Home The crystal structure of (Z)-3-hydrazono-5-nitroindolin-2-one – dimethyl sulfoxide (1/1), C8H6N4O3
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The crystal structure of (Z)-3-hydrazono-5-nitroindolin-2-one – dimethyl sulfoxide (1/1), C8H6N4O3

  • Abdulrahman M. Al-Obaid , Saeed Ali Syed , Bari Ahmed ORCID logo EMAIL logo and Eric C. Hosten
Published/Copyright: December 7, 2019

Abstract

C8H6N4O3 ⋅ C2H6OS, orthorhombic, Pnma (no. 62), a = 10.4813(5) Å, b = 6.8663(4) Å, c = 17.2605(9) Å, V = 1242.20(11) Å3, Z = 4, Rgt(F) = 0.0506, wRref(F2) = 0.1590, T = 200(2) K.

CCDC no.: 1964849

The molecular structure is shown in the figure (The asymmetric unit is labelled). Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Orange block
Size:0.47 × 0.21 × 0.12 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.28 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
θmax, completeness:28.3°, >99%
N(hkl)measured, N(hkl)unique, Rint:12634, 1674, 0.023
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 1384
N(param)refined:122
Programs:Bruker [1], SHELX [2], [3], [4], WinGX/ORTEP [5], PLATON [6], Mercury [7]
Table 2:

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

AtomxyzUiso*/Ueq
S1−0.05098(7)0.2500000.56168(4)0.0447(3)
O10.3589(2)0.2500000.68248(12)0.0479(6)
O20.6559(2)0.2500000.24584(12)0.0539(6)
O30.7985(2)0.2500000.33372(15)0.0707(9)
O40.0730(2)0.2500000.51749(13)0.0527(6)
N10.3274(2)0.2500000.54961(13)0.0332(5)
N20.6375(2)0.2500000.63323(13)0.0378(5)
N30.6233(3)0.2500000.70888(15)0.0521(7)
N40.6877(2)0.2500000.31372(14)0.0392(6)
C10.3996(3)0.2500000.61516(15)0.0347(6)
C20.5344(3)0.2500000.59057(15)0.0316(6)
C3−0.0408(3)0.4452(4)0.62820(14)0.0580(7)
H3C−0.0486020.5689650.6003260.087*
H3D0.0417430.4404820.6548620.087*
H3E−0.1097240.4343610.6662930.087*
C110.4037(2)0.2500000.48397(14)0.0274(5)
C120.5330(2)0.2500000.50603(14)0.0263(5)
C130.6278(3)0.2500000.45057(14)0.0298(5)
H130.7155140.2500000.4643940.036*
C140.5891(3)0.2500000.37356(14)0.0294(5)
C150.4622(3)0.2500000.35076(14)0.0313(6)
H150.4405730.2500000.2973150.038*
C160.3676(2)0.2500000.40660(15)0.0316(5)
H160.2800250.2500000.3923630.038*
H10.240(4)0.2500000.545(2)0.062(12)*
H3A0.679(8)0.2500000.747(5)0.16(3)*
H3B0.536(5)0.2500000.725(3)0.070(13)*

Source of materials

To a solution of 5-nitroisatin (1 mmol) in absolute ethanol was added hydrazine hydrate (1.5 mmol) followed by few drops of acetic acid. The mixture was stirred at room temperature for 30 mins and then reflux for 3 h. Ice was added directly in the hot solution and the precipitate obtained was filtered and washed several times with water affording the product in 93% yield. Recrystalization from dimethyl sulfoxide yielded orange crystals which were suitable for X-ray diffraction analysis.

Experimental details

Carbon-bound H atoms were placed in calculated positions and were included in the refinement in the riding model approximation, with U(H) set to 1.2 Ueq(C). The H atoms of the methyl group were allowed to rotate with a fixed angle around the C—C bond to best fit the experimental electron density (HFIX 137 in the SHELX system [3]), with Uiso(H) set to 1.5 Ueq(C). The nitrogen-bound H atoms were located on a difference Fourier map and refined freely.

Comment

Isatin, an indole derivative is a natural product found in plants as well as humans. It is a versatile synthetic intermediate containing both, a keto and a lactam moiety, which makes the molecule more interesting for chemists and biologists. Isatin and its analogues are associated with many biological and pharmacological processes and well known for its anti-tuberculosis and anti-microbial properties [8], [9].

The asymmetrical unit cell of the title compound contains one half of the istatin derivative and one half of the dimethyl sulfoxide solvent molecule. The structure is located on the mirror plane with only the methyl groups of the solvent out the plane (see the figure). The distance between adjacent planes is 3.433(1) Å. The bond lengths and angles of the titled compound are all in normal range and identical to the similar structure reported by Jamal et al. [10].

In the crystal structure the N3—H3A⋯O1 intermolecular hydrogen bond forms a zig-zag chain of molecules parallel to the a axis. Also in the plane of linked molecules are the intramolecular N3—H3B⋯O1 and intermolecular N1—H1⋯O4 hydrogen bonds. Between the planes there are also π—π interactions with a centroid to centroid distance of 3.5176(4) Å and slippage of 0.766 Å between the benzene C11—C16 and the pyrrole C1, C2, C11, C12, N1 rings.

Acknowledgements

The authors extend their appreciation to the Deanship of Scientific Research at King Saud University for funding this work through research group no RG-1440-009.

References

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Received: 2019-10-30
Accepted: 2019-11-11
Published Online: 2019-12-07
Published in Print: 2020-02-25

©2019 Abdulrahman M. Al-Obaid et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 Public License.

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  81. Crystal structure and photochromism of 1-(2,5-dimethyl-3-thienyl)-2-[2-methyl-5-(benzaldoxime)-3-thienyl] perfluorocyclopentene, C23H17F6NOS2
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