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

Zhang, K.; Qi, X.; Yuan, B.

doi:10.1107/S2414314616016412

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 10| October 2016| x161641

https://doi.org/10.1107/S2414314616016412

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

Kanglong Zhang,^a Xiaojin Qi ^a ^* and Bingnian Yuan ^a

^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.

Keywords: zwitterionic compound; hydrogen-bonded dimer; potential ligands; crystal structure.

CCDC reference: 1509954

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 crystal structure 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).

Table 1
Hydrogen-bond geometry (Å, °)

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.

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 refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₀H₇N₃O₄
M_r	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)
V (Å³)	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 )
T_min, T_max	0.971, 0.989
No. of measured, independent and observed [I > 2σ(I)] reflections	8958, 1589, 1460
R_int	0.041
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.28
Computer programs: CrystalClear (Rigaku, 2008 ), SHELXS97 and SHELXL97 (Sheldrick, 2008 ) and OLEX2 (Dolomanov et al., 2009 ).

Structural data

CCDC reference: 1509954

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: https://doi.org/10.1107/S2414314616016412/zs4002sup1.cif

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

checkCIF report

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

C₁₀H₇N₃O₄	F(000) = 480
M_r = 233.19	D_x = 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

Data collection top

Rigaku Pilatus 200K CCD detector diffractometer	1589 independent reflections
Radiation source: fine-focus sealed tube	1460 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.041
profile data from ω–scans	θ_max = 25.0°, θ_min = 1.8°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −13→13
T_min = 0.971, T_max = 0.989	k = −13→13
8958 measured reflections	l = −8→8

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)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.124	H-atom parameters constrained
S = 1.00	w = 1/[σ²(F_o²) + (0.080P)² + 0.5P] where P = (F_o² + 2F_c²)/3
1589 reflections	(Δ/σ)_max < 0.001
155 parameters	Δρ_max = 0.23 e Å⁻³
0 restraints	Δρ_min = −0.28 e Å⁻³

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

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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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