5-Chloro-1H-indole-3-carb­oxy­lic acid

Han, X.-L.; Luo, Y.-H.

doi:10.1107/S1600536811053384

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 68| Part 1| January 2012| Page o145

doi:10.1107/S1600536811053384

Open

access

5-Chloro-1H-indole-3-carboxylic acid

Xue-Lian Han ^a ^* and Yang-Hui Luo ^a

^aCollege of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
^*Correspondence e-mail: chmsunbw@seu.edu.cn

(Received 5 December 2011; accepted 12 December 2011; online 17 December 2011)

In the title compound, C₉H₆ClNO₂, the carboxyl group is twisted from the indole ring system by 9.00 (8)°. In the crystal, inversion dimers linked by pairs of O—H⋯O hydrogen bonds generate R₂²(8) loops and N—H⋯O hydrogen bonds link the dimers into (001) sheets. Aromatic π–π stacking interactions [centroid–centroid distance = 3.7185 (12) A °] are also observed.

Related literature

For background to indole derivatives as pharmaceuticals, see: Kunzer & Wendt (2011 ); Woodward & Bartel (2005 ).

Experimental

Crystal data

C₉H₆ClNO₂
M_r = 195.60
Orthorhombic, P b c a
a = 7.2934 (15) Å
b = 13.065 (3) Å
c = 17.902 (4) Å
V = 1705.9 (6) Å³
Z = 8
Mo Kα radiation
μ = 0.41 mm⁻¹
T = 293 K
0.30 × 0.20 × 0.15 mm

Data collection

Rigaku SCXmini CCD diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ) T_min = 0.907, T_max = 0.941
16050 measured reflections
1919 independent reflections
1590 reflections with I > 2σ(I)
R_int = 0.050

Refinement

R[F² > 2σ(F²)] = 0.037
wR(F²) = 0.104
S = 1.04
1919 reflections
123 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.17 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯O2ⁱ	0.82	1.86	2.6558 (17)	164
N1—H1B⋯O2ⁱⁱ	0.86 (2)	2.26 (2)	3.005 (2)	144.3 (19)
Symmetry codes: (i) -x, -y+2, -z+1; (ii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, z]$ .

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811053384/hb6559sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811053384/hb6559Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811053384/hb6559Isup3.cml

checkCIF report

Comment top

Indole-3-carboxylic acid and its derivatives are important chemical materials, because they are excellent auxins for plants and drug intermediates for many pharmaceutical products (Woodward, et al.,2005, Kunzer, et al.,2011). As part of our interest in these materials, we report here the crystal structure of the title compound.

The molecular structure of the title compound is shown in Fig. 1. All the non-H atoms are approximately coplanar: the carboxy O atoms deviating by 0.124 and -0.223 Å from the indole plane.

In the crystal, O—H···O hydrogen bonds linked the molecules into dimers and the dimers packed via N—H···O hydrogen bonds and π–π interactions [centroid–centroid distance = 3.7185 (12) A °] (Fig. 2).

Related literature top

For background to indole derivatives as pharmaceuticals, see: Kunzer & Wendt (2011); Woodward & Bartel (2005).

Experimental top

The title compound was purchased from ChemFuture PharmaTech, Ltd (Nanjing, Jiangsu). Colourless blocks were obstained by slow evaporation of a methanol solution.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound with displacement ellipsoids drawn at the 30% probability level.
	Fig. 2. A packing view down the a axis showing hydrogen bonds as dashed lines.

5-Chloro-1H-indole-3-carboxylic acid top

Crystal data top

C₉H₆ClNO₂	F(000) = 800
M_r = 195.60	D_x = 1.523 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 1919 reflections
a = 7.2934 (15) Å	θ = 3.1–27.4°
b = 13.065 (3) Å	µ = 0.41 mm⁻¹
c = 17.902 (4) Å	T = 293 K
V = 1705.9 (6) Å³	Block, colourless
Z = 8	0.30 × 0.20 × 0.15 mm

Data collection top

Rigaku SCXmini CCD diffractometer	1919 independent reflections
Radiation source: fine-focus sealed tube	1590 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.050
Detector resolution: 13.6612 pixels mm^-1	θ_max = 27.4°, θ_min = 3.1°
CCD_Profile_fitting scans	h = −9→9
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −16→16
T_min = 0.907, T_max = 0.941	l = −23→23
16050 measured reflections

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)] = 0.037	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.104	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ²(F_o²) + (0.052P)² + 0.5573P] where P = (F_o² + 2F_c²)/3
1919 reflections	(Δ/σ)_max < 0.001
123 parameters	Δρ_max = 0.17 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₉H₆ClNO₂	V = 1705.9 (6) Å³
M_r = 195.60	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 7.2934 (15) Å	µ = 0.41 mm⁻¹
b = 13.065 (3) Å	T = 293 K
c = 17.902 (4) Å	0.30 × 0.20 × 0.15 mm

Data collection top

Rigaku SCXmini CCD diffractometer	1919 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	1590 reflections with I > 2σ(I)
T_min = 0.907, T_max = 0.941	R_int = 0.050
16050 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.037	0 restraints
wR(F²) = 0.104	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	Δρ_max = 0.17 e Å⁻³
1919 reflections	Δρ_min = −0.23 e Å⁻³
123 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
Cl1	0.07292 (7)	0.95139 (4)	0.09595 (2)	0.05145 (18)
O2	0.05698 (16)	0.98847 (9)	0.40623 (6)	0.0402 (3)
C3	0.0835 (2)	0.89840 (12)	0.42814 (9)	0.0343 (3)
N1	0.2225 (2)	0.65957 (11)	0.33911 (8)	0.0428 (4)
C4	0.1415 (2)	0.81729 (11)	0.29670 (8)	0.0301 (3)
C6	0.1018 (2)	0.89102 (11)	0.24148 (8)	0.0329 (3)
H6	0.0636	0.9566	0.2542	0.040*
O1	0.0656 (2)	0.87130 (10)	0.49869 (6)	0.0568 (4)
H1	0.0422	0.9220	0.5240	0.085*
C5	0.1970 (2)	0.71749 (12)	0.27449 (9)	0.0350 (4)
C2	0.1353 (2)	0.81582 (11)	0.37768 (9)	0.0322 (3)
C9	0.1218 (2)	0.86192 (13)	0.16732 (9)	0.0365 (4)
C7	0.2150 (2)	0.68926 (13)	0.19938 (10)	0.0429 (4)
H7	0.2508	0.6235	0.1860	0.052*
C1	0.1853 (2)	0.71802 (13)	0.39985 (9)	0.0403 (4)
H1A	0.1924	0.6958	0.4491	0.048*
C8	0.1775 (2)	0.76284 (14)	0.14570 (9)	0.0434 (4)
H8	0.1890	0.7468	0.0953	0.052*
H1B	0.265 (3)	0.5983 (18)	0.3404 (11)	0.058 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0648 (3)	0.0559 (3)	0.0337 (2)	−0.0029 (2)	−0.00505 (19)	0.00701 (18)
O2	0.0590 (8)	0.0296 (6)	0.0320 (6)	0.0048 (5)	0.0087 (5)	0.0028 (4)
C3	0.0418 (9)	0.0338 (8)	0.0274 (7)	0.0000 (6)	0.0024 (6)	0.0008 (6)
N1	0.0569 (9)	0.0271 (7)	0.0443 (8)	0.0067 (6)	0.0023 (7)	0.0004 (6)
C4	0.0302 (7)	0.0293 (7)	0.0307 (8)	−0.0027 (6)	0.0013 (6)	−0.0031 (6)
C6	0.0350 (8)	0.0308 (7)	0.0331 (8)	−0.0013 (6)	0.0009 (6)	−0.0020 (6)
O1	0.1032 (12)	0.0388 (7)	0.0285 (6)	0.0165 (7)	0.0126 (7)	0.0045 (5)
C5	0.0353 (8)	0.0309 (8)	0.0387 (8)	−0.0004 (6)	0.0011 (6)	−0.0030 (6)
C2	0.0370 (8)	0.0302 (8)	0.0295 (8)	0.0001 (6)	0.0013 (6)	0.0011 (6)
C9	0.0369 (8)	0.0419 (9)	0.0306 (8)	−0.0046 (7)	−0.0015 (6)	−0.0005 (7)
C7	0.0498 (10)	0.0358 (9)	0.0432 (9)	0.0022 (7)	0.0038 (8)	−0.0122 (7)
C1	0.0526 (10)	0.0346 (8)	0.0338 (8)	0.0037 (7)	0.0013 (7)	0.0027 (6)
C8	0.0493 (10)	0.0496 (10)	0.0314 (8)	−0.0036 (8)	0.0023 (7)	−0.0119 (7)

Geometric parameters (Å, º) top

Cl1—C9	1.7681 (17)	C6—C9	1.389 (2)
O2—C3	1.256 (2)	C6—H6	0.9300
C3—O1	1.3181 (19)	O1—H1	0.8200
C3—C2	1.457 (2)	C5—C7	1.400 (2)
N1—C1	1.356 (2)	C2—C1	1.387 (2)
N1—C5	1.395 (2)	C9—C8	1.411 (2)
N1—H1B	0.86 (2)	C7—C8	1.387 (3)
C4—C6	1.410 (2)	C7—H7	0.9300
C4—C5	1.422 (2)	C1—H1A	0.9300
C4—C2	1.451 (2)	C8—H8	0.9300

O2—C3—O1	122.39 (14)	C1—C2—C4	106.86 (13)
O2—C3—C2	122.71 (14)	C1—C2—C3	124.96 (14)
O1—C3—C2	114.89 (14)	C4—C2—C3	128.16 (14)
C1—N1—C5	109.45 (14)	C6—C9—C8	122.94 (15)
C1—N1—H1B	125.1 (14)	C6—C9—Cl1	119.25 (13)
C5—N1—H1B	125.2 (14)	C8—C9—Cl1	117.81 (12)
C6—C4—C5	119.26 (14)	C8—C7—C5	117.67 (15)
C6—C4—C2	134.69 (14)	C8—C7—H7	121.2
C5—C4—C2	106.02 (13)	C5—C7—H7	121.2
C9—C6—C4	117.48 (14)	N1—C1—C2	109.99 (15)
C9—C6—H6	121.3	N1—C1—H1A	125.0
C4—C6—H6	121.3	C2—C1—H1A	125.0
C3—O1—H1	109.5	C7—C8—C9	120.19 (15)
N1—C5—C7	129.87 (15)	C7—C8—H8	119.9
N1—C5—C4	107.67 (14)	C9—C8—H8	119.9
C7—C5—C4	122.45 (15)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2ⁱ	0.82	1.86	2.6558 (17)	164
N1—H1B···O2ⁱⁱ	0.86 (2)	2.26 (2)	3.005 (2)	144.3 (19)

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

Experimental details

Crystal data
Chemical formula	C₉H₆ClNO₂
M_r	195.60
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	7.2934 (15), 13.065 (3), 17.902 (4)
V (Å³)	1705.9 (6)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.41
Crystal size (mm)	0.30 × 0.20 × 0.15

Data collection
Diffractometer	Rigaku SCXmini CCD diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2005)
T_min, T_max	0.907, 0.941
No. of measured, independent and observed [I > 2σ(I)] reflections	16050, 1919, 1590
R_int	0.050
(sin θ/λ)_max (Å⁻¹)	0.647

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.104, 1.04
No. of reflections	1919
No. of parameters	123
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.17, −0.23

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg & Putz, 2005).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2ⁱ	0.82	1.86	2.6558 (17)	164
N1—H1B···O2ⁱⁱ	0.86 (2)	2.26 (2)	3.005 (2)	144.3 (19)

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

Acknowledgements

We thank Southeast University for support.

References

Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Kunzer, A. R. & Wendt, M. D. (2011). Tetrahedron, 52, 1815–1818. CrossRef CAS Google Scholar
Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Woodward, A. W. & Bartel, B. (2005). Ann. Bot. (London), 95, 707–735. CrossRef CAS Google Scholar