Toward interactive scanning tunneling microscopy simulations of large-scale molecular systems in real time

We have developed a simulation tool in which structural or chemical modifications of an adsorbed molecular layer can be interactively performed, and where structural relaxation and nearly real-time evaluation of a scanning tunneling microscopy (STM) image are considered. This approach is built from an optimized integration of the atomic superposition and electron delocalization molecular orbital theory (ASED-MO) to which a van der Waals correction term is added in conjunction with a non-linear optimization algorithm based on the Broyden-Fletcher-Goldfarb-Shanno method. This integrated approach provides reliable optimized geometries for adsorbed species on metallic surfaces in a reasonable time. Although we performed a major revision of the ASED-MO parameters, the proposed computational approach can accurately reproduce the geometries of a various amount of covalent molecules and weakly bonded complexes contained in two well-defined datasets. More importantly, the relaxation of adsorbed species on a metal ...