Small molecule assembly offers a promising avenue to functionalize 2D materials and tune their optoelectronic properties. The ability to characterize the molecular assembly at the atomic-scale is crucial for systemically fabricating such surfaces and tailoring their properties. In this work, we apply low-dose, aberration-corrected scanning transmission electron microscopy (STEM) to metallated porphyrin and phthalocyanine derivatives grown on graphene substrate using thermal deposition (Fig. 1 a). We adapt data processing methods from 2D crystallography and cryo-EM to combine frames acquired from 102-105 individual molecules into a single averaged image. Our images reveal that monolayer zinc phthalocyanine (ZnPc, Fig. 1b) and monolayer copper phthalocyanine chloride (CuPcCl, Fig.1c) lay flat on the substrate as they are stabilized by the pi-pi interaction between the molecules and the graphene. While similar face-on orientation is observed for bilayer cobalt (II) meso-tetrakis (4-methoxyphenyl) porphyrin (CoTMPP, Fig. 1d), we find asymmetric spiral around bright Co atoms, suggesting that the methoxyphenyl groups adapt to interlayer bonding. Our images further allow us to identify the atomic arrangements in individual molecules. For instance, we achieve an effective resolution of 1.3 Å for CuPcCl, where we can distinguish C-C and C-N bonds in the macrocycle, as well as the Cl atoms at the edge and Cu in the center. These results indicate a new route for atomic-resolution electron microscopy imaging to directly solve the assemblies and structures of small molecules on 2D surfaces. Figure 1. Structure and atomic-resolution images of small molecule assemblies on graphene. (a) Schematic of the experiment: 1-2 layers of molecules are evaporated onto suspended graphene and imaged using aberration-corrected STEM. (b-c) 2D structural representation (top) and experimental averaged images (middle and bottom) of (b) ZnPc, (c) CuPcCl, and (d) CoMTPP. The middle row of images shows the arrangement of molecules in each 2D crystal, and the bottom row shows a magnified, filtered image of one molecule. Scale bars are 1 nm (middle) and 5 Å (bottom).

Atomic-resolution imaging of small molecule assemblies on graphene

ACS Spring 2022

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