1-(2-Methyl-5-nitro-1H-imidazol-1-yl)acetone

Abstract

In the mol­ecule of the title compound, C₇H₉N₃O₃, the nitro and carbonyl groups are tilted with respect to the imidazole ring by 9.16 (6) and 65.47 (7)°, respectively. Neighbouring chains are linked via C—H⋯N and C—H⋯O hydrogen bonds forming two-dimensional slab-like networks lying parallel to (01-1).

Related literature  

For the anti­biotic properties of metronidazole and mecnidazole, see: Lin et al. (2012 ▶); Almirall et al. (2011 ▶); Zhang et al. (2011 ▶). For the crystal structure of related imidazoles, see: Yousuf et al. (2012 ▶); Zeb et al. (2012 ▶).

Experimental  

Crystal data  

• C₇H₉N₃O₃

• M _r = 183.17

• Monoclinic,

• a = 4.7548 (4) Å

• b = 12.3971 (9) Å

• c = 14.8580 (11) Å

• β = 97.350 (2)°

• V = 868.62 (12) ų

• Z = 4

• Mo Kα radiation

• μ = 0.11 mm⁻¹

• T = 273 K

• 0.52 × 0.33 × 0.24 mm

Data collection  

• Bruker SMART APEX CCD area-detector diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2000 ▶) T _min = 0.944, T _max = 0.974

• 5030 measured reflections

• 1614 independent reflections

• 1328 reflections with I > 2σ(I)

• R _int = 0.019

Refinement  

• R[F ² > 2σ(F ²)] = 0.041

• wR(F ²) = 0.122

• S = 1.06

• 1614 reflections

• 120 parameters

• H-atom parameters constrained

• Δρ_max = 0.19 e Å⁻³

• Δρ_min = −0.15 e Å⁻³

Data collection: SMART (Bruker, 2000 ▶); cell refinement: SAINT (Bruker, 2000 ▶); 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, PARST (Nardelli, 1995 ▶) and PLATON (Spek, 2009 ▶).

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
C2—H2B⋯N2i	0.93	2.56	3.361 (2)	144
C5—H5B⋯O2ii	0.97	2.57	3.527 (2)	167
C7—H7B⋯O3iii	0.96	2.49	3.340 (2)	147

Symmetry codes: (i) ; (ii) ; (iii) .

supplementary crystallographic information

Comment

Imidazole nuclei containing metronidazole and mecnidazole are widely used antibiotics, known to be effective against anaerobic microorganisms. These drugs employed to cure amoebiasis (Almirall et al., 2011) and protozoal infections (Lin et al., 2012). Secnidazoles is also reported to have anti-inflammatory and urease inhibiton activites (Zhang et al., 2011). The title compound is a derivative of secnidazole obtained during our attempts to make more effective structure analogues of this important antibacterial drug.

The structure of the title compound (Fig. 1) is similar to that of our previously published compound 2-(2-methyl-5-nitro-1H-imidazol-1-yl)-ethyl methanesulfonate (Zeb et al., 2012) with the difference that the ethyl methanesulfonate attached to the imidazole ring is replaced by an acetone (O3/C5—C7) group. Bond length and angles were found to be similar to those reported for related structures (Yousuf et al., 2012). In the crystal, molecules are linked by C2—H2B···N2, C5—H5B···O2 and C7—H7B···O3 intermolecular interactions (Table 1) to form a three-dimensional network (Fig. 2).

Experimental

Periodic acid (2.8 mmol, 0.64 g), pyridinium chlorochromate (PCC, 4 mol%) were suspended in acetonitrile (20 ml) and stirred vigorously for five minutes. The mixture was allowed to cool on an ice-salt bath followed by the addition of secnidazole (2.7 mmol, 0.50 g) and allowed to stir for 36 h at ambient temperature. After the completion of the reaction [TLC analysis], the reaction mixture was washed with brine/water (1:1 v/v), saturated aqueous Na₂SO₃ solution, dried (Na₂SO₄) and filtered. The filtrate was evaporated in vacuum to afford off-white crystals which were washed and recrystalized by dissolving in petroleum ether to obtained colorless crystals of the title compound (0.32 g, 64% yield) found suitable for single-crystal X-ray diffraction analysis.

Refinement

H atoms of methyl, methylene and methine carbon atoms were positioned geometrically with C—H = 0.93–0.96 Å and constrained to ride on their parent atoms with U_iso(H)= 1.2U_eq(C) or 1.5U_eq(C) for methyl H atoms. A rotating group model was applied to the methyl group.

Figures

Fig. 1.

The molecular structure of the title compound with displacement ellipsoids drawn at 30% probability level.

Fig. 2.

The crystal packing of the title compound. Intermolecular hydrogen bonds are shown as dashed lines.

Crystal data

C7H9N3O3	F(000) = 384
Mr = 183.17	Dx = 1.401 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 1790 reflections
a = 4.7548 (4) Å	θ = 2.8–26.7°
b = 12.3971 (9) Å	µ = 0.11 mm−1
c = 14.8580 (11) Å	T = 273 K
β = 97.350 (2)°	Block, colorless
V = 868.62 (12) Å3	0.52 × 0.33 × 0.24 mm
Z = 4

Data collection

Bruker SMART APEX CCD area-detector diffractometer	1614 independent reflections
Radiation source: fine-focus sealed tube	1328 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.019
ω scan	θmax = 25.5°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −5→5
Tmin = 0.944, Tmax = 0.974	k = −14→15
5030 measured reflections	l = −14→17

Refinement

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)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.122	H-atom parameters constrained
S = 1.06	w = 1/[σ2(Fo2) + (0.0591P)2 + 0.2124P] where P = (Fo2 + 2Fc2)/3
1614 reflections	(Δ/σ)max < 0.001
120 parameters	Δρmax = 0.19 e Å−3
0 restraints	Δρmin = −0.15 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
O1	−0.1621 (4)	0.29596 (12)	0.33611 (13)	0.0887 (5)
O2	0.1562 (3)	0.37418 (11)	0.26792 (12)	0.0791 (5)
O3	−0.2465 (3)	0.53369 (11)	0.15962 (9)	0.0622 (4)
N1	−0.0008 (3)	0.57463 (11)	0.33181 (9)	0.0424 (4)
N2	−0.2805 (3)	0.59824 (13)	0.43940 (10)	0.0574 (4)
N3	−0.0337 (3)	0.37691 (12)	0.31638 (12)	0.0589 (4)
C1	−0.1098 (3)	0.47575 (13)	0.35252 (12)	0.0464 (4)
C2	−0.2784 (4)	0.49243 (16)	0.41793 (12)	0.0554 (5)
H2B	−0.3781	0.4389	0.4442	0.067*
C3	−0.1137 (4)	0.64611 (14)	0.38648 (11)	0.0485 (4)
C4	−0.0467 (5)	0.76284 (16)	0.38973 (15)	0.0728 (6)
H4A	−0.1214	0.7951	0.4404	0.109*
H4B	−0.1305	0.7965	0.3346	0.109*
H4C	0.1552	0.7725	0.3963	0.109*
C5	0.1509 (3)	0.60187 (13)	0.25566 (11)	0.0444 (4)
H5A	0.3240	0.5598	0.2597	0.053*
H5B	0.2034	0.6775	0.2595	0.053*
C6	−0.0235 (3)	0.58087 (13)	0.16507 (12)	0.0451 (4)
C7	0.1011 (4)	0.62131 (17)	0.08469 (13)	0.0653 (5)
H7A	−0.0270	0.6069	0.0307	0.098*
H7B	0.2783	0.5855	0.0810	0.098*
H7C	0.1326	0.6976	0.0905	0.098*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O1	0.1009 (12)	0.0431 (8)	0.1246 (15)	−0.0117 (8)	0.0248 (10)	0.0121 (8)
O2	0.0790 (10)	0.0538 (9)	0.1115 (13)	0.0122 (7)	0.0387 (9)	−0.0036 (8)
O3	0.0539 (8)	0.0678 (9)	0.0641 (9)	−0.0109 (6)	0.0049 (6)	−0.0016 (6)
N1	0.0423 (7)	0.0430 (8)	0.0437 (8)	−0.0021 (6)	0.0123 (6)	0.0018 (6)
N2	0.0622 (9)	0.0651 (10)	0.0487 (9)	−0.0007 (7)	0.0216 (7)	0.0031 (7)
N3	0.0590 (9)	0.0430 (9)	0.0751 (11)	0.0029 (7)	0.0098 (8)	0.0065 (7)
C1	0.0465 (9)	0.0426 (9)	0.0509 (10)	−0.0010 (7)	0.0098 (7)	0.0075 (7)
C2	0.0541 (10)	0.0610 (12)	0.0530 (11)	−0.0045 (9)	0.0138 (8)	0.0145 (9)
C3	0.0529 (9)	0.0508 (10)	0.0432 (9)	−0.0007 (8)	0.0112 (8)	−0.0011 (7)
C4	0.0993 (16)	0.0555 (12)	0.0684 (14)	−0.0068 (11)	0.0296 (12)	−0.0125 (10)
C5	0.0436 (8)	0.0444 (9)	0.0479 (9)	−0.0045 (7)	0.0159 (7)	0.0003 (7)
C6	0.0457 (9)	0.0395 (9)	0.0518 (10)	0.0047 (7)	0.0124 (7)	−0.0012 (7)
C7	0.0693 (12)	0.0784 (14)	0.0502 (11)	−0.0027 (10)	0.0151 (9)	0.0038 (10)

Geometric parameters (Å, º)

O1—N3	1.230 (2)	C3—C4	1.481 (3)
O2—N3	1.225 (2)	C4—H4A	0.9600
O3—C6	1.205 (2)	C4—H4B	0.9600
N1—C3	1.358 (2)	C4—H4C	0.9600
N1—C1	1.381 (2)	C5—C6	1.510 (2)
N1—C5	1.457 (2)	C5—H5A	0.9700
N2—C3	1.326 (2)	C5—H5B	0.9700
N2—C2	1.350 (3)	C6—C7	1.486 (3)
N3—C1	1.404 (2)	C7—H7A	0.9600
C1—C2	1.352 (2)	C7—H7B	0.9600
C2—H2B	0.9300	C7—H7C	0.9600
C3—N1—C1	104.93 (14)	C3—C4—H4C	109.5
C3—N1—C5	125.87 (14)	H4A—C4—H4C	109.5
C1—N1—C5	128.02 (14)	H4B—C4—H4C	109.5
C3—N2—C2	105.74 (15)	N1—C5—C6	112.47 (13)
O2—N3—O1	122.92 (17)	N1—C5—H5A	109.1
O2—N3—C1	119.63 (15)	C6—C5—H5A	109.1
O1—N3—C1	117.45 (17)	N1—C5—H5B	109.1
C2—C1—N1	107.35 (15)	C6—C5—H5B	109.1
C2—C1—N3	127.87 (16)	H5A—C5—H5B	107.8
N1—C1—N3	124.56 (15)	O3—C6—C7	123.21 (16)
N2—C2—C1	109.97 (15)	O3—C6—C5	121.44 (15)
N2—C2—H2B	125.0	C7—C6—C5	115.35 (14)
C1—C2—H2B	125.0	C6—C7—H7A	109.5
N2—C3—N1	112.01 (16)	C6—C7—H7B	109.5
N2—C3—C4	124.07 (16)	H7A—C7—H7B	109.5
N1—C3—C4	123.86 (16)	C6—C7—H7C	109.5
C3—C4—H4A	109.5	H7A—C7—H7C	109.5
C3—C4—H4B	109.5	H7B—C7—H7C	109.5
H4A—C4—H4B	109.5
C3—N1—C1—C2	−0.39 (18)	C2—N2—C3—N1	−0.6 (2)
C5—N1—C1—C2	−168.41 (15)	C2—N2—C3—C4	−177.73 (19)
C3—N1—C1—N3	−175.31 (16)	C1—N1—C3—N2	0.60 (18)
C5—N1—C1—N3	16.7 (3)	C5—N1—C3—N2	168.96 (14)
O2—N3—C1—C2	−168.38 (18)	C1—N1—C3—C4	177.77 (18)
O1—N3—C1—C2	11.0 (3)	C5—N1—C3—C4	−13.9 (3)
O2—N3—C1—N1	5.5 (3)	C3—N1—C5—C6	−106.10 (18)
O1—N3—C1—N1	−175.14 (16)	C1—N1—C5—C6	59.6 (2)
C3—N2—C2—C1	0.3 (2)	N1—C5—C6—O3	−9.0 (2)
N1—C1—C2—N2	0.1 (2)	N1—C5—C6—C7	171.59 (15)
N3—C1—C2—N2	174.76 (17)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2B···N2i	0.93	2.56	3.361 (2)	144
C5—H5B···O2ii	0.97	2.57	3.527 (2)	167
C7—H7B···O3iii	0.96	2.49	3.340 (2)	147

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