C–H···O Hydrogen Bonding in Pentamers of Isatin

Self-assembled monolayers of 1H-indole-2,3-dione (isatin), 3-methyl 2-oxindole, and 7-fluoroisatin are observed on the Au(111) surface via scanning tunneling microscopy (STM). We observed that isatin forms pentamers with density functional theory providing support for a cyclic structure stabilized by both N–H···O and C–H···O hydrogen bonds between neighboring molecules. The C–H···O bond is made between the 7-position C–H acting as the hydrogen bond donor and the 3-position carbonyl as the hydrogen bond acceptor, and calculations show that the isatin pentamer structure is 12 kJ/mol more stable than the dimer. When the 3-position carbonyl is removed and replaced with a methyl group (3-methyl 2-oxindole), we observe a monolayer with a mixture of catemer chains and pentameric clusters that are qualitatively different from those of isatin. Pentamer formation is completely broken when the 7-position hydrogen is removed and replaced with fluorine; the monolayer of 7-fluoroisatin is composed of a mixture of close packed ordered domains and hexamer clusters. The role of C–H···O bonding in forming isatin pentamers is supported by electrospray ionization mass spectrometry measurements, which show a propensity for isatin cluster formation, including magic-number isatin pentamers, while 3-methyl 2-oxindole and 7-fluoroisatin show relatively little clustering under the same conditions.