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Acta Crystallogr Sect E Struct Rep Online. 2010 June 1; 66(Pt 6): o1285–o1286.
Published online 2010 May 8. doi:  10.1107/S1600536810015448
PMCID: PMC2979540

Ethyl 1-sec-butyl-2-(2-hydroxy­phen­yl)-1H-benzimidazole-5-carboxyl­ate 0.25-hydrate

Abstract

In the title compound, C20H22N2O3·0.25H2O, the water mol­ecule (occupancy 0.25) is disordered across a crystallographic inversion center. The dihedral angle between the hydroxy­phenyl ring and the benzimidazole ring system is 59.31 (9)°. In the crystal structure, mol­ecules are connected by inter­molecular O—H(...)N and C—H(...)O hydrogen bonds. The crystal structure is further stabilized by a weak C—H(...)π inter­action involving the imidazole ring.

Related literature

For background to benzimidazoles and their biological importance, see: Garuti et al. (2004 [triangle]); Bonfanti et al. (2008 [triangle]); Ozden et al. (2008 [triangle]); Shao et al. (2005 [triangle]); Blythin et al. (1986 [triangle]); Snow (2007 [triangle]). For the synthesis of benzimidazoles, see: Arumugam et al. (2010a [triangle],b [triangle],c [triangle]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o1285-scheme1.jpg

Experimental

Crystal data

  • C20H22N2O3·0.25H2O
  • M r = 342.90
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1285-efi1.jpg
  • a = 7.0484 (11) Å
  • b = 27.262 (4) Å
  • c = 9.4673 (14) Å
  • β = 97.495 (3)°
  • V = 1803.6 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 100 K
  • 0.34 × 0.21 × 0.05 mm

Data collection

  • Bruker APEX DUO CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.971, T max = 0.996
  • 18277 measured reflections
  • 4738 independent reflections
  • 3152 reflections with I > 2σ(I)
  • R int = 0.064

Refinement

  • R[F 2 > 2σ(F 2)] = 0.066
  • wR(F 2) = 0.232
  • S = 1.08
  • 4738 reflections
  • 243 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.35 e Å−3
  • Δρmin = −0.46 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/S1600536810015448/sj2770sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810015448/sj2770Isup2.hkl

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

Acknowledgments

NA, ASAR and HO acknowledge Universiti Sains Malaysia (USM) for funding the synthetic chemistry work under Research University Grant (1001/PFARMASI/815026). NA also 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 and MH also thanks USM for a post-doctoral research fellowship.

supplementary crystallographic information

Comment

Benzimidazoles belong to one of the well known and most extensively studied class of compounds due to their biological activity such as antitumour (Garuti et al., 2004), antiviral (Bonfanti et al., 2008), antibacterial (Ozden et al., 2008) and analgesic properties (Shao et al., 2005). These derivatives are anti-inflammatory (Blythin et al., 1986) and can be carcinogenic (Snow et al., 2007). As the benzimidazole derivative is of much importance, we have undertaken the X-ray crystal structure determination of the title compound.

The asymmetric unit (Fig. 1) contains an ethyl-1-sec-butyl-2- (2-hydroxyphenyl)-1H-benzimidazole-5-carboxylate molecule and a water molecule(O1W), occupancy 0.25, which is disordered across a crystallographic inversion center (symmetry code = -x, -y+2, -z+1). The dihedral angle between the benzimidazole ring system (N1–N2/C1–C7) and the phenyl ring (C15–C20) is 59.31 (9)° .

In the crystal structure (Fig. 2), molecules are connected by intermolecular O1—H1O1···N1 and C14—H14C···O1 (Table 1) hydrogen bonds. The crystal structure is further stabilized by C—H···π interactions (Table 1), involving the imidazole ring, N1–N2/C1–C2/C7 (centroid Cg1).

Experimental

The title compound was synthesised according to the previous procedure described by us (Arumugam et al., 2010a,b,c). The product was recrystallized from EtOAc to yield the title compound as colourless crystals.

Refinement

All hydrogen atoms were positioned geometrically [C–H = 0.93 or 0.97Å] 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. In the final refinement cycles the occupancy of the water molecule, O1W, which is disordered over a crystallographic inversion centre, was fixed at 25%.

Figures

Fig. 1.
The asymmetric unit of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
The crystal packing of the title compound, showing the hydrogen-bonded (dashed lines) network. H atoms not involved in hydrogen bond interactions are omitted for clarity.

Crystal data

C20H22N2O3·0.25H2OF(000) = 730
Mr = 342.90Dx = 1.263 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3454 reflections
a = 7.0484 (11) Åθ = 2.6–28.6°
b = 27.262 (4) ŵ = 0.09 mm1
c = 9.4673 (14) ÅT = 100 K
β = 97.495 (3)°Plate, colourless
V = 1803.6 (5) Å30.34 × 0.21 × 0.05 mm
Z = 4

Data collection

Bruker APEX DUO CCD area-detector diffractometer4738 independent reflections
Radiation source: fine-focus sealed tube3152 reflections with I > 2σ(I)
graphiteRint = 0.064
[var phi] and ω scansθmax = 29.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −9→9
Tmin = 0.971, Tmax = 0.996k = −37→36
18277 measured reflectionsl = −12→12

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) = 0.232H atoms treated by a mixture of independent and constrained refinement
S = 1.08w = 1/[σ2(Fo2) + (0.1283P)2 + 0.731P] where P = (Fo2 + 2Fc2)/3
4738 reflections(Δ/σ)max < 0.001
243 parametersΔρmax = 0.35 e Å3
0 restraintsΔρmin = −0.46 e Å3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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*/UeqOcc. (<1)
O10.3724 (2)0.72773 (6)0.28243 (18)0.0229 (4)
O2−0.2905 (3)0.97944 (7)−0.0919 (2)0.0330 (5)
O3−0.1402 (3)0.95244 (8)−0.2726 (2)0.0416 (5)
N10.3512 (3)0.83123 (7)0.0078 (2)0.0194 (4)
N20.3227 (3)0.83949 (7)0.2392 (2)0.0198 (4)
C10.4138 (3)0.81661 (8)0.1391 (2)0.0185 (4)
C20.1912 (3)0.87134 (8)0.1673 (2)0.0200 (5)
C30.0594 (3)0.90402 (10)0.2134 (3)0.0257 (5)
H3A0.04780.90800.30950.031*
C4−0.0530 (3)0.93018 (9)0.1083 (3)0.0258 (5)
H4A−0.14240.95230.13490.031*
C5−0.0366 (3)0.92453 (9)−0.0362 (3)0.0243 (5)
C60.0965 (3)0.89227 (9)−0.0812 (3)0.0220 (5)
H6A0.10900.8886−0.17720.026*
C70.2102 (3)0.86571 (8)0.0232 (2)0.0191 (5)
C8−0.1585 (4)0.95277 (10)−0.1479 (3)0.0284 (5)
C9−0.4223 (4)1.00752 (11)−0.1914 (3)0.0356 (6)
H9A−0.35731.0187−0.26970.043*
H9B−0.46521.0362−0.14370.043*
C10−0.5894 (4)0.97724 (12)−0.2473 (4)0.0468 (8)
H10A−0.67970.9970−0.30720.070*
H10B−0.64900.9646−0.16940.070*
H10C−0.54810.9505−0.30180.070*
C110.3656 (3)0.83308 (9)0.3956 (2)0.0231 (5)
H11A0.45830.80630.41270.028*
C120.4596 (4)0.87887 (10)0.4644 (3)0.0286 (5)
H12A0.37420.90660.44300.034*
H12B0.47900.87450.56690.034*
C130.6503 (4)0.89027 (11)0.4137 (3)0.0350 (6)
H13A0.70750.91810.46480.053*
H13B0.63050.89750.31360.053*
H13C0.73360.86240.43050.053*
C140.1872 (3)0.81788 (11)0.4596 (3)0.0314 (6)
H14A0.12490.79140.40500.047*
H14B0.10130.84530.45800.047*
H14C0.22280.80740.55620.047*
C150.5701 (3)0.78084 (8)0.1704 (2)0.0187 (5)
C160.7463 (3)0.79107 (9)0.1229 (3)0.0217 (5)
H16A0.76270.82030.07530.026*
C170.8956 (3)0.75806 (10)0.1464 (3)0.0262 (5)
H17A1.01320.76530.11670.031*
C180.8696 (3)0.71439 (10)0.2137 (3)0.0259 (5)
H18A0.96970.69200.22820.031*
C190.6961 (3)0.70333 (9)0.2606 (3)0.0228 (5)
H19A0.68000.67360.30560.027*
C200.5463 (3)0.73679 (9)0.2401 (2)0.0195 (5)
H1O10.382 (5)0.7052 (13)0.361 (4)0.048 (10)*
O1W0.0628 (16)0.9740 (3)0.4867 (10)0.055 (3)0.25
H1W1−0.03250.98040.43200.083*0.25
H2W10.13850.99620.47850.083*0.25

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0148 (7)0.0317 (9)0.0230 (9)−0.0007 (6)0.0046 (6)0.0064 (7)
O20.0285 (9)0.0373 (11)0.0324 (10)0.0122 (8)0.0006 (8)0.0084 (8)
O30.0423 (12)0.0533 (13)0.0275 (11)0.0139 (10)−0.0021 (9)0.0073 (9)
N10.0160 (8)0.0256 (10)0.0167 (9)−0.0001 (7)0.0026 (7)−0.0001 (7)
N20.0157 (8)0.0273 (10)0.0164 (9)0.0032 (7)0.0013 (7)0.0018 (7)
C10.0149 (9)0.0238 (11)0.0169 (11)−0.0005 (8)0.0024 (7)0.0014 (8)
C20.0156 (10)0.0261 (12)0.0180 (11)0.0011 (8)0.0010 (8)0.0021 (8)
C30.0202 (11)0.0323 (13)0.0247 (12)0.0062 (9)0.0039 (9)0.0006 (10)
C40.0194 (11)0.0302 (13)0.0281 (13)0.0060 (9)0.0034 (9)0.0020 (10)
C50.0211 (11)0.0251 (12)0.0255 (12)0.0014 (9)−0.0016 (9)0.0034 (9)
C60.0222 (11)0.0259 (12)0.0175 (11)−0.0005 (9)0.0012 (8)0.0013 (9)
C70.0152 (9)0.0223 (11)0.0197 (11)−0.0006 (8)0.0013 (8)0.0006 (8)
C80.0259 (12)0.0295 (13)0.0285 (13)0.0034 (10)−0.0012 (10)0.0046 (10)
C90.0289 (13)0.0371 (15)0.0392 (16)0.0106 (11)−0.0018 (11)0.0118 (12)
C100.0392 (16)0.0443 (18)0.054 (2)0.0057 (13)−0.0043 (14)−0.0063 (15)
C110.0211 (10)0.0331 (13)0.0153 (11)0.0045 (9)0.0034 (8)0.0030 (9)
C120.0278 (12)0.0352 (14)0.0226 (12)0.0057 (10)0.0020 (9)−0.0015 (10)
C130.0280 (13)0.0375 (15)0.0375 (16)−0.0050 (11)−0.0034 (11)−0.0039 (12)
C140.0234 (12)0.0494 (16)0.0225 (13)0.0021 (11)0.0066 (9)0.0076 (11)
C150.0164 (10)0.0239 (11)0.0157 (10)−0.0001 (8)0.0019 (8)−0.0010 (8)
C160.0177 (10)0.0280 (12)0.0200 (11)−0.0010 (9)0.0050 (8)0.0018 (9)
C170.0162 (10)0.0388 (14)0.0245 (12)0.0029 (9)0.0060 (9)−0.0011 (10)
C180.0201 (11)0.0334 (13)0.0245 (12)0.0069 (9)0.0042 (9)0.0005 (10)
C190.0228 (11)0.0267 (12)0.0189 (11)0.0025 (9)0.0026 (8)0.0011 (9)
C200.0151 (10)0.0279 (12)0.0157 (10)−0.0006 (8)0.0030 (7)−0.0011 (8)
O1W0.099 (8)0.032 (4)0.046 (5)−0.004 (5)0.052 (6)0.000 (4)

Geometric parameters (Å, °)

O1—C201.361 (3)C10—H10C0.9600
O1—H1O10.96 (4)C11—C121.519 (4)
O2—C81.343 (3)C11—C141.523 (3)
O2—C91.452 (3)C11—H11A0.9800
O3—C81.204 (3)C12—C131.518 (4)
N1—C11.325 (3)C12—H12A0.9700
N1—C71.389 (3)C12—H12B0.9700
N2—C11.363 (3)C13—H13A0.9600
N2—C21.383 (3)C13—H13B0.9600
N2—C111.483 (3)C13—H13C0.9600
C1—C151.472 (3)C14—H14A0.9600
C2—C71.396 (3)C14—H14B0.9600
C2—C31.397 (3)C14—H14C0.9600
C3—C41.386 (3)C15—C201.391 (3)
C3—H3A0.9300C15—C161.403 (3)
C4—C51.396 (4)C16—C171.380 (3)
C4—H4A0.9300C16—H16A0.9300
C5—C61.393 (3)C17—C181.374 (4)
C5—C81.487 (3)C17—H17A0.9300
C6—C71.392 (3)C18—C191.388 (3)
C6—H6A0.9300C18—H18A0.9300
C9—C101.479 (4)C19—C201.389 (3)
C9—H9A0.9700C19—H19A0.9300
C9—H9B0.9700O1W—O1Wi1.708 (18)
C10—H10A0.9600O1W—H1W10.8114
C10—H10B0.9600O1W—H2W10.8187
C20—O1—H1O1112 (2)C12—C11—C14112.9 (2)
C8—O2—C9116.6 (2)N2—C11—H11A107.4
C1—N1—C7105.09 (19)C12—C11—H11A107.4
C1—N2—C2106.95 (19)C14—C11—H11A107.4
C1—N2—C11125.96 (18)C13—C12—C11112.8 (2)
C2—N2—C11127.02 (19)C13—C12—H12A109.0
N1—C1—N2112.65 (19)C11—C12—H12A109.0
N1—C1—C15122.5 (2)C13—C12—H12B109.0
N2—C1—C15124.82 (19)C11—C12—H12B109.0
N2—C2—C7105.54 (19)H12A—C12—H12B107.8
N2—C2—C3132.6 (2)C12—C13—H13A109.5
C7—C2—C3121.9 (2)C12—C13—H13B109.5
C4—C3—C2116.4 (2)H13A—C13—H13B109.5
C4—C3—H3A121.8C12—C13—H13C109.5
C2—C3—H3A121.8H13A—C13—H13C109.5
C3—C4—C5122.3 (2)H13B—C13—H13C109.5
C3—C4—H4A118.8C11—C14—H14A109.5
C5—C4—H4A118.8C11—C14—H14B109.5
C6—C5—C4120.9 (2)H14A—C14—H14B109.5
C6—C5—C8117.4 (2)C11—C14—H14C109.5
C4—C5—C8121.7 (2)H14A—C14—H14C109.5
C7—C6—C5117.4 (2)H14B—C14—H14C109.5
C7—C6—H6A121.3C20—C15—C16119.4 (2)
C5—C6—H6A121.3C20—C15—C1122.27 (19)
N1—C7—C6129.1 (2)C16—C15—C1118.3 (2)
N1—C7—C2109.77 (19)C17—C16—C15120.5 (2)
C6—C7—C2121.1 (2)C17—C16—H16A119.8
O3—C8—O2124.0 (2)C15—C16—H16A119.8
O3—C8—C5124.6 (2)C18—C17—C16119.6 (2)
O2—C8—C5111.4 (2)C18—C17—H17A120.2
O2—C9—C10110.5 (2)C16—C17—H17A120.2
O2—C9—H9A109.5C17—C18—C19120.9 (2)
C10—C9—H9A109.5C17—C18—H18A119.6
O2—C9—H9B109.5C19—C18—H18A119.6
C10—C9—H9B109.5C18—C19—C20119.9 (2)
H9A—C9—H9B108.1C18—C19—H19A120.1
C9—C10—H10A109.5C20—C19—H19A120.1
C9—C10—H10B109.5O1—C20—C19122.5 (2)
H10A—C10—H10B109.5O1—C20—C15117.73 (19)
C9—C10—H10C109.5C19—C20—C15119.8 (2)
H10A—C10—H10C109.5O1Wi—O1W—H1W160.9
H10B—C10—H10C109.5O1Wi—O1W—H2W175.8
N2—C11—C12110.6 (2)H1W1—O1W—H2W1106.0
N2—C11—C14110.99 (19)
C7—N1—C1—N2−0.1 (2)C6—C5—C8—O3−5.9 (4)
C7—N1—C1—C15−178.0 (2)C4—C5—C8—O3173.6 (3)
C2—N2—C1—N10.0 (3)C6—C5—C8—O2175.0 (2)
C11—N2—C1—N1−176.9 (2)C4—C5—C8—O2−5.5 (3)
C2—N2—C1—C15177.8 (2)C8—O2—C9—C1087.3 (3)
C11—N2—C1—C150.8 (4)C1—N2—C11—C12109.2 (2)
C1—N2—C2—C70.1 (2)C2—N2—C11—C12−67.2 (3)
C11—N2—C2—C7177.0 (2)C1—N2—C11—C14−124.7 (2)
C1—N2—C2—C3−179.9 (3)C2—N2—C11—C1459.0 (3)
C11—N2—C2—C3−2.9 (4)N2—C11—C12—C13−62.2 (3)
N2—C2—C3—C4−179.3 (2)C14—C11—C12—C13172.8 (2)
C7—C2—C3—C40.7 (4)N1—C1—C15—C20−121.4 (2)
C2—C3—C4—C5−0.1 (4)N2—C1—C15—C2061.0 (3)
C3—C4—C5—C6−0.6 (4)N1—C1—C15—C1656.0 (3)
C3—C4—C5—C8179.9 (2)N2—C1—C15—C16−121.5 (2)
C4—C5—C6—C70.7 (3)C20—C15—C16—C17−0.7 (3)
C8—C5—C6—C7−179.8 (2)C1—C15—C16—C17−178.3 (2)
C1—N1—C7—C6−179.3 (2)C15—C16—C17—C181.5 (4)
C1—N1—C7—C20.2 (2)C16—C17—C18—C19−1.0 (4)
C5—C6—C7—N1179.4 (2)C17—C18—C19—C20−0.4 (4)
C5—C6—C7—C2−0.1 (3)C18—C19—C20—O1179.3 (2)
N2—C2—C7—N1−0.2 (2)C18—C19—C20—C151.2 (4)
C3—C2—C7—N1179.8 (2)C16—C15—C20—O1−178.9 (2)
N2—C2—C7—C6179.3 (2)C1—C15—C20—O1−1.4 (3)
C3—C2—C7—C6−0.7 (4)C16—C15—C20—C19−0.6 (3)
C9—O2—C8—O32.8 (4)C1—C15—C20—C19176.8 (2)
C9—O2—C8—C5−178.2 (2)

Symmetry codes: (i) −x, −y+2, −z+1.

Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the N1,N2,C1,C2,N7 imidazole ring.
D—H···AD—HH···AD···AD—H···A
O1—H1O1···N1ii0.96 (4)1.75 (4)2.691 (3)168 (3)
C14—H14C···O1ii0.962.453.398 (3)168
C17—H17A···Cg1iii0.932.963.734 (3)142

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SJ2770).

References

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