Surface-Mediated Atomic Geometry and Decoupled States in Short Chains on a Si(553)-Au Surface

We demonstrate how the substrate fundamentally shapes atomic-scale systems on its surface and enables determination of their atomic geometry. Scanning tunneling microscopy and spectroscopy (STM/STS) measurements, supported by density functional theory and tight-binding calculations, reveal that even single adatoms exhibit a convolution with the substrate, leading to significant energy-level renormalization and a redistribution of their spectral weight beyond the energy-gapped region. In few-atom chains, this interaction drives surface-mediated dimerization, modifying both the geometry and electronic density of states, including the appearance of decoupled states. We show that, by explicitly incorporating the substrate's electronic properties, one can not only reliably determine the atomic geometry and positions of adsorbed atoms, allowing for a proper interpretation of STM topography images, but also classify and assign the origin of the STS spectral peaks. Moreover, our findings challenge the common substrate dI/dV subtraction methods and the assumption that STM conductance peaks directly reflect molecular states, an interpretation that is not valid for gapped or semiconducting surfaces.