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Zwitterionic 4-carb­­oxy-2-(pyridinium-2-yl)-1H-imidazole-5-carboxyl­ate

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aDepartment of Chemical Engineering, China University of Mining and Technology, Yinchuan College, Ningxia 750021, People's Republic of China
*Correspondence e-mail: ajinychedu@163.com

Edited by G. Smith, Queensland University of Technology, Australia (Received 29 September 2016; accepted 14 October 2016; online 25 October 2016)

The title compound, C10H7N3O4, is zwitterionic, with one carboxyl group deprotonated and the pyridyl group protonated. The pyridine ring is close to coplanar with the imidazole ring, making a dihedral angle of 2.79 (8)°, this conformation being maintained by the presence of an intra­molecular O—H⋯O hydrogen bond. In the crystal, two sets of N—H⋯O hydrogen bonds link the mol­ecules through three conjoined cyclic hydrogen-bonding inter­actions, with two R12(7) and one R22(10) motifs, forming centrosymmetric cyclic dimers. These are linked through C—H⋯O hydrogen bonds, giving a supra­molecular chain structure extending along the b-axis direction.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

In recent years, inter­est in carb­oxy­lic acid compounds having both pyridine and imidazole ring systems has increased due to their versatility in the assembly of compounds having novel structures. At the same time, their coordination chemistry has become an expanding field of study because of the potential applications in crystal engineering (Zheng et al., 2012[Zheng, W. X., Wei, Y. Q., Tian, C. B., Xiao, X. Y. & Wu, K. C. (2012). CrystEngComm, 14, 3347-3350.]; Li et al., 2010[Li, X., Wu, B. L., Wang, R. Y., Zhang, H. Y., Niu, C. Y., Niu, Y. Y. & Hou, H. W. (2010). Inorg. Chem. 49, 2600-2613.], 2013[Li, J., Yang, G. P., Hou, L., Cui, L., Li, Y. P., Wang, Y. Y. & Shi, Q. Z. (2013). Dalton Trans. 42, 13590-13598.]). Because of its structural features, the title compound may be a suitable bridging ligand for the construction of coordination polymers with inter­esting architectures. The synthesis of this acid has been reported previously (Li et al., 2012[Li, X., Liu, W., Wu, B. L., Nian, C. X. & Zhang, H. Y. (2012). Synth. React. Inorg. Met.-Org. Nano-Met. Chem. 42, 231-237.], 2014[Li, T. T., Tian, Y. Y., Zeng, R. H. & Zheng, S. R. (2014). Inorg. Chem. Commun. 50, 75-78.]; Wang, Wang et al., 2014[Wang, J. W., Wang, H. B., Wang, Z. & Tang, P. W. Y. P. (2014). Chin. J. Struct. Chem., 33, 1843-1848.]; Xin et al., 2013[Xin, R., Yu, X. Y., Gao, W. P., Wang, N., Yang, J. J., Qu, X. S. & Zhang, X. (2013). Inorg. Chem. Commun. 35, 38-41.]), but its crystal structure has not. Only the crystal structures of its coordination polymers have been described previously (Wang, Yu et al., 2014[Wang, N., Yu, X. Y., Zhang, X., Gao, W. P., Xin, R., Zhang, H., Yang, Y. Y. & Qu, X. S. (2014). J. Coord. Chem. 67, 837-846.]; Yu et al., 2013[Yu, X. Y., Xin, R., Gao, W. P., Wang, N., Zhang, X., Yang, Y. Y. & Qu, X. S. (2013). J. Solid State Chem. 204, 314-320.]).

The title compound is f zwitterionic in the solid state, with one carboxyl group (defined by O1/C1/O2) deprotonated and the pyridyl atom N3 protonated (Fig. 1[link]). The pyridine ring is close to coplanar with the imidazole ring, making a dihedral angle of 2.79 (8)°. The O1/C1/O2 and the O4/C4/O4 carboxyl groups are also essentially coplanar with the imidazole ring, making dihedral angles of 4.265 (14) and 3.48 (9)°, respectively. This conformation is maintained by the presence of an intra­molecular O3—H3⋯O2 hydrogen bond (Table 1[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O3—H3⋯O2 0.82 1.70 2.517 (2) 176
N1—H1⋯O1i 0.86 1.92 2.743 (2) 159
N3—H3A⋯O1i 0.86 1.81 2.656 (2) 169
C10—H10⋯O3ii 0.93 2.25 3.153 (3) 163
C9—H9⋯O4ii 0.93 2.52 3.239 (3) 134
Symmetry codes: (i) -x+2, -y+1, -z; (ii) x, y+1, z.
[Figure 1]
Figure 1
Mol­ecular configuration and atom-numbering scheme, with displacement ellipsoids drawn at the 50% level.

In the crystal, two sets of N—H⋯O hydrogen bonds (N1—H1⋯O1i and N3—H3A⋯O1i) link two mol­ecules through three conjoined cyclic hydrogen-bonding inter­actions, with two R21(6) and one R22(10) motifs, forming centrosymmetric cyclic dimers (Fig. 2[link]). These dimers are linked through C—H⋯O hydrogen bonds, forming a supra­molecular chain structure extending along the b-axis direction. Present also in the structure are very weak inter­actions between pyridine and imidazole rings [minimum ring-centroid separation = 3.9510 (7) Å].

[Figure 2]
Figure 2
A view of the inter­molecular associations showing the centrosymmetric hydrogen-bonded dimers and the inter-dimer C—H⋯O extensions along b. Hydrogen bonds are shown as dashed lines.

Synthesis and crystallization

The title compound was prepared by the literature method (Elagab & Alt, 2016[Elagab, H. A. & Alt, H. G. (2016). Polyhedron, 115, 17-29.]; Zheng et al., 2012[Zheng, W. X., Wei, Y. Q., Tian, C. B., Xiao, X. Y. & Wu, K. C. (2012). CrystEngComm, 14, 3347-3350.]). o-Phenyl­enedi­amine (0.05 mol) was mixed with picolinic acid (0.05 mol) and the mixture was poured into 50 ml of preheated (373 K) polyphospho­ric acid. The mixture was stirred and heated at 448 K for 3–5 h after which the reaction mixture was then poured into ice-cold water and allowed to stand overnight. The precipitate was removed by filtration and washed several times with dilute sodium hydrogen carbonate solution and finally with water. The reaction product 2-(2-pyrid­yl)benzimidazole was then air dried. To 0.04 mol of this product in 55 ml of water was added 70 ml of concentrated H2SO4 and K2Cr2O7 (37 g). The resulting mixture was allowed to react at 363 K for 15 min and then poured into ice–water. The white precipitate formed was filtered and washed with water to give the crude product in 55% yield. Crystals suitable for X-ray analysis were obtained after recrystallization from an aqueous solution of the title compound.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C10H7N3O4
Mr 233.19
Crystal system, space group Monoclinic, P21/c
Temperature (K) 113
a, b, c (Å) 11.701 (2), 10.947 (2), 7.4253 (15)
β (°) 107.68 (3)
V3) 906.2 (3)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.14
Crystal size (mm) 0.24 × 0.19 × 0.12
 
Data collection
Diffractometer Rigaku Pilatus 200K CCD detector
Absorption correction Multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.])
Tmin, Tmax 0.971, 0.989
No. of measured, independent and observed [I > 2σ(I)] reflections 8958, 1589, 1460
Rint 0.041
(sin θ/λ)max−1) 0.594
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.124, 1.00
No. of reflections 1589
No. of parameters 155
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.23, −0.28
Computer programs: CrystalClear (Rigaku, 2008[Rigaku (2008). CrystalClear. Rigaku Corporation, Tokyo, Japan.]), SHELXS97 and SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Structural data


Computing details top

Data collection: CrystalClear (Rigaku, 2008); cell refinement: CrystalClear (Rigaku, 2008); data reduction: CrystalClear (Rigaku, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

4-Carboxy-2-(pyridinium-2-yl)-1H-imidazole-5-carboxylate top
Crystal data top
C10H7N3O4F(000) = 480
Mr = 233.19Dx = 1.709 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2533 reflections
a = 11.701 (2) Åθ = 1.8–27.9°
b = 10.947 (2) ŵ = 0.14 mm1
c = 7.4253 (15) ÅT = 113 K
β = 107.68 (3)°Prism, yellow
V = 906.2 (3) Å30.24 × 0.19 × 0.12 mm
Z = 4
Data collection top
Rigaku Pilatus 200K CCD detector
diffractometer
1589 independent reflections
Radiation source: fine-focus sealed tube1460 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.041
profile data from ω–scansθmax = 25.0°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 1313
Tmin = 0.971, Tmax = 0.989k = 1313
8958 measured reflectionsl = 88
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.124H-atom parameters constrained
S = 1.00 w = 1/[σ2(Fo2) + (0.080P)2 + 0.5P]
where P = (Fo2 + 2Fc2)/3
1589 reflections(Δ/σ)max < 0.001
155 parametersΔρmax = 0.23 e Å3
0 restraintsΔρmin = 0.28 e Å3
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 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
xyzUiso*/Ueq
O11.04791 (13)0.34830 (13)0.0067 (2)0.0248 (4)
O20.99988 (13)0.15468 (13)0.0351 (2)0.0235 (4)
O30.82521 (13)0.04871 (13)0.0987 (2)0.0248 (4)
H30.88270.08520.08310.037*
O40.65300 (13)0.09509 (14)0.1472 (2)0.0298 (4)
N10.85670 (15)0.43688 (16)0.0864 (2)0.0186 (4)
H10.90340.49320.06870.022*
N20.70101 (15)0.34866 (15)0.1471 (2)0.0191 (4)
N30.76016 (15)0.67597 (16)0.1238 (2)0.0190 (4)
H3A0.82770.66830.10130.023*
C10.98184 (17)0.26779 (18)0.0321 (3)0.0189 (5)
C20.87398 (17)0.31449 (18)0.0776 (3)0.0182 (5)
C30.77614 (18)0.26033 (18)0.1155 (3)0.0184 (5)
C40.74573 (18)0.12859 (19)0.1211 (3)0.0207 (5)
C50.75262 (17)0.45424 (18)0.1280 (3)0.0179 (5)
C60.70164 (18)0.57337 (19)0.1471 (3)0.0188 (5)
C70.59330 (18)0.5860 (2)0.1861 (3)0.0210 (5)
H70.55240.51720.20660.025*
C80.54629 (19)0.7017 (2)0.1945 (3)0.0224 (5)
H80.47310.71050.21790.027*
C90.60908 (19)0.80397 (19)0.1676 (3)0.0226 (5)
H90.57830.88180.17210.027*
C100.71828 (18)0.78862 (19)0.1340 (3)0.0212 (5)
H100.76240.85640.11870.025*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0232 (8)0.0207 (8)0.0344 (9)0.0012 (6)0.0146 (7)0.0020 (6)
O20.0239 (8)0.0166 (8)0.0324 (9)0.0019 (6)0.0120 (7)0.0003 (6)
O30.0235 (8)0.0172 (8)0.0372 (9)0.0009 (6)0.0142 (7)0.0012 (6)
O40.0268 (9)0.0203 (8)0.0476 (10)0.0047 (6)0.0193 (8)0.0016 (7)
N10.0189 (9)0.0168 (9)0.0221 (9)0.0018 (6)0.0092 (7)0.0018 (7)
N20.0208 (9)0.0164 (9)0.0203 (9)0.0003 (7)0.0062 (7)0.0001 (7)
N30.0164 (8)0.0186 (9)0.0227 (9)0.0003 (7)0.0071 (7)0.0009 (7)
C10.0181 (10)0.0199 (11)0.0191 (10)0.0003 (8)0.0063 (8)0.0008 (8)
C20.0199 (11)0.0151 (10)0.0195 (10)0.0008 (8)0.0061 (8)0.0006 (8)
C30.0184 (10)0.0173 (11)0.0201 (10)0.0007 (8)0.0069 (8)0.0003 (8)
C40.0225 (11)0.0174 (11)0.0231 (11)0.0008 (8)0.0083 (9)0.0019 (8)
C50.0169 (10)0.0178 (10)0.0196 (10)0.0001 (8)0.0065 (8)0.0003 (8)
C60.0199 (10)0.0175 (10)0.0180 (10)0.0018 (8)0.0044 (8)0.0003 (8)
C70.0197 (10)0.0208 (11)0.0244 (11)0.0031 (8)0.0096 (9)0.0015 (8)
C80.0204 (10)0.0256 (11)0.0218 (11)0.0008 (8)0.0071 (9)0.0001 (9)
C90.0268 (11)0.0195 (11)0.0219 (11)0.0040 (9)0.0079 (9)0.0006 (9)
C100.0243 (11)0.0171 (11)0.0209 (11)0.0002 (8)0.0050 (9)0.0019 (8)
Geometric parameters (Å, º) top
O1—C11.262 (2)C1—C21.492 (3)
O2—C11.255 (2)C2—C31.392 (3)
O3—C41.323 (2)C3—C41.489 (3)
O3—H30.8200C5—C61.459 (3)
O4—C41.215 (2)C6—C71.390 (3)
N1—C51.358 (3)C7—C81.390 (3)
N1—C21.359 (3)C7—H70.9300
N1—H10.8600C8—C91.386 (3)
N2—C51.331 (3)C8—H80.9300
N2—C31.374 (3)C9—C101.384 (3)
N3—C101.338 (3)C9—H90.9300
N3—C61.354 (3)C10—H100.9300
N3—H3A0.8600
C4—O3—H3109.5O3—C4—C3116.96 (17)
C5—N1—C2107.80 (16)N2—C5—N1111.72 (17)
C5—N1—H1126.1N2—C5—C6123.61 (18)
C2—N1—H1126.1N1—C5—C6124.67 (18)
C5—N2—C3104.95 (17)N3—C6—C7118.21 (18)
C10—N3—C6123.33 (18)N3—C6—C5119.45 (18)
C10—N3—H3A118.3C7—C6—C5122.33 (18)
C6—N3—H3A118.3C8—C7—C6119.88 (19)
O2—C1—O1125.55 (18)C8—C7—H7120.1
O2—C1—C2118.90 (18)C6—C7—H7120.1
O1—C1—C2115.55 (18)C9—C8—C7119.69 (19)
N1—C2—C3105.46 (17)C9—C8—H8120.2
N1—C2—C1119.79 (17)C7—C8—H8120.2
C3—C2—C1134.74 (19)C10—C9—C8119.10 (19)
N2—C3—C2110.07 (18)C10—C9—H9120.4
N2—C3—C4120.39 (17)C8—C9—H9120.4
C2—C3—C4129.53 (18)N3—C10—C9119.75 (19)
O4—C4—O3121.09 (19)N3—C10—H10120.1
O4—C4—C3121.95 (18)C9—C10—H10120.1
C5—N1—C2—C30.0 (2)C3—N2—C5—N10.2 (2)
C5—N1—C2—C1179.48 (17)C3—N2—C5—C6179.00 (18)
O2—C1—C2—N1176.02 (18)C2—N1—C5—N20.1 (2)
O1—C1—C2—N14.0 (3)C2—N1—C5—C6179.07 (18)
O2—C1—C2—C34.7 (3)C10—N3—C6—C70.9 (3)
O1—C1—C2—C3175.2 (2)C10—N3—C6—C5178.23 (17)
C5—N2—C3—C20.2 (2)N2—C5—C6—N3179.50 (18)
C5—N2—C3—C4178.71 (17)N1—C5—C6—N30.4 (3)
N1—C2—C3—N20.1 (2)N2—C5—C6—C70.4 (3)
C1—C2—C3—N2179.5 (2)N1—C5—C6—C7178.63 (19)
N1—C2—C3—C4178.62 (19)N3—C6—C7—C82.0 (3)
C1—C2—C3—C40.7 (4)C5—C6—C7—C8177.13 (18)
N2—C3—C4—O42.5 (3)C6—C7—C8—C91.3 (3)
C2—C3—C4—O4176.2 (2)C7—C8—C9—C100.4 (3)
N2—C3—C4—O3176.70 (17)C6—N3—C10—C90.9 (3)
C2—C3—C4—O34.7 (3)C8—C9—C10—N31.5 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3···O20.821.702.517 (2)176
N1—H1···O1i0.861.922.743 (2)159
N3—H3A···O1i0.861.812.656 (2)169
C10—H10···O3ii0.932.253.153 (3)163
C9—H9···O4ii0.932.523.239 (3)134
Symmetry codes: (i) x+2, y+1, z; (ii) x, y+1, z.
 

Acknowledgements

We thank the Ningxia Natural Science Foundation of China (No. NZ14232) for support.

References

First citationDolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationElagab, H. A. & Alt, H. G. (2016). Polyhedron, 115, 17–29.  CrossRef CAS Google Scholar
First citationLi, X., Liu, W., Wu, B. L., Nian, C. X. & Zhang, H. Y. (2012). Synth. React. Inorg. Met.-Org. Nano-Met. Chem. 42, 231–237.  CSD CrossRef CAS Google Scholar
First citationLi, T. T., Tian, Y. Y., Zeng, R. H. & Zheng, S. R. (2014). Inorg. Chem. Commun. 50, 75–78.  CSD CrossRef Google Scholar
First citationLi, X., Wu, B. L., Wang, R. Y., Zhang, H. Y., Niu, C. Y., Niu, Y. Y. & Hou, H. W. (2010). Inorg. Chem. 49, 2600–2613.  Web of Science CSD CrossRef CAS PubMed Google Scholar
First citationLi, J., Yang, G. P., Hou, L., Cui, L., Li, Y. P., Wang, Y. Y. & Shi, Q. Z. (2013). Dalton Trans. 42, 13590–13598.  CSD CrossRef CAS PubMed Google Scholar
First citationRigaku (2008). CrystalClear. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWang, J. W., Wang, H. B., Wang, Z. & Tang, P. W. Y. P. (2014). Chin. J. Struct. Chem., 33, 1843–1848.  CAS Google Scholar
First citationWang, N., Yu, X. Y., Zhang, X., Gao, W. P., Xin, R., Zhang, H., Yang, Y. Y. & Qu, X. S. (2014). J. Coord. Chem. 67, 837–846.  CSD CrossRef CAS Google Scholar
First citationXin, R., Yu, X. Y., Gao, W. P., Wang, N., Yang, J. J., Qu, X. S. & Zhang, X. (2013). Inorg. Chem. Commun. 35, 38–41.  CSD CrossRef CAS Google Scholar
First citationYu, X. Y., Xin, R., Gao, W. P., Wang, N., Zhang, X., Yang, Y. Y. & Qu, X. S. (2013). J. Solid State Chem. 204, 314–320.  CSD CrossRef CAS Google Scholar
First citationZheng, W. X., Wei, Y. Q., Tian, C. B., Xiao, X. Y. & Wu, K. C. (2012). CrystEngComm, 14, 3347–3350.  CSD CrossRef CAS Google Scholar

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