Racemic dimers as models of chiral macrocycles self-assembled on pyrolytic graphite

0574376 - FZÚ 2024 RIV NL eng J - Journal Article
Ukraintsev, Egor - Houska, Václav - Vacek, Jaroslav - Rezek, B.
Racemic dimers as models of chiral macrocycles self-assembled on pyrolytic graphite.
Carbon Trends. Roč. 12, Sept. (2023), č. článku 100284. E-ISSN 2667-0569
R&D Projects: GA MŠMT LM2023051; GA ČR(CZ) GA20-23566S
Institutional support: RVO:68378271 ; RVO:61388963
Keywords : chiral macrocycles * self-assembly * molecular wires * atomic force microscopy * submolecular resolution * image processing * simulations
OECD category: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8); Physical chemistry (UOCHB-X)
Method of publishing: Open access

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.

Permanent Link: https://hdl.handle.net/11104/0344708