Molecules of copper(II) and cobalt(II) 5,10,15,20-tetraphenyl-21H,23H-porphine (CuTPP and CoTPP) and cobalt(II) phthalocyanine (CoPc) are spontaneously adsorbed onto reconstructed Au(100) substrate from a benzene solution containing each individual complex. In situ scanning tunneling microscopy (STM) was used to examine the real-space arrangement and the internal molecular structure of each of the individual molecules in 0.1 M HCIO4 under potential control. The adsorption of CuTPP and CoTPP produced the same highly ordered square array with an intermolecular spacing of 1.44 nm on a reconstructed Au(100) surface. These molecular superlattices and the underlying reconstructed Au(100) predominated between 0 and 0.9 V, but lifting of the reconstructed Au(100) surface and elimination of the ordered adlayers occurred at more positive potentials. Molecular resolution STM revealed propeller-shaped admolecule with its center imaged as a protrusion for Co(II) and a depression for Cu(II). In contrast, the spontaneous adsorption of CoPc molecules resulted in a rapid phase transition from the reconstructed Au(100) surface to the (1 x 1) phase, coupled with the production of locally ordered, square-shaped arrays with an intermolecular distance of 1.65 nm. This molecular adlayer and the Au(100)-(1 x 1) remained unchanged when the potential was modulated between 0 and 1.0 V. These results indicate that the subtle variation in the molecular structure of adsorbate influenced not only its spatial arrangement but also the structure of the underlying Au(100) substrate.