16)

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