A series of carboxylic acid substituted phenyleneethynylenes, having a rigid backbone of 2.7 ± 0.1 nm, were synthesized by following the Heck-Cassar-Sonagashira-Hagihara cross-coupling reaction. Hydrogen bonding, through the formation of cyclic dimers of carboxylic acid, is more preferred over catemeric structures in all the molecular systems under investigation. The formation of extended two-dimensional patterns on highly oriented pyrolitic graphite (HOPG) surface is dictated by the position as well as number of the carboxylic acid groups on the phenyleneethynylenes. Highly ordered extended arrangements, in the linear and stepwise fashion, were observed when the carboxylic acid groups are attached in the para and meta positions of phenyleneethynylenes. The vital role of the number of carboxylic acid on the organization of molecules is evident in the case of tetracarboxylic acid derivative wherein a Kagome-type structure was observed. Further, the coassembly of two types of phenyleneethynylenes was achieved on HOPG surface through acid base interaction.

The self-assembly of supramolecular architectures bound together by noncovalent interactions offers, at present, the most promising route to constructing devices at the nanoscale. However, the ability to pick molecular components that will result in a desired supramolecular structure and functionality remains a challenge. We suggest these goals can be met by using easily computed descriptors that correlate molecular form and formula with supramolecular architecture and energetics. Using a combination of theory and experiment, we show the feasibility of such an approach for a set of molecules comprised of three hosts (carboxylic acid derivatives of phenyleneethynylene) and five guests (naphthalene, phenanthrene, benzo-c-phenanthrene, benzo-ghi-perylene, and coronene), self-assembled on highly oriented pyrolitic graphite. Both scanning tunneling microscopy experiments and density functional theory calculations show that the host–guest combinations display rich structural diversity, assembling in hexagonal, linear, or random glass-like patterns. For certain host–guest combinations, the introduction of the guest triggers structural reorganization, including a disorder-to-order transition. By correlating with computed free energies, we formulate host and guest descriptors. These descriptors can be evaluated at essentially zero computational cost, as they depend only on the geometry and number of chemical motifs of specific types in the isolated molecules. However, they can successfully predict the structures and energetics of the host–guest assemblies, including systems not included in the original database used when determining the form of the descriptors. Structures of the same kind are found to cluster in the descriptor space. This suggests the way forward for the descriptor-based rational design of self-assembled nanostructured systems on surfaces.