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

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ISSN: 2056-9890

1-Allyl-5-nitro-1H-benzimidazol-2(3H)-one

aLaboratoire de Chimie Organique Appliquée, Université Sidi Mohamed Ben Abdallah, Faculté des Sciences et Techniques, Route d'immouzzer, BP 2202 Fès, Morocco, bLaboratoire de Chimie Organique Hétérocyclique URAC21, Faculté des Sciences, Université Mohammed V-Agdal, Avenue Ibn Battouta, BP 1014, Rabat, Morocco, cINANOTECH (Institute of Nanomaterials and Nanotechnology), MAScIR, Av. de l'Armée Royale, Rabat, Morocco, and dLaboratoire de Chimie du Solide Appliquée, Faculté des Sciences, Université Mohammed V-Agdal, Avenue Ibn Battouta, BP 1014, Rabat, Morocco
*Correspondence e-mail: ouzidan@yahoo.fr

(Received 18 February 2013; accepted 19 February 2013; online 23 February 2013)

The benzimidazolone residue in the title mol­ecule, C10H9N3O3, is almost planar, with the largest deviation from the mean plane being 0.016 (2) Å for the C atom linked to the nitro group. This plane is nearly perpendicular to the 1-allyl chain as indicated by the C—N—C—C torsion angle of 90.9 (3)°. The fused-ring system makes a dihedral angle of 5.6 (3)° with the nitro group, leading to a synperiplanar conformation. In the crystal, zigzag supra­molecular chains are formed along the a axis by N—H⋯O hydrogen bonds.

Related literature

For pharmacological and biochemical properties of benz­imid­azoles and derivatives, see: Al Muhaimeed (1997[Al Muhaimeed, H. (1997). J. Int. Med. Res. 25, 175-181.]); Scott et al. (2002[Scott, L. J., Dunn, C. J., Mallarkey, G. & Sharpe, M. (2002). Drugs, 62, 1503-1538.]); Nakano et al. (2000[Nakano, H., Inoue, T., Kawasaki, N., Miyataka, H., Matsumoto, H., Taguchi, T., Inagaki, N., Nagai, H. & Satoh, T. (2000). Bioorg. Med. Chem. 8, 373-380.]); Zhu et al. (2000[Zhu, Z., Lippa, B., Drach, J. C. & Townsend, L. B. (2000). J. Med. Chem. 43, 2430-2437.]); Zarrinmayeh et al. (1998[Zarrinmayeh, H., Nunes, A. M., Ornstein, P. L., Zimmerman, D. M., Arnold, M. B., Schober, D. A., Gackenheimer, S. L., Bruns, R. F., Hipskind, P. A., Britton, T. C., Cantrell, B. E. & Gehlert, D. R. (1998). J. Med. Chem. 41, 2709-2719.]). For related structures, see: Ouzidan et al. (2011a[Ouzidan, Y., Kandri Rodi, Y., Butcher, R. J., Essassi, E. M. & El Ammari, L. (2011a). Acta Cryst. E67, o283.],b[Ouzidan, Y., Kandri Rodi, Y., Saffon, N., Essassi, E. M. & Ng, S. W. (2011b). Acta Cryst. E67, o520.]).

[Scheme 1]

Experimental

Crystal data
  • C10H9N3O3

  • Mr = 219.20

  • Orthorhombic, P b c a

  • a = 8.3246 (3) Å

  • b = 14.9567 (6) Å

  • c = 16.4461 (7) Å

  • V = 2047.68 (14) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 296 K

  • 0.46 × 0.31 × 0.18 mm

Data collection
  • Bruker X8 APEXII area-detector diffractometer

  • 12145 measured reflections

  • 1940 independent reflections

  • 1483 reflections with I > 2σ(I)

  • Rint = 0.030

Refinement
  • R[F2 > 2σ(F2)] = 0.057

  • wR(F2) = 0.168

  • S = 1.05

  • 1940 reflections

  • 145 parameters

  • H-atom parameters constrained

  • Δρmax = 0.60 e Å−3

  • Δρmin = −0.38 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2N⋯O3i 0.86 1.96 2.801 (3) 164
Symmetry code: (i) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2 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: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Comment top

Benzimidazoles and their derivatives exhibit a number of important pharmacological properties, such as anti-histaminic (Al Muhaimeed, 1997) anti-ulcerative (Scott et al., 2002) and anti-allergic (Nakano et al., 2000). In addition, benzimidazole derivatives are effective against the human cytomegalovirus (HCMV) (Zhu et al., 2000) and are also efficient selective neuropeptide Y Y1 receptor antagonists (Zarrinmayeh et al., 1998).

As a continuation of our research work devoted to the development of substituted benzimidazol-2-one derivatives (Ouzidan et al., 2011a, 2011b), we report in this paper the synthesis of a new benzimidazol-2-one derivative by action of allyl-bromide with 5-nitro-1H-benzo[d]imidazol-2(3H)one using similar conditions as employed in earlier studies.

The two fused five- and six-membered rings in the molecule of the title compound, C10H9N3O3, are approximately planar, the largest deviation from the mean plane being -0.016 (2) A° at C1 (Fig. 1). The dihedral angle between the benzimidazolone mean plane and the 1-allyl chain (C4—N3—C8—C9) is 90.9 (3)°. The fused-ring system makes a dihedral angle of 5.6 (3)° with the nitro group, leading to a syn-periplanar conformation. In the crystal, each molecule is linked to symmetry equivalents by N2—H2n···O3 hydrogen bonds, Table 2, forming a supramolecular zigzag chain running along the a axis, as shown in Fig. 2.

Related literature top

For pharmacological and biochemical properties of benzimidazoles and derivatives, see: Al Muhaimeed (1997); Scott et al. (2002); Nakano et al. (2000); Zhu et al. (2000); Zarrinmayeh et al. (1998). For related structures, see: Ouzidan et al. (2011a,b).

Experimental top

To 5-Nitro-1H-benzo[d]imidazol-2(3H)-one (0.2 g, 1.11 mmol), potassium carbonate (0.3 g, 2.23 mmol), and tetra-n-butylammonium bromide (0.04 g, 0.11 mmol) in DMF (15 ml) was added allyl bromide (0.11 ml, 1.35 mmol). Stirring was continued at room temperature for 6 h. The salts were removed by filtration and the filtrate concentrated under reduced pressure. The residue was separated by chromatography on a column of silica gel with ethyl acetate/hexane (1/2) as eluent. Crystals were isolated when the solvent was allowed to evaporate.

Refinement top

H atoms were located in a difference map and treated as riding with N—H = 0.86 Å, C—H = 0.93 Å (aromatic) and C—H = 0.97 Å (methylene), and with Uiso(H) = 1.2 Ueq(parent atom). Disorder is noted in the allyl group as evidence by the shorter than normal C9C10 bond length of 1.177 (5) Å. Attempts to resolve this disorder for this room temperature data set were not successful.

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small circles.
[Figure 2] Fig. 2. Molecule and its symmetry partner linked by N2—H2n···O3 hydrogen bonds. Symmetry codes: (i) 1/2 - x, 1 - y, 1/2 + z.
1-Allyl-5-nitro-1H-benzimidazol-2(3H)-one top
Crystal data top
C10H9N3O3F(000) = 912
Mr = 219.20Dx = 1.422 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 1940 reflections
a = 8.3246 (3) Åθ = 3.0–25.7°
b = 14.9567 (6) ŵ = 0.11 mm1
c = 16.4461 (7) ÅT = 296 K
V = 2047.68 (14) Å3Block, colourless
Z = 80.46 × 0.31 × 0.18 mm
Data collection top
Bruker X8 APEXII area-detector
diffractometer
1483 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.030
Graphite monochromatorθmax = 25.7°, θmin = 3.0°
ϕ and ω scansh = 105
12145 measured reflectionsk = 1718
1940 independent reflectionsl = 2017
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)] = 0.057Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.168H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0827P)2 + 1.3415P]
where P = (Fo2 + 2Fc2)/3
1940 reflections(Δ/σ)max < 0.001
145 parametersΔρmax = 0.60 e Å3
0 restraintsΔρmin = 0.38 e Å3
Crystal data top
C10H9N3O3V = 2047.68 (14) Å3
Mr = 219.20Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 8.3246 (3) ŵ = 0.11 mm1
b = 14.9567 (6) ÅT = 296 K
c = 16.4461 (7) Å0.46 × 0.31 × 0.18 mm
Data collection top
Bruker X8 APEXII area-detector
diffractometer
1483 reflections with I > 2σ(I)
12145 measured reflectionsRint = 0.030
1940 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0570 restraints
wR(F2) = 0.168H-atom parameters constrained
S = 1.05Δρmax = 0.60 e Å3
1940 reflectionsΔρmin = 0.38 e Å3
145 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
C10.1801 (3)0.05403 (17)0.37164 (15)0.0479 (6)
C20.1529 (3)0.02563 (16)0.41211 (15)0.0469 (6)
H20.05020.04390.42690.056*
C30.2866 (3)0.07620 (16)0.42913 (14)0.0433 (6)
C40.4416 (3)0.04786 (16)0.40696 (14)0.0432 (6)
C50.4658 (3)0.03268 (18)0.36771 (16)0.0517 (6)
H50.56850.05160.35380.062*
C60.3328 (3)0.08415 (18)0.34984 (16)0.0532 (6)
H60.34490.13870.32340.064*
C70.4612 (3)0.18307 (17)0.46777 (15)0.0470 (6)
C80.7198 (3)0.11726 (18)0.41762 (15)0.0505 (6)
H8A0.76130.05670.41520.061*
H8B0.77140.14740.46280.061*
C90.7608 (4)0.1651 (3)0.3401 (2)0.0817 (10)
H90.73050.22490.33800.098*
C100.8257 (7)0.1378 (4)0.2815 (3)0.1325 (19)
H10A0.85930.07860.27940.159*
H10B0.84340.17550.23750.159*
N10.0402 (3)0.10842 (16)0.34996 (15)0.0589 (6)
N20.3035 (2)0.15796 (14)0.46649 (13)0.0506 (6)
H2N0.22570.18890.48630.061*
N30.5459 (2)0.11428 (13)0.43179 (12)0.0455 (5)
O10.0603 (3)0.17533 (15)0.30908 (16)0.0871 (8)
O20.0927 (2)0.08426 (14)0.37286 (15)0.0746 (7)
O30.5177 (2)0.25247 (13)0.49549 (13)0.0607 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0473 (13)0.0443 (14)0.0521 (13)0.0050 (11)0.0021 (10)0.0018 (11)
C20.0375 (12)0.0459 (14)0.0573 (14)0.0000 (10)0.0064 (10)0.0019 (11)
C30.0391 (12)0.0427 (13)0.0479 (13)0.0012 (10)0.0048 (9)0.0019 (10)
C40.0395 (12)0.0459 (13)0.0441 (12)0.0020 (10)0.0034 (9)0.0012 (10)
C50.0453 (13)0.0507 (15)0.0592 (15)0.0083 (11)0.0064 (11)0.0064 (12)
C60.0573 (15)0.0438 (14)0.0584 (15)0.0040 (11)0.0039 (12)0.0081 (11)
C70.0381 (12)0.0489 (14)0.0541 (14)0.0002 (10)0.0035 (10)0.0042 (11)
C80.0331 (12)0.0633 (16)0.0551 (14)0.0048 (11)0.0010 (10)0.0028 (12)
C90.0555 (17)0.110 (3)0.080 (2)0.0014 (18)0.0127 (16)0.012 (2)
C100.181 (5)0.122 (4)0.094 (3)0.021 (4)0.050 (3)0.018 (3)
N10.0592 (14)0.0470 (13)0.0704 (15)0.0068 (10)0.0009 (11)0.0055 (11)
N20.0353 (10)0.0469 (12)0.0695 (13)0.0001 (8)0.0088 (9)0.0147 (10)
N30.0332 (10)0.0492 (12)0.0542 (12)0.0002 (8)0.0036 (8)0.0051 (9)
O10.0777 (15)0.0703 (15)0.1133 (18)0.0149 (11)0.0075 (13)0.0401 (13)
O20.0483 (11)0.0586 (13)0.1169 (18)0.0083 (9)0.0026 (11)0.0109 (11)
O30.0435 (9)0.0561 (11)0.0825 (13)0.0072 (8)0.0022 (9)0.0194 (9)
Geometric parameters (Å, º) top
C1—C21.383 (3)C7—N21.365 (3)
C1—C61.396 (4)C7—N31.381 (3)
C1—N11.465 (3)C8—N31.467 (3)
C2—C31.374 (3)C8—C91.501 (4)
C2—H20.9300C8—H8A0.9700
C3—N21.376 (3)C8—H8B0.9700
C3—C41.407 (3)C9—C101.177 (5)
C4—N31.381 (3)C9—H90.9300
C4—C51.381 (3)C10—H10A0.9300
C5—C61.380 (4)C10—H10B0.9300
C5—H50.9300N1—O11.217 (3)
C6—H60.9300N1—O21.223 (3)
C7—O31.228 (3)N2—H2N0.8600
C2—C1—C6123.4 (2)N3—C8—C9111.9 (2)
C2—C1—N1117.7 (2)N3—C8—H8A109.2
C6—C1—N1118.8 (2)C9—C8—H8A109.2
C3—C2—C1116.1 (2)N3—C8—H8B109.2
C3—C2—H2122.0C9—C8—H8B109.2
C1—C2—H2122.0H8A—C8—H8B107.9
C2—C3—N2131.5 (2)C10—C9—C8129.3 (4)
C2—C3—C4121.6 (2)C10—C9—H9115.3
N2—C3—C4106.84 (19)C8—C9—H9115.3
N3—C4—C5132.4 (2)C9—C10—H10A120.0
N3—C4—C3106.5 (2)C9—C10—H10B120.0
C5—C4—C3121.2 (2)H10A—C10—H10B120.0
C6—C5—C4118.0 (2)O1—N1—O2122.5 (2)
C6—C5—H5121.0O1—N1—C1118.8 (2)
C4—C5—H5121.0O2—N1—C1118.7 (2)
C5—C6—C1119.7 (2)C7—N2—C3110.48 (19)
C5—C6—H6120.1C7—N2—H2N124.8
C1—C6—H6120.1C3—N2—H2N124.8
O3—C7—N2127.4 (2)C7—N3—C4109.99 (19)
O3—C7—N3126.4 (2)C7—N3—C8123.3 (2)
N2—C7—N3106.2 (2)C4—N3—C8126.5 (2)
C6—C1—C2—C31.2 (4)C2—C1—N1—O24.6 (4)
N1—C1—C2—C3178.0 (2)C6—C1—N1—O2176.2 (3)
C1—C2—C3—N2178.7 (2)O3—C7—N2—C3179.0 (2)
C1—C2—C3—C40.4 (4)N3—C7—N2—C31.3 (3)
C2—C3—C4—N3179.1 (2)C2—C3—N2—C7178.3 (3)
N2—C3—C4—N30.2 (3)C4—C3—N2—C70.9 (3)
C2—C3—C4—C50.6 (4)O3—C7—N3—C4179.1 (2)
N2—C3—C4—C5179.9 (2)N2—C7—N3—C41.2 (3)
N3—C4—C5—C6178.8 (2)O3—C7—N3—C83.4 (4)
C3—C4—C5—C60.9 (4)N2—C7—N3—C8176.9 (2)
C4—C5—C6—C10.1 (4)C5—C4—N3—C7179.1 (3)
C2—C1—C6—C51.0 (4)C3—C4—N3—C70.6 (3)
N1—C1—C6—C5178.2 (2)C5—C4—N3—C83.5 (4)
N3—C8—C9—C10117.9 (5)C3—C4—N3—C8176.1 (2)
C2—C1—N1—O1174.6 (3)C9—C8—N3—C784.0 (3)
C6—C1—N1—O14.6 (4)C9—C8—N3—C490.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···O3i0.861.962.801 (3)164
Symmetry code: (i) x1/2, y+1/2, z+1.

Experimental details

Crystal data
Chemical formulaC10H9N3O3
Mr219.20
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)296
a, b, c (Å)8.3246 (3), 14.9567 (6), 16.4461 (7)
V3)2047.68 (14)
Z8
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.46 × 0.31 × 0.18
Data collection
DiffractometerBruker X8 APEXII area-detector
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
12145, 1940, 1483
Rint0.030
(sin θ/λ)max1)0.610
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.057, 0.168, 1.05
No. of reflections1940
No. of parameters145
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.60, 0.38

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 2012), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···O3i0.861.962.801 (3)164
Symmetry code: (i) x1/2, y+1/2, z+1.
 

Acknowledgements

The authors thank the Unit of Support for Technical and Scientific Research (UATRS, CNRST) for the X-ray data measurements.

References

First citationAl Muhaimeed, H. (1997). J. Int. Med. Res. 25, 175–181.  CAS PubMed Web of Science
First citationBruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationFarrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.  Web of Science CrossRef CAS IUCr Journals
First citationNakano, H., Inoue, T., Kawasaki, N., Miyataka, H., Matsumoto, H., Taguchi, T., Inagaki, N., Nagai, H. & Satoh, T. (2000). Bioorg. Med. Chem. 8, 373–380.  Web of Science CrossRef PubMed CAS
First citationOuzidan, Y., Kandri Rodi, Y., Butcher, R. J., Essassi, E. M. & El Ammari, L. (2011a). Acta Cryst. E67, o283.  Web of Science CSD CrossRef IUCr Journals
First citationOuzidan, Y., Kandri Rodi, Y., Saffon, N., Essassi, E. M. & Ng, S. W. (2011b). Acta Cryst. E67, o520.  Web of Science CSD CrossRef IUCr Journals
First citationScott, L. J., Dunn, C. J., Mallarkey, G. & Sharpe, M. (2002). Drugs, 62, 1503–1538.  Web of Science CrossRef PubMed CAS
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 citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals
First citationZarrinmayeh, H., Nunes, A. M., Ornstein, P. L., Zimmerman, D. M., Arnold, M. B., Schober, D. A., Gackenheimer, S. L., Bruns, R. F., Hipskind, P. A., Britton, T. C., Cantrell, B. E. & Gehlert, D. R. (1998). J. Med. Chem. 41, 2709–2719.  Web of Science CSD CrossRef CAS PubMed
First citationZhu, Z., Lippa, B., Drach, J. C. & Townsend, L. B. (2000). J. Med. Chem. 43, 2430–2437.  Web of Science CrossRef PubMed CAS

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