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Acta Crystallogr Sect E Struct Rep Online. 2010 November 1; 66(Pt 11): o2754.
Published online 2010 October 9. doi:  10.1107/S1600536810039188
PMCID: PMC3009264

Methyl 4-(1H-benzimidazol-2-yl)benzoate trihydrate

Abstract

The title compound, C15H12N2O2·3H2O, has been prepared from the reaction of a Schiff base of benzene-1,2-diamine and iron perchlorate at room temperature. The dihedral angle between the benzimidazole ring and the 4-substituted benzene ring is 0.47 (3)°. Hydrogen bonding involving water mol­ecules, imidazole N, imidazole imine H and ester O atoms stabilizes the crystal structure.

Related literature

For literature on the pharmacological activities of benzimidazole and its derivatives, see: Matsui et al. (1994 [triangle]); Ries et al. (2003 [triangle]). For the 4-nitro analogue, see: Wu (2009 [triangle]). For the earlier reported structure, see: Bei et al. (2000 [triangle]). For the synthesis of imidazoles and benzimidazoles, see: Du & Wang (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2754-scheme1.jpg

Experimental

Crystal data

  • C15H12N2O2·3H2O
  • M r = 306.32
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2754-efi1.jpg
  • a = 6.8308 (3) Å
  • b = 10.8165 (5) Å
  • c = 11.5254 (8) Å
  • α = 114.718 (3)°
  • β = 101.718 (4)°
  • γ = 97.621 (2)°
  • V = 734.41 (7) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 296 K
  • 0.41 × 0.12 × 0.12 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • 10457 measured reflections
  • 3194 independent reflections
  • 2873 reflections with I > 2σ(I)
  • R int = 0.041

Refinement

  • R[F 2 > 2σ(F 2)] = 0.042
  • wR(F 2) = 0.142
  • S = 1.02
  • 3194 reflections
  • 218 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.34 e Å−3
  • Δρmin = −0.41 e Å−3

Data collection: APEX2 (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; 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]) and Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810039188/ds2060sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810039188/ds2060Isup2.hkl

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

Acknowledgments

PG thanks the Department of Science and Technology, India, for research grant No. SR/FT/CS-057/2009. SM thanks the CSIR, India, for his PhD fellowship. The crystal data were collected at the IISER, Kolkata. The authors thank Mr G. Ramakrishna for the data collection and Mr Bhaskar Pramanik for helping with the structure refinement.

supplementary crystallographic information

Comment

Benzimidazole and its derivatives are important heterocyclic compounds with versatile pharmacological activities and have been reportedly used as antiparasitic, antimicrobial, and antifungal agents (Ries et al., 2003, Matsui et al. 1994). They also play very important role in the synthesis of many natural products and synthetic drugs. Herein we report a facile synthesis of compound I from a Schiff's base of 1,2-phenylenediamine using iron perchlorate at room temperature. As a part of our ongoing studies of photophysical properties of metal benzimidazole complexes, the title compound (I) (Fig. 1) was obtained by the reaction of dimethyl 4,4'-(1,2-phenylenebis(azan-1-yl-1-ylidene)bis (methan-1-yl-1-ylidene)dibenzoate and iron perchlorate in presence of dil. NaOH at 298 K (scheme 1). All other previously reported syntheses were done at a higher temperature.

Both the benzimidazole (N1—C7—N2—C13—C8) and methyl benzoate (C3—C4—C5—C6—C12—C11) fragments in this molecule are essentially coplanar similar to the previously reported 4-nitro analogue (De-Hong Wu, 2009). Here, benzimidazole N—H atom does not involve in N—H···N intermolecular hydrogen bonds as in all other cases. This benzimidazole N—H interacts with O3 from one of the water molecules (H17—O3—H17) and one of the hydrogen H16 (from the same water molecule) to form hydrogen bonding interaction with O2 atom of the ester moiety. In addition, N1 atom of benzimidazole ring forms hydrogen bond with the H18 atom of H18—O4—H19 molecule. Another notable hydrogen bonding interaction involves a bridge formation by the oxygen atom O5 in (H20—O5—H21) with two water molecules (H18—O4—H19). The water molecules are contained within channels running parrllel to the a axis. However, view along c axis shows clearly the side-on substructure formed by water molecules (Fig. 2). Examination of the bond length data reveal that the distances N1—C7 and N2—C7 in the imidazole ring are respectively 1.3321 (15)Å and 1.3638 (14) Å, and is intermediate between the model C—N bond length of 1.48Å and the typical C═N distance of 1.28 Å, indicating partial double-bond character. This can be interpreted in terms of conjugation within the heterocyclic ring system. The bond angles N1—C7—N2 and C5—C6—C12 are 112.56 (10)° and 118.95 (10)° respectively, which is similar to the earlier reported structure (Bei et al., 2000). The imidazole ring (N1—C7—N2—C8—C13) of one molecule and the phenyl ring (C8—C9—C10—C15—C14—C13) of another molecule are approximately parallel with the distance between their centroids being 3.520 (3)Å indicating π-stacking interactions displaying a two-dimensional supramolecular array. The stacking interaction is highlighted in Fig. 3.

Experimental

A methanolic solution of dimethyl 4,4'-(1,2-phenylenebis(azan-1-yl-1-ylidene)bis(methan -1-yl-1-ylidene)dibenzoate) (synthesized by condensation of 1,2-phenylene diamine and 4-formyl methyl benzoate in 1:2 stoichiometric proportion) 109.40 mg (2.7 mmol) and Fe(ClO4)2.6H2O, 50 mg (1.35 mmol) were mixed and to it was added 5 drops of 5% NaOH solution. The solution immediately changes from yellow to colourless. The solution was further stirred for 30 minutes at room temperature (298 K). The resulting solution was allowed to evaporate slowly at room temperature from which colourless single crystals of the title compound were obtained (Scheme 1).

Figures

Fig. 1.
The structure of I with 50% probability displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
View of compound I along c axis, side-on substructures formed by water molecules.
Fig. 3.
Stacking interaction of compound I.
Fig. 4.
The formation of the title compound.

Crystal data

C15H12N2O2·3H2OZ = 2
Mr = 306.32F(000) = 324
Triclinic, P1Dx = 1.390 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.8308 (3) ÅCell parameters from 8743 reflections
b = 10.8165 (5) Åθ = 2.2–40.7°
c = 11.5254 (8) ŵ = 0.11 mm1
α = 114.718 (3)°T = 296 K
β = 101.718 (4)°Rod, colourless
γ = 97.621 (2)°0.41 × 0.12 × 0.12 mm
V = 734.41 (7) Å3

Data collection

Bruker APEXII CCD area-detector diffractometer2873 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.041
graphiteθmax = 27.0°, θmin = 2.0°
[var phi] and ω scansh = −8→7
10457 measured reflectionsk = −13→13
3194 independent reflectionsl = −14→14

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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.142H atoms treated by a mixture of independent and constrained refinement
S = 1.01w = 1/[σ2(Fo2) + (0.1051P)2 + 0.1366P] where P = (Fo2 + 2Fc2)/3
3194 reflections(Δ/σ)max < 0.001
218 parametersΔρmax = 0.34 e Å3
0 restraintsΔρmin = −0.41 e Å3

Special details

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
O10.31311 (14)0.28296 (9)0.39119 (8)0.0166 (2)
O50.21253 (15)0.02407 (10)0.63276 (9)0.0209 (2)
H210.155 (3)−0.050 (2)0.554 (2)0.031*
H200.122 (3)0.076 (2)0.6355 (19)0.031*
O30.37646 (14)0.87010 (9)0.26610 (9)0.0176 (2)
H170.523 (3)0.9011 (18)0.3003 (17)0.026*
H160.333 (3)0.9357 (19)0.2506 (17)0.026*
O20.22975 (14)0.07258 (9)0.20910 (9)0.0182 (2)
O40.07060 (15)0.80876 (9)0.37434 (9)0.0207 (2)
H19−0.003 (3)0.723 (2)0.3151 (19)0.031*
H180.170 (3)0.8188 (19)0.3397 (19)0.031*
N10.19210 (15)0.44471 (10)−0.18336 (10)0.0133 (2)
N20.28539 (14)0.64581 (10)0.00717 (9)0.0124 (2)
H20.31970.70170.09120.015*
C10.3320 (2)0.21255 (13)0.47386 (13)0.0211 (3)
H1A0.20920.13970.44360.032*
H1B0.35040.27900.56470.032*
H1C0.44880.17220.46820.032*
C20.26140 (17)0.20014 (12)0.25945 (12)0.0135 (3)
C30.24921 (17)0.28025 (12)0.18125 (11)0.0127 (3)
C40.29491 (18)0.42689 (12)0.24419 (12)0.0146 (3)
H40.32890.47630.33660.018*
C50.28948 (18)0.49866 (12)0.16823 (12)0.0146 (3)
H50.31930.59620.21040.017*
C60.23967 (17)0.42582 (11)0.02890 (11)0.0121 (3)
C70.23803 (17)0.50275 (12)−0.05091 (12)0.0120 (2)
C80.21047 (17)0.55767 (12)−0.21278 (11)0.0130 (3)
C90.17985 (19)0.56017 (13)−0.33573 (12)0.0166 (3)
H90.14310.4777−0.41550.020*
C100.20643 (19)0.69051 (13)−0.33395 (12)0.0179 (3)
H100.18720.6949−0.41420.021*
C110.19577 (18)0.20677 (12)0.04230 (12)0.0150 (3)
H110.16280.10920.00030.018*
C120.19151 (18)0.27840 (12)−0.03356 (12)0.0147 (3)
H120.15670.2286−0.12600.018*
C130.26809 (17)0.68429 (12)−0.09392 (11)0.0124 (3)
C140.29457 (18)0.81564 (12)−0.09143 (12)0.0155 (3)
H140.33230.8983−0.01180.019*
C150.26175 (18)0.81641 (13)−0.21382 (13)0.0170 (3)
H150.27650.9017−0.21670.020*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0222 (5)0.0159 (4)0.0151 (4)0.0054 (3)0.0048 (3)0.0102 (3)
O50.0233 (5)0.0193 (5)0.0160 (5)0.0049 (4)0.0007 (4)0.0066 (4)
O30.0199 (5)0.0138 (4)0.0189 (4)0.0043 (3)0.0029 (4)0.0084 (3)
O20.0231 (5)0.0140 (4)0.0194 (4)0.0053 (3)0.0041 (4)0.0101 (4)
O40.0223 (5)0.0161 (4)0.0179 (5)0.0009 (4)0.0056 (4)0.0035 (4)
N10.0130 (5)0.0139 (5)0.0146 (5)0.0040 (4)0.0029 (4)0.0084 (4)
N20.0135 (5)0.0127 (5)0.0118 (5)0.0036 (4)0.0025 (4)0.0069 (4)
C10.0306 (7)0.0214 (6)0.0178 (6)0.0076 (5)0.0067 (5)0.0146 (5)
C20.0113 (5)0.0154 (5)0.0165 (6)0.0045 (4)0.0041 (4)0.0093 (5)
C30.0103 (5)0.0148 (6)0.0169 (6)0.0049 (4)0.0039 (4)0.0102 (5)
C40.0167 (6)0.0147 (6)0.0130 (5)0.0047 (4)0.0037 (4)0.0069 (4)
C50.0158 (6)0.0121 (5)0.0170 (6)0.0044 (4)0.0038 (4)0.0078 (4)
C60.0094 (5)0.0142 (5)0.0160 (6)0.0049 (4)0.0038 (4)0.0093 (5)
C70.0089 (5)0.0131 (5)0.0156 (5)0.0040 (4)0.0026 (4)0.0080 (4)
C80.0108 (5)0.0140 (5)0.0155 (6)0.0043 (4)0.0028 (4)0.0080 (4)
C90.0162 (6)0.0196 (6)0.0147 (6)0.0051 (4)0.0030 (4)0.0090 (5)
C100.0162 (6)0.0245 (6)0.0178 (6)0.0062 (5)0.0035 (5)0.0144 (5)
C110.0163 (6)0.0121 (5)0.0176 (6)0.0047 (4)0.0038 (5)0.0080 (5)
C120.0162 (6)0.0143 (5)0.0130 (5)0.0045 (4)0.0022 (4)0.0066 (4)
C130.0097 (5)0.0161 (5)0.0144 (5)0.0045 (4)0.0029 (4)0.0095 (4)
C140.0143 (6)0.0151 (6)0.0189 (6)0.0045 (4)0.0042 (4)0.0094 (5)
C150.0147 (6)0.0183 (6)0.0239 (6)0.0053 (4)0.0052 (5)0.0150 (5)

Geometric parameters (Å, °)

O1—C21.3391 (14)C4—C51.3904 (16)
O1—C11.4448 (14)C4—H40.9300
O5—H210.88 (2)C5—C61.4015 (16)
O5—H200.88 (2)C5—H50.9300
O3—H170.952 (19)C6—C121.4049 (16)
O3—H160.875 (19)C6—C71.4754 (15)
O2—C21.2197 (14)C8—C91.4021 (16)
O4—H190.88 (2)C8—C131.4058 (16)
O4—H180.87 (2)C9—C101.3882 (16)
N1—C71.3321 (15)C9—H90.9300
N1—C81.3953 (14)C10—C151.4102 (18)
N2—C71.3638 (14)C10—H100.9300
N2—C131.3810 (14)C11—C121.3885 (16)
N2—H20.8600C11—H110.9300
C1—H1A0.9600C12—H120.9300
C1—H1B0.9600C13—C141.3956 (15)
C1—H1C0.9600C14—C151.3864 (17)
C2—C31.4873 (15)C14—H140.9300
C3—C111.3966 (16)C15—H150.9300
C3—C41.3978 (16)
C2—O1—C1116.02 (9)C12—C6—C7120.53 (10)
H21—O5—H20101.8 (17)N1—C7—N2112.56 (10)
H17—O3—H16107.0 (16)N1—C7—C6125.68 (10)
H19—O4—H18101.0 (17)N2—C7—C6121.76 (10)
C7—N1—C8104.98 (9)N1—C8—C9130.49 (11)
C7—N2—C13107.37 (9)N1—C8—C13109.61 (10)
C7—N2—H2126.3C9—C8—C13119.89 (10)
C13—N2—H2126.3C10—C9—C8117.47 (11)
O1—C1—H1A109.5C10—C9—H9121.3
O1—C1—H1B109.5C8—C9—H9121.3
H1A—C1—H1B109.5C9—C10—C15121.84 (11)
O1—C1—H1C109.5C9—C10—H10119.1
H1A—C1—H1C109.5C15—C10—H10119.1
H1B—C1—H1C109.5C12—C11—C3120.47 (11)
O2—C2—O1123.50 (11)C12—C11—H11119.8
O2—C2—C3123.61 (11)C3—C11—H11119.8
O1—C2—C3112.89 (10)C11—C12—C6120.20 (11)
C11—C3—C4119.73 (10)C11—C12—H12119.9
C11—C3—C2118.94 (10)C6—C12—H12119.9
C4—C3—C2121.31 (11)N2—C13—C14131.59 (11)
C5—C4—C3119.82 (11)N2—C13—C8105.47 (10)
C5—C4—H4120.1C14—C13—C8122.93 (11)
C3—C4—H4120.1C15—C14—C13116.52 (11)
C4—C5—C6120.82 (11)C15—C14—H14121.7
C4—C5—H5119.6C13—C14—H14121.7
C6—C5—H5119.6C14—C15—C10121.34 (11)
C5—C6—C12118.95 (10)C14—C15—H15119.3
C5—C6—C7120.52 (10)C10—C15—H15119.3

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2···O30.861.992.8230 (13)163
O4—H18···O30.87 (2)1.92 (2)2.7830 (13)170.1 (17)
O3—H16···O2i0.875 (19)1.910 (19)2.7840 (12)177.4 (17)
O3—H17···O5ii0.952 (19)1.745 (19)2.6932 (13)173.9 (16)
O4—H19···N1iii0.88 (2)1.89 (2)2.7614 (14)171.0 (18)
O5—H20···O4iv0.88 (2)1.95 (2)2.8291 (14)174.0 (18)
O5—H21···O4v0.88 (2)1.90 (2)2.7679 (13)168.7 (18)
C15—H15···O5vi0.932.593.4009 (15)146

Symmetry codes: (i) x, y+1, z; (ii) −x+1, −y+1, −z+1; (iii) −x, −y+1, −z; (iv) −x, −y+1, −z+1; (v) x, y−1, z; (vi) x, y+1, z−1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DS2060).

References

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  • Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst.39, 453–457.
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