The assembling of metal phthalocyanines on the rippled moiré superlattice of graphene/Ir(111) intercalated with one Co layer is driven by the site-dependent polarization field induced by the incommensurate graphene-Co interface. We have performed an X-ray absorption and photoemission study to unveil the role of the metallic centers and of the organic ligands in the molecule-Co interaction process mediated by graphene. Notably, we consider different electronic molecular orbitals, i.e. phthalocyanines with Cu and Mn metallic ions. The spectroscopic response suggests almost unaltered CuPc molecular states upon adsorption, and the rippled graphene carpet decouples completely the electronic interaction between the molecules and the Co layer, while a slight hybridization is present for MnPcs. MnPc molecules, trapped in the valleys of the moiré graphene superlattice, slightly intermix, through the orbitals protruding out of the molecular plane, with the underlying Co, while the organic ligands are almost unaltered. Graphene acts as an interlayer and mediates the interaction between metal phthalocyanines and the metallic substrate, prevent- ing a strong chemical intermixing and enabling the assembly of almost unaltered molecules, preserving their electronic/magnetic state.
