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The functionality of atomic quantum emitters is intrinsically linked to their host lattice coordination. Structural distortions that spontaneously break the lattice symmetry strongly impact their optical emission properties and spin-photon interface. Here we report on the direct imaging of charge state-dependent symmetry breaking of two prototypical atomic quantum emitters in mono- and bilayer MoS₂by scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM). By changing the built-in substrate chemical potential, different charge states of sulfur vacancies (Vac_S) and substitutional rhenium dopants (Re_Mo) can be stabilized. Vac$${}_{{{{{{{{\rm{S}}}}}}}}}^{-1}$$${}_S^{-1}$as well as Re$${}_{{{{{{{{\rm{Mo}}}}}}}}}^{0}$$${}_{\mathrm{Mo}}^0$and Re$${}_{{{{{{{{\rm{Mo}}}}}}}}}^{-1}$$${}_{\mathrm{Mo}}^{-1}$exhibit local lattice distortions and symmetry-broken defect orbitals attributed to a Jahn-Teller effect (JTE) and pseudo-JTE, respectively. By mapping the electronic and geometric structure of single point defects, we disentangle the effects of spatial averaging, charge multistability, configurational dynamics, and external perturbations that often mask the presence of local symmetry breaking.

Intercalation forms heterostructures, and over 25 elements and compounds are intercalated into graphene, but the mechanism for this process is not well understood. Here, the de‐intercalation of 2D Ag and Ga metals sandwiched between bilayer graphene and SiC are followed using photoemission electron microscopy (PEEM) and atomistic‐scale reactive molecular dynamics simulations. By PEEM, de‐intercalation “windows” (or defects) are observed in both systems, but the processes follow distinctly different dynamics. Reversible de‐ and re‐intercalation of Ag is observed through a circular defect where the intercalation velocity front is 0.5 nm s⁻¹± 0.2 nm s.⁻¹In contrast, the de‐intercalation of Ga is irreversible with faster kinetics that are influenced by the non‐circular shape of the defect. Molecular dynamics simulations support these pronounced differences and complexities between the two Ag and Ga systems. In the de‐intercalating Ga model, Ga atoms first pile up between graphene layers until ultimately moving to the graphene surface. The simulations, supported by density functional theory, indicate that the Ga atoms exhibit larger binding strength to graphene, which agrees with the faster and irreversible diffusion kinetics observed. Thus, both the thermophysical properties of the metal intercalant and its interaction with defective graphene play a key role in intercalation.