Molecular and crystal structure of 1-methyl- 5-trifluoromethoxy-1H-indole-2,3-dione 3-[4-(4-methoxyphenyl)thiosemicarbazone]

Year 2021, Volume: 51 Issue: 1, 59 - 66, 30.04.2021

Özge Soylu Eter Zeliha Atioğlu Mehmet Akkurt Cem Cüneyt Ersanlı Nilgün Karalı

Abstract

Background and Aims: The main purpose of this study is to determine the molecular structure and isomers of the new 1-methyl- 5-trifluoromethoxy-1H-indole-2,3-dione 3-[4-(4-methoxyphenyl)thiosemicarbazone] (5) and to prove the 3Z-conformer of the compound 5. Methods: The molecular structure of E- and Z-isomer mixture 5 was confirmed by analytical and spectral data (UV, IR, 1H NMR, HSQC-2D and MS). The Z-conformer of compound 5 was characterized by NMR spectroscopy and X-ray single crystal diffraction analysis method (SC-XRD). Results: The compound 5 was synthesized by condensation of 1-methyl-5-trifluoromethoxy-1H-indole-2,3-dione (2) with 4-(4-methoxyphenyl)thiosemicarbazide (4). The compound 5 was obtained in two separate forms, crystal and amorphous. It was proved by NMR data and X-ray diffraction findings that the crystal form is the Z-isomer and the amorphous form is a mixture of the E- and Z-isomers. The E- and Z-isomer ratios were determined by 1H NMR spectroscopy. The crystal structure and molecular interactions of the Z-conformer were determined by X-ray single crystal diffraction analysis. Conclusion: In the crystal, three intramolecular N—H···N, N—H···O and C—H···S hydrogen bonds provided isomer formation. Also, molecular packing was stabilized by intermolecular C—H···O hydrogen bonds, the π-π stacking interactions and weak CO···π (ring) contacts.

Keywords

Synthesis, molecular structure, isomerism, crystal structure, hydrogen bond, π-π stacking interaction

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