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Acta Crystallogr Sect E Struct Rep Online. 2010 August 1; 66(Pt 8): o2052.
Published online 2010 July 17. doi:  10.1107/S1600536810027455
PMCID: PMC3007197

4-(1H-Benzimidazol-2-ylmeth­oxy)-3-eth­oxy­benzaldehyde trihydrate

Abstract

In the title compound, C17H16N2O3·3H2O, the dihedral angle between the mean planes of the benzene and benzimidazole systems is 26.2 (3)°. These groups are slightly twisted around the eth­oxy­methane unit [C—C—O—C torsion angle = 177.64 (15)°]. The crystal packing is stabilized by N—H(...)O, O—H(...)N and O—H(...)O hydrogen-bond inter­actions involving the water mol­ecules. Weak π–π stacking inter­actions [centroid–centroid distances = 3.7943 (7), 3.6919 (13) and 3.7533 (14) Å] contribute to the mol­ecular stability.

Related literature

For the biological activity of benzimidazoles, see: Pujar et al. (1988 [triangle]); Bouwman et al. 1990 [triangle]). For related structures, see: Madkour et al. (2006 [triangle]); Jian et al. (2003 [triangle]); Odabaşoğlu et al. (2007 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

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Object name is e-66-o2052-scheme1.jpg

Experimental

Crystal data

  • C17H16N2O3·3H2O
  • M r = 350.37
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2052-efi1.jpg
  • a = 7.3020 (15) Å
  • b = 9.3170 (19) Å
  • c = 25.950 (5) Å
  • V = 1765.4 (6) Å3
  • Z = 4
  • Cu Kα radiation
  • μ = 0.84 mm−1
  • T = 100 K
  • 0.51 × 0.45 × 0.39 mm

Data collection

  • Oxford Diffraction Xcalibur with a Ruby (Gemini CCD) detector diffractometer
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007 [triangle]) T min = 0.875, T max = 1.000
  • 4635 measured reflections
  • 2130 independent reflections
  • 2030 reflections with I > 2σ(I)
  • R int = 0.019

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.102
  • S = 1.06
  • 2130 reflections
  • 246 parameters
  • 9 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.23 e Å−3
  • Δρmin = −0.16 e Å−3

Data collection: CrysAlis PRO (Oxford Diffraction, 2007 [triangle]); cell refinement: CrysAlis RED (Oxford Diffraction, 2007 [triangle]); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810027455/fl2307sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810027455/fl2307Isup2.hkl

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

Acknowledgments

SS thanks Mangalore University and the UGC SAP for financial assistance for the purchase of chemicals. HSY thanks the UOM for sabbatical leave. JPJ thanks Dr Ray Butcher and Howard University for assistance with the data collection (NSF MRI grant No. CHE-0619278).

supplementary crystallographic information

Comment

The benzimidazole ring system and its related compounds play an important role in pharmaceutical and agricultural fields due to their broad spectrum of biological activities (Pujar et al., 1988, Bouwman et al., 1990). The synthesis of novel benzimidazole derivatives remains a main focus of medicinal research. Benzimidazoles are useful as insecticides, acaricides, nematocides, herbicides and other plant-protective agents in the field of pest control (Madkour et al., 2006). In recent years, attention has increasingly been given to the synthesis of benzimidazole derivatives as a source of new antimicrobial agents. The crystal structures of some benzimidazole derivatives viz., 2-chloromethyl-1H-benzimidazole nitrate (Jian et al., 2003) and 5-methoxy-1H-benzo[d]imidazole-2(3H)-thione (Odabaşoğlu et al., 2007) have been reported. In view of the importance of benzimidazoles, the title compound, (I), ihas been synthesized and its crystal structure is reported here.

In (I) the dihedral angle between the mean planes of the benzene and benzimidazoles is 26.2 (6)° (Fig. 1). These groups are slightly twisted around the ethoxymethane structure (C2/C3/O3/C11 torsion angle = 177.64(15°). Bond distances and angles are in normal ranges (Allen et al., 1987). Crystal packing is stabilized by O—H···O, O—H..N and N—H···O hydrogen bond interactions (Fig. 2, Table 1) involving lattice crystallized water molecules which form a R22(10) graph-set motif (Fig. 3) and a two-dimensional chain along (001). Weak π-π stacking interactions (Table 2) contribute to molecular stability.

Experimental

Ethyl vanillin (0.05 mol) was dissolved in 40 ml of ethanolic KOH (0.05 mol) and the solution was stirred for 1 h. 2-Chloromethyl-1H-benzimidazole (0.05 mole) was added with continuous stirring and refluxed for 5 h. The reaction mixture was cooled at room temperature, then poured into crushed ice. The solid product that separated out was filtered off and recrystallized using 1,4-dioxane. Single crystals were grown from ethanol slow evaporation method with a yield of 48%. (m.p.: 366 K). Analytical data: Found (Calculated): C %: 68.87(68.91); H%: 5.39 (5.44); N%: 9.40 (9.45).

Refinement

The H atoms on the water molecules (H1W1, H1W2, H2W1, H2W2, H3W1, H3W2) were originally located in a difference Fourier and then their coordinates were allowed to refine with restraints to keep them in the range of 0.80 - 0.84 Å. The remaining H atoms were then positioned geometrically and allowed to ride on their parent atoms with Atom—H lengths of 0.86Å (NH), 0.93 Å (CH), 0.97Å (CH2) or 0.96Å (CH3). Isotropic displacement parameters for these atoms were set to 1.5 times (OH), 1.2 times (NH), 1.2 (CH, CH2) or 1.5 (CH3) times Ueq of the parent atom. In the absence of anomalous scattering effects Friedel opposites were merged.

Figures

Fig. 1.
Molecular structure of C17H17N2O3, with 50% probability displacement ellipsoids. Dashed lines indicate O—H···N, O—H···O and N—H···O hydrogen bonds.
Fig. 2.
Packing diagram of the title compound viewed down the c axis. Dashed lines indicate O—H···N, O—H···O and N—H···O hydrogen bonds forming a two-dimensional chain ...
Fig. 3.
R22(10) graph-set motif for C17H17N2O3 involving lattice crystallized water molecules.

Crystal data

C17H16N2O3·3H2OF(000) = 744
Mr = 350.37Dx = 1.318 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2abCell parameters from 3976 reflections
a = 7.3020 (15) Åθ = 4.7–77.2°
b = 9.3170 (19) ŵ = 0.84 mm1
c = 25.950 (5) ÅT = 100 K
V = 1765.4 (6) Å3Block, colorless
Z = 40.51 × 0.45 × 0.39 mm

Data collection

Oxford Diffraction Xcalibur with a Ruby (Gemini CCD) detector diffractometer2130 independent reflections
Radiation source: Enhance (Cu) X-ray Source2030 reflections with I > 2σ(I)
graphiteRint = 0.019
Detector resolution: 10.5081 pixels mm-1θmax = 77.4°, θmin = 5.9°
ω scansh = −9→6
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007)k = −11→5
Tmin = 0.875, Tmax = 1.000l = −32→32
4635 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.035H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.102w = 1/[σ2(Fo2) + (0.0683P)2 + 0.161P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2130 reflectionsΔρmax = 0.23 e Å3
246 parametersΔρmin = −0.16 e Å3
9 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.018 (2)

Special details

Experimental. In the absence of anomalous scattering effects Friedel opposites were merged
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)

xyzUiso*/Ueq
O10.1649 (2)0.05517 (14)0.09028 (5)0.0436 (3)
N10.1237 (2)0.36636 (17)−0.10832 (5)0.0413 (4)
C10.1274 (2)0.1882 (2)0.10989 (6)0.0380 (4)
O20.1203 (3)0.3165 (3)0.26729 (6)0.0857 (7)
N20.0561 (2)0.15054 (16)−0.07628 (5)0.0400 (3)
H2A0.02910.0857−0.05390.048*
C20.0862 (2)0.2957 (2)0.07342 (6)0.0368 (4)
O30.0958 (2)0.25276 (13)0.02315 (4)0.0436 (3)
C30.0434 (3)0.4335 (2)0.08910 (7)0.0443 (4)
H30.01560.50400.06500.053*
C40.0424 (3)0.4653 (2)0.14156 (8)0.0501 (5)
H40.01210.55740.15240.060*
C50.0857 (3)0.3622 (3)0.17741 (7)0.0483 (5)
C60.1279 (3)0.2223 (2)0.16162 (7)0.0441 (4)
H60.15610.15250.18600.053*
C70.2193 (3)−0.0543 (2)0.12644 (8)0.0484 (5)
H7A0.1208−0.07320.15060.058*
H7B0.3260−0.02310.14570.058*
C80.2631 (4)−0.1874 (2)0.09646 (11)0.0656 (7)
H8A0.1546−0.22100.07940.098*
H8B0.3073−0.26020.11950.098*
H8C0.3554−0.16610.07130.098*
C90.0857 (4)0.3982 (3)0.23244 (9)0.0662 (7)
H90.05650.49220.24130.079*
C100.0577 (3)0.35874 (19)−0.01518 (6)0.0408 (4)
H10A0.14000.4397−0.01120.049*
H10B−0.06710.3930−0.01150.049*
C110.0832 (2)0.29187 (19)−0.06693 (6)0.0369 (4)
C120.1204 (3)0.2666 (2)−0.14792 (7)0.0408 (4)
C130.0800 (2)0.1305 (2)−0.12853 (7)0.0411 (4)
C140.0735 (3)0.0092 (3)−0.15962 (9)0.0543 (5)
H140.0505−0.0814−0.14610.065*
C150.1030 (3)0.0301 (3)−0.21162 (9)0.0644 (6)
H150.1000−0.0484−0.23370.077*
C160.1372 (4)0.1668 (3)−0.23188 (8)0.0655 (7)
H160.15250.1772−0.26730.079*
C170.1488 (3)0.2858 (3)−0.20093 (7)0.0541 (5)
H170.17460.3759−0.21460.065*
O1W−0.0115 (3)−0.06193 (16)−0.00113 (5)0.0539 (4)
H1W1−0.080 (4)−0.128 (3)0.0094 (11)0.081*
H1W20.025 (4)−0.027 (3)0.0264 (9)0.081*
O2W0.2184 (4)0.65334 (19)−0.13309 (7)0.0814 (7)
H2W10.266 (5)0.660 (4)−0.1614 (10)0.122*
H2W20.206 (6)0.569 (2)−0.1259 (15)0.122*
O3W0.2942 (3)0.7793 (2)−0.04092 (7)0.0720 (5)
H3W10.272 (5)0.749 (4)−0.0708 (9)0.108*
H3W20.198 (4)0.820 (4)−0.0315 (13)0.108*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0604 (8)0.0383 (6)0.0320 (5)0.0041 (6)−0.0044 (6)0.0040 (5)
N10.0509 (8)0.0405 (7)0.0325 (7)0.0022 (7)0.0009 (6)0.0080 (6)
C10.0385 (8)0.0428 (9)0.0326 (8)−0.0030 (7)−0.0005 (7)0.0004 (7)
O20.1008 (14)0.1227 (17)0.0337 (7)−0.0013 (15)−0.0111 (8)−0.0134 (10)
N20.0478 (8)0.0384 (7)0.0337 (7)−0.0014 (7)0.0012 (6)0.0067 (6)
C20.0405 (8)0.0409 (8)0.0291 (7)−0.0008 (7)0.0006 (6)−0.0013 (6)
O30.0653 (8)0.0388 (6)0.0269 (5)0.0073 (6)−0.0005 (5)0.0022 (5)
C30.0515 (9)0.0413 (9)0.0401 (8)0.0015 (8)0.0024 (8)−0.0028 (7)
C40.0540 (10)0.0490 (10)0.0473 (10)−0.0017 (9)0.0058 (9)−0.0143 (9)
C50.0459 (9)0.0633 (12)0.0355 (8)−0.0081 (10)0.0007 (7)−0.0116 (8)
C60.0465 (9)0.0549 (10)0.0309 (8)−0.0040 (9)−0.0015 (7)0.0009 (8)
C70.0557 (10)0.0499 (10)0.0398 (8)−0.0017 (9)−0.0057 (8)0.0154 (8)
C80.0841 (16)0.0432 (10)0.0696 (14)0.0093 (11)−0.0202 (13)0.0082 (10)
C90.0687 (14)0.0878 (18)0.0420 (11)−0.0078 (14)−0.0006 (10)−0.0233 (12)
C100.0529 (10)0.0376 (8)0.0319 (7)0.0034 (8)−0.0003 (7)0.0045 (7)
C110.0403 (8)0.0375 (8)0.0330 (7)0.0029 (7)−0.0005 (7)0.0055 (6)
C120.0416 (8)0.0479 (9)0.0330 (8)0.0046 (8)−0.0010 (7)0.0054 (7)
C130.0386 (8)0.0462 (9)0.0385 (8)0.0004 (8)−0.0029 (7)0.0025 (7)
C140.0540 (11)0.0515 (11)0.0574 (11)−0.0048 (10)−0.0042 (9)−0.0096 (9)
C150.0611 (12)0.0792 (16)0.0529 (12)−0.0008 (13)−0.0085 (10)−0.0251 (12)
C160.0672 (14)0.0958 (18)0.0333 (9)0.0059 (15)−0.0025 (9)−0.0080 (11)
C170.0602 (12)0.0686 (13)0.0335 (8)0.0038 (11)0.0006 (8)0.0091 (9)
O1W0.0762 (10)0.0454 (7)0.0400 (6)−0.0085 (8)−0.0039 (7)0.0033 (6)
O2W0.1387 (19)0.0502 (9)0.0554 (9)−0.0111 (12)0.0363 (11)−0.0038 (7)
O3W0.0808 (11)0.0771 (11)0.0581 (9)0.0230 (11)−0.0052 (9)−0.0030 (9)

Geometric parameters (Å, °)

O1—C11.367 (2)C8—H8A0.9600
O1—C71.442 (2)C8—H8B0.9600
N1—C111.313 (2)C8—H8C0.9600
N1—C121.386 (2)C9—H90.9300
C1—C61.380 (2)C10—C111.492 (2)
C1—C21.410 (2)C10—H10A0.9700
O2—C91.209 (4)C10—H10B0.9700
N2—C111.354 (2)C12—C131.397 (3)
N2—C131.380 (2)C12—C171.402 (2)
N2—H2A0.8600C13—C141.389 (3)
C2—O31.3660 (19)C14—C151.380 (3)
C2—C31.383 (3)C14—H140.9300
O3—C101.429 (2)C15—C161.400 (4)
C3—C41.393 (3)C15—H150.9300
C3—H30.9300C16—C171.372 (4)
C4—C51.374 (3)C16—H160.9300
C4—H40.9300C17—H170.9300
C5—C61.400 (3)O1W—H1W10.840 (17)
C5—C91.467 (3)O1W—H1W20.829 (17)
C6—H60.9300O2W—H2W10.815 (18)
C7—C81.498 (3)O2W—H2W20.809 (19)
C7—H7A0.9700O3W—H3W10.842 (18)
C7—H7B0.9700O3W—H3W20.832 (18)
C1—O1—C7117.02 (14)H8B—C8—H8C109.5
C11—N1—C12104.39 (15)O2—C9—C5125.8 (3)
O1—C1—C6124.79 (17)O2—C9—H9117.1
O1—C1—C2115.88 (14)C5—C9—H9117.1
C6—C1—C2119.33 (17)O3—C10—C11108.28 (14)
C11—N2—C13106.84 (15)O3—C10—H10A110.0
C11—N2—H2A126.6C11—C10—H10A110.0
C13—N2—H2A126.6O3—C10—H10B110.0
O3—C2—C3124.35 (16)C11—C10—H10B110.0
O3—C2—C1114.97 (15)H10A—C10—H10B108.4
C3—C2—C1120.67 (16)N1—C11—N2113.62 (16)
C2—O3—C10116.91 (14)N1—C11—C10122.95 (16)
C2—C3—C4119.09 (18)N2—C11—C10123.31 (15)
C2—C3—H3120.5N1—C12—C13110.22 (15)
C4—C3—H3120.5N1—C12—C17129.7 (2)
C5—C4—C3120.76 (19)C13—C12—C17120.0 (2)
C5—C4—H4119.6N2—C13—C14132.61 (19)
C3—C4—H4119.6N2—C13—C12104.93 (16)
C4—C5—C6120.21 (17)C14—C13—C12122.45 (17)
C4—C5—C9119.9 (2)C15—C14—C13116.6 (2)
C6—C5—C9119.8 (2)C15—C14—H14121.7
C1—C6—C5119.92 (19)C13—C14—H14121.7
C1—C6—H6120.0C14—C15—C16121.5 (2)
C5—C6—H6120.0C14—C15—H15119.2
O1—C7—C8107.84 (16)C16—C15—H15119.2
O1—C7—H7A110.1C17—C16—C15121.76 (19)
C8—C7—H7A110.1C17—C16—H16119.1
O1—C7—H7B110.1C15—C16—H16119.1
C8—C7—H7B110.1C16—C17—C12117.5 (2)
H7A—C7—H7B108.5C16—C17—H17121.2
C7—C8—H8A109.5C12—C17—H17121.2
C7—C8—H8B109.5H1W1—O1W—H1W2102 (2)
H8A—C8—H8B109.5H2W1—O2W—H2W2109 (3)
C7—C8—H8C109.5H3W1—O3W—H3W2105 (3)
H8A—C8—H8C109.5
C7—O1—C1—C6−3.9 (3)C12—N1—C11—N20.8 (2)
C7—O1—C1—C2175.99 (16)C12—N1—C11—C10−175.35 (17)
O1—C1—C2—O3−2.2 (2)C13—N2—C11—N1−0.3 (2)
C6—C1—C2—O3177.71 (16)C13—N2—C11—C10175.87 (16)
O1—C1—C2—C3178.95 (16)O3—C10—C11—N1−154.73 (17)
C6—C1—C2—C3−1.1 (3)O3—C10—C11—N229.4 (2)
C3—C2—O3—C10−0.3 (3)C11—N1—C12—C13−1.1 (2)
C1—C2—O3—C10−179.14 (16)C11—N1—C12—C17178.2 (2)
O3—C2—C3—C4−178.37 (18)C11—N2—C13—C14178.3 (2)
C1—C2—C3—C40.4 (3)C11—N2—C13—C12−0.4 (2)
C2—C3—C4—C50.9 (3)N1—C12—C13—N20.9 (2)
C3—C4—C5—C6−1.3 (3)C17—C12—C13—N2−178.49 (18)
C3—C4—C5—C9179.4 (2)N1—C12—C13—C14−177.95 (18)
O1—C1—C6—C5−179.41 (18)C17—C12—C13—C142.7 (3)
C2—C1—C6—C50.7 (3)N2—C13—C14—C15179.3 (2)
C4—C5—C6—C10.5 (3)C12—C13—C14—C15−2.2 (3)
C9—C5—C6—C1179.83 (19)C13—C14—C15—C16−0.1 (4)
C1—O1—C7—C8−176.90 (18)C14—C15—C16—C172.1 (4)
C4—C5—C9—O2179.5 (3)C15—C16—C17—C12−1.6 (4)
C6—C5—C9—O20.2 (4)N1—C12—C17—C16−179.9 (2)
C2—O3—C10—C11177.64 (15)C13—C12—C17—C16−0.7 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2A···O1W0.861.962.822 (2)175
O1W—H1W1···O3Wi0.84 (2)1.87 (2)2.703 (2)171 (3)
O1W—H1W2···O10.83 (2)2.09 (2)2.911 (2)170 (3)
O2W—H2W1···O2ii0.82 (2)2.04 (2)2.855 (2)178 (4)
O2W—H2W2···N10.81 (2)2.04 (2)2.836 (3)169 (5)
O3W—H3W1···O2W0.84 (2)1.89 (2)2.721 (3)171 (4)
O3W—H3W2···O1Wiii0.83 (2)2.05 (2)2.870 (3)171 (4)

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

Table 2 Cg···Cg π-stacking interactions

Cg1 is the centroid of ring C11/N1/C12/C13/N2; Cg2 is the centroid of the ring C1–C6; Cg3 is the centroid of ring C12-C17.

CgI···CgJCgI···Perp (Å)CgJ···Perp (Å)
Cg1···Cg2i3.7943 (7)3.4481 (7)-3.5681 (8)
Cg1···Cg2ii3.6919 (13)-3.61041 (7)3.5404 (8)
Cg2···Cg3i3.7533 (14)3.5487 (8)3.3763 (9)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FL2307).

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