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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 4| April 2012| Page o1218
doi:10.1107/S1600536812012688

2-(2-Methyl-5-nitro-1H-imidazol-1-yl)ethyl 2-bromo­benzoate

Aurang Zeb,a Sammer Yousufa* and Fatima Z. Bashaa‡

aH.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi 75270, Pakistan
*Correspondence e-mail: dr.sammer.yousuf@gmail.com

(Received 3 March 2012; accepted 23 March 2012; online 28 March 2012)

In the title compound, C13H12BrN3O4, the dihedral angle between the benzene and imidazole rings is 30.6 (2)°. In the crystal, mol­ecules are linked into chains parallel to [001] by C—H⋯O hydrogen bonds. The crystal packing is further consolidated by π–π inter­actions [centroid–centroid distance = 3.482 (2) Å].

Related literature

For background information and the crystal structure of the 4-flouro analogue of the title compound, see: Yousuf et al. (2012[Yousuf, S., Zeb, A. & Basha, F. Z. (2012). Acta Cryst. E68, o952.]).

[Scheme 1]

Experimental

Crystal data

  • C13H12BrN3O4

  • Mr = 354.17

  • Monoclinic, P 21 /c

  • a = 14.554 (4) Å

  • b = 8.836 (2) Å

  • c = 11.563 (3) Å

  • β = 105.427 (6)°

  • V = 1433.3 (7) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 2.89 mm−1

  • T = 273 K

  • 0.33 × 0.20 × 0.19 mm
Data collection

  • Bruker SMART APEX CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2000[Bruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.449, Tmax = 0.610

  • 8200 measured reflections

  • 2601 independent reflections

  • 1959 reflections with I > 2σ(I)

  • Rint = 0.024
Refinement

  • R[F2 > 2σ(F2)] = 0.042

  • wR(F2) = 0.114

  • S = 1.04

  • 2601 reflections

  • 191 parameters

  • H-atom parameters constrained

  • Δρmax = 0.68 e Å−3

  • Δρmin = −0.51 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C8—H8A⋯O4i 0.97 2.51 3.183 (4) 127
Symmetry code: (i) [x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}].

Data collection: SMART (Bruker, 2000[Bruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2000[Bruker (2000). SMART, SAINT and SADABS. 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

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536812012688/pv2520sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812012688/pv2520Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812012688/pv2520Isup3.cml

checkCIF report


Comment top

The title compound is an ester derivative of a broad spectrum antibiotic, metronidazole, commonly known as flagyl. In continuation of our research (Yousuf et al., 2012) we have now synthesized the title compound to evaluate its antiglycation potential. In this article, we report the synthesis and crystal structure of the title compound.

The title compound (Fig. 1) is structurally similar to its 4-flouro analogue (Yousuf et al., 2012). The mean planes of the benzene (C1–C6) and imidazole (C10—C12/N1—N2) rings are inclined at 30.6 (2)° with respect to each other. In the crystal structure, the molecules are linked to form chains via C8—H8A···O4 intermolecular interactions along the c-axis (Fig. 2 and Tab. 1). The Crystal packing is further strengthened by a significant π–π interaction between centroids of imidazole rings lying about inversion centers (Cg···Cg distance = 3.482 (2) Å).

Related literature top

For background information and the crystal structure of the 4-flouro analogue of the title compound, see: Yousuf et al. (2012).

Experimental top

The synthesis of the title compounds was acheived by reacting metronidazole (171 mg, 1.0 mmole) with 2-bromobenzoic acid (1.2 equiv.) in the presence of dicyclohexylcarbodiimide (245 mg, 1.2 mmole) and 4-dimethylaminopyridine (0.35 mmole) in dichloromethane (10 ml) at room temperature for 40–45 h. The progress of the reaction was monitored by TLC. The reaction was quenched with 20 ml HCl (0.5 M) and then basified with sat. NaHCO3. It was extracted with dichloromethane and evaporated in vaccuo to obtain a crude product. The crude product was purified by using silica gel chromatography (EtOAc: hexane, 3.0: 7.0 to 7.0: 3.0) which afforded the title compound in 85% yield. Recrystallization by the slow evaporation of a dichloromethane solution of the title compound afforded pure crystals found suitable for single-crystal X-ray diffraction studies. All chemicals were purchased from Sigma-Aldrich.

Refinement top

H atoms on methyl, methylene and methine were positioned geometrically with C—H = 0.96, 0.97 and 0.93 Å respectively, and constrained to ride on their parent atoms with Uiso(H)= 1.2Ueq(CH and CH2) and 1.5Ueq(CH3). A rotating group model was applied to the methyl groups.

Structure description top

The title compound is an ester derivative of a broad spectrum antibiotic, metronidazole, commonly known as flagyl. In continuation of our research (Yousuf et al., 2012) we have now synthesized the title compound to evaluate its antiglycation potential. In this article, we report the synthesis and crystal structure of the title compound.

The title compound (Fig. 1) is structurally similar to its 4-flouro analogue (Yousuf et al., 2012). The mean planes of the benzene (C1–C6) and imidazole (C10—C12/N1—N2) rings are inclined at 30.6 (2)° with respect to each other. In the crystal structure, the molecules are linked to form chains via C8—H8A···O4 intermolecular interactions along the c-axis (Fig. 2 and Tab. 1). The Crystal packing is further strengthened by a significant π–π interaction between centroids of imidazole rings lying about inversion centers (Cg···Cg distance = 3.482 (2) Å).

For background information and the crystal structure of the 4-flouro analogue of the title compound, see: Yousuf et al. (2012).

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 the atom numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are presented as small spheres of arbitrary radius.
[Figure 2] Fig. 2. A view of the C—-H···O hydrogen bonds (dotted lines) in the crystal structure of the title compound. H atoms non-participating in hydrogen- bonding were omitted for clarity.
2-(2-Methyl-5-nitro-1H-imidazol-1-yl)ethyl 2-bromobenzoate top
Crystal data top
C13H12BrN3O4F(000) = 712
Mr = 354.17Dx = 1.641 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2494 reflections
a = 14.554 (4) Åθ = 2.7–24.1°
b = 8.836 (2) ŵ = 2.89 mm−1
c = 11.563 (3) ÅT = 273 K
β = 105.427 (6)°Block, colorles
V = 1433.3 (7) Å30.33 × 0.20 × 0.19 mm
Z = 4
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer		2601 independent reflections
Radiation source: fine-focus sealed tube1959 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
ω scansθmax = 25.5°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		h = −17→17
Tmin = 0.449, Tmax = 0.610k = −10→10
8200 measured reflectionsl = −14→13
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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.114H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0598P)2 + 0.7664P]
where P = (Fo2 + 2Fc2)/3
2601 reflections(Δ/σ)max < 0.001
191 parametersΔρmax = 0.68 e Å−3
0 restraintsΔρmin = −0.51 e Å−3
Crystal data top
C13H12BrN3O4V = 1433.3 (7) Å3
Mr = 354.17Z = 4
Monoclinic, P21/cMo Kα radiation
a = 14.554 (4) ŵ = 2.89 mm−1
b = 8.836 (2) ÅT = 273 K
c = 11.563 (3) Å0.33 × 0.20 × 0.19 mm
β = 105.427 (6)°
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer		2601 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		1959 reflections with I > 2σ(I)
Tmin = 0.449, Tmax = 0.610Rint = 0.024
8200 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0420 restraints
wR(F2) = 0.114H-atom parameters constrained
S = 1.04Δρmax = 0.68 e Å−3
2601 reflectionsΔρmin = −0.51 e Å−3
191 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
Br10.39287 (3)0.03857 (5)0.11564 (3)0.0748 (2)
O10.3629 (3)0.3331 (3)0.2376 (3)0.1003 (11)
O20.25716 (17)0.3109 (3)0.3428 (2)0.0606 (6)
O30.1411 (3)0.7613 (3)0.4002 (3)0.0981 (10)
O40.1559 (3)0.8059 (3)0.5864 (3)0.1087 (11)
N10.11680 (18)0.4509 (3)0.4402 (2)0.0471 (6)
N20.1099 (2)0.3517 (4)0.6143 (3)0.0667 (8)
N30.1438 (2)0.7198 (4)0.5010 (3)0.0696 (9)
C10.3499 (3)0.0609 (4)0.4570 (3)0.0623 (9)
H1A0.32710.12950.50380.075*
C20.3779 (3)−0.0807 (5)0.5015 (4)0.0747 (11)
H2B0.3749−0.10720.57830.090*
C30.4103 (3)−0.1832 (5)0.4319 (4)0.0778 (12)
H3A0.4292−0.27920.46200.093*
C40.4151 (3)−0.1450 (4)0.3185 (4)0.0664 (10)
H4A0.4367−0.21510.27170.080*
C50.3879 (2)−0.0030 (4)0.2746 (3)0.0498 (8)
C60.3552 (2)0.1034 (4)0.3431 (3)0.0475 (7)
C70.3277 (3)0.2592 (4)0.3011 (3)0.0541 (8)
C80.2178 (3)0.4561 (4)0.2996 (3)0.0618 (9)
H8A0.21690.46890.21600.074*
H8B0.25560.53680.34590.074*
C90.1188 (3)0.4590 (4)0.3138 (3)0.0575 (9)
H9A0.08750.55140.27850.069*
H9B0.08320.37430.27040.069*
C100.1311 (2)0.5647 (3)0.5247 (3)0.0511 (8)
C110.1268 (3)0.5010 (4)0.6297 (3)0.0631 (9)
H11A0.13430.55280.70160.076*
C120.1047 (2)0.3241 (4)0.4998 (3)0.0555 (8)
C130.0869 (3)0.1719 (4)0.4440 (4)0.0826 (12)
H13A0.06300.10580.49520.124*
H13B0.14530.13160.43320.124*
H13C0.04080.17980.36750.124*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.1056 (4)0.0702 (3)0.0535 (3)0.0046 (2)0.0298 (2)−0.00709 (18)
O10.134 (3)0.0601 (16)0.141 (3)0.0125 (17)0.096 (2)0.0205 (18)
O20.0806 (16)0.0593 (14)0.0483 (13)0.0208 (12)0.0282 (12)0.0138 (11)
O30.158 (3)0.0530 (16)0.095 (2)−0.0046 (18)0.054 (2)0.0083 (15)
O40.169 (3)0.0605 (17)0.108 (3)−0.011 (2)0.056 (2)−0.0356 (18)
N10.0498 (14)0.0417 (14)0.0480 (15)0.0060 (11)0.0097 (12)−0.0016 (12)
N20.0730 (19)0.068 (2)0.0620 (19)0.0077 (16)0.0231 (16)0.0130 (16)
N30.083 (2)0.0497 (17)0.081 (2)0.0018 (15)0.0311 (19)−0.0153 (17)
C10.067 (2)0.072 (2)0.050 (2)0.0040 (18)0.0192 (17)0.0049 (17)
C20.075 (3)0.088 (3)0.064 (2)0.010 (2)0.023 (2)0.029 (2)
C30.074 (3)0.063 (2)0.097 (3)0.010 (2)0.025 (2)0.028 (2)
C40.069 (2)0.052 (2)0.079 (3)0.0061 (18)0.020 (2)0.0020 (19)
C50.0503 (18)0.0488 (17)0.0488 (19)−0.0028 (14)0.0106 (15)−0.0015 (14)
C60.0488 (17)0.0480 (16)0.0456 (17)−0.0023 (14)0.0123 (14)−0.0019 (14)
C70.070 (2)0.0479 (17)0.0491 (19)−0.0027 (16)0.0235 (17)−0.0046 (15)
C80.088 (3)0.054 (2)0.047 (2)0.0189 (18)0.0245 (19)0.0130 (16)
C90.074 (2)0.0487 (19)0.0434 (19)0.0132 (17)0.0044 (17)0.0003 (15)
C100.0562 (19)0.0445 (17)0.054 (2)0.0075 (14)0.0159 (16)−0.0058 (14)
C110.071 (2)0.068 (2)0.051 (2)0.0093 (18)0.0186 (18)−0.0037 (17)
C120.0513 (19)0.0473 (18)0.066 (2)0.0026 (15)0.0128 (16)0.0060 (17)
C130.095 (3)0.050 (2)0.102 (3)−0.011 (2)0.024 (3)−0.002 (2)
Geometric parameters (Å, º) top
Br1—C51.895 (3)C3—C41.374 (5)
O1—C71.195 (4)C3—H3A0.9300
O2—C71.326 (4)C4—C51.372 (5)
O2—C81.439 (4)C4—H4A0.9300
O3—N31.213 (4)C5—C61.393 (4)
O4—N31.221 (4)C6—C71.479 (5)
N1—C121.351 (4)C8—C91.494 (5)
N1—C101.379 (4)C8—H8A0.9700
N1—C91.472 (4)C8—H8B0.9700
N2—C121.328 (4)C9—H9A0.9700
N2—C111.345 (5)C9—H9B0.9700
N3—C101.420 (5)C10—C111.355 (5)
C1—C21.372 (5)C11—H11A0.9300
C1—C61.391 (5)C12—C131.485 (5)
C1—H1A0.9300C13—H13A0.9600
C2—C31.376 (6)C13—H13B0.9600
C2—H2B0.9300C13—H13C0.9600
C7—O2—C8117.1 (3)O2—C7—C6111.7 (3)
C12—N1—C10105.0 (3)O2—C8—C9106.5 (3)
C12—N1—C9125.9 (3)O2—C8—H8A110.4
C10—N1—C9129.0 (3)C9—C8—H8A110.4
C12—N2—C11105.8 (3)O2—C8—H8B110.4
O3—N3—O4123.4 (4)C9—C8—H8B110.4
O3—N3—C10120.3 (3)H8A—C8—H8B108.6
O4—N3—C10116.3 (4)N1—C9—C8112.5 (3)
C2—C1—C6121.0 (3)N1—C9—H9A109.1
C2—C1—H1A119.5C8—C9—H9A109.1
C6—C1—H1A119.5N1—C9—H9B109.1
C1—C2—C3119.6 (4)C8—C9—H9B109.1
C1—C2—H2B120.2H9A—C9—H9B107.8
C3—C2—H2B120.2C11—C10—N1107.4 (3)
C4—C3—C2120.6 (4)C11—C10—N3127.8 (3)
C4—C3—H3A119.7N1—C10—N3124.8 (3)
C2—C3—H3A119.7N2—C11—C10109.8 (3)
C5—C4—C3119.6 (4)N2—C11—H11A125.1
C5—C4—H4A120.2C10—C11—H11A125.1
C3—C4—H4A120.2N2—C12—N1112.1 (3)
C4—C5—C6121.0 (3)N2—C12—C13123.8 (3)
C4—C5—Br1117.1 (3)N1—C12—C13124.1 (3)
C6—C5—Br1121.9 (2)C12—C13—H13A109.5
C1—C6—C5118.0 (3)C12—C13—H13B109.5
C1—C6—C7118.9 (3)H13A—C13—H13B109.5
C5—C6—C7123.0 (3)C12—C13—H13C109.5
O1—C7—O2122.4 (3)H13A—C13—H13C109.5
O1—C7—C6125.9 (3)H13B—C13—H13C109.5
C6—C1—C2—C3−0.9 (6)C10—N1—C9—C880.5 (4)
C1—C2—C3—C40.1 (6)O2—C8—C9—N164.2 (4)
C2—C3—C4—C50.5 (6)C12—N1—C10—C11−0.1 (4)
C3—C4—C5—C6−0.2 (5)C9—N1—C10—C11−177.1 (3)
C3—C4—C5—Br1−178.1 (3)C12—N1—C10—N3−177.7 (3)
C2—C1—C6—C51.2 (5)C9—N1—C10—N35.3 (5)
C2—C1—C6—C7−177.7 (3)O3—N3—C10—C11−176.0 (4)
C4—C5—C6—C1−0.6 (5)O4—N3—C10—C113.1 (6)
Br1—C5—C6—C1177.1 (3)O3—N3—C10—N11.1 (6)
C4—C5—C6—C7178.2 (3)O4—N3—C10—N1−179.8 (3)
Br1—C5—C6—C7−4.0 (5)C12—N2—C11—C100.5 (4)
C8—O2—C7—O15.6 (5)N1—C10—C11—N2−0.2 (4)
C8—O2—C7—C6−174.4 (3)N3—C10—C11—N2177.3 (3)
C1—C6—C7—O1145.8 (4)C11—N2—C12—N1−0.6 (4)
C5—C6—C7—O1−33.1 (6)C11—N2—C12—C13179.9 (3)
C1—C6—C7—O2−34.2 (4)C10—N1—C12—N20.5 (4)
C5—C6—C7—O2147.0 (3)C9—N1—C12—N2177.6 (3)
C7—O2—C8—C9156.0 (3)C10—N1—C12—C13179.9 (3)
C12—N1—C9—C8−95.9 (4)C9—N1—C12—C13−3.0 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C8—H8A···O4i0.972.513.183 (4)127
Symmetry code: (i) x, −y+3/2, z−1/2.

Experimental details

Crystal data
Chemical formulaC13H12BrN3O4
Mr354.17
Crystal system, space groupMonoclinic, P21/c
Temperature (K)273
a, b, c (Å)14.554 (4), 8.836 (2), 11.563 (3)
β (°) 105.427 (6)
V (Å3)1433.3 (7)
Z4
Radiation typeMo Kα
µ (mm−1)2.89
Crystal size (mm)0.33 × 0.20 × 0.19
Data collection
DiffractometerBruker SMART APEX CCD area-detector
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.449, 0.610
No. of measured, independent and
observed [I > 2σ(I)] reflections		8200, 2601, 1959
Rint0.024
(sin θ/λ)max (Å−1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.114, 1.04
No. of reflections2601
No. of parameters191
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.68, −0.51

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
C8—H8A···O4i0.972.513.183 (4)126.7
Symmetry code: (i) x, −y+3/2, z−1/2.
 

Footnotes

‡Additional corresponding author, e-mail: bashafz@gmail.com.

References

First citationBruker (2000). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationNardelli, M. (1995). J. Appl. Cryst. 28, 659.  CrossRef IUCr Journals Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationYousuf, S., Zeb, A. & Basha, F. Z. (2012). Acta Cryst. E68, o952.  CSD CrossRef IUCr Journals Google Scholar

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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 4| April 2012| Page o1218
doi:10.1107/S1600536812012688
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