First-principles simulation of scanning Tunneling microscopy images of individual molecules in alkanethiol self-assembled monolayers on Au(111)

The scanning tunneling microscopy (STM) images of individual molecules in close-packed upright alkanthiol self-assembled monolayers (SAMs) on Au(111) surface have been simulated by the density functional theory calculations with local density approximation. The internal patterns in the STM images are dependent on bias voltage and alkanethiol chain length, and have characteristic of the topographic effect modulated by the electronic effect. The electronic structure of the adsorption system is analyzed for discussing STM imaging mechanism of alkanethiol SAMs. It is also found that the chemisorption mode of the sulfur atom in alkanethiol on Au(111) surface obviously influences the pattern in STM image.