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

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) sheets.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.054
• wR factor = 0.137
• Data-to-parameter ratio = 14.5

checkCIF/PLATON results

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Alert level C
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          2
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L=  0.600          4

Alert level G
PLAT005_ALERT_5_G No _iucr_refine_instructions_details in CIF ....          ?
PLAT128_ALERT_4_G Alternate Setting of Space-group P21/c   .......      P21/n
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported   _diffrn_ambient_temperature        293 K

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   2 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   4 ALERT level G = General information/check it is not something unexpected

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check


checkCIF publication errors

Alert level G
PUBL013_ALERT_1_G The _publ_section_comment (discussion of study) is
            missing. This is required for a full paper submission (but is
            optional for an electronic paper).

   0 ALERT level A = Data missing that is essential or data in wrong format
   1 ALERT level G = General alerts. Data that may be required is missing

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Related literature

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

S1. Experimental

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.

S2. Refinement

All H atoms attached to C atoms and O atoms were fixed geometrically and treated as riding with C—H = 0.93 Å (CH), N—H = 0.86 Å and O—H = 0.86 Å with U_iso(H) = 1.2U_eq(CH), U_iso(H) = 1.3U_eq(N) and U_iso(H) = 1.5U_eq(O).

Computing details

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

	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

Crystal data

C9H6FNO2	F(000) = 368
Mr = 179.15	Dx = 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) Å^3	0.30 × 0.20 × 0.10 mm
Z = 4

Data collection

Rigaku SCXmini CCD diffractometer	1788 independent reflections
Radiation source: fine-focus sealed tube	1153 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.068
Detector resolution: 13.6612 pixels mm^-1	θmax = 27.5°, θmin = 3.2°
CCD profile–fitting scans	h = −5→5
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −14→14
Tmin = 0.982, Tmax = 0.993	l = −20→20
7874 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.054	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.137	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ^2(Fo^2) + (0.0575P)^2 + 0.142P] where P = (Fo^2 + 2Fc^2)/3
1788 reflections	(Δ/σ)max < 0.001
123 parameters	Δρmax = 0.18 e Å^−3
0 restraints	Δρmin = −0.26 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	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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2^i	0.82	1.86	2.669 (2)	171
N1—H1B···O2^ii	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.