Submolecular Imaging of Parallel Offset π-π Stacking in Nonplanar Phthalocyanine Bilayers

In aromatic systems, pi-pi interaction plays a central role in determining the stacking geometry and binding strength of molecules and thus a detailed microscopic understanding is highly desirable. Herein, by using scanning tunneling microscopy with submolecular resolution complemented with first-principles calculations based on density functional theory, we report the atomic-scale imaging of pi-pi interaction in nonplanar phthalocyanine (Pc) bilayers on different substrates, including graphite and Au(111) with weak interaction and Cu(111) with strong binding. We reveal that nonplanar Pc of the second layer on all substrates exhibits an in-plane rotation angle of 15 degrees with a parallel offset of 1.19 angstrom, which minimizes pi-pi repulsion. Interestingly, on Cu(111), it is found that the inequivalent charge distribution along with the alternating orientation of Pc molecules in the first layer creates a preferable anchoring site for Pc of the second layer, leading to the assembly of the root 2 X root 2R45 degrees superstructure, consistent with theoretical calculations showing that pi-systems with extra negative charge have weaker interlayer binding energy. Our joint experimental-theoretical efforts provide direct evidence for the most energetically favorable parallel offset pi-pi stacking and charging effects on the preferential interaction between aromatic rings, which may shed new light on molecular assembly and organic nanoelectronics.