3-Carb­oxy-5-(pyridinium-4-yl)benzoate: a redetermination

Li, S.-J.; Miao, D.-L.; Song, W.-D.; Tong, S.-W.

doi:10.1107/S1600536811016394

organic compounds

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ISSN: 2056-9890

Volume 67| Part 6| June 2011| Page o1353

doi:10.1107/S1600536811016394

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3-Carboxy-5-(pyridinium-4-yl)benzoate: a redetermination

Shi-Jie Li,^a Dong-Liang Miao,^a Wen-Dong Song ^b ^* and Shao-Wei Tong ^a

^aCollege of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, People's Republic of China, and ^bCollege of Science, Guangdong Ocean University, Zhanjiang 524088, People's Republic of China
^*Correspondence e-mail: songwd60@126.com

(Received 28 April 2011; accepted 30 April 2011; online 7 May 2011)

The title compound, C₁₃H₉NO₄, crystallizes in a zwitterionic form with the pyridine N atom protonated and the carboxyl OH group deprotonated. The benzene and pyridinium rings are inclined with a dihedral angle of 31.42 (14)° between them. A previous report of this stucture claims, we believe incorrectly, that neither of the carboxylate groups is deprotonated [Zhang et al. (2010 ). Acta Cryst. E66, o2928–o2928]. In the crystal, intermolecular O—H⋯O, N—H⋯O and weak C—H⋯O hydrogen-bonding interactions link adjacent molecules into a three-dimensional supramolecular network.

Related literature

For coordination polymers based on pyridinecarboxylate ligands, see: Lu & Luck (2003 ); Ma et al. (2009 ). For a previous report of the structure of this molecule, which claims that neither of the carboxylate groups is deprotonated, see: Zhang et al. (2010).

Experimental

Crystal data

C₁₃H₉NO₄
M_r = 243.21
Orthorhombic, F d d 2
a = 15.5702 (13) Å
b = 37.377 (3) Å
c = 7.2016 (9) Å
V = 4191.1 (7) Å³
Z = 16
Mo Kα radiation
μ = 0.12 mm⁻¹
T = 298 K
0.38 × 0.15 × 0.07 mm

Data collection

Bruker SMART 1000 CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2007 ) T_min = 0.957, T_max = 0.992
5456 measured reflections
1024 independent reflections
885 reflections with I > 2σ(I)
R_int = 0.048

Refinement

R[F² > 2σ(F²)] = 0.050
wR(F²) = 0.142
S = 1.09
1024 reflections
164 parameters
4 restraints
H-atom parameters constrained
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.26 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O4ⁱ	0.86	1.70	2.562 (4)	175
N1—H1⋯O3ⁱ	0.86	2.67	3.252 (4)	126
O1—H1A⋯O4ⁱⁱ	0.82	1.96	2.643 (5)	141
C8—H8⋯O2ⁱⁱⁱ	0.93	2.71	3.632 (5)	171
C10—H10⋯O2ⁱⁱⁱ	0.93	2.58	3.225 (6)	127
C9—H9⋯O1^iv	0.93	2.59	3.316 (6)	135
Symmetry codes: (i) $[-x+{\script{1\over 4}}, y-{\script{1\over 4}}, z-{\script{1\over 4}}]$ ; (ii) $[x+{\script{1\over 2}}, y, z-{\script{1\over 2}}]$ ; (iii) -x+1, -y, z; (iv) $[-x+{\script{3\over 4}}, y-{\script{1\over 4}}, z+{\script{1\over 4}}]$ .

Data collection: SMART (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811016394/sj5133sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811016394/sj5133Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811016394/sj5133Isup3.cml

checkCIF report

Comment top

Rigid pyridinecarboxylate ligands have been used extensively to react with metal ions and generate coordination polymers with fascinating structures and properties (Lu & Luck 2003; Ma et al., 2009). As part of an ongoing investigation into coordination polymers based on pyridinecarboxylate ligands, we report here the crystal structure of the title compound.

As shown in Fig. 1, the title compound, C₁₃H₉NO₄, crystallizes in a zwitterionic form with the pyridine N protonated and one of the carboxyl OH groups deprotonated. The locations of the N and O bound H atoms are clearly shown in a difference Fourier map. A previous report of the same structure in the same space group and with similar unit-cell parameters claims that neither of the carboxylate groups are deprotonated (Zhang et al., 2010). We believe this assignment to be in error. A conformational feature of the molecule is a rigid structure with the benzene and pyridinium rings inclined at an angle of 31.42 (14) ° to one another. In the crystal structure, molecules are interconnected by O—H···O, N—H···O and weak C—H···O hydrogen bonding interactions (Table. 1), generating a three-dimensional supramolecular network (Fig. 2).

Related literature top

For coordination polymers based on pyridinecarboxylate ligands, see: Lu & Luck (2003); Ma et al. (2009). For a previous report of the structure of this molecule, which claims that neither of the carboxylate groups is deprotonated, see: Zhang et al. (2010).

Experimental top

Commercially available 5-(pyridin-4-yl)isophthalic acid was further purified by repeated recrystallization from anhydrous ethanol. Colorless crystals suitable for X-ray analysis were obtained by slow evaporation of the ethanol solvent at room temperature.

Computing details top

Data collection: SMART (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The structure of the title compound, showing the atomic numbering scheme. Non-H atoms are shown with 30% probability displacement ellipsoids.
	Fig. 2. Crystal packing of the title compound (H atoms not involved in forming hydrogen bonds are omitted for clarity).

3-Carboxy-5-(pyridinium-4-yl)benzoate top

Crystal data top

C₁₃H₉NO₄	F(000) = 2016
M_r = 243.21	D_x = 1.542 Mg m⁻³
Orthorhombic, Fdd2	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: F 2 -2d	Cell parameters from 1702 reflections
a = 15.5702 (13) Å	θ = 2.5–25.9°
b = 37.377 (3) Å	µ = 0.12 mm⁻¹
c = 7.2016 (9) Å	T = 298 K
V = 4191.1 (7) Å³	Block, colorless
Z = 16	0.38 × 0.15 × 0.07 mm

Data collection top

Bruker SMART 1000 CCD area-detector diffractometer	1024 independent reflections
Radiation source: fine-focus sealed tube	885 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.048
ϕ and ω scans	θ_max = 25.2°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 2007)	h = −15→18
T_min = 0.957, T_max = 0.992	k = −42→44
5456 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)] = 0.050	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.142	H-atom parameters constrained
S = 1.09	w = 1/[σ²(F_o²) + (0.0985P)² + 0.9031P] where P = (F_o² + 2F_c²)/3
1024 reflections	(Δ/σ)_max < 0.001
164 parameters	Δρ_max = 0.21 e Å⁻³
4 restraints	Δρ_min = −0.26 e Å⁻³

Crystal data top

C₁₃H₉NO₄	V = 4191.1 (7) Å³
M_r = 243.21	Z = 16
Orthorhombic, Fdd2	Mo Kα radiation
a = 15.5702 (13) Å	µ = 0.12 mm⁻¹
b = 37.377 (3) Å	T = 298 K
c = 7.2016 (9) Å	0.38 × 0.15 × 0.07 mm

Data collection top

Bruker SMART 1000 CCD area-detector diffractometer	1024 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2007)	885 reflections with I > 2σ(I)
T_min = 0.957, T_max = 0.992	R_int = 0.048
5456 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.050	4 restraints
wR(F²) = 0.142	H-atom parameters constrained
S = 1.09	Δρ_max = 0.21 e Å⁻³
1024 reflections	Δρ_min = −0.26 e Å⁻³
164 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
N1	0.1480 (2)	−0.05751 (9)	0.2133 (5)	0.0409 (9)
H1	0.1190	−0.0771	0.2101	0.049*
O1	0.5435 (2)	0.10547 (10)	0.0930 (7)	0.0710 (12)
H1A	0.5939	0.1044	0.0606	0.106*
O2	0.5453 (2)	0.04721 (10)	0.0306 (6)	0.0697 (13)
O3	0.29114 (19)	0.16581 (7)	0.3311 (6)	0.0532 (9)
O4	0.18242 (19)	0.13290 (7)	0.4374 (6)	0.0482 (9)
C1	0.5099 (3)	0.07316 (11)	0.0923 (7)	0.0397 (9)
C2	0.2558 (2)	0.13670 (10)	0.3568 (7)	0.0360 (9)
C3	0.4199 (2)	0.07241 (9)	0.1660 (6)	0.0327 (9)
C4	0.3802 (2)	0.10341 (10)	0.2268 (6)	0.0328 (9)
H4A	0.4102	0.1249	0.2255	0.039*
C5	0.2964 (2)	0.10264 (10)	0.2892 (6)	0.0314 (9)
C6	0.2511 (2)	0.07076 (10)	0.2856 (6)	0.0314 (9)
H6	0.1940	0.0704	0.3236	0.038*
C7	0.2898 (2)	0.03945 (10)	0.2260 (6)	0.0315 (9)
C8	0.3750 (2)	0.04014 (10)	0.1687 (6)	0.0325 (9)
H8	0.4020	0.0191	0.1321	0.039*
C9	0.2321 (3)	−0.05851 (11)	0.2449 (7)	0.0422 (10)
H9	0.2589	−0.0804	0.2644	0.051*
C10	0.2804 (3)	−0.02736 (10)	0.2493 (7)	0.0376 (10)
H10	0.3394	−0.0285	0.2688	0.045*
C11	0.2406 (2)	0.00546 (10)	0.2248 (6)	0.0324 (9)
C12	0.1522 (3)	0.00546 (10)	0.1922 (7)	0.0399 (10)
H12	0.1229	0.0269	0.1745	0.048*
C13	0.1090 (3)	−0.02658 (11)	0.1866 (7)	0.0438 (11)
H13	0.0502	−0.0265	0.1632	0.053*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0402 (19)	0.0294 (16)	0.053 (2)	−0.0098 (14)	0.0033 (17)	−0.0067 (17)
O1	0.057 (2)	0.0575 (15)	0.098 (3)	−0.0119 (15)	0.024 (2)	−0.006 (2)
O2	0.052 (2)	0.0601 (15)	0.097 (4)	0.0054 (14)	0.018 (2)	−0.010 (2)
O3	0.0488 (18)	0.0275 (14)	0.083 (3)	−0.0033 (12)	0.0095 (17)	−0.0067 (17)
O4	0.0399 (16)	0.0334 (15)	0.071 (2)	0.0014 (12)	0.0126 (16)	−0.0045 (15)
C1	0.0301 (19)	0.0442 (18)	0.045 (2)	0.0001 (14)	0.0017 (19)	0.0004 (18)
C2	0.0335 (19)	0.028 (2)	0.046 (2)	0.0031 (15)	−0.0038 (18)	−0.0062 (18)
C3	0.0320 (19)	0.0282 (18)	0.038 (2)	−0.0014 (14)	−0.0008 (18)	0.0009 (17)
C4	0.0294 (19)	0.0310 (18)	0.038 (2)	−0.0053 (14)	0.0011 (16)	0.0001 (17)
C5	0.0300 (19)	0.0292 (18)	0.035 (2)	0.0014 (14)	−0.0026 (17)	−0.0039 (16)
C6	0.0274 (18)	0.0298 (19)	0.037 (2)	−0.0010 (14)	0.0009 (16)	−0.0012 (16)
C7	0.0291 (19)	0.0319 (19)	0.033 (2)	−0.0023 (14)	0.0006 (17)	0.0007 (18)
C8	0.032 (2)	0.0280 (18)	0.037 (2)	0.0021 (15)	0.0010 (18)	−0.0013 (16)
C9	0.048 (2)	0.0270 (19)	0.052 (3)	0.0011 (17)	0.000 (2)	−0.0019 (18)
C10	0.030 (2)	0.0340 (19)	0.049 (3)	0.0004 (15)	0.0029 (19)	−0.0046 (19)
C11	0.0336 (19)	0.028 (2)	0.035 (2)	−0.0015 (15)	0.0038 (17)	−0.0027 (17)
C12	0.032 (2)	0.0314 (19)	0.056 (3)	0.0017 (15)	0.0026 (19)	−0.003 (2)
C13	0.036 (2)	0.038 (2)	0.057 (3)	−0.0054 (17)	−0.002 (2)	−0.005 (2)

Geometric parameters (Å, º) top

N1—C13	1.320 (5)	C5—C6	1.385 (5)
N1—C9	1.329 (5)	C6—C7	1.385 (5)
N1—H1	0.8600	C6—H6	0.9300
O1—C1	1.316 (5)	C7—C8	1.389 (5)
O1—H1A	0.8200	C7—C11	1.484 (5)
O2—C1	1.201 (5)	C8—H8	0.9300
O3—C2	1.233 (5)	C9—C10	1.386 (5)
O4—C2	1.290 (5)	C9—H9	0.9300
C1—C3	1.498 (5)	C10—C11	1.386 (6)
C2—C5	1.502 (5)	C10—H10	0.9300
C3—C4	1.385 (5)	C11—C12	1.397 (6)
C3—C8	1.394 (5)	C12—C13	1.374 (6)
C4—C5	1.379 (5)	C12—H12	0.9300
C4—H4A	0.9300	C13—H13	0.9300

C13—N1—C9	120.2 (3)	C6—C7—C8	119.5 (3)
C13—N1—H1	119.9	C6—C7—C11	120.0 (3)
C9—N1—H1	119.9	C8—C7—C11	120.5 (3)
C1—O1—H1A	109.5	C7—C8—C3	119.9 (3)
O2—C1—O1	124.0 (4)	C7—C8—H8	120.0
O2—C1—C3	123.1 (4)	C3—C8—H8	120.0
O1—C1—C3	112.8 (4)	N1—C9—C10	121.0 (4)
O3—C2—O4	124.0 (3)	N1—C9—H9	119.5
O3—C2—C5	120.8 (4)	C10—C9—H9	119.5
O4—C2—C5	115.2 (3)	C11—C10—C9	119.9 (4)
C4—C3—C8	119.7 (3)	C11—C10—H10	120.1
C4—C3—C1	120.9 (3)	C9—C10—H10	120.1
C8—C3—C1	119.3 (3)	C10—C11—C12	117.5 (4)
C5—C4—C3	120.5 (3)	C10—C11—C7	121.8 (3)
C5—C4—H4A	119.7	C12—C11—C7	120.7 (3)
C3—C4—H4A	119.7	C13—C12—C11	119.2 (4)
C4—C5—C6	119.6 (3)	C13—C12—H12	120.4
C4—C5—C2	119.1 (3)	C11—C12—H12	120.4
C6—C5—C2	121.4 (3)	N1—C13—C12	122.2 (4)
C7—C6—C5	120.7 (3)	N1—C13—H13	118.9
C7—C6—H6	119.6	C12—C13—H13	118.9
C5—C6—H6	119.6

O2—C1—C3—C4	−176.6 (5)	C6—C7—C8—C3	−2.0 (6)
O1—C1—C3—C4	−0.2 (6)	C11—C7—C8—C3	178.4 (4)
O2—C1—C3—C8	1.7 (7)	C4—C3—C8—C7	2.2 (6)
O1—C1—C3—C8	178.1 (4)	C1—C3—C8—C7	−176.1 (4)
C8—C3—C4—C5	−0.3 (6)	C13—N1—C9—C10	−0.4 (7)
C1—C3—C4—C5	178.0 (4)	N1—C9—C10—C11	1.5 (7)
C3—C4—C5—C6	−1.9 (6)	C9—C10—C11—C12	−1.3 (7)
C3—C4—C5—C2	179.1 (4)	C9—C10—C11—C7	−179.2 (4)
O3—C2—C5—C4	11.1 (6)	C6—C7—C11—C10	−150.4 (4)
O4—C2—C5—C4	−170.3 (4)	C8—C7—C11—C10	29.3 (6)
O3—C2—C5—C6	−167.9 (4)	C6—C7—C11—C12	31.8 (6)
O4—C2—C5—C6	10.7 (6)	C8—C7—C11—C12	−148.5 (4)
C4—C5—C6—C7	2.2 (6)	C10—C11—C12—C13	0.2 (7)
C2—C5—C6—C7	−178.8 (4)	C7—C11—C12—C13	178.1 (4)
C5—C6—C7—C8	−0.2 (7)	C9—N1—C13—C12	−0.7 (8)
C5—C6—C7—C11	179.4 (4)	C11—C12—C13—N1	0.8 (7)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O4ⁱ	0.86	1.70	2.562 (4)	175
N1—H1···O3ⁱ	0.86	2.67	3.252 (4)	126
O1—H1A···O4ⁱⁱ	0.82	1.96	2.643 (5)	141
C8—H8···O2ⁱⁱⁱ	0.93	2.71	3.632 (5)	171
C10—H10···O2ⁱⁱⁱ	0.93	2.58	3.225 (6)	127
C9—H9···O1^iv	0.93	2.59	3.316 (6)	135

Symmetry codes: (i) −x+1/4, y−1/4, z−1/4; (ii) x+1/2, y, z−1/2; (iii) −x+1, −y, z; (iv) −x+3/4, y−1/4, z+1/4.

Experimental details

Crystal data
Chemical formula	C₁₃H₉NO₄
M_r	243.21
Crystal system, space group	Orthorhombic, Fdd2
Temperature (K)	298
a, b, c (Å)	15.5702 (13), 37.377 (3), 7.2016 (9)
V (Å³)	4191.1 (7)
Z	16
Radiation type	Mo Kα
µ (mm⁻¹)	0.12
Crystal size (mm)	0.38 × 0.15 × 0.07

Data collection
Diffractometer	Bruker SMART 1000 CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2007)
T_min, T_max	0.957, 0.992
No. of measured, independent and observed [I > 2σ(I)] reflections	5456, 1024, 885
R_int	0.048
(sin θ/λ)_max (Å⁻¹)	0.599

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.050, 0.142, 1.09
No. of reflections	1024
No. of parameters	164
No. of restraints	4
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.26

Computer programs: SMART (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O4ⁱ	0.86	1.70	2.562 (4)	175
N1—H1···O3ⁱ	0.86	2.67	3.252 (4)	126
O1—H1A···O4ⁱⁱ	0.82	1.96	2.643 (5)	141
C8—H8···O2ⁱⁱⁱ	0.93	2.71	3.632 (5)	171
C10—H10···O2ⁱⁱⁱ	0.93	2.58	3.225 (6)	127
C9—H9···O1^iv	0.93	2.59	3.316 (6)	135

Symmetry codes: (i) −x+1/4, y−1/4, z−1/4; (ii) x+1/2, y, z−1/2; (iii) −x+1, −y, z; (iv) −x+3/4, y−1/4, z+1/4.

Acknowledgements

This work was supported by the Guangdong Chinese Academy of Science Comprehensive Strategic Cooperation Project (grant No. 2009B091300121), the Science and Technology Department of Guangdong Province Project (grant No. 00087 061110314018) and the Guangdong Natural Science Foundation (No. 9252408801000002).

References

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