Ethyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate

Hakmaoui, Y.; Rakib, E.M.; Mojahidi, S.; Saadi, M.; El Ammari, L.

doi:10.1107/S2414314616005885

organic compounds

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Volume 1| Part 4| April 2016| x160588

doi:10.1107/S2414314616005885

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Ethyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate

Yassine Hakmaoui,^a ^* El Mostapha Rakib,^a Souad Mojahidi,^a Mohamed Saadi ^b and Lahcen El Ammari ^b

^aLaboratoire de Chimie Organique et Analytique, Université Sultan Moulay Slimane, Faculté des Sciences et Techniques, Béni-Mellal, BP 523, Morocco, and ^bLaboratoire de Chimie du Solide Appliquée, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, Rabat, Morocco
^*Correspondence e-mail: yhakmaoui1@gmail.com

Edited by P. Bombicz, Hungarian Academy of Sciences, Hungary (Received 2 March 2016; accepted 8 April 2016; online 15 April 2016)

In the title compound, C₈H₁₁N₃O₄, the imidazole ring and the nitro group are nearly coplanar, with the largest deviation from the mean plane being 0.119 (2) Å. The mean plane through the acetate group is approximately perpendicular to the imidazole ring, subtending a dihedral angle of 75.71 (13)°. In the crystal, molecules are linked by weak C—H⋯O and very weak C—H⋯N hydrogen bonds, forming a three-dimensional network. There is also a weak C—H⋯π(imidazole) interaction, which contributes to the stability of the crystal packing arrangement.

Keywords: crystals structure; nitro-1H-imidazole; acetate; hydrogen bonds.

CCDC reference: 1473028

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Chemical scheme

Structure description

Imidazoles are an important class of heterocyclic compounds that are abundant in the structures of many natural and synthetic pharmacologically active substances (Neildé et al., 2014 ; Adamovich et al., 2014 ). Some nitroimidazole derivatives have been identified as notable radiosensitizers, antiprotozoal, antifungal and antibacterial or anti-epileptic agents (Olender et al., 2009 ; Duan et al., 2014 ; Sutherland et al., 2010 ).

The molecule of the title compound is build up from a nitro- and methyl-substituted imidazole ring (C1–C3/N2/N3) linked to an ethylacetate moiety, as shown in Fig. 1. The nitro group and the imidazole ring are coplanar with a maximum deviation from the mean plane of 0.119 (2) Å for O1. The imidazole ring makes a dihedral angle of 75.71 (13)° with the plane through the acetate group. The title compound is achiral, although it crystallizes in a chiral space group.

Figure 1
Plot of the molecule of the title compound, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small circles.

The crystal structure cohesion is ensured by C—H⋯O and C—H⋯N hydrogen-bonding interactions (Table 1). There is also a weak C5—H5A⋯π interaction, which contributes to the stability of the crystal packing arrangement, as shown in Fig. 2.

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the imidazole ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C5—H5A⋯O3ⁱ	0.97	2.43	3.224 (2)	139
C8—H8B⋯O3ⁱⁱ	0.97	2.54	3.446 (3)	156
C5—H5B⋯N2ⁱⁱⁱ	0.97	2.65	3.586 (2)	161
C5—H5B⋯O1ⁱⁱⁱ	0.97	2.62	3.387 (2)	136
C5—H5A⋯Cgⁱ	0.97	2.98	3.651 (2)	128
Symmetry codes: (i) x+1, y, z; (ii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (iii) $[-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Figure 2
The crystal packing for the title compound, showing hydrogen bonds as dashed lines.

Synthesis and crystallization

To a solution of 2-methyl-5-nitro-1H-imidazole (7.87 mmol) in DMSO was added potassium hydroxide (8.7 mmol). After 15 min of stirring at 298 K, ethyl bromoacetate (15.74 mmol) was added dropwise. Upon disappearance of the starting material as indicated by TLC, the mixture was added to ice–water and extracted with ethyl acetate. The organic phase was washed with brine and dried over magnesium sulfate. The solvent was evaporated in vacuo. The resulting residue was purified by column chromatography (EtOAc/hexane 09/01). The title compound was recrystallized from ethanol at room temperature giving colourless crystals (m.p. 351 K, yield 68%).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₈H₁₁N₃O₄
M_r	213.20
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	296
a, b, c (Å)	4.4793 (2), 10.3596 (5), 21.5724 (11)
V (Å³)	1001.04 (8)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.12
Crystal size (mm)	0.13 × 0.12 × 0.10

Data collection
Diffractometer	Bruker X8 APEX
Absorption correction	Multi-scan (SADABS; Bruker, 2009 )
T_min, T_max	0.635, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	23416, 2802, 2488
R_int	0.040
(sin θ/λ)_max (Å⁻¹)	0.694

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.100, 1.06
No. of reflections	2802
No. of parameters	137
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.15
Computer programs: APEX2 and SAINT (Bruker, 2009), SHELXS2014 (Sheldrick, 2008 ), SHELXL2014 (Sheldrick, 2015 ), ORTEPIII (Burnett & Johnson, 1996 ), ORTEP-3 for Windows (Farrugia, 2012 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 1473028

Crystal structure: contains datablock I. DOI: 10.1107/S2414314616005885/zp4004sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2414314616005885/zp4004Isup2.hkl

Supporting information file. DOI: 10.1107/S2414314616005885/zp4004Isup3.cml

checkCIF report

Experimental top

Structure description top

Imidazoles are an important class of heterocyclic compounds that are abundant in the structures of many natural and synthetic pharmacologically active substances (Neildé et al., 2014; Adamovich et al., 2014). Some nitroimidazole derivatives have been identified as notable radiosensitizers, antiprotozoal, antifungal and antibacterial or anti-epileptic agents (Olender et al., 2009; Duan et al., 2014; Sutherland et al., 2010).

The molecule of the title compound is build up from anitro- and methyl-substituted imidazole ring (C1–C3/N2/N3) linked to an ethylacetate moiety, as shown in Fig.1. The nitro group and the imidazole ring are coplanar with a maximum deviation from the mean plane of 0.119 (2) Å for O1. The imidazole ring makes a dihedral angle of 75.71 (13)° with the plane through the acetate group. The title compound is achiral, although it crystallizes in a chiral space group.

The crystal structure cohesion is ensured by C—H···O and C—H···N hydrogen-bonding interactions (Table 1). There is also a weak C5—H5A···π interaction, which contributes to the stability of the crystal packing arrangement, as shown in Fig. 2.

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

	Fig. 1. Plot of the molecule of the title compound, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small circles.
	Fig. 2. The crystal packing for the title compound, showing hydrogen bonds as dashed lines.

Ethyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate top

Crystal data top

C₈H₁₁N₃O₄	D_x = 1.415 Mg m⁻³
M_r = 213.20	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 2802 reflections
a = 4.4793 (2) Å	θ = 2.2–29.6°
b = 10.3596 (5) Å	µ = 0.12 mm⁻¹
c = 21.5724 (11) Å	T = 296 K
V = 1001.04 (8) Å³	Block, colourless
Z = 4	0.13 × 0.12 × 0.10 mm
F(000) = 448

Data collection top

Bruker X8 APEX diffractometer	2802 independent reflections
Radiation source: fine-focus sealed tube	2488 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.040
φ and ω scans	θ_max = 29.6°, θ_min = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −6→6
T_min = 0.635, T_max = 0.746	k = −11→14
23416 measured reflections	l = −29→29

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)] = 0.037	Hydrogen site location: difference Fourier map
wR(F²) = 0.100	H-atom parameters constrained
S = 1.06	w = 1/[σ²(F_o²) + (0.0574P)² + 0.0658P] where P = (F_o² + 2F_c²)/3
2802 reflections	(Δ/σ)_max < 0.001
137 parameters	Δρ_max = 0.18 e Å⁻³
0 restraints	Δρ_min = −0.15 e Å⁻³

Crystal data top

C₈H₁₁N₃O₄	V = 1001.04 (8) Å³
M_r = 213.20	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 4.4793 (2) Å	µ = 0.12 mm⁻¹
b = 10.3596 (5) Å	T = 296 K
c = 21.5724 (11) Å	0.13 × 0.12 × 0.10 mm

Data collection top

Bruker X8 APEX diffractometer	2802 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2009)	2488 reflections with I > 2σ(I)
T_min = 0.635, T_max = 0.746	R_int = 0.040
23416 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.037	0 restraints
wR(F²) = 0.100	H-atom parameters constrained
S = 1.06	Δρ_max = 0.18 e Å⁻³
2802 reflections	Δρ_min = −0.15 e Å⁻³
137 parameters

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.6714 (4)	0.89444 (15)	0.23607 (7)	0.0340 (3)
C2	0.8179 (4)	0.78660 (15)	0.25496 (7)	0.0357 (4)
H2	0.8107	0.7045	0.2376	0.043*
C3	0.9159 (4)	0.95500 (14)	0.31441 (8)	0.0351 (4)
C4	1.0510 (5)	1.03126 (19)	0.36538 (9)	0.0512 (5)
H4A	1.0123	0.9894	0.4043	0.077*
H4B	0.9655	1.1162	0.3658	0.077*
H4C	1.2626	1.0375	0.3590	0.077*
C5	1.1594 (4)	0.74202 (18)	0.34365 (8)	0.0395 (4)
H5A	1.3374	0.7879	0.3567	0.047*
H5B	1.2214	0.6676	0.3196	0.047*
C6	0.9893 (4)	0.69707 (15)	0.40023 (8)	0.0346 (3)
C8	0.9589 (6)	0.53412 (19)	0.47602 (9)	0.0541 (5)
H8A	0.7444	0.5356	0.4698	0.065*
H8B	1.0053	0.5821	0.5134	0.065*
C9	1.0674 (7)	0.3982 (2)	0.48146 (12)	0.0703 (7)
H9A	0.9722	0.3572	0.5161	0.105*
H9B	1.0201	0.3519	0.4442	0.105*
H9C	1.2797	0.3982	0.4876	0.105*
N1	0.4717 (4)	0.90250 (14)	0.18451 (7)	0.0422 (3)
N2	0.7284 (4)	0.99894 (13)	0.27239 (6)	0.0371 (3)
N3	0.9776 (3)	0.82629 (12)	0.30513 (6)	0.0338 (3)
O1	0.3344 (4)	1.00273 (14)	0.17624 (8)	0.0603 (4)
O2	0.4468 (5)	0.80706 (15)	0.15122 (7)	0.0671 (5)
O3	0.7749 (3)	0.75150 (13)	0.42096 (6)	0.0492 (3)
O4	1.1105 (3)	0.59101 (12)	0.42288 (6)	0.0421 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0341 (8)	0.0307 (7)	0.0370 (7)	0.0001 (7)	0.0003 (7)	0.0044 (6)
C2	0.0422 (9)	0.0287 (7)	0.0364 (7)	0.0035 (7)	0.0022 (7)	0.0001 (6)
C3	0.0386 (9)	0.0282 (7)	0.0385 (8)	0.0003 (7)	0.0017 (7)	0.0029 (6)
C4	0.0637 (13)	0.0421 (9)	0.0479 (9)	−0.0055 (10)	−0.0087 (10)	−0.0026 (8)
C5	0.0324 (8)	0.0418 (8)	0.0443 (8)	0.0106 (7)	−0.0010 (7)	0.0077 (7)
C6	0.0312 (8)	0.0336 (7)	0.0389 (7)	−0.0008 (7)	−0.0065 (7)	0.0009 (6)
C8	0.0583 (13)	0.0524 (11)	0.0515 (10)	−0.0075 (10)	0.0016 (10)	0.0146 (8)
C9	0.0853 (19)	0.0504 (12)	0.0753 (15)	−0.0096 (13)	−0.0046 (14)	0.0242 (11)
N1	0.0408 (8)	0.0410 (7)	0.0449 (7)	−0.0039 (7)	−0.0071 (7)	0.0092 (6)
N2	0.0407 (8)	0.0291 (6)	0.0414 (7)	0.0036 (6)	−0.0004 (6)	0.0021 (5)
N3	0.0341 (7)	0.0305 (6)	0.0367 (6)	0.0070 (6)	0.0007 (6)	0.0031 (5)
O1	0.0571 (10)	0.0531 (8)	0.0706 (9)	0.0089 (8)	−0.0214 (8)	0.0145 (7)
O2	0.0850 (13)	0.0544 (8)	0.0619 (8)	−0.0040 (9)	−0.0289 (9)	−0.0058 (7)
O3	0.0453 (7)	0.0503 (7)	0.0521 (7)	0.0101 (7)	0.0084 (6)	0.0035 (6)
O4	0.0387 (6)	0.0392 (6)	0.0485 (7)	0.0011 (5)	−0.0035 (6)	0.0120 (5)

Geometric parameters (Å, º) top

C1—C2	1.358 (2)	C5—H5A	0.9700
C1—N2	1.360 (2)	C5—H5B	0.9700
C1—N1	1.430 (2)	C6—O3	1.200 (2)
C2—N3	1.361 (2)	C6—O4	1.3194 (19)
C2—H2	0.9300	C8—O4	1.457 (2)
C3—N2	1.317 (2)	C8—C9	1.494 (3)
C3—N3	1.3764 (19)	C8—H8A	0.9700
C3—C4	1.483 (2)	C8—H8B	0.9700
C4—H4A	0.9600	C9—H9A	0.9600
C4—H4B	0.9600	C9—H9B	0.9600
C4—H4C	0.9600	C9—H9C	0.9600
C5—N3	1.455 (2)	N1—O1	1.2200 (19)
C5—C6	1.512 (2)	N1—O2	1.227 (2)

C2—C1—N2	113.02 (14)	O3—C6—C5	124.00 (15)
C2—C1—N1	125.71 (15)	O4—C6—C5	110.36 (14)
N2—C1—N1	121.26 (14)	O4—C8—C9	106.94 (19)
C1—C2—N3	104.13 (14)	O4—C8—H8A	110.3
C1—C2—H2	127.9	C9—C8—H8A	110.3
N3—C2—H2	127.9	O4—C8—H8B	110.3
N2—C3—N3	111.28 (15)	C9—C8—H8B	110.3
N2—C3—C4	125.90 (15)	H8A—C8—H8B	108.6
N3—C3—C4	122.82 (16)	C8—C9—H9A	109.5
C3—C4—H4A	109.5	C8—C9—H9B	109.5
C3—C4—H4B	109.5	H9A—C9—H9B	109.5
H4A—C4—H4B	109.5	C8—C9—H9C	109.5
C3—C4—H4C	109.5	H9A—C9—H9C	109.5
H4A—C4—H4C	109.5	H9B—C9—H9C	109.5
H4B—C4—H4C	109.5	O1—N1—O2	123.66 (16)
N3—C5—C6	111.33 (14)	O1—N1—C1	118.61 (15)
N3—C5—H5A	109.4	O2—N1—C1	117.72 (16)
C6—C5—H5A	109.4	C3—N2—C1	103.94 (13)
N3—C5—H5B	109.4	C2—N3—C3	107.62 (14)
C6—C5—H5B	109.4	C2—N3—C5	124.56 (13)
H5A—C5—H5B	108.0	C3—N3—C5	127.64 (15)
O3—C6—O4	125.64 (17)	C6—O4—C8	115.87 (15)

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the imidazole ring.

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5A···O3ⁱ	0.97	2.43	3.224 (2)	139
C8—H8B···O3ⁱⁱ	0.97	2.54	3.446 (3)	156
C5—H5B···N2ⁱⁱⁱ	0.97	2.65	3.586 (2)	161
C5—H5B···O1ⁱⁱⁱ	0.97	2.62	3.387 (2)	136
C5—H5A···Cgⁱ	0.97	2.98	3.651 (2)	128

Symmetry codes: (i) x+1, y, z; (ii) x+1/2, −y+3/2, −z+1; (iii) −x+2, y−1/2, −z+1/2.

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the imidazole ring.

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5A···O3ⁱ	0.97	2.43	3.224 (2)	138.8
C8—H8B···O3ⁱⁱ	0.97	2.54	3.446 (3)	156.1
C5—H5B···N2ⁱⁱⁱ	0.97	2.65	3.586 (2)	161.4
C5—H5B···O1ⁱⁱⁱ	0.97	2.62	3.387 (2)	135.7
C5—H5A···Cgⁱ	0.97	2.98	3.651 (2)	128

Symmetry codes: (i) x+1, y, z; (ii) x+1/2, −y+3/2, −z+1; (iii) −x+2, y−1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₈H₁₁N₃O₄
M_r	213.20
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	296
a, b, c (Å)	4.4793 (2), 10.3596 (5), 21.5724 (11)
V (Å³)	1001.04 (8)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.12
Crystal size (mm)	0.13 × 0.12 × 0.10

Data collection
Diffractometer	Bruker X8 APEX
Absorption correction	Multi-scan (SADABS; Bruker, 2009)
T_min, T_max	0.635, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	23416, 2802, 2488
R_int	0.040
(sin θ/λ)_max (Å⁻¹)	0.694

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.100, 1.06
No. of reflections	2802
No. of parameters	137
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.15

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXS2014 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 for Windows (Farrugia, 2012), publCIF (Westrip, 2010).

Acknowledgements

The authors thank the Unit of Support for Technical and Scientific Research (UATRS, CNRST) for the X-ray measurements and the University Sultan Moulay Slimane, Beni-Mellal, Morocco, for financial support.

References

Adamovich, S. N., Ushakov, I. A., Mirskova, A. N., Mirskov, R. G. & Voronov, V. K. (2014). Mendeleev Commun. 24, 293–294. Web of Science CrossRef CAS Google Scholar
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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Ethyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

References

organic compounds