Structural and Chemical Evolution of l-Cysteine Nanofilm on Si(111)-√3×√3-Ag: From Preferential Growth at Step Edges and Antiphase Boundaries at Room Temperature to Adsorbate-Mediated Metal Cluster Formation at Elevated Temperature

Abstract

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.

Covalent and Hydrogen Bonding in Adsorption of Alanine Molecules on Si(111)7×7

“…Although the methyl group is not chemically reactive, it increases the size and complexity of the molecular structure of the amino acid, potentially introducing steric constraint, all of which could affect how alanine bonds to the surface and how it interacts with one another during film growth. Adsorption of alanine, cysteine, aspartic acid, proline, glutamic acid and methionine on single crystalline metal surfaces [Cu(110), Au(111), Ag(100), Ni(100)] and on nonreactive Si(111)- √3×√3-Ag surface, have been extensively studied by using XPS, reflection–absorption infrared spectroscopy, temperature-programmed desorption, low-energy electron diffraction, and STM. − In particular, a comprehensive adsorption phase diagram of alanine on Cu(110) has been reported to include four alaninate (NH 2 C α H­(CH 3 )­COO – ) phases depending on the coverage and substrate temperature . At room temperature, individual alanine molecules were found to bond tridentately to Cu(110) at low coverage through both carboxylate O atoms and the amino N atom, following deprotonation of the carboxylic acid group.…”

Aligned Organic Molecular Wires in Methionine Nanofilm Growth on Si(111)-√3×√3-Ag

“…The reactivities of these three surfaces were observed to follow the general trend Si(111) (most reactive) > Si(111)-√3×√3-Ag > Ag(111) (least reactive). In our recent study, we investigated the chemisorption of cysteine, the only thiol-containing amino acid, on Si(111)-√3×√3-Ag . As the thiol end group in cysteine is replaced by the methylthiomethylene end group in methionine, methionine is a more suitable candidate for the formation of physisorbed supramolecular architectures because the methylthiomethylene group is less reactive with the substrate, thereby accentuating more intermolecular interactions.…”