Importance of charging in atomic resolution scanning tunneling microscopy: study of a single phosphorus atom in a Si(001) surface

We present a detailed voltage-dependent scanning tunneling microscopy study of a single phosphorus atom in the Si(001) surface. Using density functional theory calculations we show that tip-induced charging results in reversible structural and electronic changes. These changes are caused by charge transfer from delocalized surface states to localized states associated with the presence of the phosphorus atom. While two stable geometric configurations are predicted, only the higher energy configuration is consistent with experiment.