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In this paper, we investigate by photoemission the electronic properties of an organic/organic interface consisting in a strong electron acceptor hexaazatriphenylene-hexacarbonitrile (HATCN) deposited on a physisorbed N,N′-bis(1-naphthyl)-N,N′-diphenyl-1,1′-biphenyl-4,4′-diamine (α-NPD) monolayer on Ag(111). At the first HATCN deposition steps (∼1 monolayer), the sample work function increases by 1.05 eV and the hole injection barrier (HIB) in the pre-adsorbed α-NPD monolayer is lowered by 0.65 eV. This results from HATCN diffusion to the silver surface through the α-NPD monolayer. Furthermore, this HATCN monolayer is proposed to form a compact chemisorbed monolayer, with a different structural arrangement than that observed on pristine Ag(111). In a second step, the additional deposited HATCN start growing on top of the α-NPD layer, and Fermi-level pinning, associated with the formation of HATCN negative polarons, is identified at the HATCN/α-NPD interface. Finally, HATCN is deposited on a α-NPD multilayer film. In this case, HATCN is also found to diffuse to the silver surface giving a similar HIB value in the α-NPD multilayer. This work demonstrates the importance of studying in detail the formation of organic heterostructures to understand the interplay between growth mode and electronic properties.