5-[(1H-Benzimidazol-1-yl)meth­yl]benzene-1,3-dicarb­oxy­lic acid

Cheng, X.-C.

doi:10.1107/S1600536811047416

organic compounds

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ISSN: 2056-9890

Volume 67| Part 12| December 2011| Page o3299

https://doi.org/10.1107/S1600536811047416

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5-[(1H-Benzimidazol-1-yl)methyl]benzene-1,3-dicarboxylic acid

Xiao-Chun Cheng ^a ^*

^aFaculty of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian 223003, People's Republic of China
^*Correspondence e-mail: shxycheng@163.com

(Received 4 November 2011; accepted 9 November 2011; online 12 November 2011)

Crystals of the title compound, C₁₆H₁₂N₂O₄, were obtained accidentally from a hydrothermal reaction of 5-[(1H-benzimidazol-1-yl)methyl]isophthalic acid with manganese bromide in the presence of N,N′-dimethylformamide. In the title molecule, the benzimidazole ring system is almost planar, with a maximum deviation from the mean plane of 0.010 (2) Å. The benzimidazole and central benzene rings are inclined at a dihedral angle of 71.7 (6)°. The crystal structure is stabilized by O—H⋯N and O—H⋯O hydrogen bonds.

Related literature

For background information on the title compound, see: Das & Bharadwaj (2009 ). For a related structure, see: Kuai & Cheng (2011 ).

Experimental

Crystal data

C₁₆H₁₂N₂O₄
M_r = 296.28
Triclinic, $[P \overline 1]$
a = 7.7159 (11) Å
b = 8.4559 (12) Å
c = 10.9742 (15) Å
α = 97.286 (2)°
β = 104.928 (2)°
γ = 98.029 (2)°
V = 675.07 (16) Å³
Z = 2
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 293 K
0.20 × 0.20 × 0.20 mm

Data collection

Bruker SMART APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.979, T_max = 0.979
3620 measured reflections
2499 independent reflections
1401 reflections with I > 2σ(I)
R_int = 0.024

Refinement

R[F² > 2σ(F²)] = 0.042
wR(F²) = 0.098
S = 0.84
2499 reflections
199 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H12⋯O2ⁱ	0.82	1.84	2.574 (2)	147
O1—H11⋯N2ⁱⁱ	0.82	1.76	2.553 (2)	162
Symmetry codes: (i) x, y-1, z; (ii) x-1, y, z-1.

Data collection: APEX2 (Bruker, 2008 ); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2000 ); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536811047416/pv2480sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536811047416/pv2480Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536811047416/pv2480Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S1600536811047416/pv2480Isup4.cml

checkCIF report

Comment top

The title compound is regarded as an excellent candidate for building block in molecular self-assembly engineering due to its variable conformation and coordination modes (Das & Bharadwaj, 2009). During preparation of coordination polymers, we accidentally obtained single crystals of the title compound by the hydrothermal reaction at 393 K of 5-((1H-benzo[d]imidazol-1-yl)methyl)isophthalic acid with manganese bromide in the presence of N,N'-dimethylformamide.

Although crystallized from an alkaline solution, the title compound retained the carboxylic groups in the crystal structure (Fig. 1). The benzimidazolyl ring and the central benzene ring are inclined at a dihedral angle of 71.7 (6) °. In the crystal structure, there exist O—H···N and O—H···O hydrogen bonds (Table 1). The carboxylate groups and the N atom in the benzimidazolyl group as donor or acceptor play very important role in the formation of these hydrogen bonds.

Related literature top

For background information on the title compound, see: Das & Bharadwaj (2009). For a related structure, see: Kuai & Cheng (2011).

Experimental top

A mixture of MnBr₂ (21.5 mg, 0.1 mmol), 5-((1H-benzo[d]imidazol-1-yl)methyl)isophthalic acid (29.6 mg, 0.1 mmol) and 2 ml N,N'-dimethylformamide (DMF) in 10 ml H₂O was sealed in a 16 ml Teflon-lined stainless steel container and heated to 393 K for 3 days. After cooling the stain-less steel container to room temperature, colorless block crystals of the title compound were obtained.

Structure description top

For background information on the title compound, see: Das & Bharadwaj (2009). For a related structure, see: Kuai & Cheng (2011).

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2000); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

Fig. 1. : The crystal structure of the title compound showing 30% probability displacement ellipsoids.

5-[(1H-Benzimidazol-1-yl)methyl]benzene-1,3-dicarboxylic acid top

Crystal data top

C₁₆H₁₂N₂O₄	Z = 2
M_r = 296.28	F(000) = 308
Triclinic, P1	D_x = 1.458 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.7159 (11) Å	Cell parameters from 796 reflections
b = 8.4559 (12) Å	θ = 2.8–25.0°
c = 10.9742 (15) Å	µ = 0.11 mm⁻¹
α = 97.286 (2)°	T = 293 K
β = 104.928 (2)°	Block, colorless
γ = 98.029 (2)°	0.20 × 0.20 × 0.20 mm
V = 675.07 (16) Å³

Data collection top

Bruker SMART APEXII CCD diffractometer	2499 independent reflections
Radiation source: fine-focus sealed tube	1401 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.024
φ and ω scans	θ_max = 25.6°, θ_min = 2.0°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −8→9
T_min = 0.979, T_max = 0.979	k = −10→9
3620 measured reflections	l = −11→13

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)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.098	H-atom parameters constrained
S = 0.84	w = 1/[σ²(F_o²) + (0.0392P)²] where P = (F_o² + 2F_c²)/3
2499 reflections	(Δ/σ)_max < 0.001
199 parameters	Δρ_max = 0.18 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

Crystal data top

C₁₆H₁₂N₂O₄	γ = 98.029 (2)°
M_r = 296.28	V = 675.07 (16) Å³
Triclinic, P1	Z = 2
a = 7.7159 (11) Å	Mo Kα radiation
b = 8.4559 (12) Å	µ = 0.11 mm⁻¹
c = 10.9742 (15) Å	T = 293 K
α = 97.286 (2)°	0.20 × 0.20 × 0.20 mm
β = 104.928 (2)°

Data collection top

Bruker SMART APEXII CCD diffractometer	2499 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	1401 reflections with I > 2σ(I)
T_min = 0.979, T_max = 0.979	R_int = 0.024
3620 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.042	0 restraints
wR(F²) = 0.098	H-atom parameters constrained
S = 0.84	Δρ_max = 0.18 e Å⁻³
2499 reflections	Δρ_min = −0.17 e Å⁻³
199 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
C1	0.8649 (3)	0.3096 (2)	0.61209 (17)	0.0400 (5)
C2	0.7615 (3)	0.3686 (2)	0.50979 (18)	0.0426 (5)
H1	0.7649	0.4796	0.5144	0.051*
C3	0.6533 (3)	0.2632 (2)	0.40097 (17)	0.0378 (5)
C4	0.6482 (3)	0.0979 (2)	0.39490 (17)	0.0386 (5)
H2	0.5757	0.0268	0.3222	0.046*
C5	0.7503 (3)	0.0376 (2)	0.49609 (17)	0.0368 (5)
C6	0.8591 (3)	0.1451 (2)	0.60419 (18)	0.0414 (5)
H3	0.9289	0.1052	0.6720	0.050*
C7	0.5439 (3)	0.3280 (3)	0.29147 (18)	0.0442 (6)
C8	0.7429 (3)	−0.1397 (3)	0.4906 (2)	0.0443 (6)
C9	0.9807 (3)	0.4336 (3)	0.72598 (18)	0.0572 (7)
H5	1.0883	0.4833	0.7053	0.069*
H4	0.9121	0.5180	0.7417	0.069*
C10	1.2110 (3)	0.3646 (3)	0.9087 (2)	0.0513 (6)
H6	1.3127	0.4067	0.8847	0.062*
C11	1.0403 (3)	0.2516 (2)	1.01338 (19)	0.0470 (6)
C12	0.9243 (3)	0.2953 (3)	0.9078 (2)	0.0462 (6)
C13	0.7369 (3)	0.2658 (3)	0.8840 (2)	0.0618 (7)
H7	0.6604	0.2964	0.8140	0.074*
C14	0.6703 (4)	0.1887 (3)	0.9698 (3)	0.0737 (8)
H8	0.5448	0.1652	0.9568	0.088*
C15	0.7851 (4)	0.1444 (3)	1.0760 (2)	0.0706 (8)
H9	0.7340	0.0933	1.1320	0.085*
C16	0.9705 (4)	0.1743 (3)	1.0997 (2)	0.0580 (7)
H10	1.0465	0.1443	1.1702	0.070*
N1	1.0380 (2)	0.3660 (2)	0.84266 (15)	0.0468 (5)
N2	1.2195 (2)	0.2965 (2)	1.01142 (15)	0.0500 (5)
O1	0.44624 (19)	0.21783 (16)	0.19787 (12)	0.0559 (5)
H11	0.3897	0.2606	0.1410	0.067*
O2	0.5500 (2)	0.47226 (18)	0.29074 (14)	0.0763 (6)
O3	0.6485 (2)	−0.22162 (17)	0.37611 (13)	0.0693 (5)
H12	0.6465	−0.3189	0.3759	0.083*
O4	0.8127 (2)	−0.20331 (17)	0.57734 (14)	0.0627 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0523 (13)	0.0322 (12)	0.0251 (11)	0.0059 (10)	−0.0061 (10)	0.0038 (9)
C2	0.0582 (14)	0.0295 (12)	0.0301 (11)	0.0073 (10)	−0.0053 (10)	0.0060 (9)
C3	0.0472 (12)	0.0316 (12)	0.0269 (11)	0.0057 (10)	−0.0024 (9)	0.0049 (9)
C4	0.0488 (12)	0.0319 (12)	0.0260 (11)	0.0045 (10)	−0.0026 (9)	0.0024 (9)
C5	0.0457 (12)	0.0308 (11)	0.0285 (11)	0.0074 (10)	0.0006 (10)	0.0056 (9)
C6	0.0524 (13)	0.0375 (13)	0.0277 (11)	0.0109 (10)	−0.0040 (10)	0.0103 (9)
C7	0.0560 (14)	0.0338 (13)	0.0306 (12)	0.0073 (11)	−0.0087 (10)	0.0049 (10)
C8	0.0558 (14)	0.0362 (13)	0.0347 (12)	0.0078 (11)	0.0015 (11)	0.0072 (10)
C9	0.0806 (16)	0.0403 (14)	0.0310 (12)	0.0045 (12)	−0.0160 (12)	0.0063 (10)
C10	0.0565 (14)	0.0437 (14)	0.0379 (13)	0.0015 (11)	−0.0093 (11)	0.0046 (11)
C11	0.0629 (16)	0.0365 (13)	0.0314 (12)	0.0094 (11)	−0.0025 (11)	0.0016 (10)
C12	0.0590 (15)	0.0357 (13)	0.0322 (12)	0.0090 (11)	−0.0042 (11)	−0.0013 (10)
C13	0.0595 (17)	0.0625 (18)	0.0514 (16)	0.0143 (13)	−0.0037 (13)	0.0015 (13)
C14	0.0649 (17)	0.080 (2)	0.0678 (19)	0.0068 (15)	0.0142 (16)	−0.0015 (16)
C15	0.084 (2)	0.0659 (19)	0.0587 (18)	0.0081 (16)	0.0218 (16)	0.0031 (14)
C16	0.0863 (19)	0.0445 (15)	0.0366 (14)	0.0116 (14)	0.0055 (14)	0.0072 (11)
N1	0.0584 (12)	0.0393 (11)	0.0279 (10)	0.0077 (9)	−0.0126 (9)	0.0047 (8)
N2	0.0597 (12)	0.0471 (12)	0.0320 (10)	0.0092 (10)	−0.0076 (9)	0.0081 (9)
O1	0.0717 (10)	0.0413 (9)	0.0345 (8)	0.0105 (8)	−0.0204 (8)	0.0056 (7)
O2	0.1136 (14)	0.0305 (9)	0.0515 (10)	0.0101 (9)	−0.0338 (9)	0.0070 (7)
O3	0.1078 (13)	0.0281 (9)	0.0467 (10)	0.0108 (9)	−0.0202 (9)	0.0025 (7)
O4	0.0939 (12)	0.0384 (9)	0.0431 (9)	0.0145 (9)	−0.0078 (9)	0.0142 (7)

Geometric parameters (Å, º) top

C1—C6	1.377 (3)	C9—H4	0.9700
C1—C2	1.392 (2)	C10—N2	1.320 (3)
C1—C9	1.513 (2)	C10—N1	1.347 (2)
C2—C3	1.387 (2)	C10—H6	0.9300
C2—H1	0.9300	C11—N2	1.388 (3)
C3—C4	1.386 (2)	C11—C16	1.391 (3)
C3—C7	1.493 (3)	C11—C12	1.395 (3)
C4—C5	1.385 (2)	C12—C13	1.382 (3)
C4—H2	0.9300	C12—N1	1.387 (3)
C5—C6	1.392 (2)	C13—C14	1.374 (4)
C5—C8	1.485 (3)	C13—H7	0.9300
C6—H3	0.9300	C14—C15	1.398 (3)
C7—O2	1.215 (2)	C14—H8	0.9300
C7—O1	1.286 (2)	C15—C16	1.367 (3)
C8—O4	1.197 (2)	C15—H9	0.9300
C8—O3	1.325 (2)	C16—H10	0.9300
C9—N1	1.458 (3)	O1—H11	0.8200
C9—H5	0.9700	O3—H12	0.8200

C6—C1—C2	119.24 (17)	H5—C9—H4	107.7
C6—C1—C9	123.83 (17)	N2—C10—N1	112.3 (2)
C2—C1—C9	116.92 (18)	N2—C10—H6	123.9
C3—C2—C1	120.61 (19)	N1—C10—H6	123.9
C3—C2—H1	119.7	N2—C11—C16	130.2 (2)
C1—C2—H1	119.7	N2—C11—C12	109.0 (2)
C4—C3—C2	119.40 (18)	C16—C11—C12	120.8 (2)
C4—C3—C7	120.48 (17)	C13—C12—N1	132.3 (2)
C2—C3—C7	120.12 (18)	C13—C12—C11	122.4 (2)
C5—C4—C3	120.58 (17)	N1—C12—C11	105.34 (19)
C5—C4—H2	119.7	C14—C13—C12	116.1 (2)
C3—C4—H2	119.7	C14—C13—H7	122.0
C4—C5—C6	119.27 (18)	C12—C13—H7	122.0
C4—C5—C8	120.67 (17)	C13—C14—C15	122.1 (3)
C6—C5—C8	120.06 (17)	C13—C14—H8	119.0
C1—C6—C5	120.90 (17)	C15—C14—H8	119.0
C1—C6—H3	119.6	C16—C15—C14	121.7 (3)
C5—C6—H3	119.6	C16—C15—H9	119.1
O2—C7—O1	123.42 (18)	C14—C15—H9	119.1
O2—C7—C3	122.59 (18)	C15—C16—C11	116.9 (2)
O1—C7—C3	113.98 (18)	C15—C16—H10	121.5
O4—C8—O3	123.1 (2)	C11—C16—H10	121.5
O4—C8—C5	125.28 (19)	C10—N1—C12	107.49 (17)
O3—C8—C5	111.58 (18)	C10—N1—C9	126.3 (2)
N1—C9—C1	113.68 (18)	C12—N1—C9	126.15 (19)
N1—C9—H5	108.8	C10—N2—C11	105.86 (18)
C1—C9—H5	108.8	C7—O1—H11	109.5
N1—C9—H4	108.8	C8—O3—H12	109.5
C1—C9—H4	108.8

C6—C1—C2—C3	0.1 (3)	N2—C11—C12—C13	179.95 (18)
C9—C1—C2—C3	179.18 (19)	C16—C11—C12—C13	0.5 (3)
C1—C2—C3—C4	0.2 (3)	N2—C11—C12—N1	0.4 (2)
C1—C2—C3—C7	−179.6 (2)	C16—C11—C12—N1	−179.05 (19)
C2—C3—C4—C5	−0.1 (3)	N1—C12—C13—C14	178.6 (2)
C7—C3—C4—C5	179.7 (2)	C11—C12—C13—C14	−0.8 (3)
C3—C4—C5—C6	−0.3 (3)	C12—C13—C14—C15	0.8 (4)
C3—C4—C5—C8	179.06 (19)	C13—C14—C15—C16	−0.6 (4)
C2—C1—C6—C5	−0.6 (3)	C14—C15—C16—C11	0.3 (4)
C9—C1—C6—C5	−179.6 (2)	N2—C11—C16—C15	−179.5 (2)
C4—C5—C6—C1	0.7 (3)	C12—C11—C16—C15	−0.2 (3)
C8—C5—C6—C1	−178.7 (2)	N2—C10—N1—C12	0.8 (2)
C4—C3—C7—O2	−177.0 (2)	N2—C10—N1—C9	179.20 (18)
C2—C3—C7—O2	2.9 (3)	C13—C12—N1—C10	179.8 (2)
C4—C3—C7—O1	1.7 (3)	C11—C12—N1—C10	−0.7 (2)
C2—C3—C7—O1	−178.42 (18)	C13—C12—N1—C9	1.4 (4)
C4—C5—C8—O4	−172.8 (2)	C11—C12—N1—C9	−179.11 (18)
C6—C5—C8—O4	6.6 (3)	C1—C9—N1—C10	118.4 (2)
C4—C5—C8—O3	7.3 (3)	C1—C9—N1—C12	−63.5 (3)
C6—C5—C8—O3	−173.30 (18)	N1—C10—N2—C11	−0.5 (2)
C6—C1—C9—N1	−19.5 (3)	C16—C11—N2—C10	179.4 (2)
C2—C1—C9—N1	161.5 (2)	C12—C11—N2—C10	0.1 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H12···O2ⁱ	0.82	1.84	2.574 (2)	147
O1—H11···N2ⁱⁱ	0.82	1.76	2.553 (2)	162

Symmetry codes: (i) x, y−1, z; (ii) x−1, y, z−1.

Experimental details

Crystal data
Chemical formula	C₁₆H₁₂N₂O₄
M_r	296.28
Crystal system, space group	Triclinic, P1
Temperature (K)	293
a, b, c (Å)	7.7159 (11), 8.4559 (12), 10.9742 (15)
α, β, γ (°)	97.286 (2), 104.928 (2), 98.029 (2)
V (Å³)	675.07 (16)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.20 × 0.20 × 0.20

Data collection
Diffractometer	Bruker SMART APEXII CCD
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.979, 0.979
No. of measured, independent and observed [I > 2σ(I)] reflections	3620, 2499, 1401
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.608

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.042, 0.098, 0.84
No. of reflections	2499
No. of parameters	199
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.17

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2000), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H12···O2ⁱ	0.82	1.84	2.574 (2)	147.4
O1—H11···N2ⁱⁱ	0.82	1.76	2.553 (2)	162.2

Symmetry codes: (i) x, y−1, z; (ii) x−1, y, z−1.

References

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