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Acta Crystallogr Sect E Struct Rep Online. 2010 April 1; 66(Pt 4): o845.
Published online 2010 March 17. doi:  10.1107/S1600536810007634
PMCID: PMC2983837

Ethyl 1-sec-butyl-2-(4-methoxy­phen­yl)-1H-benzimidazole-5-carboxyl­ate

Abstract

In the title mol­ecule, C21H24N2O3, the dihedral angle between the benzene and imidazole rings is 66.33 (13)°. The imidazole ring is essentially planar, with a maximum deviation of 0.004 (2) Å. In the crystal structure, mol­ecules are connected by weak C—H(...)O hydrogen bonds, forming chains along the b axis

Related literature

For the benzimidazole nucleus as a key building block for compounds showing biologically activity, see: Tanious et al. (2004 [triangle]). For the therapeutic properties of benzimidazole derivatives, see: Kohara et al. (1996 [triangle]); Mader et al. (2008 [triangle]). For 2-substituted-phen­ylbenzimidazoles with biological activity, see: Coburn et al. (1987 [triangle]); Roth et al. (1997 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0o845-scheme1.jpg

Experimental

Crystal data

  • C21H24N2O3
  • M r = 352.42
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o845-efi1.jpg
  • a = 10.5815 (3) Å
  • b = 12.1079 (3) Å
  • c = 15.1050 (3) Å
  • β = 93.678 (2)°
  • V = 1931.26 (8) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 296 K
  • 0.40 × 0.31 × 0.07 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.968, T max = 0.994
  • 19216 measured reflections
  • 4437 independent reflections
  • 2266 reflections with I > 2s(I)
  • R int = 0.065

Refinement

  • R[F 2 > 2σ(F 2)] = 0.066
  • wR(F 2) = 0.150
  • S = 1.04
  • 4437 reflections
  • 235 parameters
  • H-atom parameters constrained
  • Δρmax = 0.13 e Å−3
  • Δρmin = −0.18 e Å−3

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810007634/tk2635sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810007634/tk2635Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

NA, ASAR and HO are grateful to Universiti Sains Malaysia (USM) for funding the synthetic chemistry research under the USM Research University grant (1001/PFARMASI/815026). NA thanks USM for the award of postdoctoral fellowship. HKF and MH thank the Malaysian Government and USM for the Research University Golden Goose grant No. 1001/PFIZIK/811012. MH also thanks USM for a post-doctoral research fellowship.

supplementary crystallographic information

Comment

The benzimidazole nucleus is the key building block for a variety of compounds that play crucial roles in the function of a number of biologically important molecules (Tanious et al., 2004). Benzimidazole derivatives have shown different therapeutic properties such as antihypertensive (Kohara et al., 1996) and anti-inflammatory (Mader et al., 2008) activities. 2-(substitutedphenyl)benzimidazoles with various types of biological activities, such as antibacterial (Coburn et al., 1987) and antiviral (Roth et al., 1997), have been reported. Due to their importance, the crystal structure determination of the title compound was carried out and the results are presented here.

In the title molecule (Fig. 1), the imidazole ring is essentially planar with a maximum deviation of 0.004 (2) Å for atom C13. The dihedral angle between the imidazole ring (N1/N2/C13/C7–C8) and the benzene ring (C1–C6) is 66.33 (13)° . In the crystal structure (Fig. 2), the molecules are connected by weak C21—H21C···O1 (Table 1) hydrogen bonds, forming one-dimensional chains along the b axis.

Experimental

Ethyl-3-amino-4-(sec-butylamino)benzoate (200 mg, 0.84 mmol) and the sodium metabisulfite adduct of 4-methoxy benzaldehyde (406 mg, 1.68 mmol) were dissolved in DMF. The reaction mixture was irradiated under microwave conditions at 403 K for 2 minutes. After completion of the reaction, the reaction mixture was diluted in EtOAc (20 ml) and washed with H2O (20 ml). The organic layer was collected, dried over Na2SO4 and then evaporated in vacuo to yield the crude product. The product was recrystallized from hot EtOAc to afford the title compound as colorless crystals.

Refinement

All hydrogen atoms were positioned geometrically [C–H = 0.93–0.98 Å] and were refined using a riding model, with Uiso(H) = 1.2 or 1.5 Ueq(C). A rotating group model was applied to the methyl groups.

Figures

Fig. 1.
The title molecule, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
A view of the crystal packing of the title compound, showing C–H···O interactions as dashed lines. H atoms not involved in the hydrogen bond interactions are omitted for clarity.

Crystal data

C21H24N2O3F(000) = 752
Mr = 352.42Dx = 1.212 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1865 reflections
a = 10.5815 (3) Åθ = 2.6–19.8°
b = 12.1079 (3) ŵ = 0.08 mm1
c = 15.1050 (3) ÅT = 296 K
β = 93.678 (2)°Plate, colourless
V = 1931.26 (8) Å30.40 × 0.31 × 0.07 mm
Z = 4

Data collection

Bruker SMART APEXII CCD area-detector diffractometer4437 independent reflections
Radiation source: fine-focus sealed tube2266 reflections with I > 2s(I)
graphiteRint = 0.065
[var phi] and ω scansθmax = 27.5°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −13→13
Tmin = 0.968, Tmax = 0.994k = −15→15
19216 measured reflectionsl = −19→19

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.066Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.150H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.0461P)2 + 0.4985P] where P = (Fo2 + 2Fc2)/3
4437 reflections(Δ/σ)max < 0.001
235 parametersΔρmax = 0.13 e Å3
0 restraintsΔρmin = −0.18 e Å3

Special details

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.
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 > 2sigma(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)

xyzUiso*/Ueq
O10.50185 (18)0.95365 (16)0.17576 (12)0.0728 (6)
O20.34173 (18)1.00924 (15)0.08352 (13)0.0735 (6)
O3−0.47540 (19)0.38119 (16)0.08035 (13)0.0761 (6)
N10.07745 (19)0.58199 (16)0.20122 (13)0.0503 (5)
N20.00579 (19)0.70718 (16)0.10000 (13)0.0532 (5)
C1−0.2515 (2)0.5992 (2)0.15122 (17)0.0587 (7)
H1A−0.25050.66920.17670.070*
C2−0.3657 (3)0.5442 (2)0.13763 (16)0.0594 (7)
H2A−0.44020.57650.15430.071*
C3−0.3678 (3)0.4410 (2)0.09909 (16)0.0570 (7)
C4−0.2565 (3)0.3940 (2)0.07547 (19)0.0696 (8)
H4A−0.25780.32430.04950.084*
C5−0.1438 (3)0.4490 (2)0.08990 (18)0.0651 (8)
H5A−0.06930.41590.07390.078*
C6−0.1391 (2)0.5534 (2)0.12809 (15)0.0491 (6)
C7−0.0199 (2)0.6160 (2)0.14217 (16)0.0481 (6)
C80.1732 (2)0.65916 (19)0.19625 (15)0.0478 (6)
C90.2938 (2)0.6692 (2)0.23777 (17)0.0598 (7)
H9A0.32600.61640.27790.072*
C100.3633 (2)0.7602 (2)0.21706 (17)0.0563 (7)
H10A0.44380.76930.24450.068*
C110.3174 (2)0.8402 (2)0.15602 (15)0.0485 (6)
C120.1987 (2)0.8284 (2)0.11322 (16)0.0509 (6)
H12A0.16770.88030.07200.061*
C130.1265 (2)0.73630 (19)0.13359 (15)0.0452 (6)
C140.3975 (3)0.9378 (2)0.14099 (17)0.0548 (7)
C150.4123 (3)1.1098 (2)0.0663 (2)0.0797 (9)
H15A0.49771.09180.05150.096*
H15B0.41701.15710.11830.096*
C160.3432 (3)1.1663 (3)−0.0091 (2)0.0928 (10)
H16A0.38721.2328−0.02290.139*
H16B0.25921.18430.00670.139*
H16C0.33851.1184−0.05980.139*
C170.0678 (3)0.4949 (2)0.26963 (17)0.0600 (7)
H17A−0.01740.46340.26020.072*
C180.0755 (3)0.5434 (3)0.36209 (18)0.0758 (9)
H18A0.06170.48470.40410.091*
H18B0.16050.57150.37510.091*
C19−0.0167 (3)0.6342 (3)0.3763 (2)0.0972 (11)
H19A−0.00460.66090.43610.146*
H19B−0.10150.60670.36620.146*
H19C−0.00330.69340.33570.146*
C200.1589 (3)0.4015 (2)0.2570 (2)0.0830 (10)
H20A0.14750.37440.19730.124*
H20B0.14320.34300.29770.124*
H20C0.24420.42760.26780.124*
C21−0.5922 (3)0.4267 (3)0.1060 (2)0.0828 (10)
H21A−0.66010.37670.08940.124*
H21B−0.60720.49620.07660.124*
H21C−0.58770.43760.16900.124*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0634 (13)0.0789 (14)0.0747 (13)−0.0233 (11)−0.0070 (11)0.0058 (10)
O20.0746 (13)0.0553 (12)0.0884 (14)−0.0213 (10)−0.0109 (11)0.0173 (10)
O30.0636 (13)0.0762 (14)0.0884 (14)−0.0216 (11)0.0039 (10)−0.0165 (11)
N10.0537 (13)0.0410 (12)0.0558 (12)−0.0019 (10)−0.0002 (10)0.0107 (9)
N20.0560 (14)0.0466 (12)0.0557 (13)−0.0065 (10)−0.0052 (10)0.0079 (10)
C10.0655 (18)0.0428 (15)0.0685 (18)−0.0067 (14)0.0085 (14)−0.0055 (12)
C20.0556 (17)0.0565 (17)0.0668 (17)−0.0023 (14)0.0091 (13)−0.0005 (14)
C30.0616 (18)0.0545 (17)0.0547 (15)−0.0136 (15)0.0015 (13)−0.0006 (13)
C40.0677 (19)0.0530 (17)0.088 (2)−0.0092 (16)0.0052 (16)−0.0216 (15)
C50.0599 (18)0.0529 (17)0.083 (2)−0.0005 (15)0.0062 (15)−0.0119 (15)
C60.0534 (16)0.0412 (14)0.0524 (14)−0.0027 (13)0.0010 (12)0.0048 (12)
C70.0520 (15)0.0425 (14)0.0498 (14)−0.0003 (12)0.0039 (12)0.0028 (11)
C80.0496 (15)0.0411 (14)0.0527 (14)−0.0007 (12)0.0032 (12)0.0026 (11)
C90.0554 (17)0.0533 (17)0.0699 (18)0.0026 (14)−0.0035 (14)0.0114 (13)
C100.0494 (16)0.0539 (17)0.0643 (17)−0.0004 (13)−0.0050 (13)0.0020 (13)
C110.0500 (15)0.0440 (14)0.0516 (14)−0.0031 (12)0.0050 (12)−0.0023 (11)
C120.0575 (16)0.0440 (15)0.0506 (14)−0.0013 (13)−0.0005 (12)0.0055 (11)
C130.0492 (15)0.0399 (14)0.0462 (14)0.0016 (12)0.0002 (11)0.0005 (11)
C140.0575 (17)0.0539 (17)0.0531 (16)−0.0077 (14)0.0042 (14)−0.0047 (13)
C150.092 (2)0.0582 (19)0.087 (2)−0.0277 (17)−0.0076 (18)0.0144 (16)
C160.111 (3)0.072 (2)0.095 (2)−0.022 (2)0.003 (2)0.0107 (19)
C170.0638 (17)0.0486 (15)0.0672 (18)−0.0039 (14)0.0018 (14)0.0196 (13)
C180.081 (2)0.083 (2)0.0640 (19)−0.0050 (18)0.0050 (16)0.0213 (16)
C190.108 (3)0.110 (3)0.074 (2)0.020 (2)0.0124 (19)−0.008 (2)
C200.079 (2)0.0545 (18)0.116 (3)0.0092 (17)0.0115 (19)0.0259 (17)
C210.063 (2)0.107 (3)0.078 (2)−0.0206 (19)0.0052 (16)−0.0121 (19)

Geometric parameters (Å, °)

O1—C141.208 (3)C10—H10A0.9300
O2—C141.335 (3)C11—C121.383 (3)
O2—C151.461 (3)C11—C141.481 (3)
O3—C31.363 (3)C12—C131.396 (3)
O3—C211.429 (3)C12—H12A0.9300
N1—C71.381 (3)C15—C161.480 (4)
N1—C81.384 (3)C15—H15A0.9700
N1—C171.485 (3)C15—H15B0.9700
N2—C71.312 (3)C16—H16A0.9600
N2—C131.389 (3)C16—H16B0.9600
C1—C61.377 (3)C16—H16C0.9600
C1—C21.384 (3)C17—C201.507 (4)
C1—H1A0.9300C17—C181.512 (4)
C2—C31.379 (4)C17—H17A0.9800
C2—H2A0.9300C18—C191.495 (4)
C3—C41.375 (4)C18—H18A0.9700
C4—C51.372 (4)C18—H18B0.9700
C4—H4A0.9300C19—H19A0.9600
C5—C61.389 (3)C19—H19B0.9600
C5—H5A0.9300C19—H19C0.9600
C6—C71.475 (3)C20—H20A0.9600
C8—C91.391 (3)C20—H20B0.9600
C8—C131.397 (3)C20—H20C0.9600
C9—C101.373 (3)C21—H21A0.9600
C9—H9A0.9300C21—H21B0.9600
C10—C111.402 (3)C21—H21C0.9600
C14—O2—C15116.5 (2)O1—C14—O2122.2 (2)
C3—O3—C21117.7 (2)O1—C14—C11125.2 (3)
C7—N1—C8106.39 (19)O2—C14—C11112.6 (2)
C7—N1—C17125.4 (2)O2—C15—C16106.8 (2)
C8—N1—C17126.9 (2)O2—C15—H15A110.4
C7—N2—C13104.5 (2)C16—C15—H15A110.4
C6—C1—C2121.9 (2)O2—C15—H15B110.4
C6—C1—H1A119.0C16—C15—H15B110.4
C2—C1—H1A119.0H15A—C15—H15B108.6
C3—C2—C1119.3 (2)C15—C16—H16A109.5
C3—C2—H2A120.3C15—C16—H16B109.5
C1—C2—H2A120.3H16A—C16—H16B109.5
O3—C3—C4116.4 (2)C15—C16—H16C109.5
O3—C3—C2124.0 (3)H16A—C16—H16C109.5
C4—C3—C2119.6 (3)H16B—C16—H16C109.5
C5—C4—C3120.5 (3)N1—C17—C20111.8 (2)
C5—C4—H4A119.7N1—C17—C18111.4 (2)
C3—C4—H4A119.7C20—C17—C18114.3 (2)
C4—C5—C6121.0 (3)N1—C17—H17A106.2
C4—C5—H5A119.5C20—C17—H17A106.2
C6—C5—H5A119.5C18—C17—H17A106.2
C1—C6—C5117.6 (2)C19—C18—C17114.9 (2)
C1—C6—C7120.1 (2)C19—C18—H18A108.5
C5—C6—C7122.3 (2)C17—C18—H18A108.5
N2—C7—N1113.3 (2)C19—C18—H18B108.5
N2—C7—C6124.3 (2)C17—C18—H18B108.5
N1—C7—C6122.4 (2)H18A—C18—H18B107.5
N1—C8—C9133.5 (2)C18—C19—H19A109.5
N1—C8—C13105.1 (2)C18—C19—H19B109.5
C9—C8—C13121.4 (2)H19A—C19—H19B109.5
C10—C9—C8117.2 (2)C18—C19—H19C109.5
C10—C9—H9A121.4H19A—C19—H19C109.5
C8—C9—H9A121.4H19B—C19—H19C109.5
C9—C10—C11122.4 (2)C17—C20—H20A109.5
C9—C10—H10A118.8C17—C20—H20B109.5
C11—C10—H10A118.8H20A—C20—H20B109.5
C12—C11—C10120.2 (2)C17—C20—H20C109.5
C12—C11—C14121.5 (2)H20A—C20—H20C109.5
C10—C11—C14118.3 (2)H20B—C20—H20C109.5
C11—C12—C13118.2 (2)O3—C21—H21A109.5
C11—C12—H12A120.9O3—C21—H21B109.5
C13—C12—H12A120.9H21A—C21—H21B109.5
N2—C13—C12128.7 (2)O3—C21—H21C109.5
N2—C13—C8110.8 (2)H21A—C21—H21C109.5
C12—C13—C8120.5 (2)H21B—C21—H21C109.5
C6—C1—C2—C3−0.6 (4)C13—C8—C9—C102.4 (4)
C21—O3—C3—C4178.6 (2)C8—C9—C10—C11−0.8 (4)
C21—O3—C3—C2−2.9 (4)C9—C10—C11—C12−0.8 (4)
C1—C2—C3—O3−178.0 (2)C9—C10—C11—C14177.5 (2)
C1—C2—C3—C40.5 (4)C10—C11—C12—C130.9 (3)
O3—C3—C4—C5178.6 (3)C14—C11—C12—C13−177.3 (2)
C2—C3—C4—C50.0 (4)C7—N2—C13—C12−178.3 (2)
C3—C4—C5—C6−0.4 (4)C7—N2—C13—C80.8 (3)
C2—C1—C6—C50.2 (4)C11—C12—C13—N2179.7 (2)
C2—C1—C6—C7178.8 (2)C11—C12—C13—C80.6 (3)
C4—C5—C6—C10.3 (4)N1—C8—C13—N2−0.6 (3)
C4—C5—C6—C7−178.3 (3)C9—C8—C13—N2178.5 (2)
C13—N2—C7—N1−0.7 (3)N1—C8—C13—C12178.6 (2)
C13—N2—C7—C6−179.7 (2)C9—C8—C13—C12−2.3 (4)
C8—N1—C7—N20.3 (3)C15—O2—C14—O1−1.6 (4)
C17—N1—C7—N2168.1 (2)C15—O2—C14—C11178.4 (2)
C8—N1—C7—C6179.4 (2)C12—C11—C14—O1−179.9 (2)
C17—N1—C7—C6−12.9 (4)C10—C11—C14—O11.9 (4)
C1—C6—C7—N2−66.1 (3)C12—C11—C14—O20.1 (3)
C5—C6—C7—N2112.4 (3)C10—C11—C14—O2−178.1 (2)
C1—C6—C7—N1114.9 (3)C14—O2—C15—C16170.8 (2)
C5—C6—C7—N1−66.5 (3)C7—N1—C17—C20120.4 (3)
C7—N1—C8—C9−178.8 (3)C8—N1—C17—C20−74.4 (3)
C17—N1—C8—C913.8 (4)C7—N1—C17—C18−110.3 (3)
C7—N1—C8—C130.2 (2)C8—N1—C17—C1854.9 (3)
C17—N1—C8—C13−167.3 (2)N1—C17—C18—C1953.6 (3)
N1—C8—C9—C10−178.9 (2)C20—C17—C18—C19−178.5 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C21—H21C···O1i0.962.473.389 (4)161

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2635).

References

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