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 Fréchet-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.