Insight into (Co)Pyrphyrin Adsorption on Au(111): Effects of Herringbone Reconstruction and Dynamics of Metalation

Understanding molecule–metal interfaces is crucial for technologies such as molecular electronics, magnetism, and photovoltaic cells. However, due to the complex nature of the Au(111) surface, which possesses herringbone reconstruction, the interactions between molecules and the reconstructed Au(111) surface are still unclear. To fill this fundamental gap in the literature, we apply Density Functional Theory (DFT) to address the role of this reconstruction and more in general of the registry of the molecule and assembly with respect to the underlying metal on the adsorption strength and on the modification of the molecular properties. We find that the type of van der Waals schemes is important to get accurate herringbone reconstruction of the Au(111) surface. Adsorption simulations verify that the dominant contribution to the adsorption energy are dispersion forces, followed by the interaction of the cyano groups with the metal. The insertion of the Co atom further stabilizes the adsorption, due to the attractive interaction between Co and the surface. While changes in adsorption registry of the molecule lead to have weaker binding energy and different conformation of the molecule on the surface, adsorption energies, and structural parameters of the molecules on different surface domains are very similar. The formation of the monolayer and the geometrical configuration of the assembly are mainly driven by the molecule/molecule interactions. Experimental observation indicated that the metalation of pyrphyrin by coadsorption of Co atoms occurs slowly or upon annealing. In order to address these issues, we investigate the assembly and metalation process by means of ab initio molecular dynamics. We show the presence of intermediate states that hinder the process. Moreover, rearrangements within the monolayer are observed upon metalation, which are in agreement with experimental evidence.