1H-Benzimidazol-3-ium-2-carboxyl­ate dihydrate

Yao, X.-J.; Yuan, Q.

doi:10.1107/S1600536811017399

organic compounds

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ISSN: 2056-9890

Volume 67| Part 6| June 2011| Page o1399

doi:10.1107/S1600536811017399

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1H-Benzimidazol-3-ium-2-carboxylate dihydrate

Xing-Jun Yao ^a ^* and Qian Yuan ^b

^aCollege of Chemistry and Chemical Engineering, Liaocheng University, 252059 Liaocheng, Shandong, People's Republic of China, and ^bGuodian Liaocheng Power Co. Ltd, 252033 Liaocheng, Shandong, People's Republic of China
^*Correspondence e-mail: y_xingjun01@163.com

(Received 29 April 2011; accepted 9 May 2011; online 14 May 2011)

The title compound, C₈H₆N₂O₂·2H₂O, crystallized as a zwitterion with the carboxyl group deprotonated and the imidazole group protonated. The dihedral angle between the benzimidazole ring and the pendant –CO₂ group is 0.62 (2)°. In the crystal, molecules are linked into a three-dimensional network by N—H⋯O and O—H⋯O hydrogen bonds.

Related literature

For the crystal structure of related zwitterionic benzimidazole-2-carboxylic acid monohydrate, see: Krawczyk et al. (2005 ). For the synthesis of the title compound, see: Thakurdesai et al. (2007 ).

Experimental

Crystal data

C₈H₆N₂O₂·2H₂O
M_r = 198.18
Monoclinic, P 2₁ /c
a = 6.8503 (15) Å
b = 7.3679 (17) Å
c = 18.939 (4) Å
β = 109.728 (7)°
V = 899.8 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.12 mm⁻¹
T = 298 K
0.42 × 0.38 × 0.35 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2005 ) T_min = 0.952, T_max = 0.960
4496 measured reflections
1760 independent reflections
1342 reflections with I > 2σ(I)
R_int = 0.095

Refinement

R[F² > 2σ(F²)] = 0.043
wR(F²) = 0.111
S = 1.03
1760 reflections
128 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H6⋯O1	0.85	2.01	2.8608 (19)	174
N1—H1⋯O3ⁱ	0.86	1.86	2.7135 (18)	170
O4—H9⋯O3ⁱ	0.84	2.06	2.874 (2)	163
N2—H2A⋯O2ⁱⁱ	0.86	1.87	2.6708 (18)	155
O3—H7⋯O4ⁱⁱⁱ	0.84	1.93	2.756 (2)	165
O4—H8⋯O1^iv	0.85	2.53	3.142 (2)	130
Symmetry codes: (i) $[-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) -x+1, -y+1, -z+2; (iii) x-1, y, z; (iv) $[-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811017399/cv5086sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811017399/cv5086Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811017399/cv5086Isup3.cml

checkCIF report

Comment top

Recently, the crystal structure of zwitterionic compound benzimidazole-2-carboxylic acid monohydrate (I) has been reported by Krawczyk et al. (2005). Herewith we present the crystal structure of its dihydrate form, the title compound (II).

In (II) (Fig. 1), the bond lengths and angles are normal and comparable with those observed in (I). The equal bond lengths of C7—N1 and C7—N2 of the imidazolium fragment, and C8—O1 and C8—O2 of the carboxylate group show both N atoms of the benzimidazole group are protonated and both O atoms of the carboxylate group are deprotonated. The dihedral angle between the benzimidazole and carboxylate groupe is 0.62 (2) °. The molecule is essentially planar, the r.m.s. deviation for all non-H atoms being 0.0249 Å. An extensive three-dimensional hydrogen-bonding network (Table 1) stabilize the crystal packing.

Related literature top

For the crystal structure of related zwitterionic benzimidazole-2-carboxylic acid monohydrate, see: Krawczyk et al. (2005). For the synthesis of the title compound, see: Thakurdesai et al. (2007).

Experimental top

The title compound was synthesized according to the method reported in the literature (Thakurdesai et al., 2007). Colourless single crystals suitable for X-ray diffraction were obtained by slow evaporation of an ethanol solution of the compound.

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

Fig. 1. View of the title compound showing the atomic labeling and 30% probability displacement ellipsoids.

1H-Benzimidazol-3-ium-2-carboxylate dihydrate top

Crystal data top

C₈H₆N₂O₂·2H₂O	F(000) = 416
M_r = 198.18	D_x = 1.463 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1540 reflections
a = 6.8503 (15) Å	θ = 2.3–26.2°
b = 7.3679 (17) Å	µ = 0.12 mm⁻¹
c = 18.939 (4) Å	T = 298 K
β = 109.728 (7)°	Block, colorless
V = 899.8 (3) Å³	0.42 × 0.38 × 0.35 mm
Z = 4

Data collection top

Bruker APEXII CCD diffractometer	1760 independent reflections
Radiation source: fine-focus sealed tube	1342 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.095
ϕ and ω scans	θ_max = 26.0°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −6→8
T_min = 0.952, T_max = 0.960	k = −9→9
4496 measured reflections	l = −23→17

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.043	H-atom parameters constrained
wR(F²) = 0.111	w = 1/[σ²(F_o²) + (0.041P)² + 0.0001P] where P = (F_o² + 2F_c²)/3
S = 1.03	(Δ/σ)_max = 0.001
1760 reflections	Δρ_max = 0.18 e Å⁻³
128 parameters	Δρ_min = −0.16 e Å⁻³
0 restraints	Extinction correction: SHELXTL (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.097 (8)

Crystal data top

C₈H₆N₂O₂·2H₂O	V = 899.8 (3) Å³
M_r = 198.18	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.8503 (15) Å	µ = 0.12 mm⁻¹
b = 7.3679 (17) Å	T = 298 K
c = 18.939 (4) Å	0.42 × 0.38 × 0.35 mm
β = 109.728 (7)°

Data collection top

Bruker APEXII CCD diffractometer	1760 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2005)	1342 reflections with I > 2σ(I)
T_min = 0.952, T_max = 0.960	R_int = 0.095
4496 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.043	0 restraints
wR(F²) = 0.111	H-atom parameters constrained
S = 1.03	Δρ_max = 0.18 e Å⁻³
1760 reflections	Δρ_min = −0.16 e Å⁻³
128 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
O1	0.4666 (2)	0.4099 (2)	0.80063 (6)	0.0549 (4)
O2	0.36643 (18)	0.48692 (18)	0.89664 (6)	0.0503 (4)
N1	0.8395 (2)	0.27481 (18)	0.90210 (7)	0.0352 (4)
H1	0.8355	0.2552	0.8569	0.042*
N2	0.74817 (19)	0.35912 (18)	0.99579 (7)	0.0354 (4)
H2A	0.6754	0.4029	1.0209	0.043*
C8	0.4882 (3)	0.4223 (2)	0.86784 (9)	0.0378 (4)
C7	0.6902 (3)	0.3506 (2)	0.92144 (8)	0.0346 (4)
C1	1.0037 (2)	0.2319 (2)	0.96623 (9)	0.0338 (4)
C2	1.1954 (3)	0.1538 (2)	0.97674 (9)	0.0392 (4)
H2	1.2351	0.1172	0.9366	0.047*
C3	1.3236 (3)	0.1332 (2)	1.04979 (10)	0.0443 (5)
H3	1.4546	0.0830	1.0594	0.053*
C4	1.2623 (3)	0.1857 (3)	1.11020 (10)	0.0451 (5)
H4	1.3532	0.1678	1.1588	0.054*
C5	1.0734 (3)	0.2625 (2)	1.10005 (9)	0.0415 (5)
H5	1.0331	0.2970	1.1403	0.050*
C6	0.9443 (2)	0.2864 (2)	1.02604 (9)	0.0344 (4)
O3	0.1521 (2)	0.67445 (19)	0.73470 (6)	0.0542 (4)
H7	0.0403	0.6248	0.7338	0.081*
H6	0.2413	0.5942	0.7569	0.081*
O4	0.7592 (2)	0.5359 (2)	0.70601 (8)	0.0747 (5)
H8	0.6747	0.5904	0.7228	0.112*
H9	0.7617	0.4321	0.7248	0.112*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0504 (8)	0.0778 (10)	0.0330 (7)	0.0132 (7)	0.0096 (6)	−0.0016 (6)
O2	0.0422 (7)	0.0669 (9)	0.0417 (8)	0.0109 (7)	0.0138 (6)	−0.0024 (6)
N1	0.0398 (8)	0.0360 (8)	0.0295 (7)	0.0008 (6)	0.0114 (6)	−0.0015 (6)
N2	0.0344 (8)	0.0386 (9)	0.0340 (8)	0.0029 (6)	0.0126 (6)	−0.0001 (6)
C8	0.0391 (10)	0.0389 (10)	0.0336 (9)	−0.0026 (8)	0.0099 (7)	−0.0008 (7)
C7	0.0379 (9)	0.0324 (9)	0.0334 (9)	−0.0022 (7)	0.0118 (7)	−0.0006 (7)
C1	0.0357 (9)	0.0299 (9)	0.0341 (9)	−0.0029 (7)	0.0097 (7)	0.0013 (7)
C2	0.0407 (10)	0.0342 (9)	0.0446 (10)	−0.0003 (8)	0.0169 (8)	−0.0006 (7)
C3	0.0390 (10)	0.0387 (11)	0.0523 (11)	0.0026 (8)	0.0114 (8)	0.0028 (8)
C4	0.0430 (11)	0.0422 (11)	0.0411 (10)	−0.0019 (8)	0.0025 (8)	0.0042 (8)
C5	0.0471 (11)	0.0415 (10)	0.0338 (9)	−0.0015 (8)	0.0110 (7)	−0.0009 (7)
C6	0.0354 (9)	0.0314 (9)	0.0350 (9)	−0.0036 (7)	0.0101 (7)	−0.0001 (7)
O3	0.0540 (8)	0.0618 (9)	0.0446 (8)	0.0048 (7)	0.0137 (6)	0.0122 (6)
O4	0.0629 (10)	0.0848 (12)	0.0758 (11)	−0.0023 (8)	0.0225 (8)	0.0131 (8)

Geometric parameters (Å, º) top

O1—C8	1.234 (2)	C2—H2	0.9300
O2—C8	1.236 (2)	C3—C4	1.400 (3)
N1—C7	1.321 (2)	C3—H3	0.9300
N1—C1	1.385 (2)	C4—C5	1.366 (2)
N1—H1	0.8600	C4—H4	0.9300
N2—C7	1.3291 (18)	C5—C6	1.393 (2)
N2—C6	1.379 (2)	C5—H5	0.9300
N2—H2A	0.8601	O3—H7	0.8435
C8—C7	1.508 (2)	O3—H6	0.8525
C1—C2	1.385 (2)	O4—H8	0.8496
C1—C6	1.386 (2)	O4—H9	0.8415
C2—C3	1.374 (2)

C7—N1—C1	109.21 (13)	C3—C2—H2	121.8
C7—N1—H1	125.4	C1—C2—H2	121.8
C1—N1—H1	125.4	C2—C3—C4	121.77 (17)
C7—N2—C6	108.83 (13)	C2—C3—H3	119.1
C7—N2—H2A	125.6	C4—C3—H3	119.1
C6—N2—H2A	125.5	C5—C4—C3	122.08 (16)
O1—C8—O2	128.31 (16)	C5—C4—H4	119.0
O1—C8—C7	115.57 (15)	C3—C4—H4	119.0
O2—C8—C7	116.11 (14)	C4—C5—C6	116.33 (16)
N1—C7—N2	109.33 (13)	C4—C5—H5	121.8
N1—C7—C8	125.56 (14)	C6—C5—H5	121.8
N2—C7—C8	125.09 (14)	N2—C6—C1	106.67 (13)
N1—C1—C2	132.13 (15)	N2—C6—C5	131.73 (15)
N1—C1—C6	105.95 (14)	C1—C6—C5	121.59 (15)
C2—C1—C6	121.92 (15)	H7—O3—H6	101.8
C3—C2—C1	116.30 (16)	H8—O4—H9	100.9

C1—N1—C7—N2	−0.27 (19)	C1—C2—C3—C4	1.0 (3)
C1—N1—C7—C8	177.85 (15)	C2—C3—C4—C5	−0.9 (3)
C6—N2—C7—N1	0.32 (18)	C3—C4—C5—C6	−0.1 (3)
C6—N2—C7—C8	−177.81 (16)	C7—N2—C6—C1	−0.25 (17)
O1—C8—C7—N1	−1.3 (3)	C7—N2—C6—C5	−179.71 (17)
O2—C8—C7—N1	179.22 (16)	N1—C1—C6—N2	0.09 (17)
O1—C8—C7—N2	176.57 (16)	C2—C1—C6—N2	179.40 (15)
O2—C8—C7—N2	−2.9 (3)	N1—C1—C6—C5	179.61 (15)
C7—N1—C1—C2	−179.11 (17)	C2—C1—C6—C5	−1.1 (2)
C7—N1—C1—C6	0.11 (18)	C4—C5—C6—N2	−179.49 (17)
N1—C1—C2—C3	179.09 (17)	C4—C5—C6—C1	1.1 (2)
C6—C1—C2—C3	0.0 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H6···O1	0.85	2.01	2.8608 (19)	174
N1—H1···O3ⁱ	0.86	1.86	2.7135 (18)	170
O4—H9···O3ⁱ	0.84	2.06	2.874 (2)	163
N2—H2A···O2ⁱⁱ	0.86	1.87	2.6708 (18)	155
O3—H7···O4ⁱⁱⁱ	0.84	1.93	2.756 (2)	165
O4—H8···O1^iv	0.85	2.53	3.142 (2)	130

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

Experimental details

Crystal data
Chemical formula	C₈H₆N₂O₂·2H₂O
M_r	198.18
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	298
a, b, c (Å)	6.8503 (15), 7.3679 (17), 18.939 (4)
β (°)	109.728 (7)
V (Å³)	899.8 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.12
Crystal size (mm)	0.42 × 0.38 × 0.35

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.952, 0.960
No. of measured, independent and observed [I > 2σ(I)] reflections	4496, 1760, 1342
R_int	0.095
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.111, 1.03
No. of reflections	1760
No. of parameters	128
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.16

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H6···O1	0.85	2.01	2.8608 (19)	174
N1—H1···O3ⁱ	0.86	1.86	2.7135 (18)	170
O4—H9···O3ⁱ	0.84	2.06	2.874 (2)	163
N2—H2A···O2ⁱⁱ	0.86	1.87	2.6708 (18)	155
O3—H7···O4ⁱⁱⁱ	0.84	1.93	2.756 (2)	165
O4—H8···O1^iv	0.85	2.53	3.142 (2)	130

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

References

Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Krawczyk, S., Gdaniec, M. & Sa˛czewski, F. (2005). Acta Cryst. E61, o4185–o4187. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Thakurdesai, P. A., Wadodkar, S. G. & Chopade, C. T. (2007). Pharmacologyonline, 1, 314–329. Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 67| Part 6| June 2011| Page o1399

doi:10.1107/S1600536811017399

Open

access