organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

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[Lin, Y., Su, Y., Liao, X., Yang, N., Yang, X. & Choi, M. M. F. (2012). Talanta, 88, 646-652.]); Almirall et al. (2011[Almirall, P., Escobedo, A. A., Ayala, I., Alfonso, M., Salazar, Y., Cañete, R., Cimerman, S., Galloso, M., Olivero, I., Robaina, M. & Tornés, K. (2011). J. Parasitol. Res., Article ID 636857, doi:10.1155/2011/636857.]); Zhang et al. (2011[Zhang, H.-J., Zhu, D.-D., Li, Z.-L., Sun, J. & Zhu, H. L. (2011). Bioorg. Med. Chem. 19, 4513-4519.]). For the crystal structure of related imidazoles, see: Yousuf et al. (2012[Yousuf, S., Zeb, A., Batool, F. & Basha, F. Z. (2012). Acta Cryst. E68, o2781.]); Zeb et al. (2012[Zeb, A., Yousuf, S. & Basha, F. Z. (2012). Acta Cryst. E68, o1218.]).

[Scheme 1]

Experimental

Crystal data
  • C7H9N3O3

  • Mr = 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[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.944, Tmax = 0.974

  • 5030 measured reflections

  • 1614 independent reflections

  • 1328 reflections with I > 2σ(I)

  • Rint = 0.019

Refinement
  • R[F2 > 2σ(F2)] = 0.041

  • wR(F2) = 0.122

  • S = 1.06

  • 1614 reflections

  • 120 parameters

  • H-atom parameters constrained

  • Δρmax = 0.19 e Å−3

  • Δρmin = −0.15 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL, PARST (Nardelli, 1995[Nardelli, M. (1995). J. Appl. Cryst. 28, 659.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


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.

Refinement top

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 Uiso(H)= 1.2Ueq(C) or 1.5Ueq(C) for methyl H atoms. A rotating group model was applied to the methyl group.

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
[Figure 1] Fig. 1. The molecular structure of the title compound with displacement ellipsoids drawn at 30% probability level.
[Figure 2] 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
C7H9N3O3F(000) = 384
Mr = 183.17Dx = 1.401 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1790 reflections
a = 4.7548 (4) Åθ = 2.8–26.7°
b = 12.3971 (9) ŵ = 0.11 mm1
c = 14.8580 (11) ÅT = 273 K
β = 97.350 (2)°Block, colorless
V = 868.62 (12) Å30.52 × 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 tube1328 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
ω scanθmax = 25.5°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
h = 55
Tmin = 0.944, Tmax = 0.974k = 1415
5030 measured reflectionsl = 1417
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.122H-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 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = 0.15 e Å3
Crystal data top
C7H9N3O3V = 868.62 (12) Å3
Mr = 183.17Z = 4
Monoclinic, P21/nMo Kα radiation
a = 4.7548 (4) ŵ = 0.11 mm1
b = 12.3971 (9) ÅT = 273 K
c = 14.8580 (11) Å0.52 × 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)
Tmin = 0.944, Tmax = 0.974Rint = 0.019
5030 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0410 restraints
wR(F2) = 0.122H-atom parameters constrained
S = 1.06Δρmax = 0.19 e Å3
1614 reflectionsΔρmin = 0.15 e Å3
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
xyzUiso*/Ueq
O10.1621 (4)0.29596 (12)0.33611 (13)0.0887 (5)
O20.1562 (3)0.37418 (11)0.26792 (12)0.0791 (5)
O30.2465 (3)0.53369 (11)0.15962 (9)0.0622 (4)
N10.0008 (3)0.57463 (11)0.33181 (9)0.0424 (4)
N20.2805 (3)0.59824 (13)0.43940 (10)0.0574 (4)
N30.0337 (3)0.37691 (12)0.31638 (12)0.0589 (4)
C10.1098 (3)0.47575 (13)0.35252 (12)0.0464 (4)
C20.2784 (4)0.49243 (16)0.41793 (12)0.0554 (5)
H2B0.37810.43890.44420.067*
C30.1137 (4)0.64611 (14)0.38648 (11)0.0485 (4)
C40.0467 (5)0.76284 (16)0.38973 (15)0.0728 (6)
H4A0.12140.79510.44040.109*
H4B0.13050.79650.33460.109*
H4C0.15520.77250.39630.109*
C50.1509 (3)0.60187 (13)0.25566 (11)0.0444 (4)
H5A0.32400.55980.25970.053*
H5B0.20340.67750.25950.053*
C60.0235 (3)0.58087 (13)0.16507 (12)0.0451 (4)
C70.1011 (4)0.62131 (17)0.08469 (13)0.0653 (5)
H7A0.02700.60690.03070.098*
H7B0.27830.58550.08100.098*
H7C0.13260.69760.09050.098*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.1009 (12)0.0431 (8)0.1246 (15)0.0117 (8)0.0248 (10)0.0121 (8)
O20.0790 (10)0.0538 (9)0.1115 (13)0.0122 (7)0.0387 (9)0.0036 (8)
O30.0539 (8)0.0678 (9)0.0641 (9)0.0109 (6)0.0049 (6)0.0016 (6)
N10.0423 (7)0.0430 (8)0.0437 (8)0.0021 (6)0.0123 (6)0.0018 (6)
N20.0622 (9)0.0651 (10)0.0487 (9)0.0007 (7)0.0216 (7)0.0031 (7)
N30.0590 (9)0.0430 (9)0.0751 (11)0.0029 (7)0.0098 (8)0.0065 (7)
C10.0465 (9)0.0426 (9)0.0509 (10)0.0010 (7)0.0098 (7)0.0075 (7)
C20.0541 (10)0.0610 (12)0.0530 (11)0.0045 (9)0.0138 (8)0.0145 (9)
C30.0529 (9)0.0508 (10)0.0432 (9)0.0007 (8)0.0112 (8)0.0011 (7)
C40.0993 (16)0.0555 (12)0.0684 (14)0.0068 (11)0.0296 (12)0.0125 (10)
C50.0436 (8)0.0444 (9)0.0479 (9)0.0045 (7)0.0159 (7)0.0003 (7)
C60.0457 (9)0.0395 (9)0.0518 (10)0.0047 (7)0.0124 (7)0.0012 (7)
C70.0693 (12)0.0784 (14)0.0502 (11)0.0027 (10)0.0151 (9)0.0038 (10)
Geometric parameters (Å, º) top
O1—N31.230 (2)C3—C41.481 (3)
O2—N31.225 (2)C4—H4A0.9600
O3—C61.205 (2)C4—H4B0.9600
N1—C31.358 (2)C4—H4C0.9600
N1—C11.381 (2)C5—C61.510 (2)
N1—C51.457 (2)C5—H5A0.9700
N2—C31.326 (2)C5—H5B0.9700
N2—C21.350 (3)C6—C71.486 (3)
N3—C11.404 (2)C7—H7A0.9600
C1—C21.352 (2)C7—H7B0.9600
C2—H2B0.9300C7—H7C0.9600
C3—N1—C1104.93 (14)C3—C4—H4C109.5
C3—N1—C5125.87 (14)H4A—C4—H4C109.5
C1—N1—C5128.02 (14)H4B—C4—H4C109.5
C3—N2—C2105.74 (15)N1—C5—C6112.47 (13)
O2—N3—O1122.92 (17)N1—C5—H5A109.1
O2—N3—C1119.63 (15)C6—C5—H5A109.1
O1—N3—C1117.45 (17)N1—C5—H5B109.1
C2—C1—N1107.35 (15)C6—C5—H5B109.1
C2—C1—N3127.87 (16)H5A—C5—H5B107.8
N1—C1—N3124.56 (15)O3—C6—C7123.21 (16)
N2—C2—C1109.97 (15)O3—C6—C5121.44 (15)
N2—C2—H2B125.0C7—C6—C5115.35 (14)
C1—C2—H2B125.0C6—C7—H7A109.5
N2—C3—N1112.01 (16)C6—C7—H7B109.5
N2—C3—C4124.07 (16)H7A—C7—H7B109.5
N1—C3—C4123.86 (16)C6—C7—H7C109.5
C3—C4—H4A109.5H7A—C7—H7C109.5
C3—C4—H4B109.5H7B—C7—H7C109.5
H4A—C4—H4B109.5
C3—N1—C1—C20.39 (18)C2—N2—C3—N10.6 (2)
C5—N1—C1—C2168.41 (15)C2—N2—C3—C4177.73 (19)
C3—N1—C1—N3175.31 (16)C1—N1—C3—N20.60 (18)
C5—N1—C1—N316.7 (3)C5—N1—C3—N2168.96 (14)
O2—N3—C1—C2168.38 (18)C1—N1—C3—C4177.77 (18)
O1—N3—C1—C211.0 (3)C5—N1—C3—C413.9 (3)
O2—N3—C1—N15.5 (3)C3—N1—C5—C6106.10 (18)
O1—N3—C1—N1175.14 (16)C1—N1—C5—C659.6 (2)
C3—N2—C2—C10.3 (2)N1—C5—C6—O39.0 (2)
N1—C1—C2—N20.1 (2)N1—C5—C6—C7171.59 (15)
N3—C1—C2—N2174.76 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2B···N2i0.932.563.361 (2)144
C5—H5B···O2ii0.972.573.527 (2)167
C7—H7B···O3iii0.962.493.340 (2)147
Symmetry codes: (i) x1, y+1, z+1; (ii) x+1/2, y+1/2, z+1/2; (iii) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC7H9N3O3
Mr183.17
Crystal system, space groupMonoclinic, P21/n
Temperature (K)273
a, b, c (Å)4.7548 (4), 12.3971 (9), 14.8580 (11)
β (°) 97.350 (2)
V3)868.62 (12)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.52 × 0.33 × 0.24
Data collection
DiffractometerBruker SMART APEX CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.944, 0.974
No. of measured, independent and
observed [I > 2σ(I)] reflections
5030, 1614, 1328
Rint0.019
(sin θ/λ)max1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.122, 1.06
No. of reflections1614
No. of parameters120
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
C2—H2B···N2i0.93002.56003.361 (2)144.00
C5—H5B···O2ii0.97002.57003.527 (2)167.00
C7—H7B···O3iii0.96002.49003.340 (2)147.00
Symmetry codes: (i) x1, 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

First citationAlmirall, P., Escobedo, A. A., Ayala, I., Alfonso, M., Salazar, Y., Cañete, R., Cimerman, S., Galloso, M., Olivero, I., Robaina, M. & Tornés, K. (2011). J. Parasitol. Res., Article ID 636857, doi:10.1155/2011/636857.
First citationBruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationLin, Y., Su, Y., Liao, X., Yang, N., Yang, X. & Choi, M. M. F. (2012). Talanta, 88, 646–652.  Web of Science CrossRef CAS PubMed
First citationNardelli, M. (1995). J. Appl. Cryst. 28, 659.  CrossRef IUCr Journals
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals
First citationYousuf, S., Zeb, A., Batool, F. & Basha, F. Z. (2012). Acta Cryst. E68, o2781.  CSD CrossRef IUCr Journals
First citationZeb, A., Yousuf, S. & Basha, F. Z. (2012). Acta Cryst. E68, o1218.  CSD CrossRef IUCr Journals
First citationZhang, H.-J., Zhu, D.-D., Li, Z.-L., Sun, J. & Zhu, H. L. (2011). Bioorg. Med. Chem. 19, 4513–4519.  Web of Science CrossRef CAS PubMed

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