Three-dimensional hydrogen bonding between Landers and planar molecules facilitated by electrostatic interactions with Ni adatoms.

Using a combination of UHV-STM and molecular mechanics calculations, we investigate the surface self-assembly of a complex multi-component metal-molecule system with synergistic non-covalent interactions. Hydrogen bonding between three-dimensional Lander-DAT molecules and planar PTCDI molecules, adsorbed closer to the surface, is found to be facilitated by electrostatic interactions between co-adsorbed Ni adatoms and the flexible molecular DAT groups.

Water clustering on nanostructured iron oxide films.

The adhesion of water to solid surfaces is characterized by the tendency to balance competing molecule-molecule and molecule-surface interactions. Hydroxyl groups form strong hydrogen bonds to water molecules and are known to substantially influence the wetting behaviour of oxide surfaces, but it is not well-understood how these hydroxyl groups and their distribution on a surface affect the molecular-scale structure at the interface. Here we report a study of water clustering on a moiré-structured iron oxide thin film with a controlled density of hydroxyl groups. While large amorphous monolayer islands form on the bare film, the hydroxylated iron oxide film acts as a hydrophilic nanotemplate, causing the formation of a regular array of ice-like hexameric nanoclusters. The formation of this ordered phase is localized at the nanometre scale; with increasing water coverage, ordered and amorphous water are found to coexist at adjacent hydroxylated and hydroxyl-free domains of the moiré structure.

Chiral induction with chiral conformational switches in the limit of low "sergeants to soldiers" ratio.

Molecular-level insights into chiral adsorption phenomena are highly relevant within the fields of asymmetric heterogeneous catalysis or chiral separation and may contribute to understand the origins of homochirality in nature. Here, we investigate chiral induction by the "sergeants and soldiers" mechanism for an oligo(phenylene ethynylene) based chiral conformational switch by coadsorbing it with an intrinsically chiral seed on Au(111). Through statistical analysis of scanning tunneling microscopy (STM) data, we demonstrate successful chiral induction with a very low concentration of seeding molecules down to 3%. The microscopic mechanism for the observed chiral induction is suggested to involve nucleation of the intrinsically chiral seeds, allowing for effective transfer and amplification of chirality to large numbers of soldier target molecules.

Adsorption of the organic salt TAB(HCl)4 on Cu(111) studied using STM and XPS.

Sublimation of Tetra-Amino Benzene (TAB) in its tetrahydrochlorinated form onto Cu(111) leads to the formation of long range ordered structures consisting of TAB molecules with partially protonated amino groups interspersed with Cl species.

Atomic-scale structures and interactions between the guanine quartet and potassium.

The atomic-scale identification of the G4K1 structural motif is achieved using an interplay of STM imaging and DFT calculations. Its high stability is found to be caused by the delicate balance between hydrogen bonding and metal-ligand interaction, which is of utmost relevance to model interactions of the G-quadruplex with cations in vivo.

Identification of molecular-adsorption geometries and intermolecular hydrogen-bonding configurations by in situ STM manipulation.

Don't be dim! By combining the technique with DFT calculations, STM manipulation was extended to the probing of intermolecular hydrogen-bonding configurations in self-assembled nanostructures. It was also possible to convert one configuration into another in a controlled fashion through the careful manipulation of a particular structural unit (see picture).

A molecular conformational change induced self-assembly: from randomness to order.

From an interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations we reveal how a molecular conformational change induced self-assembly process can result in the conversion from a random molecular phase to the formation of two types of ordered surface nanostructures with different apparent heights.

Graphene coatings: probing the limits of the one atom thick protection layer.

The limitations of graphene as an effective corrosion-inhibiting coating on metal surfaces, here exemplified by the hex-reconstructed Pt(100) surface, are probed by scanning tunneling microscopy measurements and density functional theory calculations. While exposure of small molecules directly onto the Pt(100) surface will lift the reconstruction, a single graphene layer is observed to act as an effective coating, protecting the reactive surface from O(2) exposure and thus preserving the reconstruction underneath the graphene layer in O(2) pressures as high as 10(-4) mbar. A similar protective effect against CO is observed at CO pressures below 10(-6) mbar. However, at higher pressures CO is observed to intercalate under the graphene coating layer, thus lifting the reconstruction. The limitations of the coating effect are further tested by exposure to hot atomic hydrogen. While the coating can withstand these extreme conditions for a limited amount of time, after substantial exposure, the Pt(100) reconstruction is lifted. Annealing experiments and density functional theory calculations demonstrate that the basal plane of the graphene stays intact and point to a graphene-mediated mechanism for the H-induced lifting of the reconstruction.

Scanning tunneling microscopy reveals single-molecule insights into the self-assembly of amyloid fibrils.

Many severe diseases are associated with amyloid fibril deposits in the body caused by protein misfolding. Structural information on amyloid fibrils is accumulating rapidly, but little is known about the assembly of peptides into fibrils at the level of individual molecules. Here we investigate self-assembly of the fibril-forming tetrapeptides KFFE and KVVE on a gold surface under ultraclean vacuum conditions using scanning tunneling microscopy. Combined with restrained molecular dynamics modeling, we identify peptide arrangements with interesting similarities to fibril structures. By resolving individual peptide residues and revealing conformational heterogeneities and dynamics, we demonstrate how conformational correlations may be involved in cooperative fibril growth. Most interestingly, intermolecular interactions prevail over intramolecular interactions, and assembly of the phenyl-rich KFFE peptide appears not to be dominated by π-π interactions. This study offers interesting perspectives for obtaining fundamental single-molecule insights into fibril formation using a surface science approach to study idealized model systems.

Water-mediated proton hopping on an iron oxide surface.

The diffusion of hydrogen atoms across solid oxide surfaces is often assumed to be accelerated by the presence of water molecules. Here we present a high-resolution, high-speed scanning tunneling microscopy (STM) study of the diffusion of H atoms on an FeO thin film. STM movies directly reveal a water-mediated hydrogen diffusion mechanism on the oxide surface at temperatures between 100 and 300 kelvin. Density functional theory calculations and isotope-exchange experiments confirm the STM observations, and a proton-transfer mechanism that proceeds via an H(3)O(+)-like transition state is revealed. This mechanism differs from that observed previously for rutile TiO(2)(110), where water dissociation is a key step in proton diffusion.

Ethanol Diffusion on Rutile TiO2(110) Mediated by H Adatoms.

We have studied the diffusion of ethanol on rutile TiO2(110)-(1 × 1) by high-resolution scanning tunneling microscopy (STM) measurements and density functional theory (DFT) calculations. Time-lapsed STM images recorded at ∼200 K revealed the diffusion of ethanol molecules both parallel and perpendicular to the rows of surface Ti atoms. The diffusion of ethanol molecules perpendicular to the rows of surface Ti atoms was found to be mediated by H adatoms in the rows of bridge-bonded O (Obr) atoms similarly to previous results obtained for water monomers. In contrast, the diffusion of H adatoms across the Ti rows, mediated by ethanol molecules, was observed only very rarely and exclusively on fully hydrogenated TiO2(110) surfaces. Possible reasons why the diffusion of H adatoms across the Ti rows mediated by ethanol molecules occurs less frequently than the cross-row diffusion of ethanol molecules mediated by H adatoms are discussed.

Chiral induction by seeding surface assemblies of chiral switches.

It is demonstrated by scanning tunneling microscopy that coadsorption of a molecular chiral switch with a complementary, intrinsically chiral induction seed on the Au(111) surface leads to the formation of globally homochiral molecular assemblies.

Homochiral xanthine quintet networks self-assembled on Au(111) surfaces.

Xanthine molecule is an intermediate in nucleic acid degradation from the deamination of guanine and is also a compound present in the ancient solar system that is found in high concentrations in extraterrestrial meteorites. The self-assembly of xanthine molecules on inorganic surfaces is therefore of interest for the study of biochemical processes, and it may also be relevant to the fundamental understanding of prebiotic biosynthesis. Using a combination of high-resolution scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, two new homochiral xanthine structures have been found on Au(111) under ultrahigh vacuum conditions. Xanthine molecules are found to be self-assembled into two extended homochiral networks tiled by two types of di-pentamer units and stabilized by intermolecular double hydrogen bonding. Our findings indicate that the deamination of guanine into xanthine leads to a very different base pairing potential and the chemical properties of the base which may be of relevance to the function of the cell and potential development of human diseases. Moreover, the adsorption of xanthine molecules on inorganic surfaces leading to homochiral assemblies may be of interest for the fundamental understanding of the emerged chirality at early stages of life.

CO-induced embedding of Pt adatoms in a partially reduced FeO(x) film on Pt(111).

The reduction of a single-layer FeO film grown on Pt(111) by CO at elevated pressures and temperatures has been studied through an interplay of scanning tunneling microscopy, ambient-pressure X-ray photoelectron spectroscopy, and density functional theory calculations. Exposure of the FeO thin film to CO at pressures between 1 and 30 Torr and temperatures between 500 and 530 K leads to formation of a honeycomb-structured Fe(3)O(2) film with hollow sites occupied by single Pt atoms extracted from the substrate surface. The formation of these adatoms is driven by an increase in CO adsorption energy. In addition, the structure incorporates undercoordinated Fe centers, which are proposed to have substantial effects on the catalytic properties of the surface.

The importance of bulk Ti3+ defects in the oxygen chemistry on titania surfaces.

The role of bulk defects in the oxygen chemistry on reduced rutile TiO(2)(110)-(1 × 1) has been studied by means of temperature-programmed desorption spectroscopy and scanning tunneling microscopy measurements. Following O(2) adsorption at 130 K, the amount of O(2) desorbing at ∼410 K initially increased with increasing density of surface oxygen vacancies but decreased after further reduction of the TiO(2)(110) crystal. We explain these results by withdrawal of excess charge (Ti(3+)) from the TiO(2)(110) lattice to oxygen species on the surface and by a reaction of Ti interstitials with O adatoms upon heating. Important consequences for the understanding of the O(2)-TiO(2) interaction are discussed.

Controlling chiral organization of molecular rods on Au(111) by molecular design.

Chiral self-assembled structures formed from organic molecules adsorbed on surfaces have been the subject of intense investigation in the recent decade, owing both to relevance in applications such as enantiospecific heterogeneous catalysis or chiral separation as well as to fundamental interest, for example, in relation to the origin of biomolecular homochirality. A central target is rational design of molecular building blocks allowing transfer of chirality from the molecular to the supramolecular level. We previously studied the surface self-assembly of a class of linear compounds based on an oligo(phenylene ethynylene) backbone, which were shown to form a characteristic windmill adsorption pattern on the Au(111) surface. However, since these prochiral compounds were intrinsically achiral, domains with oppositely oriented windmill motifs and related conformational surface enantiomers were always realized in equal proportion. Here we report on the enantioselective, high yield chemical synthesis of a structurally related but intrinsically chiral compound in which two peripheral tert-butyl substituents are replaced by sec-butyl groups, each containing an (S) chiral center. Using scanning tunneling microscopy under ultrahigh vacuum conditions, we characterize the adsorption structures formed from this compound on the Au(111) surface. The perturbation introduced by the modified molecular design is found to be sufficiently small so structures form that are closely analogous to those observed for the original tert-butyl substituted compound. However, as demonstrated from careful statistical analysis of high-resolution STM images, the introduction of the two chiral (S)-sec-butyl substituents leads to a strong preference for windmill motifs with one orientation, demonstrating control of the chiral organization of the molecular backbones through rational molecular design.

Guanine- and potassium-based two-dimensional coordination network self-assembled on Au(111).

In this study, through the choice of the well-known G-K biological coordination system, bioligand-alkali metal coordination has for the first time been brought onto an inert Au(111) surface. Using the interplay between high-resolution scanning tunneling microscopy and density functional theory calculations, we show that the mobile G molecules on Au(111) can effectively coordinate with the K atoms, resulting in a metallosupramolecular porous network that is stabilized by a delicate balance between hydrogen bonding and metal-organic coordination.

Low-temperature CO oxidation on Ni(111) and on a Au/Ni(111) surface alloy.

From an interplay between scanning tunneling microscopy, temperature programmed desorption, X-ray photoelectron spectroscopy, and density functional theory calculations we have studied low-temperature CO oxidation on Au/Ni(111) surface alloys and on Ni(111). We show that an oxide is formed on both the Ni(111) and the Au/Ni(111) surfaces when oxygen is dosed at 100 K, and that CO can be oxidized at 100 K on both of these surfaces in the presence of weakly bound oxygen. We suggest that low-temperature CO oxidation can be rationalized by CO oxidation on O(2)-saturated NiO(111) surfaces, and show that the main effect of Au in the Au/Ni(111) surface alloy is to block the formation of carbonate and thereby increase the low-temperature CO(2) production.

Size threshold in the dibenzothiophene adsorption on MoS2 nanoclusters.

In hydrodesulfurization (HDS) of fossil fuels, the sulfur levels are reduced by sulfur extraction from hydrocarbons through a series of catalyzed reaction steps on low-coordinated sites on molybdenum disulfide (MoS(2)) nanoclusters. By means of scanning tunneling microscopy (STM), we show that the adsorption properties of MoS(2) nanoclusters toward the HDS refractory dibenzothiophene (DBT) vary dramatically with small changes in the cluster size. STM images reveal that MoS(2) nanoclusters with a size above a threshold value of 1.5 nm react with hydrogen to form so-called sulfur vacancies predominately located at edge sites, but these edge vacancies are not capable of binding DBT directly. In contrast, MoS(2) nanoclusters below the threshold perform remarkably better. Here, sulfur vacancies form predominantly at the corner sites, and these vacancies show a high affinity for DBT. The results thus indicate that very small MoS(2) nanoclusters may have unique catalytic properties for the production of clean fuels.