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−His 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 7position 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.

A series of experiments and electronic structure calculations were performed to identify metastable 1,1′-ferrocenedicarboxylic acid supramolecular structures formed during solution deposition in a vacuum on a Au(111) substrate, as well as to observe their evolution into more stable species under mild annealing conditions. Electrospray ionization mass spectrometry measurments were performed to determine which species are likely to be present in the rapidly evaporating droplet, and these experiments found that a hexamer can exist in solution during deposition, albeit as a metastable species. The molecular clusters present after solution deposition were observed and analyzed using ultrahigh-vacuum scanning tunneling microscopy, and the initial monolayer contains four basic classes of structures: ordered dimer domains, tilted dimer rows, square tetramers, and rectangular chiral hexamers. Electronic structure calculations indicate that the chiral hexamers consist of a central dimer surrounded by four molecules oriented to form birfurcated hydrogen bonds with other carboxylic acid groups and weaker hydrogen bonds with hydrogens from the aromatic rings. The calculations also indicated that the tetramers are clusters held together by carboxylic acid dimer bonds on each ring oriented perpendicular to each other, and that this conformation is slightly more stable than two dimers for a cluster of four molecules. Annealing this surface at 50 °C for 1 h results in the formation of both isolated tetramers and ordered tetramer rows at the expense of the end-to-end dimer domains, with few chiral hexamers remaining. Further annealing at 50 °C, as well as annealing at 65 °C drives the system to form chiral dimer domains, as well as several other minor structures. Annealing at 75 °C resulted in a dramatic decrease in apparent surface coverage, and most ordered structures existed as large tilted dimer rows, whether isolated or in ordered domains. This drop in surface coverage is likely due to some combination of decomposition of the molecule, desorption, or the growth of three-dimensional crystal structures. The observed coexistence of many forms of ordered dimer structures after annealing indicates that the equilbrium conformation of 1,1′-ferrocenedicarboxylic acid is some array of ordered dimers, and the variety of supramolecular structures present after annealing is an indicator that this system evolves under kinetically controlled growth conditions.