We investigate the dynamical features of the adsorption of diphenylalanine molecules on the Cu(I 10) surface and of their assembling into supramolecular structures by a combination of quantum and classical atomistic modeling with dynamic scanning tunneling microscopy and spectroscopic experiments. Our results reveal a self-assembling mechanism in which isolated adsorbed molecules change their conformation and adsorption mode as a consequence of their mutual interactions. In particular, the formation of zwitterions after proton transfer between initially neutral molecules is found to be the key event of the assembling process, which stabilizes the supramolecular structures. Because of the constraints on the intermolecular bonds exerted by the surface-molecule interactions, the assembly process is strictly stereoselective, And may suggest a general model for patterning and functionalization of bare metal surfaces with short chiral peptides.