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).

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.

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.

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.

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.

Bandgap opening in graphene induced by patterned hydrogen adsorption.

Graphene, a single layer of graphite, has recently attracted considerable attention owing to its remarkable electronic and structural properties and its possible applications in many emerging areas such as graphene-based electronic devices. The charge carriers in graphene behave like massless Dirac fermions, and graphene shows ballistic charge transport, turning it into an ideal material for circuit fabrication. However, graphene lacks a bandgap around the Fermi level, which is the defining concept for semiconductor materials and essential for controlling the conductivity by electronic means. Theory predicts that a tunable bandgap may be engineered by periodic modulations of the graphene lattice, but experimental evidence for this is so far lacking. Here, we demonstrate the existence of a bandgap opening in graphene, induced by the patterned adsorption of atomic hydrogen onto the Moiré superlattice positions of graphene grown on an Ir(111) substrate.

Unzipping of functionalized multiwall carbon nanotubes induced by STM.

Carbon nanotubes (CNTs), functionalized by a cycloaddition reaction, were studied by ultrahigh vacuum scanning tunneling microscopy (STM). The STM images provided evidence for partial or total unzipping of the outer CNT layer. The formation of graphene ribbons was triggered by the STM tip, under specific operating conditions. A model for the unzipping is proposed, based on the perturbation of the pi-conjugation along the CNT surface induced by the cycloaddition reaction.

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.

Atomic hydrogen adsorbate structures on graphene.

The adsorbate structures of atomic hydrogen on the basal plane of graphene on a SiC substrate is revealed by Scanning Tunneling Microscopy (STM). At low hydrogen coverage the formation of hydrogen dimer structures is observed, while at higher coverage larger disordered clusters are seen. We find that hydrogenation preferentially occurs on the protruding/high tunneling probability areas of the graphene layer modulated by the underlying 6 x 6 reconstruction of SiC. Hydrogenation offers the interesting possibility to manipulate both the electronic and chemical properties of graphene.

Hydrogen-bonded molecular networks of melamine and cyanuric acid on thin films of NaCl on Au(111).

Self-assembly of organized molecular structures on insulators is technologically very relevant, but in general rather challenging to achieve due to the comparatively weak molecule-substrate interactions. Here the self-assembly of a bimolecular hydrogen-bonded network formed by melamine (M) and cyanuric acid (CA) on ultrathin NaCl films grown on a Au(111) surface is reported. Using scanning tunneling microscopy under ultrahigh-vacuum conditions it is demonstrated that it is possible to exploit strong intermolecular forces in the M-CA system, resulting from complementary triple hydrogen bonds, to grow 2D bimolecular networks on an ultrathin NaCl film that are stable at a relatively high temperature of approximately 160 K and at a coverage below saturation of the first molecular monolayer. These hydrogen-bonded structures on NaCl are identical to the self-assembled structures observed for the M-CA system on Au(111), which indicates that the molecular self-assembly is not significantly affected by the isolating NaCl substrate.

Adenine monolayers on the Au(111) surface: structure identification by scanning tunneling microscopy experiment and ab initio calculations.

From an interplay between scanning tunneling microscopy (STM) and ab initio density functional theory (DFT) we have identified and characterized two different self-assembled adenine (A) structures formed on the Au(111) surface. The STM observations reveal that both structures have a hexagonal geometry in which each molecule forms double hydrogen bonds with three nearest neighbors. One of the A structures, with four molecules in the primitive cell, has p2gg space group symmetry, while the other one, with two molecules in the cell, has p2 symmetry. The first structure is observed more frequently and is found to be the dominating structure after annealing. Experimental as well as theoretical findings indicate that the interaction of A molecules with the gold surface is rather weak and smooth across the surface. This enabled us to unequivocally characterize the observed structures, systematically predict all structural possibilities, based on all known A-A dimers, and provisionally optimize positions of the A molecules in the cell prior to full-scale DFT calculations. The theoretical method is a considerable improvement compared to the approach suggested previously by Kelly and Kantorovich [Surf. Sci. 589, 139 (2005)]. We propose that the less ordered p2gg symmetry structure is observed more frequently due to kinetic effects during island formation upon deposition at room temperature.

Formation of trioctylamine from octylamine on Au(111).

The adsorption of octylamine on Au(111) under ultrahigh vacuum conditions is investigated. The molecules surprisingly undergo a thermally activated chemical reaction, resulting in formation of trioctylamine as confirmed both by X-ray photoelectron spectroscopy (XPS) and by comparison to the scanning tunneling microscopy (STM) signature of trioctylamine deposited directly onto the surface.

An investigation into the interactions between self-assembled adenine molecules and a Au(111) surface.

Two molecular phases of the DNA base adenine (A) on a Au(111) surface are observed by using STM under ultrahigh-vacuum conditions. One of these phases is reported for the first time. A systematic approach that considers all possible gas-phase two-dimensional arrangements of A molecules connected by double hydrogen bonds with each other and subsequent ab initio DFT calculations are used to characterize and identify the two phases. The influence of the gold surface on the structure of A assemblies is also discussed. DFT is found to predict a smooth corrugation potential of the gold surface that will enable A molecules to move freely across the surface at room temperature. This conclusion remains unchanged if van der Waals interaction between A and gold is also approximately taken into account. DFT calculations of the A pairs on the Au(111) surface show its negligible effect on the hydrogen bonding between the molecules. These results justify the gas-phase analysis of possible assemblies on flat metal surfaces. Nevertheless, the fact that it is not the most stable gas-phase monolayer that is actually observed on the gold surface indicates that the surface still plays a subtle role, which needs to be properly addressed.

Understanding the disorder of the DNA base cytosine on the Au(111) surface.

Using ultrahigh vacuum scanning tunneling microscopy (STM) and ab initio density functional theory, we have investigated in detail structures formed by cytosine on the Au(111) surface in clean ultrahigh vacuum conditions. In spite of the fact that the ground state of this DNA base on the surface is shown to be an ordered arrangement of cytosine one-dimensional branches (filaments), this structure has never been observed in our STM experiments. Instead, disordered structures are observed, which can be explained by only a few elementary structural motifs: filaments, five- and sixfold rings, which randomly interconnect with each other forming bent chains, T junctions, and nanocages. The latter may have trapped smaller structures inside. The formation of such an unusual assembly is explained by simple kinetic arguments as a liquid-glass transition.

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.

Influence of molecular geometry on the adsorption orientation for oligophenylene-ethynylenes on Au(111).

The adsorption structures formed from a class of oligophenylene-ethynylenes on Au(111) under ultrahigh vacuum conditions is compared based on high-resolution scanning tunneling microscopy (STM) measurements. The molecules consist of three or four benzene rings connected by ethynylene spokes and are all functionalized identically with an aldehyde, a hydroxyl, and a bulky tert-butyl group. Compounds with the conjugated spokes placed in the para, meta, and threefold configurations were previously found to exclusively form molecular layers with flat-lying adsorption geometries. In contrast, the associated compound with spokes in the ortho configuration surprisingly differs in its adsorption by forming only structures with an upright adsorption orientation. The packing density for the structures formed by the compound with the ortho configuration is less dense than that in conventional self-assembled monolayers while still keeping the conducting backbone in an upright orientation. These structures are thus interesting from the perspective of performing single-molecule conduction measurements on the oligophenylene-ethynylene backbones.

Chiral ordering and conformational dynamics for a class of oligo-phenylene-ethynylenes on Au(111).

Adsorption structures formed from a class of planar organic molecules on the Au(111) surface under ultrahigh vacuum conditions have been characterized using scanning tunneling microscopy (STM). The molecules have different geometries, linear, bent, or three-spoke, but all consist of a conjugated aromatic backbone formed from three or four benzene rings connected by ethynylene spokes and functionalized at all ends with an aldehyde, a hydroxyl, and a bulky tert-butyl group. Upon adsorption, the molecules adopt different surface conformations some of which are chiral. For the majority of the observed adsorption structures, chirality is expressed also in the molecular tiling pattern, and the two levels of chirality display a high degree of correlation. The formation and chiral ordering of the self-assembled structures are shown to result from dynamic interchanges between a diffusing lattice gas and the nucleated islands, as well as from a chiral switching process in which molecules alter their conformation by an intramolecular rotation around a molecular spoke, enabling them to accommodate to the tiling pattern of the surrounding molecular structures. The kinetics of the conformational switching is investigated from time-resolved, variable temperature STM, showing the process to involve an activation energy of approximately 0.3 eV depending on the local molecular environment. The molecule-molecule interactions appear primarily to be of van der Waals character, despite the investigated compounds having functional moieties capable of forming intermolecular hydrogen bonds.

Chiral close-packing of achiral star-shaped molecules on solid surfaces.

From the interplay of scanning tunneling microscopy and theoretical calculations, we study the chiral self-assembly of achiral HtB-HBC molecules upon adsorption on the Cu(110) surface. We find that chirality is expressed at two different levels: a +/-5 degrees rotation of the molecular axis with respect to the close-packed direction of the Cu(110) substrate and a chiral close-packed arrangement expected for star-shaped molecules in 2D. Out of the four possible chiral expressions, only two are found to exist due the effect of van der Waals (vdW) interactions forcing the molecules to simultaneously adjust to the atomic template of the substrate geometry and self-assemble in a close-packed geometry.

The adsorption structure of NO on Pd(111) at high pressures studied by STM and DFT.

Using a combination of scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, we study the adsorption structure of NO on Pd(111) at pressures of up to 720 Torr. From atomically resolved STM images, we identify, at high pressures, only the (2 x 2)-3NO structure, which is identical with the highest NO-coverage structure found at low pressure and low temperature. DFT calculations confirm that the (2 x 2)-3NO structure is indeed the most stable adsorption structure at high pressures. Contrary to recent suggestions in the literature, we therefore conclude that we find no evidence for a (3 x 3)-7NO structure on Pd(111) at high NO pressure.