supplementary materials


hb6559 scheme

Acta Cryst. (2012). E68, o145    [ doi:10.1107/S1600536811053384 ]

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

X.-L. Han and Y.-H. Luo

Abstract top

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 [pi]-[pi] stacking interactions [centroid-centroid distance = 3.7185 (12) A °] are also observed.

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 ππ 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.

Refinement top

All H atoms attached to C, N and O atoms were fixed geometrically and treated as riding with C—H = 0.93 Å (CH), O—H = 0.82 Å and N—H = 0.86 Å with Uiso(H) = 1.2Ueq(CH), Uiso(H) = 1.35Ueq(N) and Uiso(H) = 1.5Ueq(O).

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
[Figure 1] Fig. 1. The molecular structure of the title compound with displacement ellipsoids drawn at the 30% probability level.
[Figure 2] 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
C9H6ClNO2F(000) = 800
Mr = 195.60Dx = 1.523 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 1919 reflections
a = 7.2934 (15) Åθ = 3.1–27.4°
b = 13.065 (3) ŵ = 0.41 mm1
c = 17.902 (4) ÅT = 293 K
V = 1705.9 (6) Å3Block, colourless
Z = 80.30 × 0.20 × 0.15 mm
Data collection top
Rigaku SCXmini CCD
diffractometer
1919 independent reflections
Radiation source: fine-focus sealed tube1590 reflections with I > 2σ(I)
graphiteRint = 0.050
Detector resolution: 13.6612 pixels mm-1θmax = 27.4°, θmin = 3.1°
CCD_Profile_fitting scansh = 99
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
k = 1616
Tmin = 0.907, Tmax = 0.941l = 2323
16050 measured reflections
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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.104H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.052P)2 + 0.5573P]
where P = (Fo2 + 2Fc2)/3
1919 reflections(Δ/σ)max < 0.001
123 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = 0.23 e Å3
Crystal data top
C9H6ClNO2V = 1705.9 (6) Å3
Mr = 195.60Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 7.2934 (15) ŵ = 0.41 mm1
b = 13.065 (3) ÅT = 293 K
c = 17.902 (4) Å0.30 × 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)
Tmin = 0.907, Tmax = 0.941Rint = 0.050
16050 measured reflectionsθmax = 27.4°
Refinement top
R[F2 > 2σ(F2)] = 0.037H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.104Δρmax = 0.17 e Å3
S = 1.04Δρmin = 0.23 e Å3
1919 reflectionsAbsolute structure: ?
123 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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
xyzUiso*/Ueq
Cl10.07292 (7)0.95139 (4)0.09595 (2)0.05145 (18)
O20.05698 (16)0.98847 (9)0.40623 (6)0.0402 (3)
C30.0835 (2)0.89840 (12)0.42814 (9)0.0343 (3)
N10.2225 (2)0.65957 (11)0.33911 (8)0.0428 (4)
C40.1415 (2)0.81729 (11)0.29670 (8)0.0301 (3)
C60.1018 (2)0.89102 (11)0.24148 (8)0.0329 (3)
H60.06360.95660.25420.040*
O10.0656 (2)0.87130 (10)0.49869 (6)0.0568 (4)
H10.04220.92200.52400.085*
C50.1970 (2)0.71749 (12)0.27449 (9)0.0350 (4)
C20.1353 (2)0.81582 (11)0.37768 (9)0.0322 (3)
C90.1218 (2)0.86192 (13)0.16732 (9)0.0365 (4)
C70.2150 (2)0.68926 (13)0.19938 (10)0.0429 (4)
H70.25080.62350.18600.052*
C10.1853 (2)0.71802 (13)0.39985 (9)0.0403 (4)
H1A0.19240.69580.44910.048*
C80.1775 (2)0.76284 (14)0.14570 (9)0.0434 (4)
H80.18900.74680.09530.052*
H1B0.265 (3)0.5983 (18)0.3404 (11)0.058 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0648 (3)0.0559 (3)0.0337 (2)0.0029 (2)0.00505 (19)0.00701 (18)
O20.0590 (8)0.0296 (6)0.0320 (6)0.0048 (5)0.0087 (5)0.0028 (4)
C30.0418 (9)0.0338 (8)0.0274 (7)0.0000 (6)0.0024 (6)0.0008 (6)
N10.0569 (9)0.0271 (7)0.0443 (8)0.0067 (6)0.0023 (7)0.0004 (6)
C40.0302 (7)0.0293 (7)0.0307 (8)0.0027 (6)0.0013 (6)0.0031 (6)
C60.0350 (8)0.0308 (7)0.0331 (8)0.0013 (6)0.0009 (6)0.0020 (6)
O10.1032 (12)0.0388 (7)0.0285 (6)0.0165 (7)0.0126 (7)0.0045 (5)
C50.0353 (8)0.0309 (8)0.0387 (8)0.0004 (6)0.0011 (6)0.0030 (6)
C20.0370 (8)0.0302 (8)0.0295 (8)0.0001 (6)0.0013 (6)0.0011 (6)
C90.0369 (8)0.0419 (9)0.0306 (8)0.0046 (7)0.0015 (6)0.0005 (7)
C70.0498 (10)0.0358 (9)0.0432 (9)0.0022 (7)0.0038 (8)0.0122 (7)
C10.0526 (10)0.0346 (8)0.0338 (8)0.0037 (7)0.0013 (7)0.0027 (6)
C80.0493 (10)0.0496 (10)0.0314 (8)0.0036 (8)0.0023 (7)0.0119 (7)
Geometric parameters (Å, °) top
Cl1—C91.7681 (17)C6—C91.389 (2)
O2—C31.256 (2)C6—H60.9300
C3—O11.3181 (19)O1—H10.8200
C3—C21.457 (2)C5—C71.400 (2)
N1—C11.356 (2)C2—C11.387 (2)
N1—C51.395 (2)C9—C81.411 (2)
N1—H1B0.86 (2)C7—C81.387 (3)
C4—C61.410 (2)C7—H70.9300
C4—C51.422 (2)C1—H1A0.9300
C4—C21.451 (2)C8—H80.9300
O2—C3—O1122.39 (14)C1—C2—C4106.86 (13)
O2—C3—C2122.71 (14)C1—C2—C3124.96 (14)
O1—C3—C2114.89 (14)C4—C2—C3128.16 (14)
C1—N1—C5109.45 (14)C6—C9—C8122.94 (15)
C1—N1—H1B125.1 (14)C6—C9—Cl1119.25 (13)
C5—N1—H1B125.2 (14)C8—C9—Cl1117.81 (12)
C6—C4—C5119.26 (14)C8—C7—C5117.67 (15)
C6—C4—C2134.69 (14)C8—C7—H7121.2
C5—C4—C2106.02 (13)C5—C7—H7121.2
C9—C6—C4117.48 (14)N1—C1—C2109.99 (15)
C9—C6—H6121.3N1—C1—H1A125.0
C4—C6—H6121.3C2—C1—H1A125.0
C3—O1—H1109.5C7—C8—C9120.19 (15)
N1—C5—C7129.87 (15)C7—C8—H8119.9
N1—C5—C4107.67 (14)C9—C8—H8119.9
C7—C5—C4122.45 (15)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O2i0.821.862.6558 (17)164
N1—H1B···O2ii0.86 (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.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
O1—H1···O2i0.821.862.6558 (17)164
N1—H1B···O2ii0.86 (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 top

We thank Southeast University for support.

references
References top

Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.

Kunzer, A. R. & Wendt, M. D. (2011). Tetrahedron, 52, 1815–1818.

Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Woodward, A. W. & Bartel, B. (2005). Ann. Bot. (London), 95, 707–735.