Simulating STM transport in alkanes from first principles

Simulations of scanning tunneling microscopy (STM) measurements for molecules on surfaces are traditionally based on a perturbative approach, most typically employing the Tersoff-Hamann method. This assumes that the STM tip is far from the sample so that the two do not interact with each other. However, when the tip gets close to the molecule to perform measurements, its electrostatic interplay with the substrate may generate nontrivial potential distribution, charge transfer, and forces, all of which may alter the electronic and physical structure of the molecule. These effects are investigated with the ab initio quantum transport code SMEAGOL, combining the nonequilibrium Green’s-function formalism with density functional theory. In particular, we investigate alkanethiol molecules terminated with either CH₃ or CF₃ end-groups on gold surfaces for which recent experimental data are available. We discuss the effects connected to the interaction between the STM tip and the molecule, as well as the asymmetric charge transfer between the molecule and the electrodes.