Nanostructures, fabricated by locating molecular building blocks in well-defined positions, for example, on a lattice, are ideal platforms for studying atomic-scale quantum effects. In this context, STM data obtained from self-assembled Bis(phthalocyaninato) Terbium (III) (TbPc2) single-molecule magnets on various substrates have raised questions about the conformation of the TbPc2 molecules within the lattice. In order to address this issue, molecular dynamics simulations were carried out on a 2D assembly of TbPc2 molecules. The calculations are in excellent agreement with the experiment, and thus improve our understanding of the self-assembly process. In particular, the calculated electron density of the molecular assembly compares well with STM contrast of self-assembled TbPc2 on Au(111), simultaneously providing the conformation of the two Pc ligands of the individual double-decker molecule. This approach proves valuable in the identification of the STM contrast of LnPc2 layers and could be used in similar cases where it is difficult to interpret the STM images of an assembly of molecular complexes.
Keywords: 2D self-assembly; STM; ab initio; bis(phthalocyaninato) terbium (III); double-decker; electronic contrast; molecular conformation; molecular dynamics; molecular magnets; quantum computation.