Atomic Scale Modeling of Two-Dimensional Molecular Self-Assembly on a Passivated Si Surface

International audienceThe self-assembly of two-dimensional (2D) molecular structures on a solid surface relies on the subtle balance between non covalent intermolecular and molecule-surface forces. The energetics of 2D molecular lattices forming different patterns on a passivated semiconductor surface are here investigated by a combination of atomistic simulation methods. Density-functional theory provides structure and charges of the molecules, while metadynamics with empirical forces provides a best guess for the lowest-energy adsorption sites of single molecules and dimers. Subsequently, molecular dynamics simulations of extended molecular assemblies with empirical forces yield the most favorable lattice structures at finite temperature and pressure