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.

The direct injection of a 9,10-phenanthrenequinone in tetrahydrofuran solution on a Au(111) substrate in high vacuum results in the formation of metastable clusters with a non-intuitive structure. Metastable, rectangular tetramers of this molecule form in which the net molecular dipoles all orient toward the center of the cluster. This structure does not allow for additional hydrogen bonding and thus the origin of its metastability is not clear. We compare this feature to other structures observed on this surface, as well as those formed during the deposition of 9-fluorenone, which does not exhibit this anomalous clustering behavior.

Scanning tunneling microscopy was used to study the self-assembly of three molecules on the Au(111) surface: 2-naphthoic acid, quinaldic acid, and 3-quinoline carboxylic acid. All three compounds consist of two fused six-membered rings functionalized at the same position with a carboxylic acid group. Despite their chemical similarity, widely different structures were observed to result from selfassembly after pulse deposition. 2-Naphthoic acid forms cyclically hydrogen-bonded pentamers, a metastable structure that transitions to rows of dimers upon gentle annealing. Quinaldic acid and 3-quinoline carboxylic acid form dimers, tetramers, and hexamers, but no pentamers. Differences in self-assembly between these three compounds are attributed to the ability of quinaldic acid and 3-quinoline carboxylic acid to form zwitterionic species.

Monolayers of two pairs of structural isomers were deposited on Au(111) and observed via scanning tunneling microscopy in ultrahigh vacuum. We observe exclusively cyclic pentamers of isatin (1H-indole-2,3-dione), whereas its structural isomer, phthalimide (isoindole-1,3-dione), self-assembles primarily into close-packed arrays, with alternate structures that include kinetically locked disordered clusters and tetramer networks. Removal of the phthalimide NH group and its replacement with a CH2 group produces 1,3-indandione, which, despite the loss of the hydrogen-bond donor site, self-assembles into similar structures: close-packed areas and tetramer networks. The equivalent analog for isatin, 1,2-indandione, does not form pentamers and instead forms only close-packed areas and disordered regions. By iteratively altering the chemical structure, we demonstrate the influence that the chemical structure has on the resulting two-dimensional self-assembly.

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