Molecular dynamics simulation of non-contact atomic force microscopy of self-assembled monolayers on Au(111)

We attempted molecular dynamics (MD) simulation of non-contact atomic force microscopy (nc-AFM) of a self-assembled monolayer (SAM) on Au(111) by modifying a previously developed MD simulation method. In the previous simulation, the interaction between a single gold atom tip and a SAM sample consisting of the united atoms (CH3) with a mass (m(0)) and a continuum gold substrate was treated explicitly in terms of microscopic potentials. On the other hand, the probe tip with an artificial reduced mass (m(sl)) was bound to a cantilever spring in order to describe its macroscopic nc-AFM behaviour. In the present study, we treated explicitly the interaction between a gold probe tip (the radius = R) having a single gold atom at the apex and the same SAM on gold. By using this new MD method, we succeeded in interpreting our recent experimental nc-AFM observation. Namely, the local atom-atom interactions in terms of Lennard-Jones potentials together with the long-range sphere-substrate interaction are responsible for inversion and molecular-dependent imaging of van der Waals (i.e. chemically inert) molecules bound on gold substrates.