Molecules intercalating two-dimensional (2D) materials form complex structures that have been mostly characterized by spatially averaged techniques. Here we use aberration-corrected scanning transmission electron microscopy and density-functional-theory (DFT) calculations to study the atomic structure of bilayer graphene (BLG) and few-layer graphene (FLG) intercalated with FeCl$_3$. In BLG we discover two distinct intercalated structures that we identify as monolayer-FeCl$_3$ and monolayer-FeCl$_2$. The two structures are separated by atomically sharp boundaries and induce large but different free-carrier densities in the graphene layers, $7.1times10^{13}$ cm$^{-2}$ and $7.1times10^{13}$ cm$^{-2}$ respectively. In FLG, we observe multiple FeCl$_3$ layers stacked in a variety of possible configurations with respect to one another. Finally, we find that the microscopes electron beam can convert the FeCl$_3$ monolayer into FeOCl monolayers in a rectangular lattice. These results reveal the need for a combination of atomically-resolved microscopy, spectroscopy, and DFT calculations to identify intercalated structures and study their properties.
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