Deciphering rich non-covalent interactions that govern many chemical and biological processes is crucial for the design of drugs and controlling molecular assemblies and their chemical transformations. However, real-space characterization of these weak interactions in complex molecular architectures at the single bond level has been a longstanding challenge. Here, we employed bond-resolved scanning probe microscopy combined with an exhaustive structural search algorithm and quantum chemistry calculations to elucidate multiple non-covalent interactions that control the cohesive molecular clustering of well-designed precursor molecules and their chemical reactions. The presence of two flexible bromo-triphenyl moieties in the precursor leads to the assembly of distinct non-planar dimer and trimer clusters by manifold non-covalent interactions, including hydrogen bonding, halogen bonding, C-H⋯π and lone pair⋯π interactions. The dynamic nature of weak interactions allows for transforming dimers into energetically more favourable trimers as molecular density increases. The formation of trimers also facilitates thermally-triggered intermolecular Ullmann coupling reactions, while the disassembly of dimers favours intramolecular cyclization, as evidenced by bond-resolved imaging of metalorganic intermediates and final products. The richness of manifold non-covalent interactions offers unprecedented opportunities for controlling the assembly of complex molecular architectures and steering on-surface synthesis of quantum nanostructures.
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