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Scanning probe microscopy has become an essential tool to not only study pristine surfaces but also on-surface reactions and molecular self-assembly. Nonetheless, due to inherent limitations, some atoms or (parts of) molecules are either not imaged or cannot be unambiguously identified. Herein, we discuss the arrangement of two different nonplanar molecular assemblies of para-hexaphenyl-dicarbonitrile (Ph6(CN)2) on Au(111) based on a combined theoretical and experimental approach. For deposition of Ph6(CN)2 on Au(111) kept at room tempe
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