Adsorbate-Promoted Tunneling-Electron-Induced Local Faceting of D/Pd{110}-(1 × 2)

We have utilized tunneling electrons and thiophene adsorption to draw deuterium (D) from within the single-crystal bulk beneath Pd{110} up to subsurface adsorption sites. We found local faceting induced by this process, and determined the energy threshold of drawing bulk D to subsurface sites to be 0.38 ± 0.02 eV. We show that these facets propagate along the ⟨11̅0⟩ direction of the substrate, and that Pd{110} adopts the (1 × 1) surface reconstruction on the induced facets, yet maintains the paired row (1 × 2) structure on unaffected regions. After producing subsurface D, the facet plane tilts 3.2 ± 0.8° off the substrate plane

Adsorbate-Promoted Tunneling-Electron-Induced Local Faceting of D/Pd{110}-(1 × 2)

We have utilized tunneling electrons and thiophene adsorption to draw deuterium (D) from within the single-crystal bulk beneath Pd{110} up to subsurface adsorption sites. We found local faceting induced by this process, and determined the energy threshold of drawing bulk D to subsurface sites to be 0.38 ± 0.02 eV. We show that these facets propagate along the ⟨11̅0⟩ direction of the substrate, and that Pd{110} adopts the (1 × 1) surface reconstruction on the induced facets, yet maintains the paired row (1 × 2) structure on unaffected regions. After producing subsurface D, the facet plane tilts 3.2 ± 0.8° off the substrate plane

Differentiating Amino Acid Residues and Side Chain Orientations in Peptides Using Scanning Tunneling Microscopy

Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structures at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer’s and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level

Exchange Reactions between Alkanethiolates and Alkaneselenols on Au{111}

When alkanethiolate self-assembled monolayers on Au{111} are exchanged with alkaneselenols from solution, replacement of thiolates by selenols is rapid and complete, and is well described by perimeter-dependent island growth kinetics. The monolayer structures change as selenolate coverage increases, from being epitaxial and consistent with the initial thiolate structure to being characteristic of selenolate monolayer structures. At room temperature and at positive sample bias in scanning tunneling microscopy, the selenolate–gold attachment is labile, and molecules exchange positions with neighboring thiolates. The scanning tunneling microscope probe can be used to induce these place-exchange reactions

Mapping Buried Hydrogen-Bonding Networks

We map buried hydrogen-bonding networks within self-assembled monolayers of 3-mercapto-<i>N</i>-nonylpropionamide on Au{111}. The contributing interactions include the buried S–Au bonds at the substrate surface and the buried plane of linear networks of hydrogen bonds. Both are simultaneously mapped with submolecular resolution, in addition to the exposed interface, to determine the orientations of molecular segments and directional bonding. Two-dimensional mode-decomposition techniques are used to elucidate the directionality of these networks. We find that amide-based hydrogen bonds cross molecular domain boundaries and areas of local disorder

Self-Assembled <i>p</i>‑Carborane Analogue of <i>p</i>‑Mercaptobenzoic Acid on Au{111}

The <i>p</i>-carborane cluster analogue of <i>p</i>-mercaptobenzoic acid, 1-HS-12-COOH-1,12-C₂B₁₀H₁₀, has been synthesized and characterized using nuclear magnetic resonance spectroscopy, single-crystal X-ray diffraction analysis, quantum-chemical calculations, and scanning tunneling microscopy. The single-crystal structure and selected packing aspects are discussed and presented in comparison with the two-dimensional periodic arrangements. Scanning tunneling micrographs, recorded under ambient conditions, are used to compare pure monolayers of 1-HS-1,12-C₂B₁₀H₁₁ to coadsorbed monolayers of both the parental precursor and carboxyl-functionalized <i>p</i>-carboranethiolate on Au{111}. Monolayers of both constituents are further characterized by X-ray photoelectron spectroscopy, which shows good agreement between the stoichiometry of each pure monolayer and the nominal stoichiometries of the respective molecules. Results indicate that most of the molecules of both derivatives adsorb as thiolates but that a small fraction of each adsorbs as thiols, without complete SH bond scission, and consequently are labile relative to desorption. Wetting-angle measurements confirm the hydrophilic character of monolayers containing the carboxylic acid constituents. Mixed self-assembled monolayers with functionalized constituents of high axial symmetry provide a convenient basis for grafting two- and three-dimensional structures

Defect-Tolerant Aligned Dipoles within Two-Dimensional Plastic Lattices

Carboranethiol molecules self-assemble into upright molecular monolayers on Au{111} with aligned dipoles in two dimensions. The positions and offsets of each molecule’s geometric apex and local dipole moment are measured and correlated with sub-Ångström precision. Juxtaposing simultaneously acquired images, we observe monodirectional offsets between the molecular apexes and dipole extrema. We determine dipole orientations using efficient new image analysis techniques and find aligned dipoles to be highly defect tolerant, crossing molecular domain boundaries and substrate step edges. The alignment observed, consistent with Monte Carlo simulations, forms through favorable intermolecular dipole–dipole interactions