6-Fluoro-1H-indole-3-carb­oxy­lic acid

Abstract

In the title compound, C₉H₆FNO₂, all the non-H atoms are approximately coplanar, the carb­oxy O atoms deviating by 0.0809 and −0.1279 Å from the indole plane. In the crystal, O—H⋯O hydrogen bonds link the mol­ecules into dimers which are linked via N—H⋯O hydrogen bonds and π–π inter­actions [centroid–centroid distance = 3.680 (2) Å]

Related literature  

For the origin of the material studied, see: Kunzer & Wendt (2011 ▶). For a related structure, see: Luo et al. (2011 ▶).

Experimental  

Crystal data  

• C₉H₆FNO₂

• M _r = 179.15

• Monoclinic,

• a = 7.0054 (14) Å

• b = 11.699 (2) Å

• c = 9.2947 (19) Å

• β = 104.15 (3)°

• V = 738.7 (3) ų

• Z = 4

• Mo Kα radiation

• μ = 0.13 mm⁻¹

• T = 293 K

• 0.3 × 0.3 × 0.2 mm

Data collection  

• Rigaku SCXmini diffractometer

• Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ▶) T _min = 0.961, T _max = 0.974

• 7541 measured reflections

• 1693 independent reflections

• 1418 reflections with I > 2σ(I)

• R _int = 0.033

Refinement  

• R[F ² > 2σ(F ²)] = 0.043

• wR(F ²) = 0.115

• S = 1.08

• 1693 reflections

• 123 parameters

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.21 e Å⁻³

• Δρ_min = −0.21 e Å⁻³

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.

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536812016935/rn2099Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1i	0.86 (2)	2.159 (19)	2.8925 (17)	142.8 (17)
O2—H2⋯O1ii	0.82	1.78	2.5954 (17)	170

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

Comment

Indole-3-carboxylic acid and its derivatives are important chemical materials, because they are excellent auxins for plants ( Kunzer & Wendt, 2011) and drug intermediates for many pharmaceutical products (Luo et al., 2011).

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 0.0809 and -0.1279 Å from the indole plane..

In the crystal structure of the title compound, intermolecular O—H···O hydrogen bonds linked the molecules into dimers and the dimers are linked via intermolecular N—H···O hydrogen bonds and π–π interactions [centroid–centroid distance = 3.680 (2) Å] (Fig. 2).

Experimental

The title compound was purchased commercially from ChemFuture PharmaTech, Ltd (Jiangsu) and used as received without further purification. Crystals of it were obtained by slow evaporation of a methanol solution.

Refinement

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 U_iso(H) = 1.2U_eq(CH), U_iso(H) = 1.35U_eq(N) and U_iso(H) = 1.5U_eq(O).

Figures

Fig. 1.

The molecular structure of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii.

Fig. 2.

A packing view down the a axis showing the three dimensional network. Intermolecular hydrogen bonds are shown as dashed lines.

Crystal data

C9H6FNO2	F(000) = 368
Mr = 179.15	Dx = 1.611 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1693 reflections
a = 7.0054 (14) Å	θ = 3.5–27.5°
b = 11.699 (2) Å	µ = 0.13 mm−1
c = 9.2947 (19) Å	T = 293 K
β = 104.15 (3)°	Block, brown
V = 738.7 (3) Å3	0.3 × 0.3 × 0.2 mm
Z = 4

Data collection

Rigaku SCXmini diffractometer	1693 independent reflections
Radiation source: fine-focus sealed tube	1418 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.033
Detector resolution: 13.6612 pixels mm-1	θmax = 27.5°, θmin = 3.5°
CCD_Profile_fitting scans	h = −9→9
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −15→15
Tmin = 0.961, Tmax = 0.974	l = −12→12
7541 measured reflections

Refinement

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)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	w = 1/[σ2(Fo2) + (0.0591P)2 + 0.1428P] where P = (Fo2 + 2Fc2)/3
1693 reflections	(Δ/σ)max < 0.001
123 parameters	Δρmax = 0.21 e Å−3
0 restraints	Δρmin = −0.21 e Å−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
O2	0.60596 (19)	−0.07115 (8)	0.16978 (12)	0.0489 (3)
H2	0.5681	−0.0785	0.0795	0.073*
O1	0.5438 (2)	0.11097 (9)	0.10977 (12)	0.0514 (3)
F1	0.96927 (19)	−0.13190 (10)	0.89741 (12)	0.0727 (4)
N1	0.70843 (19)	0.17044 (11)	0.55849 (14)	0.0394 (3)
C3	0.5997 (2)	0.03550 (12)	0.20426 (16)	0.0377 (3)
C2	0.6606 (2)	0.06339 (11)	0.35810 (16)	0.0343 (3)
C4	0.74187 (19)	−0.00793 (11)	0.48256 (15)	0.0330 (3)
C9	0.7914 (2)	−0.12279 (12)	0.50269 (18)	0.0397 (4)
H9	0.7736	−0.1718	0.4217	0.048*
C6	0.8487 (2)	0.02441 (13)	0.74928 (18)	0.0432 (4)
H6	0.8692	0.0722	0.8316	0.052*
C8	0.8663 (2)	−0.16262 (13)	0.6426 (2)	0.0465 (4)
H8	0.8991	−0.2394	0.6583	0.056*
C5	0.7710 (2)	0.06329 (12)	0.60672 (16)	0.0351 (3)
C1	0.6428 (2)	0.17026 (12)	0.41164 (16)	0.0382 (3)
H1A	0.5925	0.2335	0.3542	0.046*
C7	0.8931 (2)	−0.08866 (15)	0.76066 (19)	0.0475 (4)
H1	0.702 (3)	0.2305 (17)	0.611 (2)	0.053 (5)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O2	0.0787 (8)	0.0289 (6)	0.0382 (6)	−0.0018 (5)	0.0127 (6)	−0.0044 (4)
O1	0.0856 (9)	0.0304 (6)	0.0364 (6)	−0.0084 (5)	0.0116 (6)	0.0019 (4)
F1	0.0872 (8)	0.0638 (8)	0.0524 (7)	0.0055 (6)	−0.0111 (6)	0.0161 (5)
N1	0.0514 (7)	0.0270 (6)	0.0399 (7)	−0.0006 (5)	0.0114 (6)	−0.0068 (5)
C3	0.0479 (8)	0.0291 (7)	0.0388 (8)	−0.0050 (6)	0.0156 (6)	−0.0007 (5)
C2	0.0397 (7)	0.0281 (7)	0.0370 (8)	−0.0039 (5)	0.0128 (6)	−0.0025 (5)
C4	0.0321 (6)	0.0291 (7)	0.0393 (8)	−0.0030 (5)	0.0115 (6)	−0.0025 (5)
C9	0.0417 (8)	0.0300 (7)	0.0475 (9)	0.0004 (6)	0.0114 (7)	−0.0042 (6)
C6	0.0450 (8)	0.0430 (8)	0.0388 (8)	−0.0053 (7)	0.0046 (6)	−0.0044 (6)
C8	0.0456 (9)	0.0329 (8)	0.0585 (10)	0.0055 (6)	0.0079 (7)	0.0050 (7)
C5	0.0342 (7)	0.0306 (7)	0.0411 (8)	−0.0034 (5)	0.0101 (6)	−0.0038 (6)
C1	0.0477 (8)	0.0287 (7)	0.0392 (8)	−0.0010 (6)	0.0124 (6)	0.0001 (6)
C7	0.0442 (8)	0.0477 (9)	0.0447 (9)	0.0006 (7)	−0.0005 (7)	0.0089 (7)

Geometric parameters (Å, º)

O2—C3	1.2916 (17)	C4—C9	1.389 (2)
O2—H2	0.8200	C4—C5	1.3974 (19)
O1—C3	1.2394 (18)	C9—C8	1.360 (2)
F1—C7	1.351 (2)	C9—H9	0.9300
N1—C1	1.330 (2)	C6—C7	1.357 (2)
N1—C5	1.3668 (19)	C6—C5	1.381 (2)
N1—H1	0.86 (2)	C6—H6	0.9300
C3—C2	1.426 (2)	C8—C7	1.373 (3)
C2—C1	1.363 (2)	C8—H8	0.9300
C2—C4	1.427 (2)	C1—H1A	0.9300
C3—O2—H2	109.5	C7—C6—C5	115.15 (14)
C1—N1—C5	109.75 (12)	C7—C6—H6	122.4
C1—N1—H1	121.7 (13)	C5—C6—H6	122.4
C5—N1—H1	128.4 (13)	C9—C8—C7	119.56 (15)
O1—C3—O2	122.44 (14)	C9—C8—H8	120.2
O1—C3—C2	120.84 (13)	C7—C8—H8	120.2
O2—C3—C2	116.72 (13)	N1—C5—C6	129.53 (14)
C1—C2—C3	122.98 (14)	N1—C5—C4	107.80 (13)
C1—C2—C4	107.12 (12)	C6—C5—C4	122.67 (14)
C3—C2—C4	129.88 (13)	N1—C1—C2	109.68 (13)
C9—C4—C5	118.97 (13)	N1—C1—H1A	125.2
C9—C4—C2	135.39 (13)	C2—C1—H1A	125.2
C5—C4—C2	105.64 (12)	F1—C7—C6	117.94 (16)
C8—C9—C4	119.04 (14)	F1—C7—C8	117.45 (15)
C8—C9—H9	120.5	C6—C7—C8	124.61 (15)
C4—C9—H9	120.5

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1i	0.86 (2)	2.159 (19)	2.8925 (17)	142.8 (17)
O2—H2···O1ii	0.82	1.78	2.5954 (17)	170

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