Crystal structure of 1-ethyl-5-iodo­indolin-2-one

Mol­ecules of 1-ethyl-5-iodo­indolin-2-one are arranged in columns extending along the a axis and inter­act with the mol­ecules in adjacent columns via inter­molecular C—H⋯O hydrogen bonds and I⋯I short contacts. A one-dimensional zigzag iodine chain along the a axis can be recognized between two neighbouring columns.

Abstract

In the title indolinone derivative, C₁₀H₁₀INO, all the non-H atoms, except the terminal methyl C atom, are almost coplanar. The mol­ecules are arranged into columns extending along the a-axis direction and inter­act with the mol­ecules in adjacent columns via C—H⋯O hydrogen bonds [H⋯O distance = 2.57 (3) Å] and I⋯I short contacts of 3.8986 (3) Å. A one-dimensional zigzag iodine chain along the a axis is apparent between two neighbouring columns.

Chemical context  

Indolinone derivatives play an important role in the pharma­ceutical industry and some of them show anti­neoplastic (Cane et al., 2000 ▸), anti­bacterial (Kumar et al., 2013 ▸) and anti-inflammatory (Mammone et al., 2006 ▸) activities. The indolinone skeleton can be also found in many known bioactive drugs, such as horsfiline (Murphy et al., 2005 ▸), rhynchophylline (Deiters et al., 2006 ▸) and the gelsemium alkaloids (Kitajima et al., 2006 ▸). In addition, indolinone derivatives are widely used in the spice industry and agriculture, as functional materials (Ji et al., 2010 ▸) and dye inter­mediates.

In recent years, the synthesis and crystal structures of many indolinone derivatives have been reported including 6-chloro-5-(2-chloro­eth­yl)oxindole (Nadkarni & Hallissey, 2008 ▸). We have recently synthesized and reported the crystal structures of several indolin-2-one derivatives including 1-phenyl-indolin-2-one (Wang et al., 2015 ▸). As a continuation of our work in this field, we report here the synthesis and crystal structure of the title compound, 1-ethyl-5-iodo­indolin-2-one.

Structural commentary  

The title mol­ecule is shown in Fig. 1 ▸. The non-H atoms of the indoline core are virtually coplanar [mean deviation is 0.011 (3) Å with a maximum deviation of 0.023 (3) Å for C1]. The atoms C9, O1 and I1 are essentially co-planar with the indoline core, with deviations of 0.019 (4) Å for C9, 0.070 (3) Å for O1, and 0.127 (1) Å for I1. The sum of valence angles around N1 is 360.0°, indicating an sp ² hybridization of this atom. The two C—N bonds in the five-membered ring have a partial double-bond character [N1 C1 1.370 (4) Å; N1 C8 1.400 (3) Å], indicating conjugation of the π-electrons of the NC=O group with the π-electrons of the benzene ring.

Figure 1.

The mol­ecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.

Supra­molecular features  

The crystal packing in the title compound is shown in Figs. 2 ▸ and 3 ▸. The mol­ecules are face-to-face parallel-packed forming a column along the a axis with π–π inter­actions centroid–centroid distances = 4.130 (2) and 4.462 (2) Å]. Mol­ecules from neighbouring columns are connected by a C—H⋯O hydrogen bond (Table 1 ▸) with the formation of a layer-type aggregate parallel to (001). There is an I⋯I contact shorter than the sum (3.96 Å) of the van der Waals radii [I⋯Iⁱ 3.8986 (3) Å, C—I⋯Iⁱ 173.3 (3)°; symmetry code: (i) x − , −y − , −z + 2] joining the columns of mol­ecules in adjacent layers and forming a kind of 1-D zigzag chain along the a-axis direction (see Fig. 3 ▸). An important feature of the columns is that they are polar, i.e. all mol­ecular dipole moments in the same column point in the same direction.

Figure 2.

The view of the structure along the a axis, showing the C—H⋯O hydrogen bond between columns and the I⋯I inter­actions between columns. [Symmetry codes: (i) −x + 3, y + , −z + ; (ii) −x + 3, y − , −z + ; (iii) x − , −y − , −z + 2.]

Figure 3.

The view of the structure along the b axis, showing the one-dimensional columnar structure and the zigzag iodine chains along the a axis.

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C2H2AO1i	0.99(3)	2.57(4)	3.554(4)	169(3)

Symmetry code: (i) .

DFT/b3lyp/genecp calculations were carried out, which took the pseudopotential basis set LanL2DZ for the iodine atom and the 6–311g(d) basis set for the other atoms, to optimize the mol­ecular geometry and calculate the dipole moment using the GAUSSIAN03 program (Frisch et al., 2003 ▸). The dipole moment of the title mol­ecule (1.707 D) is much smaller than that of its precursor mol­ecule, 1-ethyl-5-iodo­indolin-2,3-dione (5.432 D). This difference may partly explain the non-centrosymmetry of the title crystal (space group P2₁2₁2₁) and the centrosymmetry of the crystal of the precursor (Wang et al.,2014 ▸). On the other hand, the non-centrosymmetry of the title crystal may be better explained by the I⋯I inter­molecular inter­actions, for there are no I⋯I short contacts in the above centrosymmetric precursor crystal.

Database survey  

A search of the Cambridge Structural Database (WebCSD, Version 5.36; last update April 2015; Groom & Allen, 2014 ▸) for 5-iodo­indolin-2-one derivatives gave 15 hits. Of these 16 structures (with the title structure included), the number of non-centrosymmetric structures (9) is slightly greater than the number of centrosymmetric structures (7). In these 16 structures, there are four structures which exhibit I⋯I short inter­molecular contacts and all the four structures are non-centrosymmetric (three of them belong to the P2₁2₁2₁ space group and the other one belongs to the P6₃ space group; Takahashi et al., 2014 ▸). Therefore, the I⋯I contacts seem to promote non-centrosymmetric packing in this kind of compound.

Synthesis and crystallization  

The title compound was synthesized by reduction of the precursor with an 80% hydrazine hydrate (see reaction scheme) . 1-Ethyl-5-iodo­indolin-2,3-dione precursor (1.714 g, 5.69 mmol) and 80% NH₂NH₂·H₂O (19.0 mL) were added into a 50 mL flask and the mixture was stirred under reflux. The reaction progress was tracked by TLC. After 4.5 h, the reaction mixture was cooled down and poured into 100 mL water with precipitation of yellow solid. Then the mixture was extracted with CH₂Cl₂, the organic phase was washed with water and dried with MgSO₄. The solvent was removed under reduced pressure and the crude product was purified by silica gel column chromatography with CHCl₃ as eluent. The title compound was obtained as a colorless solid (1.509 g, yield 92.3%). m.p. 403–404 K. Crystals suitable for X-ray diffraction were obtained by slow evaporation of a CHCl₃ solution.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. H atoms bound to aromatic C atoms and methyl­ene C atoms were located in difference maps and freely refined, leading to C—H distances of 0.91 to 1.02 Å. The three H atoms bound to methyl C atoms could also be located in difference maps but they were placed at calculated positions and treated using a riding-model approximation with C—H = 0.96 Å and U _iso(H) = 1.5 U _eq(C).

Table 2. Experimental details.

Crystal data
Chemical formula	C10H10INO
M r	287.09
Crystal system, space group	Orthorhombic, P212121
Temperature (K)	295
a, b, c ()	4.4622(1), 8.2664(2), 27.4400(5)
V (3)	1012.16(4)
Z	4
Radiation type	Mo K
(mm1)	3.12
Crystal size (mm)	0.42 0.32 0.16
Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2005 ▸)
T min, T max	0.354, 0.635
No. of measured, independent and observed [I > 2(I)] reflections	12175, 2938, 2878
R int	0.020
(sin /)max (1)	0.704
Refinement
R[F 2 > 2(F 2)], wR(F 2), S	0.021, 0.050, 1.21
No. of reflections	2938
No. of parameters	148
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
max, min (e 3)	0.47, 0.69
Absolute structure	Flack (1983 ▸), 1183 Friedel pairs
Absolute structure parameter	0.02(2)

Computer programs: APEX2 and SAINT (Bruker, 2005 ▸), SHELXS97, SHELXL97 and SHELXTL (Sheldrick, 2008 ▸).

Supplementary Material

CCDC reference: 1028641

Additional supporting information: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Crystal data

C10H10INO	Dx = 1.884 Mg m−3
Mr = 287.09	Melting point = 403–404 K
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 9948 reflections
a = 4.4622 (1) Å	θ = 2.5–30.0°
b = 8.2664 (2) Å	µ = 3.12 mm−1
c = 27.4400 (5) Å	T = 295 K
V = 1012.16 (4) Å3	Parallelepiped, orange
Z = 4	0.42 × 0.32 × 0.16 mm
F(000) = 552

Data collection

Bruker APEXII CCD diffractometer	2938 independent reflections
Radiation source: fine-focus sealed tube	2878 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.020
Detector resolution: 8.3 pixels mm-1	θmax = 30.0°, θmin = 2.6°
ω scans	h = −6→6
Absorption correction: multi-scan (SADABS; Bruker, 2005)	k = −11→9
Tmin = 0.354, Tmax = 0.635	l = −37→33
12175 measured reflections

Refinement

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)] = 0.021	w = 1/[σ2(Fo2) + (0.0144P)2 + 0.4592P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.050	(Δ/σ)max = 0.002
S = 1.21	Δρmax = 0.47 e Å−3
2938 reflections	Δρmin = −0.69 e Å−3
148 parameters	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraints	Extinction coefficient: 0.0014 (3)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 1183 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.02 (2)

Special details

Experimental. Scan width 0.4° ω, Crystal to detector distance 6.20 cm, exposure time 20 s, 17 h for data collection

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
I1	0.57349 (4)	−0.10015 (2)	0.963176 (7)	0.05126 (7)
C5	0.7961 (6)	0.0703 (3)	0.91955 (9)	0.0404 (5)
O1	1.3877 (6)	0.3521 (3)	0.74792 (8)	0.0644 (7)
C4	0.8354 (6)	0.0383 (3)	0.87003 (10)	0.0410 (5)
C3	0.9948 (5)	0.1476 (3)	0.84294 (9)	0.0386 (6)
C8	1.1096 (6)	0.2881 (3)	0.86420 (9)	0.0394 (5)
N1	1.2652 (5)	0.3781 (3)	0.82916 (8)	0.0429 (5)
C9	1.4198 (8)	0.5309 (4)	0.83826 (12)	0.0505 (6)
C10	1.2102 (8)	0.6717 (4)	0.84543 (12)	0.0539 (7)
H10A	1.0772	0.6795	0.8180	0.081*
H10B	1.3242	0.7698	0.8482	0.081*
H10C	1.0955	0.6557	0.8746	0.081*
C1	1.2634 (7)	0.3027 (3)	0.78470 (10)	0.0472 (6)
C2	1.0825 (9)	0.1476 (3)	0.78985 (10)	0.0488 (6)
C7	1.0700 (8)	0.3218 (3)	0.91288 (10)	0.0456 (5)
C6	0.9096 (8)	0.2096 (4)	0.94064 (9)	0.0472 (6)
H2A	1.216 (8)	0.054 (4)	0.7827 (11)	0.053 (9)*
H2B	0.899 (12)	0.165 (5)	0.7685 (17)	0.103 (16)*
H4	0.754 (8)	−0.062 (4)	0.8534 (12)	0.058 (9)*
H6	0.884 (8)	0.234 (4)	0.9737 (11)	0.051 (9)*
H7	1.143 (7)	0.419 (4)	0.9266 (11)	0.053 (9)*
H9A	1.548 (9)	0.555 (4)	0.8089 (13)	0.067 (11)*
H9B	1.528 (10)	0.520 (5)	0.8662 (14)	0.075 (12)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
I1	0.05236 (10)	0.05416 (11)	0.04726 (10)	−0.00328 (9)	0.00305 (9)	0.01516 (8)
C5	0.0395 (12)	0.0407 (14)	0.0410 (12)	0.0021 (10)	0.0017 (10)	0.0086 (10)
O1	0.0785 (16)	0.0576 (13)	0.0570 (13)	−0.0032 (13)	0.0277 (13)	0.0062 (10)
C4	0.0445 (13)	0.0333 (12)	0.0451 (13)	0.0004 (9)	0.0016 (10)	0.0007 (10)
C3	0.0434 (14)	0.0350 (12)	0.0374 (12)	0.0044 (8)	0.0043 (9)	−0.0006 (9)
C8	0.0386 (12)	0.0356 (11)	0.0440 (12)	0.0026 (10)	0.0029 (10)	0.0009 (10)
N1	0.0479 (11)	0.0335 (11)	0.0473 (11)	−0.0035 (10)	0.0100 (10)	−0.0003 (9)
C9	0.0432 (13)	0.0488 (15)	0.0596 (17)	−0.0113 (14)	0.0002 (15)	0.0038 (12)
C10	0.0615 (18)	0.0403 (15)	0.0598 (17)	−0.0119 (14)	−0.0008 (15)	−0.0031 (13)
C1	0.0537 (16)	0.0393 (13)	0.0486 (15)	0.0047 (13)	0.0125 (13)	0.0039 (12)
C2	0.0664 (17)	0.0389 (13)	0.0412 (13)	−0.0003 (15)	0.0159 (15)	−0.0040 (10)
C7	0.0526 (14)	0.0414 (13)	0.0428 (13)	−0.0052 (14)	−0.0023 (13)	−0.0048 (10)
C6	0.0530 (14)	0.0538 (15)	0.0349 (12)	−0.0018 (15)	0.0015 (13)	0.0009 (11)

Geometric parameters (Å, º)

I1—C5	2.099 (3)	C9—C10	1.506 (5)
C5—C6	1.384 (4)	C9—H9A	1.01 (4)
C5—C4	1.395 (4)	C9—H9B	0.91 (4)
O1—C1	1.222 (3)	C10—H10A	0.9600
C4—C3	1.369 (4)	C10—H10B	0.9600
C4—H4	1.02 (3)	C10—H10C	0.9600
C3—C8	1.397 (4)	C1—C2	1.521 (4)
C3—C2	1.508 (4)	C2—H2A	0.99 (3)
C8—C7	1.376 (4)	C2—H2B	1.02 (5)
C8—N1	1.400 (3)	C7—C6	1.398 (4)
N1—C1	1.370 (4)	C7—H7	0.95 (3)
N1—C9	1.461 (4)	C6—H6	0.94 (3)
C6—C5—C4	121.3 (2)	C9—C10—H10A	109.5
C6—C5—I1	119.53 (19)	C9—C10—H10B	109.5
C4—C5—I1	119.2 (2)	H10A—C10—H10B	109.5
C3—C4—C5	118.0 (3)	C9—C10—H10C	109.5
C3—C4—H4	118.8 (19)	H10A—C10—H10C	109.5
C5—C4—H4	123.3 (19)	H10B—C10—H10C	109.5
C4—C3—C8	120.8 (2)	O1—C1—N1	125.5 (3)
C4—C3—C2	131.2 (3)	O1—C1—C2	126.8 (3)
C8—C3—C2	108.0 (2)	N1—C1—C2	107.7 (2)
C7—C8—C3	121.8 (3)	C3—C2—C1	103.1 (2)
C7—C8—N1	128.5 (3)	C3—C2—H2A	110.2 (18)
C3—C8—N1	109.7 (2)	C1—C2—H2A	108 (2)
C1—N1—C8	111.5 (2)	C3—C2—H2B	110 (3)
C1—N1—C9	123.3 (2)	C1—C2—H2B	105 (3)
C8—N1—C9	125.2 (2)	H2A—C2—H2B	118 (3)
N1—C9—C10	113.4 (3)	C8—C7—C6	117.4 (3)
N1—C9—H9A	107 (2)	C8—C7—H7	121 (2)
C10—C9—H9A	108 (2)	C6—C7—H7	121.6 (19)
N1—C9—H9B	108 (3)	C5—C6—C7	120.8 (2)
C10—C9—H9B	107 (3)	C5—C6—H6	122 (2)
H9A—C9—H9B	113 (3)	C7—C6—H6	117 (2)
C6—C5—C4—C3	1.2 (4)	C8—N1—C1—O1	−178.2 (3)
I1—C5—C4—C3	−176.70 (19)	C9—N1—C1—O1	0.1 (5)
C5—C4—C3—C8	−1.1 (4)	C8—N1—C1—C2	1.3 (3)
C5—C4—C3—C2	178.5 (3)	C9—N1—C1—C2	179.6 (3)
C4—C3—C8—C7	0.5 (4)	C4—C3—C2—C1	−178.6 (3)
C2—C3—C8—C7	−179.1 (3)	C8—C3—C2—C1	1.0 (3)
C4—C3—C8—N1	179.4 (2)	O1—C1—C2—C3	178.1 (3)
C2—C3—C8—N1	−0.3 (3)	N1—C1—C2—C3	−1.4 (3)
C7—C8—N1—C1	178.0 (3)	C3—C8—C7—C6	0.0 (4)
C3—C8—N1—C1	−0.7 (3)	N1—C8—C7—C6	−178.6 (3)
C7—C8—N1—C9	−0.2 (5)	C4—C5—C6—C7	−0.7 (5)
C3—C8—N1—C9	−178.9 (3)	I1—C5—C6—C7	177.2 (2)
C1—N1—C9—C10	108.7 (3)	C8—C7—C6—C5	0.0 (5)
C8—N1—C9—C10	−73.2 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2A···O1i	0.99 (3)	2.57 (4)	3.554 (4)	169 (3)

Symmetry code: (i) −x+3, y−1/2, −z+3/2.