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

Yousuf, S.; Khan, K.M.; Naz, F.; Perveen, S.; Miana, G.A.

doi:10.1107/S1600536813006569

organic compounds

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ISSN: 2056-9890

Volume 69| Part 4| April 2013| Page o552

doi:10.1107/S1600536813006569

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

Sammer Yousuf,^a ^* Khalid M. Khan,^a Frazana Naz,^a Shahanaz Perveen ^b and Ghulam A. Miana ^c

^aH.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan, ^bPCSIR Laboratories Complex Karachi, Shahrah-e-Dr Salimuzzaman Siddiqui, Karachi 75280, Pakistan, and ^cRipha Insititue of Pharmaceutical Sciences, Ripha International University, 7th Avenue G-7/4 Islamambad, Pakistan
^*Correspondence e-mail: dr.sammer.yousuf@gmail.com

(Received 2 March 2013; accepted 7 March 2013; online 16 March 2013)

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, P 2₁ /n
a = 4.7548 (4) Å
b = 12.3971 (9) Å
c = 14.8580 (11) Å
β = 97.350 (2)°
V = 868.62 (12) Å³
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[F² > 2σ(F²)] = 0.041
wR(F²) = 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

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) -x-1, -y+1, -z+1; (ii) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) x+1, y, z.

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 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536813006569/rz5048sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813006569/rz5048Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813006569/rz5048Isup3.cml

checkCIF report

Comment top

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).

Related literature top

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 top

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.

Computing details top

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

Figures top

	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.

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

Crystal data top

C₇H₉N₃O₃	F(000) = 384
M_r = 183.17	D_x = 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 top

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

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)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.122	H-atom parameters constrained
S = 1.06	w = 1/[σ²(F_o²) + (0.0591P)² + 0.2124P] where P = (F_o² + 2F_c²)/3
1614 reflections	(Δ/σ)_max < 0.001
120 parameters	Δρ_max = 0.19 e Å⁻³
0 restraints	Δρ_min = −0.15 e Å⁻³

Crystal data top

C₇H₉N₃O₃	V = 868.62 (12) Å³
M_r = 183.17	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 4.7548 (4) Å	µ = 0.11 mm⁻¹
b = 12.3971 (9) Å	T = 273 K
c = 14.8580 (11) Å	0.52 × 0.33 × 0.24 mm
β = 97.350 (2)°

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	1614 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2000)	1328 reflections with I > 2σ(I)
T_min = 0.944, T_max = 0.974	R_int = 0.019
5030 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.041	0 restraints
wR(F²) = 0.122	H-atom parameters constrained
S = 1.06	Δρ_max = 0.19 e Å⁻³
1614 reflections	Δρ_min = −0.15 e Å⁻³
120 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
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 (Å²) top

	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) top

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) top

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.

Experimental details

Crystal data
Chemical formula	C₇H₉N₃O₃
M_r	183.17
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	273
a, b, c (Å)	4.7548 (4), 12.3971 (9), 14.8580 (11)
β (°)	97.350 (2)
V (Å³)	868.62 (12)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.52 × 0.33 × 0.24

Data collection
Diffractometer	Bruker SMART APEX CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2000)
T_min, T_max	0.944, 0.974
No. of measured, independent and observed [I > 2σ(I)] reflections	5030, 1614, 1328
R_int	0.019
(sin θ/λ)_max (Å⁻¹)	0.606

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.122, 1.06
No. of reflections	1614
No. of parameters	120
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.19, −0.15

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2B···N2ⁱ	0.9300	2.5600	3.361 (2)	144.00
C5—H5B···O2ⁱⁱ	0.9700	2.5700	3.527 (2)	167.00
C7—H7B···O3ⁱⁱⁱ	0.9600	2.4900	3.340 (2)	147.00

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

Acknowledgements

The authors gratefully acknowledge the Pakistan Academy of Sciences for funding project No. 5-9/PAS/8418 entitled `Biology-oriented Parallel Synthesis on Nitroimidazoles in Search of Better Therapeutic Agents'.

References

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