Squaraine dyes form aggregates in solution and in the solid state. We have found that squaraines form two-dimensional (2D) ordered layers when adsorbed onto HOPG from phenyloctane and from liquid crystalline solvents. We investigated with scanning tunneling microscopy the 2D structures of the adsorbed phases of five bis(4-alkylamino-2-hydroxyphenyl) squaraines (both symmetric and asymmetric) and mixtures of these squaraines. Differences in the stability of the 2D structures and molecular packing are observed when the alkyl tail length and symmetry are varied. A transition in the 2D structure from a herringbone packing to a lamellar packing occurs between the tail lengths of 4 carbons and 8 carbons. Many of the compounds form a number of 2D polytypes on HOPG. Multilayers of squaraine molecules were observed for most of the studied molecules. Squaraines with tail lengths of 12 carbons exhibited a tendency toward registry with the HOPG substrate whereas all other squaraine compounds investigated showed a lack of molecule-substrate registry. Domain sizes of the investigated molecules varied from tens of nanometers to a micron.

The 2D structures of a variety of n-alkyl-substituted perylene diimides adsorbed onto HOPG and MoS2 surfaces from phenyloctane solutions were studied using scanning tunneling microscopy (STM). Both rectangular, or herringbone-like, structures and row structures were observed. Surprisingly, the lattice constants, and thus the area per molecule of the rectangular structures, did not increase as expected when the alkyl chain length was increased. Protrusion of the alkyl tails into the solvent above the 2D layer is proposed to account for this behavior. Row structures, where the alkyl tails lie flat on the substrate surface, were also observed wherein the area per molecule increases as expected for the increase in the length of the alkyl tail. The formation of domains with a particular orientation with respect to the underlying lattice was observed for many of the 2D structures. The alignment of the molecular layers with the substrate could be explained with a point-on-line coincidence model. Formation and filling of missing molecule defects within the oriented domains was observed during continuous scanning of the STM.