1) Département de génie physique and Regroupement québécois sur les matériaux de pointe (RQMP), 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 surface leads to molecular geometries in good agreement with experimental and Density Functional Theory results. Then, the electronic structure obtained from ASED-MO is used to compute the STM image of the system nearly in real-time using the Tersoff-Hamann formalism. We developed a parallelization strategy that use Graphics Processing Units (GPU) to reduce the computing time of STM simulation by a factor of 30. Such improvements allow one to simulate STM images of large supramolecular arrangements and to investigate the influence of realistic local chemical or structural defects on metal surfaces.