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

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

doi:10.1107/S2414314616007008

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 4| April 2016| x160700

doi:10.1107/S2414314616007008

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access

6-Iodo-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 H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 24 April 2016; accepted 25 April 2016; online 29 April 2016)

The molecule of the title compound, C₈H₄INO₂, is almost planar, having an r.m.s. deviation from planarity of 0.019 Å for all non-H atoms. In the crystal, molecules are linked by pairs of N—H⋯O hydrogen bonds, forming inversion dimers with an R₂²(8) ring motif. The dimers are further linked by I⋯O close contacts of 3.078 (2) Å, forming chains along [10-1]. The nine-membered fused rings of the isatin molecules stack along the b axis, with parallel slipped π–π interactions [intercentroid distance = 3.594 (2) Å, interplanar distance = 3.379 (1) Å and slippage = 1.243 Å]. These interactions lead to the formation of a three-dimensional network.

Keywords: crystal structure; isatins; halogen–oxygen interactions; hydrogen bonding; π–π interactions.

CCDC reference: 1476500

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Chemical scheme

Structure description

In a continuing study of the structure of halogenated isatins, we report herein on the crystal structure of 6-iodoisatin (Fig. 1). The molecule possesses bond lengths and angles similar to those observed in the parent isatin (Goldschmidt & Llewellyn, 1950 ). The isatins dimerize in the solid state through pairs N1—H1⋯O1 hydrogen bonds, forming inversion dimers with an $[R_{2}^{2}]$ (8) ring motif. These dimers are further linked through I1⋯O1 close contacts of 3.078 (2) Å that result in infinite chains along [10 $[\overline{1}]$ ]; see Fig. 2 and Table 1. The nine-membered fused rings of the isatin stack along b with parallel slipped π–π interactions [Cg2⋯Cg1ⁱ = 3.594 (2) Å, inter-planar distance: 3.379 (1) Å, slippage: 1.243 Å; Cg1 and Cg2 are the centroids of rings N1/C1–C3/C8 and C3–C8, respectively; symmetry code: (i) − x + 1, − y + 1, − z + 1]. The result of these interactions is the formation of a three-dimensional network.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1ⁱ	0.87 (1)	2.10 (2)	2.888 (3)	152 (3)
Symmetry code: (i) -x+1, -y, -z.

Figure 1
Molecular structure of the title compound, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.

Figure 2
Crystal packing of the title compound viewed along the b axis, with hydrogen bonds shown as dashed lines (see Table 1

), and Iodine-oxygen interactions shown as thin solid lines.

The I⋯O close contacts reported in the title compound are observed in the other three isomers of iodoisatin (Garden et al., 2006 ; Golen & Manke, 2016a ,b ). The crystal structure of 6-bromoisatin (Turbitt et al., 2016 ) also exhibits a similar halogen–oxygen interaction.

Synthesis and crystallization

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

Refinement

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

Table 2
Experimental details

Crystal data
Chemical formula	C₈H₄INO₂
M_r	273.02
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	200
a, b, c (Å)	6.4152 (12), 7.5089 (12), 8.9546 (15)
α, β, γ (°)	110.162 (7), 96.120 (8), 91.997 (8)
V (Å³)	401.43 (12)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	3.94
Crystal size (mm)	0.22 × 0.2 × 0.1

Data collection
Diffractometer	Bruker Venture D8 CMOS
Absorption correction	Multi-scan (SADABS; Bruker, 2014 )
T_min, T_max	0.197, 0.259
No. of measured, independent and observed [I > 2σ(I)] reflections	7043, 1533, 1428
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.613

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.020, 0.044, 1.13
No. of reflections	1533
No. of parameters	112
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	1.12, −0.74
Computer programs: APEX2and SAINT (Bruker, 2014), SHELXS97 (Sheldrick, 2008 ), SHELXL2014 (Sheldrick, 2015 ), OLEX2 (Dolomanov et al., 2009 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 1476500

Crystal structure: contains datablocks Global, I. DOI: 10.1107/S2414314616007008/su4042sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2414314616007008/su4042Isup2.hkl

Supporting information file. DOI: 10.1107/S2414314616007008/su4042Isup3.cml

checkCIF report

Experimental top

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 1.

Results and discussion top

Experimental top

Structure description top

In a continuing study of the structure of halogenated isatins, we report herein on the crystal structure of 6-iodoisatin (Fig. 1). The molecule possesses bond lengths and angles similar to those observed in the parent isatin (Goldschmidt & Llewellyn, 1950). The isatins dimerize in the solid state through pairs N1—H1···O1 hydrogen bonds, forming inversion dimers with an R₂²(8) ring motif. These dimers are further linked through I1···O1 close contacts of 3.078 (2) Å that result in infinite chains along [101]; see Fig. 2 and Table 1. The nine-membered rings of the isatin stack along b with parallel slipped π–π interactions [Cg2···Cg1ⁱ = 3.594 (2) Å, inter-planar distance: 3.379 (1) Å, slippage: 1.243 Å; Cg1 and Cg2 are the centroids of rings N1/C1–C3/C8 and C3–C8, respectively; symmetry code: (i) - x + 1, - y + 1, - z + 1]. The result of these interactions is the formation of a three-dimensional structure. The I···O close contacts reported in the title compound are observed in the other three isomers of iodoisatin (Garden et al., 2006; Golen & Manke, 2016a,b). The crystal structure of 6-bromoisatin (Turbitt et al., 2016) also exhibits a similar halogen–oxygen interaction.

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).

Figures top

	Fig. 1. Molecular structure of the title compound, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. Crystal packing of the title compound viewed along the b axis, with hydrogen bonds shown as dashed lines (see Table 1), and Iodine-oxygen interactions shown as thin solid lines.

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

Crystal data top

C₈H₄INO₂	Z = 2
M_r = 273.02	F(000) = 256
Triclinic, P1	D_x = 2.259 Mg m⁻³
a = 6.4152 (12) Å	Mo Kα radiation, λ = 0.71073 Å
b = 7.5089 (12) Å	Cell parameters from 5053 reflections
c = 8.9546 (15) Å	θ = 2.9–25.9°
α = 110.162 (7)°	µ = 3.94 mm⁻¹
β = 96.120 (8)°	T = 200 K
γ = 91.997 (8)°	BLOCK, yellow
V = 401.43 (12) Å³	0.22 × 0.2 × 0.1 mm

Data collection top

Bruker Venture D8 CMOS diffractometer	1428 reflections with I > 2σ(I)
Radiation source: Mo	R_int = 0.030
φ and ω scans	θ_max = 25.9°, θ_min = 2.9°
Absorption correction: multi-scan (SADABS; Bruker, 2014)	h = −7→7
T_min = 0.197, T_max = 0.259	k = −9→9
7043 measured reflections	l = −10→10
1533 independent reflections

Refinement top

Refinement on F²	1 restraint
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.020	H-atom parameters constrained
wR(F²) = 0.044	w = 1/[σ²(F_o²) + (0.0052P)² + 0.5065P] where P = (F_o² + 2F_c²)/3
S = 1.13	(Δ/σ)_max = 0.001
1533 reflections	Δρ_max = 1.12 e Å⁻³
112 parameters	Δρ_min = −0.74 e Å⁻³

Crystal data top

C₈H₄INO₂	γ = 91.997 (8)°
M_r = 273.02	V = 401.43 (12) Å³
Triclinic, P1	Z = 2
a = 6.4152 (12) Å	Mo Kα radiation
b = 7.5089 (12) Å	µ = 3.94 mm⁻¹
c = 8.9546 (15) Å	T = 200 K
α = 110.162 (7)°	0.22 × 0.2 × 0.1 mm
β = 96.120 (8)°

Data collection top

Bruker Venture D8 CMOS diffractometer	1533 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2014)	1428 reflections with I > 2σ(I)
T_min = 0.197, T_max = 0.259	R_int = 0.030
7043 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.020	1 restraint
wR(F²) = 0.044	H-atom parameters constrained
S = 1.13	Δρ_max = 1.12 e Å⁻³
1533 reflections	Δρ_min = −0.74 e Å⁻³
112 parameters

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
I1	0.88468 (3)	0.23586 (3)	0.83188 (2)	0.03175 (8)
O1	0.2881 (4)	0.1534 (3)	0.0076 (2)	0.0348 (5)
O2	0.0321 (3)	0.3232 (3)	0.2659 (3)	0.0326 (5)
N1	0.5260 (4)	0.1523 (4)	0.2204 (3)	0.0246 (5)
H1	0.621 (4)	0.087 (4)	0.168 (4)	0.030*
C1	0.3425 (5)	0.1870 (4)	0.1497 (3)	0.0244 (6)
C2	0.2080 (5)	0.2776 (4)	0.2872 (3)	0.0230 (6)
C3	0.3404 (4)	0.2856 (4)	0.4329 (3)	0.0208 (6)
C4	0.3091 (5)	0.3516 (4)	0.5932 (3)	0.0263 (6)
H4	0.1825	0.4068	0.6248	0.032*
C5	0.4653 (5)	0.3358 (4)	0.7071 (3)	0.0275 (7)
H5	0.4460	0.3788	0.8173	0.033*
C6	0.6502 (5)	0.2565 (4)	0.6580 (3)	0.0242 (6)
C7	0.6862 (5)	0.1905 (4)	0.4976 (3)	0.0229 (6)
H7	0.8137	0.1373	0.4662	0.028*
C8	0.5280 (5)	0.2063 (4)	0.3870 (3)	0.0205 (6)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
I1	0.03483 (13)	0.03183 (12)	0.02774 (12)	−0.00684 (8)	−0.01217 (8)	0.01497 (9)
O1	0.0388 (13)	0.0438 (13)	0.0224 (11)	0.0155 (11)	0.0011 (9)	0.0120 (10)
O2	0.0264 (12)	0.0370 (12)	0.0334 (12)	0.0136 (10)	0.0013 (9)	0.0106 (10)
N1	0.0219 (13)	0.0325 (13)	0.0186 (12)	0.0105 (11)	0.0028 (10)	0.0070 (10)
C1	0.0289 (16)	0.0229 (14)	0.0207 (15)	0.0066 (12)	0.0010 (12)	0.0071 (12)
C2	0.0220 (16)	0.0198 (13)	0.0264 (15)	0.0032 (12)	−0.0010 (12)	0.0079 (12)
C3	0.0214 (15)	0.0194 (13)	0.0219 (14)	0.0030 (11)	0.0008 (11)	0.0080 (11)
C4	0.0277 (17)	0.0265 (15)	0.0233 (15)	0.0036 (13)	0.0053 (12)	0.0063 (12)
C5	0.0350 (18)	0.0274 (15)	0.0189 (14)	0.0014 (13)	0.0051 (13)	0.0064 (12)
C6	0.0268 (17)	0.0222 (14)	0.0230 (14)	−0.0027 (12)	−0.0037 (12)	0.0096 (12)
C7	0.0204 (15)	0.0236 (14)	0.0242 (14)	0.0040 (11)	0.0007 (12)	0.0080 (12)
C8	0.0224 (15)	0.0196 (13)	0.0193 (14)	0.0015 (11)	0.0028 (11)	0.0066 (11)

Geometric parameters (Å, º) top

I1—C6	2.096 (3)	C3—C8	1.400 (4)
O1—C1	1.217 (3)	C4—H4	0.9500
O2—C2	1.206 (3)	C4—C5	1.390 (4)
N1—H1	0.867 (10)	C5—H5	0.9500
N1—C1	1.354 (4)	C5—C6	1.392 (4)
N1—C8	1.403 (4)	C6—C7	1.396 (4)
C1—C2	1.553 (4)	C7—H7	0.9500
C2—C3	1.460 (4)	C7—C8	1.378 (4)
C3—C4	1.388 (4)

C1—N1—H1	124 (2)	C5—C4—H4	120.4
C1—N1—C8	111.5 (2)	C4—C5—H5	120.4
C8—N1—H1	124 (2)	C4—C5—C6	119.3 (3)
O1—C1—N1	128.2 (3)	C6—C5—H5	120.4
O1—C1—C2	125.7 (3)	C5—C6—I1	118.7 (2)
N1—C1—C2	106.1 (2)	C5—C6—C7	122.6 (3)
O2—C2—C1	123.7 (3)	C7—C6—I1	118.7 (2)
O2—C2—C3	131.6 (3)	C6—C7—H7	121.6
C3—C2—C1	104.7 (2)	C8—C7—C6	116.9 (3)
C4—C3—C2	132.3 (3)	C8—C7—H7	121.6
C4—C3—C8	120.3 (3)	C3—C8—N1	110.3 (2)
C8—C3—C2	107.4 (2)	C7—C8—N1	127.9 (3)
C3—C4—H4	120.4	C7—C8—C3	121.8 (3)
C3—C4—C5	119.2 (3)

I1—C6—C7—C8	179.9 (2)	C2—C3—C8—C7	−179.2 (3)
O1—C1—C2—O2	0.6 (5)	C3—C4—C5—C6	0.8 (4)
O1—C1—C2—C3	179.2 (3)	C4—C3—C8—N1	−179.1 (3)
O2—C2—C3—C4	−1.8 (6)	C4—C3—C8—C7	0.2 (4)
O2—C2—C3—C8	177.5 (3)	C4—C5—C6—I1	179.6 (2)
N1—C1—C2—O2	−178.5 (3)	C4—C5—C6—C7	−0.2 (4)
N1—C1—C2—C3	0.1 (3)	C5—C6—C7—C8	−0.3 (4)
C1—N1—C8—C3	−1.5 (3)	C6—C7—C8—N1	179.5 (3)
C1—N1—C8—C7	179.2 (3)	C6—C7—C8—C3	0.4 (4)
C1—C2—C3—C4	179.8 (3)	C8—N1—C1—O1	−178.2 (3)
C1—C2—C3—C8	−1.0 (3)	C8—N1—C1—C2	0.8 (3)
C2—C3—C4—C5	178.4 (3)	C8—C3—C4—C5	−0.7 (4)
C2—C3—C8—N1	1.5 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.87 (1)	2.10 (2)	2.888 (3)	152 (3)

Symmetry code: (i) −x+1, −y, −z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.87 (1)	2.095 (18)	2.888 (3)	152 (3)

Symmetry code: (i) −x+1, −y, −z.

Experimental details

Crystal data
Chemical formula	C₈H₄INO₂
M_r	273.02
Crystal system, space group	Triclinic, P1
Temperature (K)	200
a, b, c (Å)	6.4152 (12), 7.5089 (12), 8.9546 (15)
α, β, γ (°)	110.162 (7), 96.120 (8), 91.997 (8)
V (Å³)	401.43 (12)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	3.94
Crystal size (mm)	0.22 × 0.2 × 0.1

Data collection
Diffractometer	Bruker Venture D8 CMOS
Absorption correction	Multi-scan (SADABS; Bruker, 2014)
T_min, T_max	0.197, 0.259
No. of measured, independent and observed [I > 2σ(I)] reflections	7043, 1533, 1428
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.613

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.020, 0.044, 1.13
No. of reflections	1533
No. of parameters	112
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	1.12, −0.74

Computer programs: APEX2 (Bruker, 2014), SAINT (Bruker, 2014), SHELXS97 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), OLEX2 (Dolomanov et al., 2009) and publCIF (Westrip, 2010).

Acknowledgements

We gratefully 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
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Goldschmidt, G. H. & Llewellyn, F. J. (1950). Acta Cryst. 3, 294–305. CSD CrossRef CAS IUCr Journals Web of Science Google Scholar
Golen, J. A. & Manke, D. R. (2016a). IUCrData, 1, x160215. Google Scholar
Golen, J. A. & Manke, D. R. (2016b). IUCrData, 1, x160412. 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
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar

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IUCrDATA

ISSN: 2414-3146

Volume 1| Part 4| April 2016| x160700

doi:10.1107/S2414314616007008

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

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

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

References

organic compounds