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.

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.

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.

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.

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.

Supramolecular architectures on surfaces formed through hydrogen bonding optimized in three dimensions.

Supramolecular self-assembly on surfaces, guided by hydrogen bonding interactions, has been widely studied, most often involving planar compounds confined directly onto surfaces in a planar two-dimensional (2-D) geometry and equipped with structurally rigid chemical functionalities to direct the self-assembly. In contrast, so-called molecular Landers are a class of compounds that exhibit a pronounced three-dimensional (3-D) structure once adsorbed on surfaces, arising from a molecular backboard equipped with bulky groups which act as spacer legs. Here we demonstrate the first examples of extended, hydrogen-bonded surface architectures formed from molecular Landers. Using high-resolution scanning tunnelling microscopy (STM) under well controlled ultrahigh vacuum conditions we characterize both one-dimensional (1-D) chains as well as five distinct long-range ordered 2-D supramolecular networks formed on a Au(111) surface from a specially designed Lander molecule equipped with dual diamino-triazine (DAT) functional moieties, enabling complementary NH...N hydrogen bonding. Most interestingly, comparison of experimental results to STM image calculations and molecular mechanics structural modeling demonstrates that the observed molecular Lander-DAT structures can be rationalized through characteristic intermolecular hydrogen bonding coupling motifs which would not have been possible in purely planar 2-D surface assembly because they involve pronounced 3-D optimization of the bonding configurations. The described 1-D and 2-D patterns of Lander-DAT molecules may potentially be used as extended molecular molds for the nucleation and growth of complex metallic nanostructures.

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.

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.

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.

Elementary structural motifs in a random network of cytosine adsorbed on a gold(111) surface.

Nonsymmetrical organic molecules adsorbed on solid surfaces may assemble into random networks, thereby providing model systems for organic glasses that can be directly observed by scanning tunneling microscopy (STM). We investigated the structure of a disordered cytosine network on a gold(111) surface created by thermal quenching, to temperatures below 150 K, of the two-dimensional fluid present on the surface at room temperature. Comparison of STM images to density functional theory calculations allowed us to identify three elementary structural motifs (zigzag filaments and five- and six-membered rings) that underlie the whole supramolecular random network. The identification of elementary structural motifs may provide a new framework for understanding medium-range order in amorphous and glassy systems.

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.

Adsorbate-induced alloy phase separation: a direct view by high-pressure scanning tunneling microscopy.

The influence of high pressures of carbon monoxide (CO) on the stability of a Au/Ni(111) surface alloy has been studied by high-pressure scanning tunneling microscopy. We show that CO induces a phase separation of the surface alloy at high pressures, and by means of time-lapsed STM movies we find that Ni atoms are removed from the surface layer during the process. Density functional theory calculations reveal the thermodynamic driving force for the phase separation to be the Au-induced compression of the CO overlayer with a resulting CO-CO repulsion. Furthermore, the atomistic mechanism of the process is shown to be kink-site carbonyl formation and evaporation which is found to be enhanced by the presence of Au.