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

Miao, J.; Nie, Y.; Chen, H.; Li, J.; Wang, D.

doi:10.1107/S1600536809027391

organic compounds

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ISSN: 2056-9890

Volume 65| Part 8| August 2009| Page o2005

doi:10.1107/S1600536809027391

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

Jinling Miao,^a ^* Yong Nie,^a Hongwei Chen,^a Jingtao Li ^a and Daqi Wang ^b

^aSchool of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, People's Republic of China, and ^bCollege of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252059, People's Republic of China.
^*Correspondence e-mail: chm_miaojl@ujn.edu.cn

(Received 27 June 2009; accepted 12 July 2009; online 25 July 2009)

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 ).

Experimental

Crystal data

C₁₁H₁₀N₂O₄·H₂O
M_r = 252.23
Monoclinic, C 2/c
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 ) 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[F² > 2σ(F²)] = 0.041
wR(F²) = 0.120
S = 1.00
2213 reflections
173 parameters
1 restraint
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.18 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H3⋯O2ⁱ	0.925 (17)	1.592 (18)	2.487 (2)	162 (2)
O5—H5⋯O1	0.88 (3)	1.95 (3)	2.825 (2)	172 (3)
O6—H6⋯O1	0.84 (3)	2.11 (3)	2.943 (2)	173 (3)
Symmetry code: (i) $[x+{\script{1\over 2}}, y+{\script{1\over 2}}, z]$ .

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809027391/hk2729sup1.cif

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

checkCIF report

Comment top

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).

Related literature top

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

Experimental top

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.

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	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.

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

Crystal data top

C₁₁H₁₀N₂O₄·H₂O	F(000) = 1056
M_r = 252.23	D_x = 1.475 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 1932 reflections
a = 16.0731 (15) Å	θ = 2.4–26.4°
b = 8.1619 (11) Å	µ = 0.12 mm⁻¹
c = 18.8678 (17) Å	T = 298 K
β = 113.368 (1)°	Plate, colorless
V = 2272.2 (4) Å³	0.50 × 0.40 × 0.20 mm
Z = 8

Data collection top

Bruker SMART 1000 CCD area-detector diffractometer	2213 independent reflections
Radiation source: fine-focus sealed tube	1495 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.048
ϕ and ω scans	θ_max = 26.0°, θ_min = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −14→19
T_min = 0.943, T_max = 0.977	k = −10→10
5875 measured reflections	l = −23→23

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.120	H atoms treated by a mixture of independent and constrained refinement
S = 1.00	w = 1/[σ²(F_o²) + (0.0647P)² + 0.9016P] where P = (F_o² + 2F_c²)/3
2213 reflections	(Δ/σ)_max = 0.001
173 parameters	Δρ_max = 0.25 e Å⁻³
1 restraint	Δρ_min = −0.18 e Å⁻³

Crystal data top

C₁₁H₁₀N₂O₄·H₂O	V = 2272.2 (4) Å³
M_r = 252.23	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 16.0731 (15) Å	µ = 0.12 mm⁻¹
b = 8.1619 (11) Å	T = 298 K
c = 18.8678 (17) Å	0.50 × 0.40 × 0.20 mm
β = 113.368 (1)°

Data collection top

Bruker SMART 1000 CCD area-detector diffractometer	2213 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2001)	1495 reflections with I > 2σ(I)
T_min = 0.943, T_max = 0.977	R_int = 0.048
5875 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.041	1 restraint
wR(F²) = 0.120	H atoms treated by a mixture of independent and constrained refinement
S = 1.00	Δρ_max = 0.25 e Å⁻³
2213 reflections	Δρ_min = −0.18 e Å⁻³
173 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
O1	0.64155 (9)	0.6138 (2)	0.28621 (9)	0.0608 (5)
O2	0.75932 (9)	0.5077 (2)	0.38158 (10)	0.0658 (6)
O3	1.16479 (10)	0.80460 (19)	0.41440 (9)	0.0501 (4)
H3	1.1979 (16)	0.867 (3)	0.3937 (14)	0.075*
O4	1.20178 (11)	0.6063 (2)	0.35149 (10)	0.0646 (5)
O5	0.5000	0.8452 (3)	0.2500	0.0582 (6)
H5	0.5476 (18)	0.782 (4)	0.2614 (17)	0.087*
O6	0.5000	0.3611 (3)	0.2500	0.0688 (8)
H6	0.544 (2)	0.427 (4)	0.2634 (19)	0.103*
N1	0.87906 (10)	0.7126 (2)	0.36403 (9)	0.0349 (4)
N2	1.01818 (10)	0.62393 (18)	0.40836 (9)	0.0337 (4)
C1	0.72276 (12)	0.6073 (3)	0.32812 (11)	0.0377 (5)
C2	0.78365 (12)	0.7326 (3)	0.31305 (11)	0.0416 (5)
H2A	0.7772	0.7230	0.2599	0.050*
H2B	0.7641	0.8417	0.3199	0.050*
C3	1.16099 (12)	0.6581 (3)	0.38815 (11)	0.0372 (5)
C4	1.10076 (13)	0.5451 (3)	0.41022 (13)	0.0411 (5)
H4A	1.0840	0.4524	0.3752	0.049*
H4B	1.1348	0.5034	0.4618	0.049*
C5	0.94014 (13)	0.6308 (2)	0.34744 (11)	0.0376 (5)
H5A	0.9297	0.5845	0.2996	0.045*
C6	1.00799 (12)	0.7058 (2)	0.46895 (11)	0.0322 (4)
C7	0.91917 (12)	0.7614 (2)	0.44087 (10)	0.0320 (4)
C8	0.88646 (14)	0.8494 (3)	0.48694 (12)	0.0429 (5)
H8	0.8271	0.8877	0.4683	0.052*
C9	0.94620 (17)	0.8773 (3)	0.56172 (13)	0.0494 (6)
H9	0.9265	0.9350	0.5947	0.059*
C10	1.03527 (16)	0.8218 (3)	0.58943 (12)	0.0480 (6)
H10	1.0736	0.8443	0.6403	0.058*
C11	1.06811 (14)	0.7353 (3)	0.54415 (11)	0.0409 (5)
H11	1.1277	0.6981	0.5628	0.049*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0289 (8)	0.0773 (13)	0.0644 (10)	−0.0032 (8)	0.0059 (7)	0.0195 (9)
O2	0.0296 (8)	0.0579 (11)	0.0966 (13)	−0.0030 (7)	0.0107 (8)	0.0402 (10)
O3	0.0451 (9)	0.0378 (10)	0.0757 (11)	−0.0041 (7)	0.0328 (8)	0.0023 (8)
O4	0.0649 (11)	0.0641 (12)	0.0884 (12)	0.0002 (9)	0.0552 (10)	−0.0062 (9)
O5	0.0550 (15)	0.0519 (16)	0.0612 (14)	0.000	0.0161 (13)	0.000
O6	0.0574 (16)	0.0520 (17)	0.0872 (19)	0.000	0.0181 (15)	0.000
N1	0.0279 (8)	0.0388 (10)	0.0393 (9)	−0.0036 (7)	0.0147 (7)	0.0031 (7)
N2	0.0306 (9)	0.0294 (9)	0.0451 (9)	−0.0026 (7)	0.0193 (8)	−0.0003 (7)
C1	0.0250 (10)	0.0426 (13)	0.0433 (11)	0.0014 (9)	0.0111 (9)	0.0025 (10)
C2	0.0323 (11)	0.0449 (13)	0.0440 (11)	0.0004 (10)	0.0115 (9)	0.0092 (10)
C3	0.0276 (10)	0.0401 (13)	0.0428 (11)	0.0054 (9)	0.0129 (9)	0.0027 (10)
C4	0.0383 (11)	0.0327 (12)	0.0576 (12)	0.0032 (9)	0.0246 (10)	0.0002 (10)
C5	0.0378 (11)	0.0383 (12)	0.0410 (11)	−0.0087 (9)	0.0203 (9)	−0.0027 (9)
C6	0.0343 (10)	0.0242 (10)	0.0419 (11)	−0.0019 (8)	0.0191 (9)	0.0028 (9)
C7	0.0318 (10)	0.0281 (11)	0.0391 (10)	−0.0016 (8)	0.0172 (8)	0.0060 (8)
C8	0.0441 (12)	0.0381 (13)	0.0551 (13)	0.0084 (10)	0.0287 (11)	0.0078 (10)
C9	0.0702 (16)	0.0377 (13)	0.0503 (13)	0.0032 (11)	0.0345 (12)	−0.0009 (10)
C10	0.0603 (15)	0.0413 (13)	0.0389 (11)	−0.0061 (11)	0.0158 (11)	−0.0014 (10)
C11	0.0379 (11)	0.0351 (12)	0.0457 (12)	−0.0012 (9)	0.0124 (10)	0.0051 (10)

Geometric parameters (Å, º) top

O1—C1	1.230 (2)	C2—H2B	0.9700
O2—C1	1.246 (2)	C3—C4	1.511 (3)
O3—C3	1.286 (3)	C4—H4A	0.9700
O3—H3	0.925 (17)	C4—H4B	0.9700
O4—C3	1.203 (2)	C5—H5A	0.9300
O5—H5	0.88 (3)	C6—C11	1.385 (3)
O6—H6	0.84 (3)	C6—C7	1.387 (3)
N1—C5	1.323 (2)	C7—C8	1.382 (3)
N1—C7	1.391 (2)	C8—C9	1.375 (3)
N1—C2	1.461 (2)	C8—H8	0.9300
N2—C5	1.324 (2)	C9—C10	1.391 (3)
N2—C6	1.389 (2)	C9—H9	0.9300
N2—C4	1.463 (2)	C10—C11	1.366 (3)
C1—C2	1.519 (3)	C10—H10	0.9300
C2—H2A	0.9700	C11—H11	0.9300

C3—O3—H3	107.1 (16)	C3—C4—H4B	108.9
C5—N1—C7	108.08 (16)	H4A—C4—H4B	107.7
C5—N1—C2	125.76 (17)	N1—C5—N2	110.62 (17)
C5—N2—C6	108.28 (15)	N1—C5—H5A	124.7
C5—N2—C4	125.26 (16)	N2—C5—H5A	124.7
C6—N2—C4	126.45 (16)	C11—C6—C7	121.93 (18)
C7—N1—C2	125.85 (16)	C11—C6—N2	131.65 (18)
O1—C1—O2	126.00 (19)	C7—C6—N2	106.41 (16)
O1—C1—C2	116.68 (18)	C8—C7—C6	121.35 (18)
O2—C1—C2	117.31 (16)	C8—C7—N1	132.04 (18)
N1—C2—C1	112.79 (16)	C6—C7—N1	106.60 (16)
N1—C2—H2A	109.0	C9—C8—C7	116.5 (2)
C1—C2—H2A	109.0	C9—C8—H8	121.7
N1—C2—H2B	109.0	C7—C8—H8	121.7
C1—C2—H2B	109.0	C8—C9—C10	121.8 (2)
H2A—C2—H2B	107.8	C8—C9—H9	119.1
O4—C3—O3	126.48 (19)	C10—C9—H9	119.1
O4—C3—C4	119.9 (2)	C11—C10—C9	121.9 (2)
O3—C3—C4	113.53 (17)	C11—C10—H10	119.0
N2—C4—C3	113.53 (16)	C9—C10—H10	119.0
N2—C4—H4A	108.9	C10—C11—C6	116.4 (2)
C3—C4—H4A	108.9	C10—C11—H11	121.8
N2—C4—H4B	108.9	C6—C11—H11	121.8

C5—N1—C2—C1	95.5 (2)	C11—C6—C7—C8	0.1 (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—N1	179.22 (17)
O2—C1—C2—N1	1.7 (3)	N2—C6—C7—N1	−0.61 (19)
C5—N2—C4—C3	89.6 (2)	C5—N1—C7—C8	179.7 (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—C6	0.7 (2)
O3—C3—C4—N2	38.8 (2)	C2—N1—C7—C6	174.70 (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—N1	0.2 (2)	C7—C8—C9—C10	0.7 (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—C6	0.1 (3)
C4—N2—C6—C11	−0.3 (3)	C7—C6—C11—C10	0.1 (3)
C5—N2—C6—C7	0.30 (19)	N2—C6—C11—C10	179.90 (19)
C4—N2—C6—C7	179.50 (16)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O2ⁱ	0.93 (2)	1.59 (2)	2.487 (2)	162 (2)
O5—H5···O1	0.88 (3)	1.95 (3)	2.825 (2)	172 (3)
O6—H6···O1	0.84 (3)	2.11 (3)	2.943 (2)	173 (3)

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

Experimental details

Crystal data
Chemical formula	C₁₁H₁₀N₂O₄·H₂O
M_r	252.23
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	298
a, b, c (Å)	16.0731 (15), 8.1619 (11), 18.8678 (17)
β (°)	113.368 (1)
V (Å³)	2272.2 (4)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.12
Crystal size (mm)	0.50 × 0.40 × 0.20

Data collection
Diffractometer	Bruker SMART 1000 CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2001)
T_min, T_max	0.943, 0.977
No. of measured, independent and observed [I > 2σ(I)] reflections	5875, 2213, 1495
R_int	0.048
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.120, 1.00
No. of reflections	2213
No. of parameters	173
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.25, −0.18

Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O2ⁱ	0.925 (17)	1.592 (18)	2.487 (2)	162 (2)
O5—H5···O1	0.88 (3)	1.95 (3)	2.825 (2)	172 (3)
O6—H6···O1	0.84 (3)	2.11 (3)	2.943 (2)	173 (3)

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

Acknowledgements

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

References

Bruker (2001). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Chen, D.-B. & Huang, L. (2006). Acta Cryst. E62, o4686–o4688. 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