Racemic Dimers as Models of Chiral Macrocycles Self-Assembled on Pyrolytic Graphite

Fully aromatic helicenes are fascinating building blocks for the construction of inherently chiral macrocyclic nanocarbons. Such helicene-based non-planar macrocycles interact with each other and underlying substrate and form various 2D crystals. However, the role of their chirality remains unknown. In Atomic Force Microscopy (AFM) the macrocycles show stripes with six-fold symmetry but only faintly visible internal structure that is not sufficient to see individual adsorbed molecules and identify their chirality. Here, AFM data of self-assembled helicene-based 2D molecular crystals are analyzed by a new computational method that combines various information from AFM image and expected molecular shape taken from molecular dynamic simulations. Possible molecule arrangements are thereby computed and four basic structural elements (dimers) with the smallest deviation from AFM topography image are found. Validation procedure using larger AFM image with many 2D crystal domains improves the resolution in AFM data and allows reliable and reproducible reconstruction of molecular sub-structure, precise molecules position within the 2D crystal as well as their chirality. The presented results and developed mathematical method are generally applicable to study ensembles of molecules with known atom coordinates and to any image with periodic pattern.