6-Fluoro-1H-indole-2,3-dione

Golen, J.A.; Manke, D.R.

doi:10.1107/S2414314616001656

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 2| February 2016| x160165

https://doi.org/10.1107/S2414314616001656

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6-Fluoro-1H-indole-2,3-dione

James A. Golen ^a and David R. Manke ^a ^*

^aDepartment of Chemistry and Biochemistry, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA 02747, USA
^*Correspondence e-mail: dmanke@umassd.edu

Edited by J. Simpson, University of Otago, New Zealand (Received 22 January 2016; accepted 27 January 2016; online 3 February 2016)

The title compound, C₈H₄FNO₂, has a single, almost planar, molecule in the asymmetric unit, with the non-H atoms having a mean deviation from planarity of 0.042 Å. Intermolecular N—H⋯O hydrogen bonds result in infinite chains along [100]. The molecules are further linked through weak C—H⋯O and C—H⋯F interactions.

Keywords: crystal structure; hydrogen bonding; isatins.

CCDC reference: 1450254

Structure description

Herein we report the crystal structure of 6-fluoroisatin as part of a continuing study on the structure of halogenated isatins. The structure exhibits a near planar molecule with the non-hydrogen atoms possessing a mean deviation from planarity of 0.042 Å (Fig. 1). The bond lengths and angles were similar to those observed in the parent isatin (Goldschmidt et al., 1950 ). In the crystal, the molecule exhibits N1—H1⋯O1 hydrogen bonds that result in infinite chains along [100]. There are also C7—H7⋯O2 interactions and C5—H5⋯F1 interactions that further link the molecules in the solid state (Table 1, Fig. 2). These C—H⋯F interactions are unique to this class of compounds as there are no halogen interactions reported in other fluoroisatin derivatives (Mohamed et al., 2007a ,b ; Shankland et al., 2007 ; Wu et al., 2011 ; Wang et al., 2012 ; Mudududdla et al., 2014 ). The structure of the only other 6-haloisatin reported, 6-bromoisatin, also possesses a halogen interaction, with a Br⋯O close contact being observed (Turbitt et al., 2016 ).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1ⁱ	0.86 (1)	2.03 (1)	2.889 (3)	177 (3)
C5—H5⋯F1ⁱⁱ	0.93	2.60	3.425 (4)	148
C7—H7⋯O2ⁱⁱⁱ	0.93	2.36	3.273 (4)	169
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (ii) $[-x, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (iii) x-1, y+1, z.

Figure 1
The molecular structure of the title compound, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are drawn as spheres of arbitrary radius.

Figure 2
The molecular packing of the title compound, shown along the a axis, with hydrogen bonds drawn as dashed lines.

Synthesis and crystallization

A commercial sample (Matrix Scientific) of 6-fluoro-1H-indole-2,3-dione was used for the crystallization. A sample suitable for single-crystal X-ray analysis was grown from the slow evaporation of its acetone solution.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₈H₄FNO₂
M_r	165.12
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	298
a, b, c (Å)	4.9880 (3), 5.5522 (3), 24.2578 (12)
V (Å³)	671.80 (6)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	1.19
Crystal size (mm)	0.25 × 0.15 × 0.1

Data collection
Diffractometer	Bruker D8 Venture CMOS
Absorption correction	Multi-scan (SADABS; Bruker, 2014 )
T_min, T_max	0.528, 0.753
No. of measured, independent and observed [I > 2σ(I)] reflections	7354, 1205, 1184
R_int	0.043
(sin θ/λ)_max (Å⁻¹)	0.603

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.112, 1.10
No. of reflections	1205
No. of parameters	112
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.49, −0.23
Absolute structure	Flack x determined using 451 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.03 (7)
Computer programs: APEX2 (Bruker, 2014), SAINT (Bruker, 2014), SHELXS97 (Sheldrick, 2008 ), SHELXL2014 (Sheldrick, 2015 ), OLEX2 (Dolomanov et al., 2009 ), publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 1450254

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314616001656/sj4011sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616001656/sj4011Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314616001656/sj4011Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009) and publCIF (Westrip, 2010).

6-Fluoro-1H-indole-2,3-dione top

Crystal data top

C₈H₄FNO₂	D_x = 1.633 Mg m⁻³
M_r = 165.12	Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 6268 reflections
a = 4.9880 (3) Å	θ = 5.5–68.3°
b = 5.5522 (3) Å	µ = 1.19 mm⁻¹
c = 24.2578 (12) Å	T = 298 K
V = 671.80 (6) Å³	BLOCK, orange
Z = 4	0.25 × 0.15 × 0.1 mm
F(000) = 336

Data collection top

Bruker D8 Venture CMOS diffractometer	1205 independent reflections
Radiation source: Cu	1184 reflections with I > 2σ(I)
HELIOS MX monochromator	R_int = 0.043
φ and ω scans	θ_max = 68.3°, θ_min = 9.1°
Absorption correction: multi-scan (SADABS; Bruker, 2014)	h = −6→5
T_min = 0.528, T_max = 0.753	k = −6→6
7354 measured reflections	l = −29→29

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.039	w = 1/[σ²(F_o²) + (0.0688P)² + 0.1919P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.112	(Δ/σ)_max < 0.001
S = 1.10	Δρ_max = 0.49 e Å⁻³
1205 reflections	Δρ_min = −0.23 e Å⁻³
112 parameters	Absolute structure: Flack x determined using 451 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
1 restraint	Absolute structure parameter: 0.03 (7)

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
F1	0.0765 (5)	0.5676 (5)	0.70923 (9)	0.0721 (7)
O1	1.0503 (4)	0.4748 (4)	0.50142 (8)	0.0409 (5)
O2	1.0523 (4)	0.0601 (4)	0.57698 (9)	0.0438 (6)
N1	0.6855 (5)	0.5829 (4)	0.55480 (9)	0.0345 (6)
H1	0.644 (7)	0.712 (4)	0.5368 (11)	0.041*
C1	0.8919 (5)	0.4412 (5)	0.53884 (10)	0.0317 (6)
C2	0.8971 (6)	0.2246 (4)	0.57986 (10)	0.0310 (6)
C3	0.6835 (5)	0.2782 (5)	0.61916 (10)	0.0327 (6)
C4	0.6008 (7)	0.1608 (5)	0.66655 (11)	0.0398 (7)
H4	0.6838	0.0190	0.6777	0.048*
C5	0.3914 (7)	0.2583 (6)	0.69712 (12)	0.0467 (7)
H5	0.3297	0.1827	0.7289	0.056*
C6	0.2774 (6)	0.4711 (7)	0.67891 (11)	0.0432 (7)
C7	0.3538 (6)	0.5951 (6)	0.63205 (12)	0.0398 (7)
H7	0.2705	0.7371	0.6211	0.048*
C8	0.5624 (5)	0.4936 (5)	0.60257 (10)	0.0308 (6)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.0613 (12)	0.0928 (17)	0.0622 (12)	0.0084 (15)	0.0169 (10)	−0.0181 (12)
O1	0.0407 (11)	0.0395 (10)	0.0426 (10)	−0.0048 (9)	0.0053 (8)	0.0086 (9)
O2	0.0450 (11)	0.0342 (10)	0.0522 (11)	0.0089 (10)	−0.0021 (9)	0.0043 (9)
N1	0.0393 (12)	0.0250 (11)	0.0394 (12)	0.0020 (10)	−0.0016 (10)	0.0107 (9)
C1	0.0330 (12)	0.0272 (12)	0.0348 (12)	−0.0046 (11)	−0.0039 (10)	0.0040 (10)
C2	0.0329 (12)	0.0251 (12)	0.0349 (12)	−0.0017 (12)	−0.0048 (11)	0.0026 (10)
C3	0.0345 (13)	0.0290 (13)	0.0346 (13)	−0.0024 (12)	−0.0036 (11)	0.0027 (10)
C4	0.0482 (16)	0.0348 (14)	0.0365 (13)	−0.0038 (14)	−0.0022 (14)	0.0090 (11)
C5	0.0508 (17)	0.0541 (16)	0.0354 (13)	−0.0104 (18)	0.0032 (13)	0.0026 (13)
C6	0.0373 (14)	0.0546 (19)	0.0377 (14)	−0.0023 (14)	0.0031 (11)	−0.0128 (13)
C7	0.0388 (16)	0.0349 (14)	0.0458 (14)	0.0032 (13)	−0.0060 (13)	−0.0059 (11)
C8	0.0321 (13)	0.0265 (12)	0.0337 (12)	−0.0022 (11)	−0.0055 (10)	0.0006 (10)

Geometric parameters (Å, º) top

F1—C6	1.353 (4)	C3—C8	1.399 (4)
O1—C1	1.218 (3)	C4—H4	0.9300
O2—C2	1.199 (3)	C4—C5	1.391 (5)
N1—H1	0.864 (13)	C5—H5	0.9300
N1—C1	1.352 (4)	C5—C6	1.383 (5)
N1—C8	1.402 (3)	C6—C7	1.382 (4)
C1—C2	1.561 (3)	C7—H7	0.9300
C2—C3	1.460 (4)	C7—C8	1.383 (4)
C3—C4	1.384 (4)

C1—N1—H1	121 (2)	C5—C4—H4	120.5
C1—N1—C8	111.4 (2)	C4—C5—H5	121.0
C8—N1—H1	127 (2)	C6—C5—C4	118.1 (3)
O1—C1—N1	128.2 (2)	C6—C5—H5	121.0
O1—C1—C2	125.6 (2)	F1—C6—C5	118.0 (3)
N1—C1—C2	106.2 (2)	F1—C6—C7	117.0 (3)
O2—C2—C1	124.1 (2)	C7—C6—C5	125.1 (3)
O2—C2—C3	131.6 (2)	C6—C7—H7	122.3
C3—C2—C1	104.3 (2)	C6—C7—C8	115.5 (3)
C4—C3—C2	131.6 (3)	C8—C7—H7	122.3
C4—C3—C8	120.8 (3)	C3—C8—N1	110.6 (2)
C8—C3—C2	107.5 (2)	C7—C8—N1	127.8 (3)
C3—C4—H4	120.5	C7—C8—C3	121.6 (2)
C3—C4—C5	118.9 (3)

F1—C6—C7—C8	179.0 (2)	C2—C3—C8—C7	−179.1 (2)
O1—C1—C2—O2	−3.9 (4)	C3—C4—C5—C6	−0.8 (4)
O1—C1—C2—C3	175.1 (3)	C4—C3—C8—N1	177.9 (2)
O2—C2—C3—C4	3.0 (5)	C4—C3—C8—C7	−1.1 (4)
O2—C2—C3—C8	−179.4 (3)	C4—C5—C6—F1	−179.0 (3)
N1—C1—C2—O2	178.2 (3)	C4—C5—C6—C7	0.6 (5)
N1—C1—C2—C3	−2.8 (3)	C5—C6—C7—C8	−0.6 (5)
C1—N1—C8—C3	−1.9 (3)	C6—C7—C8—N1	−177.9 (3)
C1—N1—C8—C7	177.0 (3)	C6—C7—C8—C3	0.8 (4)
C1—C2—C3—C4	−176.0 (3)	C8—N1—C1—O1	−175.0 (3)
C1—C2—C3—C8	1.7 (3)	C8—N1—C1—C2	2.8 (3)
C2—C3—C4—C5	178.4 (3)	C8—C3—C4—C5	1.1 (4)
C2—C3—C8—N1	−0.1 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.86 (1)	2.03 (1)	2.889 (3)	177 (3)
C5—H5···F1ⁱⁱ	0.93	2.60	3.425 (4)	148
C7—H7···O2ⁱⁱⁱ	0.93	2.36	3.273 (4)	169

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

Acknowledgements

We greatly acknowledge support from the National Science Foundation (CHE-1429086)

References

Bruker (2014). APEX2, SAINT, and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341. Web of Science CrossRef CAS IUCr Journals Google Scholar
Goldschmidt, G. H. & Llewellyn, F. J. (1950). Acta Cryst. 3, 294–305. CSD CrossRef CAS IUCr Journals Web of Science Google Scholar
Mohamed, S., Barnett, S. A. & Tocher, D. A. (2007a). Acta Cryst. E63, o3575. Web of Science CSD CrossRef IUCr Journals Google Scholar
Mohamed, S., Barnett, S. A. & Tocher, D. A. (2007b). Acta Cryst. E63, o3576. Web of Science CSD CrossRef IUCr Journals Google Scholar
Mudududdla, R., Sharma, R., Guru, S. K., Kushwaha, M., Gupta, A. P., Bharate, S. S., Aravinda, S., Kant, R., Bhushan, S., Vishwakarma, R. A. & Bharate, S. B. (2014). RSC Adv. 4, 14081–14088. Web of Science CSD CrossRef CAS Google Scholar
Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. Web of Science CrossRef CAS IUCr Journals Google Scholar
Shankland, K., Leech, C. K., Mohamed, S., Barnett, S. A. & Tocher, D. A. (2007). Acta Cryst. E63, o3574. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Turbitt, J. R., Golen, J. A. & Manke, D. R. (2016). IUCrData, 1, x152434. Google Scholar
Wang, Y., Lin, H.-H. & Cao, S.-L. (2012). Acta Cryst. E68, o94–o95. Web of Science CSD CrossRef IUCr Journals Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar
Wu, W., Lin, H., Wan, C.-Q. & Cao, S.-L. (2011). Acta Cryst. E67, o1834. Web of Science CSD CrossRef IUCr Journals Google Scholar

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IUCrDATA

ISSN: 2414-3146

Volume 1| Part 2| February 2016| x160165

https://doi.org/10.1107/S2414314616001656

Open

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

6-Fluoro-1H-indole-2,3-dione

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

References

organic compounds