Molecular and Crystal Structure of 1-Methyl 5-Trifluoromethoxy-1h-indole-2,3-dione 3-[4-(4-Methoxyphenyl)thiosemicarbazone]

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, H-1 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 H-1 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 center dot center dot center dot N, N-H center dot center dot center dot O and C-H center dot center dot center dot S hydrogen bonds provided isomer formation. Also, molecular packing was stabilized by intermolecular C-H center dot center dot center dot O hydrogen bonds, the pi-pi stacking interactions and weak CO center dot center dot center dot pi (ring) contacts.