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

Lu, W.-J.; Zou, Z.-H.; Luo, Y.-H.

doi:10.1107/S1600536811053426

organic compounds

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Volume 68| Part 1| January 2012| Page o187

doi:10.1107/S1600536811053426

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

Wen-Jun Lu,^a Zhi-Hong Zou ^a ^* and Yang-Hui Luo ^a

^aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
^*Correspondence e-mail: seuzzh@sina.com

(Received 2 December 2011; accepted 12 December 2011; online 21 December 2011)

In the title compound, C₉H₆FNO₂, the carboxyl group is twisted slightly away from the indole-ring plane [dihedral angle = 7.39 (10)°]. In the crystal, carboxyl inversion dimers linked by pairs of O—H⋯O hydrogen bonds generate R₂²(8) loops and N—H⋯O hydrogen bonds connect the dimers into (10 $[\overline{1}]$ ) sheets.

Related literature

For background to indoles as pharmaceuticals, see: Lang et al. (2011 ).

Experimental

Crystal data

C₉H₆FNO₂
M_r = 179.15
Monoclinic, P 2₁ /n
a = 4.4176 (9) Å
b = 11.073 (2) Å
c = 16.014 (3) Å
β = 96.63 (3)°
V = 778.1 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.13 mm⁻¹
T = 293 K
0.30 × 0.20 × 0.10 mm

Data collection

Rigaku SCXmini CCD diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ) T_min = 0.982, T_max = 0.993
7874 measured reflections
1788 independent reflections
1153 reflections with I > 2σ(I)
R_int = 0.068

Refinement

R[F² > 2σ(F²)] = 0.054
wR(F²) = 0.137
S = 1.02
1788 reflections
123 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.18 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
O1—H1⋯O2ⁱ	0.82	1.86	2.669 (2)	171
N1—H1B⋯O2ⁱⁱ	0.89 (3)	2.18 (3)	3.026 (2)	159 (2)
Symmetry codes: (i) -x+2, -y+1, -z+2; (ii) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

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/S1600536811053426/hb6548sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811053426/hb6548Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811053426/hb6548Isup3.cml

checkCIF report

Related literature top

For background to indoles as pharmaceuticals, see: Lang et al. (2011).

Experimental top

A commercial sample of the title compound was obtained. Colourlss prisms were obtained by slow evaporation of a methanol solution over a period of seven days.

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

Crystal data top

C₉H₆FNO₂	F(000) = 368
M_r = 179.15	D_x = 1.529 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 1954 reflections
a = 4.4176 (9) Å	θ = 3.2–25.0°
b = 11.073 (2) Å	µ = 0.13 mm⁻¹
c = 16.014 (3) Å	T = 293 K
β = 96.63 (3)°	Prism, colourless
V = 778.1 (3) Å³	0.30 × 0.20 × 0.10 mm
Z = 4

Data collection top

Rigaku SCXmini CCD diffractometer	1788 independent reflections
Radiation source: fine-focus sealed tube	1153 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.068
Detector resolution: 13.6612 pixels mm^-1	θ_max = 27.5°, θ_min = 3.2°
CCD profile–fitting scans	h = −5→5
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −14→14
T_min = 0.982, T_max = 0.993	l = −20→20
7874 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)] = 0.054	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.137	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ²(F_o²) + (0.0575P)² + 0.142P] where P = (F_o² + 2F_c²)/3
1788 reflections	(Δ/σ)_max < 0.001
123 parameters	Δρ_max = 0.18 e Å⁻³
0 restraints	Δρ_min = −0.26 e Å⁻³

Crystal data top

C₉H₆FNO₂	V = 778.1 (3) Å³
M_r = 179.15	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 4.4176 (9) Å	µ = 0.13 mm⁻¹
b = 11.073 (2) Å	T = 293 K
c = 16.014 (3) Å	0.30 × 0.20 × 0.10 mm
β = 96.63 (3)°

Data collection top

Rigaku SCXmini CCD diffractometer	1788 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	1153 reflections with I > 2σ(I)
T_min = 0.982, T_max = 0.993	R_int = 0.068
7874 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.054	0 restraints
wR(F²) = 0.137	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	Δρ_max = 0.18 e Å⁻³
1788 reflections	Δρ_min = −0.26 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
O2	1.0621 (4)	0.51786 (13)	0.89866 (9)	0.0431 (4)
F1	1.4484 (3)	0.55381 (14)	0.59940 (9)	0.0624 (5)
N1	0.7010 (4)	0.21726 (17)	0.71693 (12)	0.0388 (5)
C4	1.0013 (4)	0.38262 (17)	0.73456 (12)	0.0295 (5)
C7	0.9558 (5)	0.2922 (2)	0.59302 (14)	0.0410 (6)
H7	0.8767	0.2328	0.5556	0.049*
O1	0.8085 (4)	0.36747 (14)	0.95496 (9)	0.0544 (5)
H1	0.8432	0.4097	0.9970	0.082*
C5	0.8845 (5)	0.29428 (17)	0.67573 (14)	0.0322 (5)
C3	0.9254 (5)	0.41935 (19)	0.89110 (13)	0.0341 (5)
C6	1.1989 (4)	0.47175 (18)	0.70871 (13)	0.0333 (5)
H6	1.2837	0.5308	0.7456	0.040*
C2	0.8776 (5)	0.35426 (18)	0.81256 (13)	0.0320 (5)
C1	0.6979 (5)	0.25319 (19)	0.79748 (14)	0.0367 (5)
H1A	0.5906	0.2154	0.8368	0.044*
C9	1.2604 (5)	0.4674 (2)	0.62638 (14)	0.0387 (5)
C8	1.1466 (5)	0.3805 (2)	0.56824 (14)	0.0441 (6)
H8	1.1984	0.3819	0.5136	0.053*
H1B	0.599 (5)	0.154 (2)	0.6945 (16)	0.052 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O2	0.0677 (11)	0.0344 (9)	0.0267 (8)	−0.0101 (8)	0.0033 (8)	−0.0006 (6)
F1	0.0725 (10)	0.0703 (10)	0.0478 (9)	−0.0232 (8)	0.0220 (8)	0.0004 (7)
N1	0.0464 (11)	0.0336 (10)	0.0360 (11)	−0.0070 (9)	0.0027 (9)	−0.0069 (8)
C4	0.0299 (10)	0.0297 (11)	0.0280 (11)	0.0059 (8)	−0.0011 (9)	−0.0021 (9)
C7	0.0449 (13)	0.0454 (14)	0.0320 (13)	0.0019 (11)	0.0012 (10)	−0.0135 (10)
O1	0.0903 (14)	0.0477 (10)	0.0262 (9)	−0.0222 (9)	0.0116 (9)	−0.0019 (7)
C5	0.0328 (11)	0.0304 (11)	0.0326 (12)	0.0038 (9)	0.0005 (9)	−0.0034 (9)
C3	0.0436 (12)	0.0324 (11)	0.0253 (11)	0.0029 (10)	0.0004 (9)	0.0039 (9)
C6	0.0339 (11)	0.0332 (11)	0.0318 (12)	0.0017 (9)	−0.0002 (9)	−0.0039 (9)
C2	0.0383 (11)	0.0298 (11)	0.0270 (11)	0.0016 (9)	0.0006 (9)	−0.0002 (9)
C1	0.0449 (12)	0.0331 (11)	0.0322 (12)	0.0008 (10)	0.0046 (10)	0.0006 (9)
C9	0.0378 (12)	0.0425 (13)	0.0372 (13)	−0.0015 (10)	0.0099 (10)	0.0018 (10)
C8	0.0489 (14)	0.0565 (15)	0.0281 (12)	0.0038 (12)	0.0092 (11)	−0.0048 (11)

Geometric parameters (Å, º) top

O2—C3	1.246 (2)	C7—H7	0.9300
F1—C9	1.369 (2)	O1—C3	1.328 (2)
N1—C1	1.351 (3)	O1—H1	0.8200
N1—C5	1.394 (3)	C3—C2	1.444 (3)
N1—H1B	0.89 (3)	C6—C9	1.378 (3)
C4—C5	1.414 (3)	C6—H6	0.9300
C4—C6	1.411 (3)	C2—C1	1.377 (3)
C4—C2	1.454 (3)	C1—H1A	0.9300
C7—C8	1.378 (3)	C9—C8	1.392 (3)
C7—C5	1.397 (3)	C8—H8	0.9300

C1—N1—C5	110.02 (18)	C9—C6—C4	116.95 (19)
C1—N1—H1B	123.9 (16)	C9—C6—H6	121.5
C5—N1—H1B	126.1 (16)	C4—C6—H6	121.5
C5—C4—C6	118.62 (19)	C1—C2—C3	125.57 (19)
C5—C4—C2	106.17 (18)	C1—C2—C4	106.92 (18)
C6—C4—C2	135.20 (19)	C3—C2—C4	127.49 (19)
C8—C7—C5	118.3 (2)	N1—C1—C2	109.7 (2)
C8—C7—H7	120.9	N1—C1—H1A	125.1
C5—C7—H7	120.9	C2—C1—H1A	125.1
C3—O1—H1	109.5	F1—C9—C6	118.10 (19)
C7—C5—N1	130.24 (19)	F1—C9—C8	117.23 (19)
C7—C5—C4	122.58 (19)	C6—C9—C8	124.7 (2)
N1—C5—C4	107.18 (18)	C7—C8—C9	118.9 (2)
O2—C3—O1	122.08 (19)	C7—C8—H8	120.6
O2—C3—C2	122.83 (19)	C9—C8—H8	120.6
O1—C3—C2	115.09 (19)

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	2.669 (2)	171
N1—H1B···O2ⁱⁱ	0.89 (3)	2.18 (3)	3.026 (2)	159 (2)

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

Experimental details

Crystal data
Chemical formula	C₉H₆FNO₂
M_r	179.15
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	4.4176 (9), 11.073 (2), 16.014 (3)
β (°)	96.63 (3)
V (Å³)	778.1 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.13
Crystal size (mm)	0.30 × 0.20 × 0.10

Data collection
Diffractometer	Rigaku SCXmini CCD diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2005)
T_min, T_max	0.982, 0.993
No. of measured, independent and observed [I > 2σ(I)] reflections	7874, 1788, 1153
R_int	0.068
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.054, 0.137, 1.02
No. of reflections	1788
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)	0.18, −0.26

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	2.669 (2)	171
N1—H1B···O2ⁱⁱ	0.89 (3)	2.18 (3)	3.026 (2)	159 (2)

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

References

Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Lang, L., Wu, J.-L., Shi, L.-J., Xia, C.-G. & Li, F.-W. (2011). Chem. Commun. 47, 12553–12555. Web of Science CSD 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

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 68| Part 1| January 2012| Page o187

doi:10.1107/S1600536811053426

Open

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