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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o2005.
Published online 2009 July 25. doi:  10.1107/S1600536809027391
PMCID: PMC2977158

3-Carboxy­methyl-1,3-benzimidazolium-1-acetate monohydrate

Abstract

The title compound, C11H10N2O4·H2O, has a zwitterionic structure, in which the benzimidazole ring system is planar, with a maximum deviation of 0.007 (3) Å. The carbox­yl/carboxyl­ate groups adopt a trans configuration. In the crystal structure, inter­molecular O—H(...)O hydrogen bonds involving the hydr­oxy/oxide O atoms link the mol­ecules into a one-dimensional chain. These chains are further linked by O—H(...)O hydrogen bonds involving the water mol­ecules into a two-dimensional network. π–π contacts between the benzimidazole rings [centroid–centroid distance = 3.5716 (4) Å] lead to the formation of a three-dimensional supra­molecular structure.

Related literature

For a related structure, see: Chen & Huang (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2005-scheme1.jpg

Experimental

Crystal data

  • C11H10N2O4·H2O
  • M r = 252.23
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2005-efi1.jpg
  • a = 16.0731 (15) Å
  • b = 8.1619 (11) Å
  • c = 18.8678 (17) Å
  • β = 113.3680 (10)°
  • V = 2272.2 (4) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 298 (2) K
  • 0.50 × 0.40 × 0.20 mm

Data collection

  • Bruker SMART 1000 CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.943, T max = 0.977
  • 5875 measured reflections
  • 2213 independent reflections
  • 1495 reflections with I > 2σ(I)
  • R int = 0.048

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.120
  • S = 1.00
  • 2213 reflections
  • 173 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.25 e Å−3
  • Δρmin = −0.18 e Å−3

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT (Bruker, 2001 [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]); 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/S1600536809027391/hk2729sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809027391/hk2729Isup2.hkl

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

Acknowledgments

The authors thank the University of Jinan (grant No. B0604) for support of this work.

supplementary crystallographic information

Comment

Benzimidazole carboxylic acids have received much attention because of their application in the design of therapeutic agents and in construction of supramolecular metal complexes. Previously, the synthesis and crystal structure of 1-(carboxymethyl)-1,3-benzimidazol-3-ium-3-acetate, (II), have been described (Chen & Huang, 2006). We report herein the crystal struture of the title compound, (I).

In the molecule of the title compound (Fig. 1), the benzimidazole ring system is planar with a maximum deviation of 0.007 (3) Å for atom N1, and the two carboxyl groups adopt a trans configuration with respect to the benzimidazole ring plane. The C—N bonds on the imidazolium rings are found to be within 1.323 (2)–1.391 (2) Å, which are between the C—N single and C=N double bonds, suggesting charge delocalization on the imidazolium rings. The torsion angles of C5—N1—C2—C1 [95.5 (2)°] and C6—N2—C4—C3 [-89.5 (2)°] are much smaller than the corresponding values in (II). The lattice water molecules have site symmetries 2.

In the crystal structure, intermolecular O-H···O hydrogen bonds involving the hydroxy O atoms (Table 1) link the molecules into a one-dimensional chain (Fig. 2), in which they are further linked by O-H···O hydrogen bonds of lattice water molecules (Table 1) into a two-dimensional network (Fig. 3). The π···π contacts between the benzene rings of the benzimidazole groups (Fig. 4), Cg2···Cg2i [symmetry code: (i) -x, 2 - y, -z, where Cg2 is centroid of the ring (C6-C11)] may further stabilize the structure, with centroid-centroid distance of 3.5716 (4) Å and lead to the formation of a three-dimensional supramolecular structure (Fig. 5).

Experimental

For the preparation of the title compound, benzimidazole (0.714 g,6 mmol) was added to an aqueous solution (35 ml) of iodoacetic acid (1.859 g, 10 mmol) and NaOH (0.405 g, 10 mmol). The resulting mixture was heated at reflux during which benzimidazole was gradually dissolved and the colorless solution changed to yellow. The pH was adjusted using saturated NaOH solution at 20 min intervals, keeping in the range of 8–9. When no pH change was detected, the solution was further refluxed for 30 min, cooled, acidified with hydrochloric acid until pH = 2–3. The brown precipitate formed was filtered and recrystallized using water during which the deep yellow solution changed to colorless. The colorless plate crystals were formed after 5 d.

Refinement

Atoms H3, H5 and H6 were located in a difference Fourier map and refined isotropically. The remaining H atoms were positioned geometrically with C-H = 0.93 and 0.97 Å for aromatic and methylene H atoms, respectively, and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 25% probability level.
Fig. 2.
The one-dimensional chain constructed by hydrogen bondings.
Fig. 3.
The two-dimensional network viewed along [001] direction.
Fig. 4.
The π-π stacking between the benzene rings.
Fig. 5.
The three-dimensional network viewed along the b axis.

Crystal data

C11H10N2O4·H2OF(000) = 1056
Mr = 252.23Dx = 1.475 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 1932 reflections
a = 16.0731 (15) Åθ = 2.4–26.4°
b = 8.1619 (11) ŵ = 0.12 mm1
c = 18.8678 (17) ÅT = 298 K
β = 113.368 (1)°Plate, colorless
V = 2272.2 (4) Å30.50 × 0.40 × 0.20 mm
Z = 8

Data collection

Bruker SMART 1000 CCD area-detector diffractometer2213 independent reflections
Radiation source: fine-focus sealed tube1495 reflections with I > 2σ(I)
graphiteRint = 0.048
[var phi] and ω scansθmax = 26.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −14→19
Tmin = 0.943, Tmax = 0.977k = −10→10
5875 measured reflectionsl = −23→23

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)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.120H atoms treated by a mixture of independent and constrained refinement
S = 1.00w = 1/[σ2(Fo2) + (0.0647P)2 + 0.9016P] where P = (Fo2 + 2Fc2)/3
2213 reflections(Δ/σ)max = 0.001
173 parametersΔρmax = 0.25 e Å3
1 restraintΔρmin = −0.18 e Å3

Special details

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
O10.64155 (9)0.6138 (2)0.28621 (9)0.0608 (5)
O20.75932 (9)0.5077 (2)0.38158 (10)0.0658 (6)
O31.16479 (10)0.80460 (19)0.41440 (9)0.0501 (4)
H31.1979 (16)0.867 (3)0.3937 (14)0.075*
O41.20178 (11)0.6063 (2)0.35149 (10)0.0646 (5)
O50.50000.8452 (3)0.25000.0582 (6)
H50.5476 (18)0.782 (4)0.2614 (17)0.087*
O60.50000.3611 (3)0.25000.0688 (8)
H60.544 (2)0.427 (4)0.2634 (19)0.103*
N10.87906 (10)0.7126 (2)0.36403 (9)0.0349 (4)
N21.01818 (10)0.62393 (18)0.40836 (9)0.0337 (4)
C10.72276 (12)0.6073 (3)0.32812 (11)0.0377 (5)
C20.78365 (12)0.7326 (3)0.31305 (11)0.0416 (5)
H2A0.77720.72300.25990.050*
H2B0.76410.84170.31990.050*
C31.16099 (12)0.6581 (3)0.38815 (11)0.0372 (5)
C41.10076 (13)0.5451 (3)0.41022 (13)0.0411 (5)
H4A1.08400.45240.37520.049*
H4B1.13480.50340.46180.049*
C50.94014 (13)0.6308 (2)0.34744 (11)0.0376 (5)
H5A0.92970.58450.29960.045*
C61.00799 (12)0.7058 (2)0.46895 (11)0.0322 (4)
C70.91917 (12)0.7614 (2)0.44087 (10)0.0320 (4)
C80.88646 (14)0.8494 (3)0.48694 (12)0.0429 (5)
H80.82710.88770.46830.052*
C90.94620 (17)0.8773 (3)0.56172 (13)0.0494 (6)
H90.92650.93500.59470.059*
C101.03527 (16)0.8218 (3)0.58943 (12)0.0480 (6)
H101.07360.84430.64030.058*
C111.06811 (14)0.7353 (3)0.54415 (11)0.0409 (5)
H111.12770.69810.56280.049*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0289 (8)0.0773 (13)0.0644 (10)−0.0032 (8)0.0059 (7)0.0195 (9)
O20.0296 (8)0.0579 (11)0.0966 (13)−0.0030 (7)0.0107 (8)0.0402 (10)
O30.0451 (9)0.0378 (10)0.0757 (11)−0.0041 (7)0.0328 (8)0.0023 (8)
O40.0649 (11)0.0641 (12)0.0884 (12)0.0002 (9)0.0552 (10)−0.0062 (9)
O50.0550 (15)0.0519 (16)0.0612 (14)0.0000.0161 (13)0.000
O60.0574 (16)0.0520 (17)0.0872 (19)0.0000.0181 (15)0.000
N10.0279 (8)0.0388 (10)0.0393 (9)−0.0036 (7)0.0147 (7)0.0031 (7)
N20.0306 (9)0.0294 (9)0.0451 (9)−0.0026 (7)0.0193 (8)−0.0003 (7)
C10.0250 (10)0.0426 (13)0.0433 (11)0.0014 (9)0.0111 (9)0.0025 (10)
C20.0323 (11)0.0449 (13)0.0440 (11)0.0004 (10)0.0115 (9)0.0092 (10)
C30.0276 (10)0.0401 (13)0.0428 (11)0.0054 (9)0.0129 (9)0.0027 (10)
C40.0383 (11)0.0327 (12)0.0576 (12)0.0032 (9)0.0246 (10)0.0002 (10)
C50.0378 (11)0.0383 (12)0.0410 (11)−0.0087 (9)0.0203 (9)−0.0027 (9)
C60.0343 (10)0.0242 (10)0.0419 (11)−0.0019 (8)0.0191 (9)0.0028 (9)
C70.0318 (10)0.0281 (11)0.0391 (10)−0.0016 (8)0.0172 (8)0.0060 (8)
C80.0441 (12)0.0381 (13)0.0551 (13)0.0084 (10)0.0287 (11)0.0078 (10)
C90.0702 (16)0.0377 (13)0.0503 (13)0.0032 (11)0.0345 (12)−0.0009 (10)
C100.0603 (15)0.0413 (13)0.0389 (11)−0.0061 (11)0.0158 (11)−0.0014 (10)
C110.0379 (11)0.0351 (12)0.0457 (12)−0.0012 (9)0.0124 (10)0.0051 (10)

Geometric parameters (Å, °)

O1—C11.230 (2)C2—H2B0.9700
O2—C11.246 (2)C3—C41.511 (3)
O3—C31.286 (3)C4—H4A0.9700
O3—H30.925 (17)C4—H4B0.9700
O4—C31.203 (2)C5—H5A0.9300
O5—H50.88 (3)C6—C111.385 (3)
O6—H60.84 (3)C6—C71.387 (3)
N1—C51.323 (2)C7—C81.382 (3)
N1—C71.391 (2)C8—C91.375 (3)
N1—C21.461 (2)C8—H80.9300
N2—C51.324 (2)C9—C101.391 (3)
N2—C61.389 (2)C9—H90.9300
N2—C41.463 (2)C10—C111.366 (3)
C1—C21.519 (3)C10—H100.9300
C2—H2A0.9700C11—H110.9300
C3—O3—H3107.1 (16)C3—C4—H4B108.9
C5—N1—C7108.08 (16)H4A—C4—H4B107.7
C5—N1—C2125.76 (17)N1—C5—N2110.62 (17)
C5—N2—C6108.28 (15)N1—C5—H5A124.7
C5—N2—C4125.26 (16)N2—C5—H5A124.7
C6—N2—C4126.45 (16)C11—C6—C7121.93 (18)
C7—N1—C2125.85 (16)C11—C6—N2131.65 (18)
O1—C1—O2126.00 (19)C7—C6—N2106.41 (16)
O1—C1—C2116.68 (18)C8—C7—C6121.35 (18)
O2—C1—C2117.31 (16)C8—C7—N1132.04 (18)
N1—C2—C1112.79 (16)C6—C7—N1106.60 (16)
N1—C2—H2A109.0C9—C8—C7116.5 (2)
C1—C2—H2A109.0C9—C8—H8121.7
N1—C2—H2B109.0C7—C8—H8121.7
C1—C2—H2B109.0C8—C9—C10121.8 (2)
H2A—C2—H2B107.8C8—C9—H9119.1
O4—C3—O3126.48 (19)C10—C9—H9119.1
O4—C3—C4119.9 (2)C11—C10—C9121.9 (2)
O3—C3—C4113.53 (17)C11—C10—H10119.0
N2—C4—C3113.53 (16)C9—C10—H10119.0
N2—C4—H4A108.9C10—C11—C6116.4 (2)
C3—C4—H4A108.9C10—C11—H11121.8
N2—C4—H4B108.9C6—C11—H11121.8
C5—N1—C2—C195.5 (2)C11—C6—C7—C80.1 (3)
C7—N1—C2—C1−77.4 (2)N2—C6—C7—C8−179.74 (17)
O1—C1—C2—N1−178.35 (18)C11—C6—C7—N1179.22 (17)
O2—C1—C2—N11.7 (3)N2—C6—C7—N1−0.61 (19)
C5—N2—C4—C389.6 (2)C5—N1—C7—C8179.7 (2)
C6—N2—C4—C3−89.5 (2)C2—N1—C7—C8−6.3 (3)
O4—C3—C4—N2−143.40 (19)C5—N1—C7—C60.7 (2)
O3—C3—C4—N238.8 (2)C2—N1—C7—C6174.70 (16)
C7—N1—C5—N2−0.5 (2)C6—C7—C8—C9−0.5 (3)
C2—N1—C5—N2−174.54 (16)N1—C7—C8—C9−179.39 (19)
C6—N2—C5—N10.2 (2)C7—C8—C9—C100.7 (3)
C4—N2—C5—N1−179.06 (16)C8—C9—C10—C11−0.6 (3)
C5—N2—C6—C11−179.5 (2)C9—C10—C11—C60.1 (3)
C4—N2—C6—C11−0.3 (3)C7—C6—C11—C100.1 (3)
C5—N2—C6—C70.30 (19)N2—C6—C11—C10179.90 (19)
C4—N2—C6—C7179.50 (16)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O3—H3···O2i0.93 (2)1.59 (2)2.487 (2)162 (2)
O5—H5···O10.88 (3)1.95 (3)2.825 (2)172 (3)
O6—H6···O10.84 (3)2.11 (3)2.943 (2)173 (3)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HK2729).

References

  • Bruker (2001). SMART, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Chen, D.-B. & Huang, L. (2006). Acta Cryst. E62, o4686–o4688.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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