organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

A monoclinic polymorph of 5-[(1H-benzimidazol-1-yl)meth­yl]benzene-1,3-dicarb­­oxy­lic acid

aFaculty of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaian 223003, People's Republic of China
*Correspondence e-mail: hyitshy@126.com

(Received 22 September 2012; accepted 29 September 2012; online 6 October 2012)

Crystals of the title compound, C16H12N2O4, were obtained accidentally by the hydro­thermal reaction of 5-[(1H-benzo[d]imidazol-1-yl)meth­yl]isophthalic acid with manganese chloride tetra­hydrate in the presence of KOH as alkaline reagent for the deprotonation. A triclinic polymorph of this structure has been reported previously from a similar reaction [Cheng (2011[Cheng, X.-C. (2011). Acta Cryst. E67, o3299.]). Acta Cryst. E67, o3299]. The benzimidazole ring system is almost planar, with a maximum deviation from the mean plane of 0.020 (4) Å. The benzimidazole unit and benzene ring are inclined at a dihedral angle of 68.17 (4)°, reflecting the axial rotation of the flexible benzimidazolyl arm. In the crystal, pairs of O—H⋯O hydrogen bonds link adjacent mol­ecules into inversion dimers. O—H⋯N contacts connect these dimers into zigzag chains along [010].

Related literature

For a triclinic polymorph of the title compound, see: Cheng (2011[Cheng, X.-C. (2011). Acta Cryst. E67, o3299.]).

[Scheme 1]

Experimental

Crystal data
  • C16H12N2O4

  • Mr = 296.28

  • Monoclinic, P 21 /c

  • a = 7.401 (5) Å

  • b = 16.589 (5) Å

  • c = 11.762 (4) Å

  • β = 111.53 (3)°

  • V = 1343.3 (11) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 293 K

  • 0.20 × 0.10 × 0.10 mm

Data collection
  • Bruker Smart APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.979, Tmax = 0.989

  • 6722 measured reflections

  • 2358 independent reflections

  • 1239 reflections with I > 2σ(I)

  • Rint = 0.072

Refinement
  • R[F2 > 2σ(F2)] = 0.056

  • wR(F2) = 0.152

  • S = 0.96

  • 2358 reflections

  • 200 parameters

  • H-atom parameters constrained

  • Δρmax = 0.21 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O3—H5⋯O4i 0.84 1.82 2.649 (3) 171
O1—H4⋯N1ii 0.84 1.76 2.576 (4) 164
Symmetry codes: (i) -x+2, -y+2, -z+1; (ii) x-1, y, z-1.

Data collection: APEX2 (Bruker, 2008[Bruker (2008). APEX2 and SAINT. Bruker AXS Inc., Madison, wisconsin, USA.]); cell refinement: SAINT (Bruker, 2008[Bruker (2008). APEX2 and SAINT. Bruker AXS Inc., Madison, wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg, 2000[Brandenburg, K. (2000). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]); software used to prepare material for publication: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information


Comment top

5-((1H-benzo[d]imidazol-1-yl)methyl)isophthalic acid (H2L), is usually regarded as an excellent candidate for use as a building block in molecular self-assembly engineerings due to its variable conformations and coordination modes. During an attempt to assemble a coordination polymer, we accidentally obtained some single crystals of the title compound, C16H12N2O4, as a result of the hydrothermal reaction of 5-((1H-benzo[d]imidazol-1-yl)methyl)isophthalic acid with manganese chloride tetrahydrate at 453 K in the presence of KOH as alkaline reagent for the deprotonation. A triclinic polymorph of this structure has been reported previously (Cheng, 2011) from a very similar hydrothermal reaction involving manganese bromide. The bond distances and angles in that molecule are reasonably similar to those reported here. As shown in Fig. 1, the asymmetric unit consists of only one H2L molecule. Interestingly, though crystallizing from alkaline solution, the H2L retains the intact carboxylic acid groups in the crystal structure. The flexible benzimidazolyl arm is apt to rotate axially. As a result, the benzimidazolyl ring and central benzene rings are inclined at a dihedral angle of 68.17 °.

In the crystal structure O3–H5..O4 hydrogen bonds, Table 1, link adjacent molecules into inversion dimers. O1—H4···N1 contacts connect these dimers into zig-zag chains in the 010 plane, Fig. 2.

Related literature top

For a triclinic polymorph of the title compound, see: Cheng (2011).

Experimental top

A reaction mixture comprising manganese chloride tetrahydrate (23.3 mg, 0.1 mmol), 5-((1H-benzo[d]imidazol-1-yl)methyl)isophthalic acid (29.6 mg, 0.1 mmol) and KOH (11.2 mg, 0.2 mmol) in 10 ml H2O was sealed in a 16 ml Teflon-lined stainless steel container and heated to 453 K for 3 days. After cooling to the room temperature, colorless block like crystals of the title compound were obtained.

Refinement top

Hydrogen atoms of the OH groups were found in difference Fourier maps and their coordinates were allowed to ride on those of the O atoms with Uiso(H) = 1.2Ueq(O). Other hydrogen atoms were included in geometrically idealized positions and constrained to ride on their parent atoms, with C—H = 0.93–0.97 Å and Uiso(H) = 1.2Ueq(C).

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) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. : The crystal structure of the title compound showing 30% probability displacement ellipsoids.
[Figure 2] Fig. 2. Crystal packing of the title compound.
5-[(1H-benzimidazol-1-yl)methyl]benzene-1,3-dicarboxylic acid top
Crystal data top
C16H12N2O4F(000) = 616
Mr = 296.28Dx = 1.465 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 479 reflections
a = 7.401 (5) Åθ = 2.2–18.5°
b = 16.589 (5) ŵ = 0.11 mm1
c = 11.762 (4) ÅT = 293 K
β = 111.53 (3)°Block, colorless
V = 1343.3 (11) Å30.20 × 0.10 × 0.10 mm
Z = 4
Data collection top
Bruker Smart APEXII CCD
diffractometer
2358 independent reflections
Radiation source: fine-focus sealed tube1239 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.072
ϕ and ω scansθmax = 25.0°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 86
Tmin = 0.979, Tmax = 0.989k = 1919
6722 measured reflectionsl = 1313
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.056H-atom parameters constrained
wR(F2) = 0.152 w = 1/[σ2(Fo2) + (0.0659P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.96(Δ/σ)max < 0.001
2358 reflectionsΔρmax = 0.21 e Å3
200 parametersΔρmin = 0.22 e Å3
0 restraintsExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0052 (15)
Crystal data top
C16H12N2O4V = 1343.3 (11) Å3
Mr = 296.28Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.401 (5) ŵ = 0.11 mm1
b = 16.589 (5) ÅT = 293 K
c = 11.762 (4) Å0.20 × 0.10 × 0.10 mm
β = 111.53 (3)°
Data collection top
Bruker Smart APEXII CCD
diffractometer
2358 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
1239 reflections with I > 2σ(I)
Tmin = 0.979, Tmax = 0.989Rint = 0.072
6722 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0560 restraints
wR(F2) = 0.152H-atom parameters constrained
S = 0.96Δρmax = 0.21 e Å3
2358 reflectionsΔρmin = 0.22 e Å3
200 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
xyzUiso*/Ueq
C10.4929 (4)0.81173 (19)0.6457 (3)0.0337 (8)
C20.3157 (4)0.81097 (19)0.5499 (3)0.0359 (8)
H10.21280.78280.55860.043*
C30.2869 (4)0.85118 (19)0.4407 (3)0.0334 (8)
C40.4398 (4)0.89389 (18)0.4285 (3)0.0322 (8)
H20.42240.92110.35610.039*
C50.6190 (4)0.89614 (19)0.5242 (3)0.0335 (8)
C60.6444 (4)0.85508 (19)0.6319 (3)0.0369 (8)
H30.76450.85660.69570.044*
C110.5228 (4)0.7621 (2)0.7587 (2)0.0393 (9)
H70.40320.73360.74800.047*
H60.62220.72200.76660.047*
C120.7566 (4)0.8106 (2)0.9604 (3)0.0419 (9)
H80.86430.78490.95420.050*
C130.5734 (5)0.87902 (19)1.0306 (3)0.0391 (9)
C140.4574 (4)0.85280 (19)0.9137 (3)0.0359 (8)
C150.2615 (5)0.8708 (2)0.8615 (3)0.0526 (10)
H90.18550.85350.78330.063*
C160.1854 (6)0.9155 (2)0.9315 (4)0.0641 (11)
H100.05450.92930.89930.077*
C170.2977 (6)0.9410 (2)1.0494 (4)0.0616 (11)
H110.23940.96981.09450.074*
C180.4931 (5)0.9243 (2)1.1002 (3)0.0529 (10)
H120.56880.94241.17800.063*
C310.0929 (5)0.8454 (2)0.3395 (3)0.0421 (9)
C510.7854 (5)0.9411 (2)0.5135 (3)0.0393 (8)
N10.7629 (4)0.85258 (17)1.0568 (2)0.0451 (8)
N20.5798 (3)0.80875 (16)0.8720 (2)0.0363 (7)
O10.0865 (3)0.87513 (17)0.23681 (19)0.0661 (8)
H40.02850.86930.18800.079*
O20.0442 (3)0.81489 (18)0.3545 (2)0.0756 (9)
O30.7501 (3)0.97884 (14)0.41101 (19)0.0493 (7)
H50.85281.00180.41510.059*
O40.9450 (3)0.94199 (15)0.5985 (2)0.0584 (8)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0290 (18)0.043 (2)0.0258 (17)0.0006 (16)0.0059 (15)0.0014 (15)
C20.0313 (18)0.041 (2)0.0351 (18)0.0055 (15)0.0113 (15)0.0018 (16)
C30.0288 (18)0.040 (2)0.0296 (17)0.0005 (15)0.0088 (14)0.0001 (16)
C40.0318 (18)0.037 (2)0.0259 (16)0.0018 (15)0.0086 (15)0.0012 (15)
C50.0295 (18)0.040 (2)0.0282 (17)0.0039 (15)0.0077 (15)0.0017 (15)
C60.0283 (19)0.047 (2)0.0283 (17)0.0037 (16)0.0022 (15)0.0040 (16)
C110.0355 (19)0.046 (2)0.0304 (17)0.0040 (16)0.0052 (15)0.0010 (17)
C120.033 (2)0.054 (2)0.0341 (19)0.0039 (17)0.0064 (16)0.0062 (18)
C130.037 (2)0.047 (2)0.0307 (18)0.0021 (17)0.0093 (16)0.0076 (17)
C140.0298 (19)0.044 (2)0.0327 (18)0.0008 (16)0.0096 (15)0.0020 (16)
C150.040 (2)0.067 (3)0.049 (2)0.0017 (19)0.0143 (19)0.007 (2)
C160.048 (2)0.076 (3)0.074 (3)0.008 (2)0.029 (2)0.012 (2)
C170.063 (3)0.065 (3)0.071 (3)0.014 (2)0.042 (2)0.008 (2)
C180.070 (3)0.054 (3)0.039 (2)0.003 (2)0.026 (2)0.0002 (18)
C310.033 (2)0.052 (2)0.034 (2)0.0013 (17)0.0048 (17)0.0042 (18)
C510.035 (2)0.050 (2)0.0307 (18)0.0049 (17)0.0092 (17)0.0014 (17)
N10.0376 (17)0.059 (2)0.0304 (15)0.0002 (14)0.0031 (13)0.0004 (15)
N20.0275 (15)0.0483 (18)0.0257 (14)0.0005 (13)0.0011 (12)0.0013 (13)
O10.0401 (15)0.115 (2)0.0312 (13)0.0222 (14)0.0014 (12)0.0127 (15)
O20.0357 (15)0.123 (3)0.0534 (16)0.0303 (15)0.0005 (13)0.0262 (16)
O30.0402 (14)0.0641 (17)0.0421 (14)0.0163 (12)0.0134 (11)0.0060 (13)
O40.0310 (14)0.088 (2)0.0449 (14)0.0173 (13)0.0008 (12)0.0130 (14)
Geometric parameters (Å, º) top
C1—C21.380 (4)C13—N11.392 (4)
C1—C61.390 (4)C13—C181.394 (4)
C1—C111.510 (4)C13—C141.397 (4)
C2—C31.393 (4)C14—C151.384 (4)
C2—H10.9300C14—N21.386 (4)
C3—C41.386 (4)C15—C161.374 (5)
C3—C311.494 (4)C15—H90.9300
C4—C51.390 (4)C16—C171.395 (5)
C4—H20.9300C16—H100.9300
C5—C61.389 (4)C17—C181.375 (5)
C5—C511.484 (4)C17—H110.9300
C6—H30.9300C18—H120.9300
C11—N21.463 (4)C31—O21.203 (4)
C11—H70.9700C31—O11.289 (4)
C11—H60.9700C51—O41.236 (3)
C12—N11.317 (4)C51—O31.297 (3)
C12—N21.340 (4)O1—H40.8397
C12—H80.9300O3—H50.8356
C2—C1—C6118.4 (3)C18—C13—C14120.4 (3)
C2—C1—C11120.1 (3)C15—C14—N2132.1 (3)
C6—C1—C11121.4 (3)C15—C14—C13122.3 (3)
C1—C2—C3121.7 (3)N2—C14—C13105.5 (3)
C1—C2—H1119.1C16—C15—C14116.3 (3)
C3—C2—H1119.1C16—C15—H9121.8
C4—C3—C2119.1 (3)C14—C15—H9121.8
C4—C3—C31122.2 (3)C15—C16—C17122.3 (4)
C2—C3—C31118.8 (3)C15—C16—H10118.9
C3—C4—C5120.2 (3)C17—C16—H10118.9
C3—C4—H2119.9C18—C17—C16121.2 (4)
C5—C4—H2119.9C18—C17—H11119.4
C6—C5—C4119.6 (3)C16—C17—H11119.4
C6—C5—C51119.1 (3)C17—C18—C13117.4 (3)
C4—C5—C51121.3 (3)C17—C18—H12121.3
C5—C6—C1121.0 (3)C13—C18—H12121.3
C5—C6—H3119.5O2—C31—O1123.7 (3)
C1—C6—H3119.5O2—C31—C3121.7 (3)
N2—C11—C1114.4 (3)O1—C31—C3114.6 (3)
N2—C11—H7108.7O4—C51—O3123.6 (3)
C1—C11—H7108.7O4—C51—C5120.9 (3)
N2—C11—H6108.7O3—C51—C5115.6 (3)
C1—C11—H6108.7C12—N1—C13105.2 (3)
H7—C11—H6107.6C12—N2—C14107.0 (3)
N1—C12—N2113.4 (3)C12—N2—C11126.3 (3)
N1—C12—H8123.3C14—N2—C11126.4 (3)
N2—C12—H8123.3C31—O1—H4106.1
N1—C13—C18130.7 (3)C51—O3—H5107.3
N1—C13—C14109.0 (3)
C6—C1—C2—C31.0 (5)C16—C17—C18—C131.7 (5)
C11—C1—C2—C3175.2 (3)N1—C13—C18—C17179.7 (3)
C1—C2—C3—C40.8 (5)C14—C13—C18—C170.4 (5)
C1—C2—C3—C31178.0 (3)C4—C3—C31—O2172.8 (3)
C2—C3—C4—C50.1 (5)C2—C3—C31—O28.5 (5)
C31—C3—C4—C5178.6 (3)C4—C3—C31—O17.6 (5)
C3—C4—C5—C60.3 (4)C2—C3—C31—O1171.1 (3)
C3—C4—C5—C51179.7 (3)C6—C5—C51—O40.3 (5)
C4—C5—C6—C10.1 (5)C4—C5—C51—O4179.2 (3)
C51—C5—C6—C1179.6 (3)C6—C5—C51—O3179.1 (3)
C2—C1—C6—C50.5 (5)C4—C5—C51—O31.5 (4)
C11—C1—C6—C5175.6 (3)N2—C12—N1—C131.3 (4)
C2—C1—C11—N2121.4 (3)C18—C13—N1—C12178.4 (3)
C6—C1—C11—N262.6 (4)C14—C13—N1—C121.7 (4)
N1—C13—C14—C15179.2 (3)N1—C12—N2—C140.5 (4)
C18—C13—C14—C150.7 (5)N1—C12—N2—C11174.7 (3)
N1—C13—C14—N21.4 (3)C15—C14—N2—C12179.9 (3)
C18—C13—C14—N2178.7 (3)C13—C14—N2—C120.6 (3)
N2—C14—C15—C16178.6 (3)C15—C14—N2—C115.7 (5)
C13—C14—C15—C160.6 (5)C13—C14—N2—C11173.6 (3)
C14—C15—C16—C170.7 (5)C1—C11—N2—C12106.8 (3)
C15—C16—C17—C181.9 (6)C1—C11—N2—C1480.2 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H5···O4i0.841.822.649 (3)171
O1—H4···N1ii0.841.762.576 (4)164
Symmetry codes: (i) x+2, y+2, z+1; (ii) x1, y, z1.

Experimental details

Crystal data
Chemical formulaC16H12N2O4
Mr296.28
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)7.401 (5), 16.589 (5), 11.762 (4)
β (°) 111.53 (3)
V3)1343.3 (11)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.20 × 0.10 × 0.10
Data collection
DiffractometerBruker Smart APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.979, 0.989
No. of measured, independent and
observed [I > 2σ(I)] reflections
6722, 2358, 1239
Rint0.072
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.056, 0.152, 0.96
No. of reflections2358
No. of parameters200
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.21, 0.22

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2000) and Mercury (Macrae et al., 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H5···O4i0.841.822.649 (3)171.4
O1—H4···N1ii0.841.762.576 (4)164.1
Symmetry codes: (i) x+2, y+2, z+1; (ii) x1, y, z1.
 

References

First citationBrandenburg, K. (2000). DIAMOND. Crystal Impact GbR, Bonn, Germany.
First citationBruker (2008). APEX2 and SAINT. Bruker AXS Inc., Madison, wisconsin, USA.
First citationCheng, X.-C. (2011). Acta Cryst. E67, o3299.  Web of Science CSD CrossRef IUCr Journals
First citationMacrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.  Web of Science CrossRef CAS IUCr Journals
First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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