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

Ouzidan, Y.; Kandri Rodi, Y.; Kandri Rodi, A.; Essassi, E.M.; Saadi, M.; El Ammari, L.

doi:10.1107/S1600536813004790

organic compounds

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ISSN: 2056-9890

Volume 69| Part 3| March 2013| Page o431

doi:10.1107/S1600536813004790

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

Younès Ouzidan,^a ^* Youssef Kandri Rodi,^a Adiba Kandri Rodi,^a El Mokhtar Essassi,^b,^c Mohamed Saadi ^d and Lahcen El Ammari ^d

^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 ); 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

Crystal data

C₁₀H₉N₃O₃
M_r = 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)
R_int = 0.030

Refinement

R[F² > 2σ(F²)] = 0.057
wR(F²) = 0.168
S = 1.05
1940 reflections
145 parameters
H-atom parameters constrained
Δρ_max = 0.60 e Å⁻³
Δρ_min = −0.38 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT; 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 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536813004790/tk5200sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813004790/tk5200Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813004790/tk5200Isup3.cml

checkCIF report

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.

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

	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.
	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

C₁₀H₉N₃O₃	F(000) = 912
M_r = 219.20	D_x = 1.422 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 1940 reflections
a = 8.3246 (3) Å	θ = 3.0–25.7°
b = 14.9567 (6) Å	µ = 0.11 mm⁻¹
c = 16.4461 (7) Å	T = 296 K
V = 2047.68 (14) Å³	Block, colourless
Z = 8	0.46 × 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 tube	R_int = 0.030
Graphite monochromator	θ_max = 25.7°, θ_min = 3.0°
ϕ and ω scans	h = −10→5
12145 measured reflections	k = −17→18
1940 independent reflections	l = −20→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)] = 0.057	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.168	H-atom parameters constrained
S = 1.05	w = 1/[σ²(F_o²) + (0.0827P)² + 1.3415P] where P = (F_o² + 2F_c²)/3
1940 reflections	(Δ/σ)_max < 0.001
145 parameters	Δρ_max = 0.60 e Å⁻³
0 restraints	Δρ_min = −0.38 e Å⁻³

Crystal data top

C₁₀H₉N₃O₃	V = 2047.68 (14) Å³
M_r = 219.20	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 8.3246 (3) Å	µ = 0.11 mm⁻¹
b = 14.9567 (6) Å	T = 296 K
c = 16.4461 (7) Å	0.46 × 0.31 × 0.18 mm

Data collection top

Bruker X8 APEXII area-detector diffractometer	1483 reflections with I > 2σ(I)
12145 measured reflections	R_int = 0.030
1940 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.057	0 restraints
wR(F²) = 0.168	H-atom parameters constrained
S = 1.05	Δρ_max = 0.60 e Å⁻³
1940 reflections	Δρ_min = −0.38 e Å⁻³
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

	x	y	z	U_iso*/U_eq
C1	0.1801 (3)	−0.05403 (17)	0.37164 (15)	0.0479 (6)
C2	0.1529 (3)	0.02563 (16)	0.41211 (15)	0.0469 (6)
H2	0.0502	0.0439	0.4269	0.056*
C3	0.2866 (3)	0.07620 (16)	0.42913 (14)	0.0433 (6)
C4	0.4416 (3)	0.04786 (16)	0.40696 (14)	0.0432 (6)
C5	0.4658 (3)	−0.03268 (18)	0.36771 (16)	0.0517 (6)
H5	0.5685	−0.0516	0.3538	0.062*
C6	0.3328 (3)	−0.08415 (18)	0.34984 (16)	0.0532 (6)
H6	0.3449	−0.1387	0.3234	0.064*
C7	0.4612 (3)	0.18307 (17)	0.46777 (15)	0.0470 (6)
C8	0.7198 (3)	0.11726 (18)	0.41762 (15)	0.0505 (6)
H8A	0.7613	0.0567	0.4152	0.061*
H8B	0.7714	0.1474	0.4628	0.061*
C9	0.7608 (4)	0.1651 (3)	0.3401 (2)	0.0817 (10)
H9	0.7305	0.2249	0.3380	0.098*
C10	0.8257 (7)	0.1378 (4)	0.2815 (3)	0.1325 (19)
H10A	0.8593	0.0786	0.2794	0.159*
H10B	0.8434	0.1755	0.2375	0.159*
N1	0.0402 (3)	−0.10842 (16)	0.34996 (15)	0.0589 (6)
N2	0.3035 (2)	0.15796 (14)	0.46649 (13)	0.0506 (6)
H2N	0.2257	0.1889	0.4863	0.061*
N3	0.5459 (2)	0.11428 (13)	0.43179 (12)	0.0455 (5)
O1	0.0603 (3)	−0.17533 (15)	0.30908 (16)	0.0871 (8)
O2	−0.0927 (2)	−0.08426 (14)	0.37286 (15)	0.0746 (7)
O3	0.5177 (2)	0.25247 (13)	0.49549 (13)	0.0607 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0473 (13)	0.0443 (14)	0.0521 (13)	−0.0050 (11)	0.0021 (10)	−0.0018 (11)
C2	0.0375 (12)	0.0459 (14)	0.0573 (14)	0.0000 (10)	0.0064 (10)	−0.0019 (11)
C3	0.0391 (12)	0.0427 (13)	0.0479 (13)	0.0012 (10)	0.0048 (9)	−0.0019 (10)
C4	0.0395 (12)	0.0459 (13)	0.0441 (12)	0.0020 (10)	0.0034 (9)	−0.0012 (10)
C5	0.0453 (13)	0.0507 (15)	0.0592 (15)	0.0083 (11)	0.0064 (11)	−0.0064 (12)
C6	0.0573 (15)	0.0438 (14)	0.0584 (15)	0.0040 (11)	0.0039 (12)	−0.0081 (11)
C7	0.0381 (12)	0.0489 (14)	0.0541 (14)	−0.0002 (10)	0.0035 (10)	−0.0042 (11)
C8	0.0331 (12)	0.0633 (16)	0.0551 (14)	0.0048 (11)	0.0010 (10)	−0.0028 (12)
C9	0.0555 (17)	0.110 (3)	0.080 (2)	0.0014 (18)	0.0127 (16)	0.012 (2)
C10	0.181 (5)	0.122 (4)	0.094 (3)	0.021 (4)	0.050 (3)	0.018 (3)
N1	0.0592 (14)	0.0470 (13)	0.0704 (15)	−0.0068 (10)	0.0009 (11)	−0.0055 (11)
N2	0.0353 (10)	0.0469 (12)	0.0695 (13)	−0.0001 (8)	0.0088 (9)	−0.0147 (10)
N3	0.0332 (10)	0.0492 (12)	0.0542 (12)	−0.0002 (8)	0.0036 (8)	−0.0051 (9)
O1	0.0777 (15)	0.0703 (15)	0.1133 (18)	−0.0149 (11)	0.0075 (13)	−0.0401 (13)
O2	0.0483 (11)	0.0586 (13)	0.1169 (18)	−0.0083 (9)	0.0026 (11)	−0.0109 (11)
O3	0.0435 (9)	0.0561 (11)	0.0825 (13)	−0.0072 (8)	0.0022 (9)	−0.0194 (9)

Geometric parameters (Å, º) top

C1—C2	1.383 (3)	C7—N2	1.365 (3)
C1—C6	1.396 (4)	C7—N3	1.381 (3)
C1—N1	1.465 (3)	C8—N3	1.467 (3)
C2—C3	1.374 (3)	C8—C9	1.501 (4)
C2—H2	0.9300	C8—H8A	0.9700
C3—N2	1.376 (3)	C8—H8B	0.9700
C3—C4	1.407 (3)	C9—C10	1.177 (5)
C4—N3	1.381 (3)	C9—H9	0.9300
C4—C5	1.381 (3)	C10—H10A	0.9300
C5—C6	1.380 (4)	C10—H10B	0.9300
C5—H5	0.9300	N1—O1	1.217 (3)
C6—H6	0.9300	N1—O2	1.223 (3)
C7—O3	1.228 (3)	N2—H2N	0.8600

C2—C1—C6	123.4 (2)	N3—C8—C9	111.9 (2)
C2—C1—N1	117.7 (2)	N3—C8—H8A	109.2
C6—C1—N1	118.8 (2)	C9—C8—H8A	109.2
C3—C2—C1	116.1 (2)	N3—C8—H8B	109.2
C3—C2—H2	122.0	C9—C8—H8B	109.2
C1—C2—H2	122.0	H8A—C8—H8B	107.9
C2—C3—N2	131.5 (2)	C10—C9—C8	129.3 (4)
C2—C3—C4	121.6 (2)	C10—C9—H9	115.3
N2—C3—C4	106.84 (19)	C8—C9—H9	115.3
N3—C4—C5	132.4 (2)	C9—C10—H10A	120.0
N3—C4—C3	106.5 (2)	C9—C10—H10B	120.0
C5—C4—C3	121.2 (2)	H10A—C10—H10B	120.0
C6—C5—C4	118.0 (2)	O1—N1—O2	122.5 (2)
C6—C5—H5	121.0	O1—N1—C1	118.8 (2)
C4—C5—H5	121.0	O2—N1—C1	118.7 (2)
C5—C6—C1	119.7 (2)	C7—N2—C3	110.48 (19)
C5—C6—H6	120.1	C7—N2—H2N	124.8
C1—C6—H6	120.1	C3—N2—H2N	124.8
O3—C7—N2	127.4 (2)	C7—N3—C4	109.99 (19)
O3—C7—N3	126.4 (2)	C7—N3—C8	123.3 (2)
N2—C7—N3	106.2 (2)	C4—N3—C8	126.5 (2)

C6—C1—C2—C3	1.2 (4)	C2—C1—N1—O2	−4.6 (4)
N1—C1—C2—C3	−178.0 (2)	C6—C1—N1—O2	176.2 (3)
C1—C2—C3—N2	178.7 (2)	O3—C7—N2—C3	179.0 (2)
C1—C2—C3—C4	−0.4 (4)	N3—C7—N2—C3	−1.3 (3)
C2—C3—C4—N3	179.1 (2)	C2—C3—N2—C7	−178.3 (3)
N2—C3—C4—N3	−0.2 (3)	C4—C3—N2—C7	0.9 (3)
C2—C3—C4—C5	−0.6 (4)	O3—C7—N3—C4	−179.1 (2)
N2—C3—C4—C5	−179.9 (2)	N2—C7—N3—C4	1.2 (3)
N3—C4—C5—C6	−178.8 (2)	O3—C7—N3—C8	−3.4 (4)
C3—C4—C5—C6	0.9 (4)	N2—C7—N3—C8	176.9 (2)
C4—C5—C6—C1	−0.1 (4)	C5—C4—N3—C7	179.1 (3)
C2—C1—C6—C5	−1.0 (4)	C3—C4—N3—C7	−0.6 (3)
N1—C1—C6—C5	178.2 (2)	C5—C4—N3—C8	3.5 (4)
N3—C8—C9—C10	−117.9 (5)	C3—C4—N3—C8	−176.1 (2)
C2—C1—N1—O1	174.6 (3)	C9—C8—N3—C7	−84.0 (3)
C6—C1—N1—O1	−4.6 (4)	C9—C8—N3—C4	90.9 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N···O3ⁱ	0.86	1.96	2.801 (3)	164

Symmetry code: (i) x−1/2, −y+1/2, −z+1.

Experimental details

Crystal data
Chemical formula	C₁₀H₉N₃O₃
M_r	219.20
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	296
a, b, c (Å)	8.3246 (3), 14.9567 (6), 16.4461 (7)
V (Å³)	2047.68 (14)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.46 × 0.31 × 0.18

Data collection
Diffractometer	Bruker X8 APEXII area-detector diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	12145, 1940, 1483
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.610

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.057, 0.168, 1.05
No. of reflections	1940
No. of parameters	145
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	D—H···A
N2—H2N···O3ⁱ	0.86	1.96	2.801 (3)	164

Symmetry code: (i) x−1/2, −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.

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