The moiré superstructure of graphene grown on metals can drive the assembly of molecular architectures, such as iron−phthalocyanine (FePc) molecules, allowing for the production of artificial molecular configurations. A detailed analysis of the Gr/Co interaction upon intercalation (including a modeling of the resulting moiré pattern) is performed here by density functional theory, which provides an accurate description of the template as a function of the corrugation parameters. The theoretical results are a preliminary step to describe the interaction process of the FePc molecules adsorption on the Gr/Co system. Core level photoemission and absorption spectroscopies have been employed to control the preferential adsorption regions of the FePc on the graphene moiré superstructure and the interaction of the central Fe ion with the underlying Co. Our results show that, upon molecular adsorption, the distance of C atoms from the Co template mainly drives the strength of the molecules-substrate interaction, thereby allowing for locally different electronic properties within the corrugated interface.
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