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organic compounds
Zwitterionic 4-carboxy-2-(pyridinium-2-yl)-1H-imidazole-5-carboxylate
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
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.
CCDC reference: 1509954
![[Scheme 3D1]](zs4002scheme3D1.gif)
![[Scheme 1]](zs4002scheme1.gif)
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; Li et al., 2010
, 2013
). 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
, 2014
; Wang, Wang et al., 2014
; Xin et al., 2013
), but its has not. Only the crystal structures of its coordination polymers have been described previously (Wang, Yu et al., 2014
; Yu et al., 2013
).
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). 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
).
|
![]() | 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). 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 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; Zheng et al., 2012
). 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 .
|
Structural data
CCDC reference: 1509954
https://doi.org/10.1107/S2414314616016412/zs4002sup1.cif
contains datablocks I, New_Global_Publ_Block. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616016412/zs4002Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314616016412/zs4002Isup3.cml
Data collection: CrystalClear (Rigaku, 2008); cell
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).C10H7N3O4 | F(000) = 480 |
Mr = 233.19 | Dx = 1.709 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 2533 reflections |
a = 11.701 (2) Å | θ = 1.8–27.9° |
b = 10.947 (2) Å | µ = 0.14 mm−1 |
c = 7.4253 (15) Å | T = 113 K |
β = 107.68 (3)° | Prism, yellow |
V = 906.2 (3) Å3 | 0.24 × 0.19 × 0.12 mm |
Z = 4 |
Rigaku Pilatus 200K CCD detector diffractometer | 1589 independent reflections |
Radiation source: fine-focus sealed tube | 1460 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.041 |
profile data from ω–scans | θmax = 25.0°, θmin = 1.8° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −13→13 |
Tmin = 0.971, Tmax = 0.989 | k = −13→13 |
8958 measured reflections | l = −8→8 |
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)] = 0.047 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.124 | H-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 parameters | Δρmax = 0.23 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 1.04791 (13) | 0.34830 (13) | −0.0067 (2) | 0.0248 (4) | |
O2 | 0.99988 (13) | 0.15468 (13) | 0.0351 (2) | 0.0235 (4) | |
O3 | 0.82521 (13) | 0.04871 (13) | 0.0987 (2) | 0.0248 (4) | |
H3 | 0.8827 | 0.0852 | 0.0831 | 0.037* | |
O4 | 0.65300 (13) | 0.09509 (14) | 0.1472 (2) | 0.0298 (4) | |
N1 | 0.85670 (15) | 0.43688 (16) | 0.0864 (2) | 0.0186 (4) | |
H1 | 0.9034 | 0.4932 | 0.0687 | 0.022* | |
N2 | 0.70101 (15) | 0.34866 (15) | 0.1471 (2) | 0.0191 (4) | |
N3 | 0.76016 (15) | 0.67597 (16) | 0.1238 (2) | 0.0190 (4) | |
H3A | 0.8277 | 0.6683 | 0.1013 | 0.023* | |
C1 | 0.98184 (17) | 0.26779 (18) | 0.0321 (3) | 0.0189 (5) | |
C2 | 0.87398 (17) | 0.31449 (18) | 0.0776 (3) | 0.0182 (5) | |
C3 | 0.77614 (18) | 0.26033 (18) | 0.1155 (3) | 0.0184 (5) | |
C4 | 0.74573 (18) | 0.12859 (19) | 0.1211 (3) | 0.0207 (5) | |
C5 | 0.75262 (17) | 0.45424 (18) | 0.1280 (3) | 0.0179 (5) | |
C6 | 0.70164 (18) | 0.57337 (19) | 0.1471 (3) | 0.0188 (5) | |
C7 | 0.59330 (18) | 0.5860 (2) | 0.1861 (3) | 0.0210 (5) | |
H7 | 0.5524 | 0.5172 | 0.2066 | 0.025* | |
C8 | 0.54629 (19) | 0.7017 (2) | 0.1945 (3) | 0.0224 (5) | |
H8 | 0.4731 | 0.7105 | 0.2179 | 0.027* | |
C9 | 0.60908 (19) | 0.80397 (19) | 0.1676 (3) | 0.0226 (5) | |
H9 | 0.5783 | 0.8818 | 0.1721 | 0.027* | |
C10 | 0.71828 (18) | 0.78862 (19) | 0.1340 (3) | 0.0212 (5) | |
H10 | 0.7624 | 0.8564 | 0.1187 | 0.025* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0232 (8) | 0.0207 (8) | 0.0344 (9) | −0.0012 (6) | 0.0146 (7) | 0.0020 (6) |
O2 | 0.0239 (8) | 0.0166 (8) | 0.0324 (9) | 0.0019 (6) | 0.0120 (7) | 0.0003 (6) |
O3 | 0.0235 (8) | 0.0172 (8) | 0.0372 (9) | −0.0009 (6) | 0.0142 (7) | 0.0012 (6) |
O4 | 0.0268 (9) | 0.0203 (8) | 0.0476 (10) | −0.0047 (6) | 0.0193 (8) | −0.0016 (7) |
N1 | 0.0189 (9) | 0.0168 (9) | 0.0221 (9) | −0.0018 (6) | 0.0092 (7) | 0.0018 (7) |
N2 | 0.0208 (9) | 0.0164 (9) | 0.0203 (9) | −0.0003 (7) | 0.0062 (7) | −0.0001 (7) |
N3 | 0.0164 (8) | 0.0186 (9) | 0.0227 (9) | −0.0003 (7) | 0.0071 (7) | 0.0009 (7) |
C1 | 0.0181 (10) | 0.0199 (11) | 0.0191 (10) | 0.0003 (8) | 0.0063 (8) | 0.0008 (8) |
C2 | 0.0199 (11) | 0.0151 (10) | 0.0195 (10) | −0.0008 (8) | 0.0061 (8) | 0.0006 (8) |
C3 | 0.0184 (10) | 0.0173 (11) | 0.0201 (10) | −0.0007 (8) | 0.0069 (8) | 0.0003 (8) |
C4 | 0.0225 (11) | 0.0174 (11) | 0.0231 (11) | −0.0008 (8) | 0.0083 (9) | −0.0019 (8) |
C5 | 0.0169 (10) | 0.0178 (10) | 0.0196 (10) | −0.0001 (8) | 0.0065 (8) | 0.0003 (8) |
C6 | 0.0199 (10) | 0.0175 (10) | 0.0180 (10) | −0.0018 (8) | 0.0044 (8) | 0.0003 (8) |
C7 | 0.0197 (10) | 0.0208 (11) | 0.0244 (11) | −0.0031 (8) | 0.0096 (9) | −0.0015 (8) |
C8 | 0.0204 (10) | 0.0256 (11) | 0.0218 (11) | 0.0008 (8) | 0.0071 (9) | 0.0001 (9) |
C9 | 0.0268 (11) | 0.0195 (11) | 0.0219 (11) | 0.0040 (9) | 0.0079 (9) | −0.0006 (9) |
C10 | 0.0243 (11) | 0.0171 (11) | 0.0209 (11) | −0.0002 (8) | 0.0050 (9) | 0.0019 (8) |
O1—C1 | 1.262 (2) | C1—C2 | 1.492 (3) |
O2—C1 | 1.255 (2) | C2—C3 | 1.392 (3) |
O3—C4 | 1.323 (2) | C3—C4 | 1.489 (3) |
O3—H3 | 0.8200 | C5—C6 | 1.459 (3) |
O4—C4 | 1.215 (2) | C6—C7 | 1.390 (3) |
N1—C5 | 1.358 (3) | C7—C8 | 1.390 (3) |
N1—C2 | 1.359 (3) | C7—H7 | 0.9300 |
N1—H1 | 0.8600 | C8—C9 | 1.386 (3) |
N2—C5 | 1.331 (3) | C8—H8 | 0.9300 |
N2—C3 | 1.374 (3) | C9—C10 | 1.384 (3) |
N3—C10 | 1.338 (3) | C9—H9 | 0.9300 |
N3—C6 | 1.354 (3) | C10—H10 | 0.9300 |
N3—H3A | 0.8600 | ||
C4—O3—H3 | 109.5 | O3—C4—C3 | 116.96 (17) |
C5—N1—C2 | 107.80 (16) | N2—C5—N1 | 111.72 (17) |
C5—N1—H1 | 126.1 | N2—C5—C6 | 123.61 (18) |
C2—N1—H1 | 126.1 | N1—C5—C6 | 124.67 (18) |
C5—N2—C3 | 104.95 (17) | N3—C6—C7 | 118.21 (18) |
C10—N3—C6 | 123.33 (18) | N3—C6—C5 | 119.45 (18) |
C10—N3—H3A | 118.3 | C7—C6—C5 | 122.33 (18) |
C6—N3—H3A | 118.3 | C8—C7—C6 | 119.88 (19) |
O2—C1—O1 | 125.55 (18) | C8—C7—H7 | 120.1 |
O2—C1—C2 | 118.90 (18) | C6—C7—H7 | 120.1 |
O1—C1—C2 | 115.55 (18) | C9—C8—C7 | 119.69 (19) |
N1—C2—C3 | 105.46 (17) | C9—C8—H8 | 120.2 |
N1—C2—C1 | 119.79 (17) | C7—C8—H8 | 120.2 |
C3—C2—C1 | 134.74 (19) | C10—C9—C8 | 119.10 (19) |
N2—C3—C2 | 110.07 (18) | C10—C9—H9 | 120.4 |
N2—C3—C4 | 120.39 (17) | C8—C9—H9 | 120.4 |
C2—C3—C4 | 129.53 (18) | N3—C10—C9 | 119.75 (19) |
O4—C4—O3 | 121.09 (19) | N3—C10—H10 | 120.1 |
O4—C4—C3 | 121.95 (18) | C9—C10—H10 | 120.1 |
C5—N1—C2—C3 | 0.0 (2) | C3—N2—C5—N1 | −0.2 (2) |
C5—N1—C2—C1 | 179.48 (17) | C3—N2—C5—C6 | 179.00 (18) |
O2—C1—C2—N1 | 176.02 (18) | C2—N1—C5—N2 | 0.1 (2) |
O1—C1—C2—N1 | −4.0 (3) | C2—N1—C5—C6 | −179.07 (18) |
O2—C1—C2—C3 | −4.7 (3) | C10—N3—C6—C7 | −0.9 (3) |
O1—C1—C2—C3 | 175.2 (2) | C10—N3—C6—C5 | 178.23 (17) |
C5—N2—C3—C2 | 0.2 (2) | N2—C5—C6—N3 | −179.50 (18) |
C5—N2—C3—C4 | −178.71 (17) | N1—C5—C6—N3 | −0.4 (3) |
N1—C2—C3—N2 | −0.1 (2) | N2—C5—C6—C7 | −0.4 (3) |
C1—C2—C3—N2 | −179.5 (2) | N1—C5—C6—C7 | 178.63 (19) |
N1—C2—C3—C4 | 178.62 (19) | N3—C6—C7—C8 | 2.0 (3) |
C1—C2—C3—C4 | −0.7 (4) | C5—C6—C7—C8 | −177.13 (18) |
N2—C3—C4—O4 | 2.5 (3) | C6—C7—C8—C9 | −1.3 (3) |
C2—C3—C4—O4 | −176.2 (2) | C7—C8—C9—C10 | −0.4 (3) |
N2—C3—C4—O3 | −176.70 (17) | C6—N3—C10—C9 | −0.9 (3) |
C2—C3—C4—O3 | 4.7 (3) | C8—C9—C10—N3 | 1.5 (3) |
D—H···A | D—H | H···A | D···A | 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. |
Acknowledgements
We thank the Ningxia Natural Science Foundation of China (No. NZ14232) for support.
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