organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

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[Lang, L., Wu, J.-L., Shi, L.-J., Xia, C.-G. & Li, F.-W. (2011). Chem. Commun. 47, 12553-12555.]).

[Scheme 1]

Experimental

Crystal data
  • C9H6FNO2

  • Mr = 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[Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.982, Tmax = 0.993

  • 7874 measured reflections

  • 1788 independent reflections

  • 1153 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.26 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg & Putz, 2005[Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: SHELXL97.

Supporting information


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.

Refinement top

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 Uiso(H) = 1.2Ueq(CH), Uiso(H) = 1.3Ueq(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-Fluoro-1H-indole-3-carboxylic acid top
Crystal data top
C9H6FNO2F(000) = 368
Mr = 179.15Dx = 1.529 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1954 reflections
a = 4.4176 (9) Åθ = 3.2–25.0°
b = 11.073 (2) ŵ = 0.13 mm1
c = 16.014 (3) ÅT = 293 K
β = 96.63 (3)°Prism, colourless
V = 778.1 (3) Å30.30 × 0.20 × 0.10 mm
Z = 4
Data collection top
Rigaku SCXmini CCD
diffractometer
1788 independent reflections
Radiation source: fine-focus sealed tube1153 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.068
Detector resolution: 13.6612 pixels mm-1θmax = 27.5°, θmin = 3.2°
CCD profile–fitting scansh = 55
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
k = 1414
Tmin = 0.982, Tmax = 0.993l = 2020
7874 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)] = 0.054Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.137H atoms treated by a mixture of independent and constrained refinement
S = 1.02 w = 1/[σ2(Fo2) + (0.0575P)2 + 0.142P]
where P = (Fo2 + 2Fc2)/3
1788 reflections(Δ/σ)max < 0.001
123 parametersΔρmax = 0.18 e Å3
0 restraintsΔρmin = 0.26 e Å3
Crystal data top
C9H6FNO2V = 778.1 (3) Å3
Mr = 179.15Z = 4
Monoclinic, P21/nMo Kα radiation
a = 4.4176 (9) ŵ = 0.13 mm1
b = 11.073 (2) ÅT = 293 K
c = 16.014 (3) Å0.30 × 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)
Tmin = 0.982, Tmax = 0.993Rint = 0.068
7874 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0540 restraints
wR(F2) = 0.137H atoms treated by a mixture of independent and constrained refinement
S = 1.02Δρmax = 0.18 e Å3
1788 reflectionsΔρmin = 0.26 e Å3
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
xyzUiso*/Ueq
O21.0621 (4)0.51786 (13)0.89866 (9)0.0431 (4)
F11.4484 (3)0.55381 (14)0.59940 (9)0.0624 (5)
N10.7010 (4)0.21726 (17)0.71693 (12)0.0388 (5)
C41.0013 (4)0.38262 (17)0.73456 (12)0.0295 (5)
C70.9558 (5)0.2922 (2)0.59302 (14)0.0410 (6)
H70.87670.23280.55560.049*
O10.8085 (4)0.36747 (14)0.95496 (9)0.0544 (5)
H10.84320.40970.99700.082*
C50.8845 (5)0.29428 (17)0.67573 (14)0.0322 (5)
C30.9254 (5)0.41935 (19)0.89110 (13)0.0341 (5)
C61.1989 (4)0.47175 (18)0.70871 (13)0.0333 (5)
H61.28370.53080.74560.040*
C20.8776 (5)0.35426 (18)0.81256 (13)0.0320 (5)
C10.6979 (5)0.25319 (19)0.79748 (14)0.0367 (5)
H1A0.59060.21540.83680.044*
C91.2604 (5)0.4674 (2)0.62638 (14)0.0387 (5)
C81.1466 (5)0.3805 (2)0.56824 (14)0.0441 (6)
H81.19840.38190.51360.053*
H1B0.599 (5)0.154 (2)0.6945 (16)0.052 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O20.0677 (11)0.0344 (9)0.0267 (8)0.0101 (8)0.0033 (8)0.0006 (6)
F10.0725 (10)0.0703 (10)0.0478 (9)0.0232 (8)0.0220 (8)0.0004 (7)
N10.0464 (11)0.0336 (10)0.0360 (11)0.0070 (9)0.0027 (9)0.0069 (8)
C40.0299 (10)0.0297 (11)0.0280 (11)0.0059 (8)0.0011 (9)0.0021 (9)
C70.0449 (13)0.0454 (14)0.0320 (13)0.0019 (11)0.0012 (10)0.0135 (10)
O10.0903 (14)0.0477 (10)0.0262 (9)0.0222 (9)0.0116 (9)0.0019 (7)
C50.0328 (11)0.0304 (11)0.0326 (12)0.0038 (9)0.0005 (9)0.0034 (9)
C30.0436 (12)0.0324 (11)0.0253 (11)0.0029 (10)0.0004 (9)0.0039 (9)
C60.0339 (11)0.0332 (11)0.0318 (12)0.0017 (9)0.0002 (9)0.0039 (9)
C20.0383 (11)0.0298 (11)0.0270 (11)0.0016 (9)0.0006 (9)0.0002 (9)
C10.0449 (12)0.0331 (11)0.0322 (12)0.0008 (10)0.0046 (10)0.0006 (9)
C90.0378 (12)0.0425 (13)0.0372 (13)0.0015 (10)0.0099 (10)0.0018 (10)
C80.0489 (14)0.0565 (15)0.0281 (12)0.0038 (12)0.0092 (11)0.0048 (11)
Geometric parameters (Å, º) top
O2—C31.246 (2)C7—H70.9300
F1—C91.369 (2)O1—C31.328 (2)
N1—C11.351 (3)O1—H10.8200
N1—C51.394 (3)C3—C21.444 (3)
N1—H1B0.89 (3)C6—C91.378 (3)
C4—C51.414 (3)C6—H60.9300
C4—C61.411 (3)C2—C11.377 (3)
C4—C21.454 (3)C1—H1A0.9300
C7—C81.378 (3)C9—C81.392 (3)
C7—C51.397 (3)C8—H80.9300
C1—N1—C5110.02 (18)C9—C6—C4116.95 (19)
C1—N1—H1B123.9 (16)C9—C6—H6121.5
C5—N1—H1B126.1 (16)C4—C6—H6121.5
C5—C4—C6118.62 (19)C1—C2—C3125.57 (19)
C5—C4—C2106.17 (18)C1—C2—C4106.92 (18)
C6—C4—C2135.20 (19)C3—C2—C4127.49 (19)
C8—C7—C5118.3 (2)N1—C1—C2109.7 (2)
C8—C7—H7120.9N1—C1—H1A125.1
C5—C7—H7120.9C2—C1—H1A125.1
C3—O1—H1109.5F1—C9—C6118.10 (19)
C7—C5—N1130.24 (19)F1—C9—C8117.23 (19)
C7—C5—C4122.58 (19)C6—C9—C8124.7 (2)
N1—C5—C4107.18 (18)C7—C8—C9118.9 (2)
O2—C3—O1122.08 (19)C7—C8—H8120.6
O2—C3—C2122.83 (19)C9—C8—H8120.6
O1—C3—C2115.09 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O2i0.821.862.669 (2)171
N1—H1B···O2ii0.89 (3)2.18 (3)3.026 (2)159 (2)
Symmetry codes: (i) x+2, y+1, z+2; (ii) x+3/2, y1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC9H6FNO2
Mr179.15
Crystal system, space groupMonoclinic, P21/n
Temperature (K)293
a, b, c (Å)4.4176 (9), 11.073 (2), 16.014 (3)
β (°) 96.63 (3)
V3)778.1 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.13
Crystal size (mm)0.30 × 0.20 × 0.10
Data collection
DiffractometerRigaku SCXmini CCD
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.982, 0.993
No. of measured, independent and
observed [I > 2σ(I)] reflections
7874, 1788, 1153
Rint0.068
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.054, 0.137, 1.02
No. of reflections1788
No. of parameters123
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
O1—H1···O2i0.821.862.669 (2)171
N1—H1B···O2ii0.89 (3)2.18 (3)3.026 (2)159 (2)
Symmetry codes: (i) x+2, y+1, z+2; (ii) x+3/2, y1/2, z+3/2.
 

References

First citationBrandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.
First citationLang, 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
First citationRigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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COMMUNICATIONS
ISSN: 2056-9890
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