Single-molecule manipulation and chemistry with the STM

We review recent theoretical work on the manipulation of single molecules with scanning probes, in particular the scanning tunnelling microscope (STM). The aim of theories and simulations is to account for the processes, ideally at a quantitative level, that permit the controlled manipulation of matter at the atomic scale in adsorbed molecular systems. In order to achieve this, simulations rely on total energy and electronic structure calculations where a trade-off is made between the size of the system and the accuracy of the calculation. This first stage of the calculation yields the basic quantities used for the second stage: the evaluation of the coupled electron-nuclear dynamics. This second stage is a formidable task and many approximations are involved. In this review, we will present some of the customary approximations regarding the theoretical study of mechanical and inelastic manipulations. Mechanical manipulations use the interaction between the acting probe (usually a metallic tip) and the targeted adsorbate. We review recent results in the field of adsorbate mechanical manipulations and explain how manipulations can be effected by using the interaction between the probe's tip and certain molecular groups of complex chemisorbed molecular systems. On the other hand, inelastic manipulations use the tunnelling current to convey energy with sub-angstrom precision. This current can excite localized vibrations that can induce measurable variations of the tunnelling conductance, hence providing a means of detecting singlemolecule vibrations. This current can also inject energy in a few reaction coordinates. Recently, the possibility of vibrational selective manipulations of NH3/Cu(100) has been experimentally demonstrated. The theory presented here addresses the actual pathways accessed when the molecule is excited by the tunnelling current from an STM.