The interaction of cysteine molecules with the Si(111)-√3×√3-Ag
surface has been investigated over the submonolayer to multilayer
regime using X-ray photoelectron spectroscopy, scanning tunneling
microscopy, and density functional theory calculations. With both
upper step and lower step terraces, step edges, and antiphase boundaries,
the √3×√3-Ag overlayer supported on Si(111) provides
a rich two-dimensional template for studying site-specific biomolecular
interactions. As an amino acid with three functional groups, cysteine
is found to chemisorb through S−H bond cleavage and S−Ag
bond linkage first at step edges and antiphase boundaries followed
by island formation and expanded growth onto terraces. Intermolecular
interactions are dominated by zwitterionic hydrogen bonding at higher
coverages, producing a porous unordered interfacial layer composed
of cysteine agglomerates at room temperature. Upon annealing, cysteine
adsorbates induce structural transformation of the uniform √3×√3-Ag
reconstructed surface lattice into metallic Ag clusters with a narrow
size distribution and short-range ordering. Preferential nanoaggregate
formation of cysteine at defect sites and cysteine-induced metal cluster
formation promise a new approach to fabricating nanoclusters for potential
applications in chemical sensing and catalysis.