Issue contents
Download PDF of article
Download CIF
3D view
Navigation
Highlighting
Dictionary of Crystallography reference
IUPAC Gold Book reference
more ...
Download citation
FormatBIBTeX
EndNote
RefMan
Refer
Medline
CIF
SGML
Plain Text
share
Previous article
Next article
Previous article
Issue contents
Download PDF of article
Download CIF
3D view
Navigation
Highlighting
Dictionary of Crystallography reference
IUPAC Gold Book reference
more ...
Download citation
FormatBIBTeX
EndNote
RefMan
Refer
Medline
CIF
SGML
Plain Text
share
Next article

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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 5| May 2012| Page o1580
doi:10.1107/S1600536812016935

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

Ming Loua* and Yang-Hui Luoa

aCollege of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, People's Republic of China
*Correspondence e-mail: chmsunbw@seu.edu.cn

(Received 2 December 2011; accepted 18 April 2012; online 28 April 2012)

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[Kunzer, A. R. & Wendt, M. D. (2011). Tetrahedron, 52, 1815-1818.]). For a related structure, see: Luo et al. (2011[Luo, Y.-H., Qian, X.-M., Gao, G., Li, J.-F. & Mao, S.-L. (2011). Acta Cryst. E67, m172.]).

[Scheme 1]

Experimental

Crystal data

  • C9H6FNO2

  • Mr = 179.15

  • Monoclinic, P 21 /c

  • a = 7.0054 (14) Å

  • b = 11.699 (2) Å

  • c = 9.2947 (19) Å

  • β = 104.15 (3)°

  • V = 738.7 (3) Å3

  • 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[Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.961, Tmax = 0.974

  • 7541 measured reflections

  • 1693 independent reflections

  • 1418 reflections with I > 2σ(I)

  • Rint = 0.033
Refinement

  • R[F2 > 2σ(F2)] = 0.043

  • wR(F2) = 0.115

  • S = 1.08

  • 1693 reflections

  • 123 parameters

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

  • Δρmax = 0.21 e Å−3

  • Δρmin = −0.21 e Å−3

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) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (ii) -x+1, -y, -z.

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

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812016935/rn2099sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812016935/rn2099Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812016935/rn2099Isup3.cml

checkCIF report


Comment top

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).

Related literature top

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

Experimental top

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 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 the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii.
[Figure 2] Fig. 2. A packing view down the a axis showing the three dimensional network. Intermolecular hydrogen bonds are shown as dashed lines.
6-Fluoro-1H-indole-3-carboxylic acid top
Crystal data top
C9H6FNO2F(000) = 368
Mr = 179.15Dx = 1.611 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1693 reflections
a = 7.0054 (14) Åθ = 3.5–27.5°
b = 11.699 (2) ŵ = 0.13 mm−1
c = 9.2947 (19) ÅT = 293 K
β = 104.15 (3)°Block, brown
V = 738.7 (3) Å30.3 × 0.3 × 0.2 mm
Z = 4
Data collection top
Rigaku SCXmini
diffractometer		1693 independent reflections
Radiation source: fine-focus sealed tube1418 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.033
Detector resolution: 13.6612 pixels mm-1θmax = 27.5°, θmin = 3.5°
CCD_Profile_fitting scansh = −9→9
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)		k = −15→15
Tmin = 0.961, Tmax = 0.974l = −12→12
7541 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)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115H 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 parametersΔρmax = 0.21 e Å−3
0 restraintsΔρmin = −0.21 e Å−3
Crystal data top
C9H6FNO2V = 738.7 (3) Å3
Mr = 179.15Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.0054 (14) ŵ = 0.13 mm−1
b = 11.699 (2) ÅT = 293 K
c = 9.2947 (19) Å0.3 × 0.3 × 0.2 mm
β = 104.15 (3)°
Data collection top
Rigaku SCXmini
diffractometer		1693 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)		1418 reflections with I > 2σ(I)
Tmin = 0.961, Tmax = 0.974Rint = 0.033
7541 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0430 restraints
wR(F2) = 0.115H atoms treated by a mixture of independent and constrained refinement
S = 1.08Δρmax = 0.21 e Å−3
1693 reflectionsΔρmin = −0.21 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
xyzUiso*/Ueq
O20.60596 (19)−0.07115 (8)0.16978 (12)0.0489 (3)
H20.5681−0.07850.07950.073*
O10.5438 (2)0.11097 (9)0.10977 (12)0.0514 (3)
F10.96927 (19)−0.13190 (10)0.89741 (12)0.0727 (4)
N10.70843 (19)0.17044 (11)0.55849 (14)0.0394 (3)
C30.5997 (2)0.03550 (12)0.20426 (16)0.0377 (3)
C20.6606 (2)0.06339 (11)0.35810 (16)0.0343 (3)
C40.74187 (19)−0.00793 (11)0.48256 (15)0.0330 (3)
C90.7914 (2)−0.12279 (12)0.50269 (18)0.0397 (4)
H90.7736−0.17180.42170.048*
C60.8487 (2)0.02441 (13)0.74928 (18)0.0432 (4)
H60.86920.07220.83160.052*
C80.8663 (2)−0.16262 (13)0.6426 (2)0.0465 (4)
H80.8991−0.23940.65830.056*
C50.7710 (2)0.06329 (12)0.60672 (16)0.0351 (3)
C10.6428 (2)0.17026 (12)0.41164 (16)0.0382 (3)
H1A0.59250.23350.35420.046*
C70.8931 (2)−0.08866 (15)0.76066 (19)0.0475 (4)
H10.702 (3)0.2305 (17)0.611 (2)0.053 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O20.0787 (8)0.0289 (6)0.0382 (6)−0.0018 (5)0.0127 (6)−0.0044 (4)
O10.0856 (9)0.0304 (6)0.0364 (6)−0.0084 (5)0.0116 (6)0.0019 (4)
F10.0872 (8)0.0638 (8)0.0524 (7)0.0055 (6)−0.0111 (6)0.0161 (5)
N10.0514 (7)0.0270 (6)0.0399 (7)−0.0006 (5)0.0114 (6)−0.0068 (5)
C30.0479 (8)0.0291 (7)0.0388 (8)−0.0050 (6)0.0156 (6)−0.0007 (5)
C20.0397 (7)0.0281 (7)0.0370 (8)−0.0039 (5)0.0128 (6)−0.0025 (5)
C40.0321 (6)0.0291 (7)0.0393 (8)−0.0030 (5)0.0115 (6)−0.0025 (5)
C90.0417 (8)0.0300 (7)0.0475 (9)0.0004 (6)0.0114 (7)−0.0042 (6)
C60.0450 (8)0.0430 (8)0.0388 (8)−0.0053 (7)0.0046 (6)−0.0044 (6)
C80.0456 (9)0.0329 (8)0.0585 (10)0.0055 (6)0.0079 (7)0.0050 (7)
C50.0342 (7)0.0306 (7)0.0411 (8)−0.0034 (5)0.0101 (6)−0.0038 (6)
C10.0477 (8)0.0287 (7)0.0392 (8)−0.0010 (6)0.0124 (6)0.0001 (6)
C70.0442 (8)0.0477 (9)0.0447 (9)0.0006 (7)−0.0005 (7)0.0089 (7)
Geometric parameters (Å, º) top
O2—C31.2916 (17)C4—C91.389 (2)
O2—H20.8200C4—C51.3974 (19)
O1—C31.2394 (18)C9—C81.360 (2)
F1—C71.351 (2)C9—H90.9300
N1—C11.330 (2)C6—C71.357 (2)
N1—C51.3668 (19)C6—C51.381 (2)
N1—H10.86 (2)C6—H60.9300
C3—C21.426 (2)C8—C71.373 (3)
C2—C11.363 (2)C8—H80.9300
C2—C41.427 (2)C1—H1A0.9300
C3—O2—H2109.5C7—C6—C5115.15 (14)
C1—N1—C5109.75 (12)C7—C6—H6122.4
C1—N1—H1121.7 (13)C5—C6—H6122.4
C5—N1—H1128.4 (13)C9—C8—C7119.56 (15)
O1—C3—O2122.44 (14)C9—C8—H8120.2
O1—C3—C2120.84 (13)C7—C8—H8120.2
O2—C3—C2116.72 (13)N1—C5—C6129.53 (14)
C1—C2—C3122.98 (14)N1—C5—C4107.80 (13)
C1—C2—C4107.12 (12)C6—C5—C4122.67 (14)
C3—C2—C4129.88 (13)N1—C1—C2109.68 (13)
C9—C4—C5118.97 (13)N1—C1—H1A125.2
C9—C4—C2135.39 (13)C2—C1—H1A125.2
C5—C4—C2105.64 (12)F1—C7—C6117.94 (16)
C8—C9—C4119.04 (14)F1—C7—C8117.45 (15)
C8—C9—H9120.5C6—C7—C8124.61 (15)
C4—C9—H9120.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.86 (2)2.159 (19)2.8925 (17)142.8 (17)
O2—H2···O1ii0.821.782.5954 (17)170
Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x+1, −y, −z.

Experimental details

Crystal data
Chemical formulaC9H6FNO2
Mr179.15
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)7.0054 (14), 11.699 (2), 9.2947 (19)
β (°) 104.15 (3)
V (Å3)738.7 (3)
Z4
Radiation typeMo Kα
µ (mm−1)0.13
Crystal size (mm)0.3 × 0.3 × 0.2
Data collection
DiffractometerRigaku SCXmini
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.961, 0.974
No. of measured, independent and
observed [I > 2σ(I)] reflections		7541, 1693, 1418
Rint0.033
(sin θ/λ)max (Å−1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.115, 1.08
No. of reflections1693
No. of parameters123
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.21, −0.21

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
N1—H1···O1i0.86 (2)2.159 (19)2.8925 (17)142.8 (17)
O2—H2···O1ii0.821.782.5954 (17)170.3
Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x+1, −y, −z.
 

Acknowledgements

LM thanks Southeast University, Jiangsu Province, PRC.

References

First citationBrandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.  Google Scholar
 First citationKunzer, A. R. & Wendt, M. D. (2011). Tetrahedron, 52, 1815–1818.  CrossRef CAS Google Scholar
 First citationLuo, Y.-H., Qian, X.-M., Gao, G., Li, J.-F. & Mao, S.-L. (2011). Acta Cryst. E67, m172.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationRigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.  Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 5| May 2012| Page o1580
doi:10.1107/S1600536812016935
Follow Acta Cryst. E
Sign up for e-alerts
E-alerts
Follow Acta Cryst. on Twitter
Twitter
Follow us on facebook
Facebook
Sign up for RSS feeds
RSS