Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}

Nanofabrication and the growth of self-assembled monolayers (SAM) of organic molecules are increasingly important in various industries, including microelectronics and health care. Glycine adsorbed on Cu{110} provides a good model with a rich phenomenological space to explore and understand the self-assembly of more complex amino acids. Our focus is on (a) the dynamics exhibited by glycine molecules already adsorbed on Cu{110} when diffusing on the metal surface and (b) the chemical kinetics of how these molecules form clusters, networks, and islands. The stochastic discrete event algorithm we employ can be viewed as a multiscale approach, based on density functional energies and transition barriers. The method extends from the femtosecond time-scale of molecular rotations to the nano- and microsecond range of molecular self-assembly. Hydrogen-bonds and van der Waals forces play a crucial role in pattern formation. Investigations of chemical kinetics show that enantiopure, homochiral islands are an intermediate step during the formation process of larger stable racemic, heterochiral islands, especially when two islands merge. At lower temperature, defects stabilize mainly homochiral clusters and prevent the molecules from synchronizing their footprint orientation, in contrast to higher temperature. On the way, we solve the long-standing puzzle of how the pseudocentered (3 × 2) enantiopure clusters can have glide plane symmetry. We end with a comparison to similar amino acids, such as alanine and proline. The results provide insight into mechanisms for fine-tuning the self-organization of organic molecules on metal surfaces