Simulating self-organized molecular patterns using interaction-site models.

Molecular building blocks interacting at the nanoscale organize spontaneously into stable monolayers that display intriguing long-range ordering motifs on the surface of atomic substrates. The patterning process, if appropriately controlled, represents a viable route to manufacture practical nanodevices. With this goal in mind, we seek to capture the salient features of the self-assembly process by means of an interaction-site model. The geometry of the building blocks, the symmetry of the underlying substrate, and the strength and range of interactions encode the self-assembly process. By means of Monte Carlo simulations, we have predicted an ample variety of ordering motifs which nicely reproduce the experimental results. Here, we explore in detail the phase behavior of the system in terms of the temperature and the lattice constant of the underlying substrate.

Molecular jigsaw: pattern diversity encoded by elementary geometrical features.

Scanning tunneling microscopy (STM) images of self-organized monolayers of Frechet dendrons display a variety of two-dimensional ordering motifs, which are influenced by engineering the molecular interactions. An interaction-site model condenses the essential molecular properties determined by molecular mechanics modeling, which in a Monte Carlo approach successfully predicts the various ordering motifs. This confirms that geometry as well as a few salient weak interaction sites encode these structural motifs.

Conformational analysis of self-organized monolayers with scanning tunneling microscopy at near-atomic resolution.

We describe the synthesis and a novel approach to the conformational analysis of 2,2'-bipyridines (bpy) bearing aromatic rich Frechet-type dendritic wedges of the first and second generation as substituents. The evaporation of solutions of these new ligands on graphite surfaces under ambient conditions results in the formation of self-organized monolayers. Scanning tunneling microscopy (STM) investigations of the monolayers under ambient conditions (air, 298 K) gave images at submolecular and near-atomic resolution. The analysis of the STM images includes the following processes: (i) identification and reproduction of potential homoconformational domains, (ii) exclusion of improper data using quality criteria for drift and feedback artifacts, (iii) compilation of running averages and checking for averaging artifacts, (iv) analysis of three-dimensional and contour plots, (v) calculation of the HOMO properties of the free molecules, and (vi) final conformational assignment based on all accessible information. Following this procedure, two different conformations could be assigned to domains observed in the monolayers of the first-generation (G1) and second-generation (G2) dendritic compounds. Homoconformational domains are observed side-by-side. The different conformations arise from syn or anti arrangements at the ether substituents. An additional conformational effect is found upon treating the G1 domains with HCl gas, when a partial rearrangement of the bpy from trans to cis occurs, concomitant with protonation.

Octyl-decorated Fréchet-type dendrons: a general motif for visualisation of static and dynamic behaviour using scanning tunnelling microscopy?

A detailed STM study of monolayers of 3,5-bis[(3,5-bisoctyloxyphenyl)methyloxy]benzaldehyde and 3,5-bis[(3,5-bisoctyloxyphenyl)methyloxy]benzyl alcohol adsorbed on graphite is presented. Very highly resolved scanning tunnelling microscopy images are observed at room temperature in air allowing the analysis of the conformation of the adsorbed molecules. These long-chain alkyl-decorated Fréchet-type dendrons are a powerful assembly motif and initially form a pattern based on trimeric units, assembled into hexagonal host structures with a pseudo-unit cell of seven molecules, one of which remains highly mobile. Over time, the supramolecular ordering changes from a trimeric into a dimeric pattern. The chirality arising from the adsorption onto a surface of the dendrons is discussed.