1. The Scanning Tunneling Microscopy of Adsorbed Molecules on Semiconductors: Some Theoretical Answers to the Experimental Observations

The present chapter depicts various theoretical methods that have been used in the context of experimental studies at the nanoscale. With the scanning tunneling microscopy (STM), we can investigate the manipulation of individual molecules and their electronic properties through electronically induced excitations. To explore in details the surface dynamics of a molecule in a bistable or quadristable motion, the nudged elastic band method is used to describe the energy barrier of the saddle point located along the molecular reaction pathway. When the physisorbed stilbene molecule is studied on the bare Si(100), the tight binding method is associated to the density functional theory (DFT) to simulate the scanning tunneling topographies. The physisorption of a molecule such as the hexaphenyle-benzene at the step edge of the Si(100) show particular lateral movements which diffusion barrier can be described accurately by the dispersive term added to the DFT to describe van der Waals interactions (DFT-D). In order to identify the nature of bonding of a porphyrin molecule adsorbed on a boron doped silicon surface, we have analyzed the Laplacian of the charge density. Finally, we present a full DFT-D study of a bidimensional nanoporous supramolecular network on a silicon surface. We have evaluated the molecule-molecule and molecule-substrate interactions energies that are key parameters to understand the mechanism of formation of these networks. In this context, the simulations of STM images with multi-diffusion with the presence of a tungsten tip show a better agreement with the experimental observations than the Tersoff-Hamann approach.