Self-assembly of s-indacene-tetrone on Cu(111): molecular trapping and patterning of Cu adatoms.

The supramolecular self-assembly of s-indacene-1,3,5,7(2H,6H)-tetrone on the Cu(111) surface was investigated under ultrahigh vacuum by room-temperature scanning tunneling microscopy supported by theoretical modelling based on density functional theory. In total, six different phases were found, driven by hydrogen bonding, metal ligand coordination or covalent coupling. Host-guest interactions allowed for the accommodation of molecular or metal clusters inside the open nanoporous patterns. In one phase, molecular trapping was stochastically observed inside the large periodic nanopores created inside the supramolecular network. The three metal-organic networks observed resulted in the creation of different kinds of regular arrays of isolated metal adatoms or adatom clusters with a lattice period larger than 1 nm.

Portable Device for Multipurpose Research on Dendritic Yanson Point Contacts and Quantum Sensing.

Quantum structures are ideal objects by which to discover and study new sensor mechanisms and implement advanced approaches in sensor analysis to develop innovative sensor devices. Among them, one of the most interesting representatives is the Yanson point contact. It allows the implementation of a simple technological chain to activate the quantum mechanisms of selective detection in gaseous and liquid media. In this work, a portable device for multipurpose research on dendritic Yanson point contacts and quantum sensing was developed and manufactured. The device allows one to create dendritic Yanson point contacts and study their quantum properties, which are clearly manifested in the process of the electrochemical cyclic switchover effect. The device tests demonstrated that it was possible to gather data on the compositions and characteristics of the synthesized substances, and on the electrochemical processes that influence the production of dendritic Yanson point contacts, as well as on the electrophysical processes that provide information on the quantum nature of the electrical conductance of dendritic Yanson point contacts. The small size of the device makes it simple to integrate into a micro-Raman spectrometer setup. The developed device may be used as a prototype for designing a quantum sensor that will serve as the foundation for cutting-edge sensor technologies, as well as be applied to research into atomic-scale junctions, single-atom transistors, and any relative subjects.

Self-Accommodating Honeycomb Networks from Supramolecular Self-Assembly of s-Indacene-tetrone on Silver Surfaces.

We describe the self-assembly of s-indacene-tetrone on Ag(111), Ag(100), and Ag(110) surfaces and the formation of three hydrogen-bonded supramolecular phases representing a complex self-accommodating honeycomb network. The differences in terms of relative host-guest stability and molecular density are analyzed and discussed. Different epitaxial behaviors of the two-dimensional self-assembly are found as a response to the variations in the crystallographic orientation of the surface.

Electronic effects of the Bernal stacking of graphite on self-assembled aromatic adsorbates.

We compare by Scanning Tunneling Microscopy (STM) self-organized honeycomb monolayers of aromatic molecules formed either on graphite or on graphene. A differential contrast between the adsorption sites observed exclusively on graphite evidences the electronic effects of the symmetry breaking by the staggered atomic layers forming this substrate.

Molecular adaptation in supramolecular self-assembly: brickwall-type phases of indacene-tetrone on silver surfaces.

The supramolecular self-assembly of s-indacene-1,3,5,7(2H,6H)-tetrone (INDO4) on Ag(111), Ag(100) and Ag(110) surfaces was studied using scanning tunneling microscopy (STM). Four similar brickwall-type phases were found and in two of them the molecules appeared with distinct alternating contrast. The origin of this effect is discussed in terms of molecular adaptation.

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.

Strain relaxation and epitaxial relationship of perylene overlayer on Ag(110).

We present a room temperature STM study of perylene self-assembly on Ag(110) beyond the monolayer coverage regime. Coupling of the perylene aromatic boards yields π-π bonded stacks. The perylene stacks self-assemble into a continuous three-dimensional epitaxial overlayer of (3 × 5) symmetry. The self-assembly is driven by thermodynamic balance established under coupling of the intra- and intermolecular interactions and the molecule-substrate interaction all accommodating the short-range thermal motion of the constituent molecules. The balance bestows to the overlayer the unique ability to accommodate the underlying substrate morphology and to spread over the surface steps as a single structure preserving its lateral order and keeping epitaxial relationship with every surface terrace. The complete epitaxy is driven by (i) anchoring of half of the perylene stacks into specific adsorption sites on each terrace, (ii) interlacing of the perylene stacks across the steps within the entire H-bonded network, and (iii) relaxation of the overlayer strain via enhancement of the overlayer-specific vibrational modes and short-range thermal motion of the constituent molecules. This complete epitaxy phenomenon is described via (i) structural and statistical analysis of the molecularly resolved STM topographies, (ii) monitoring of the short-range molecular displacements under the strain relaxation, (iii) highlighting of specific intra-molecular and inter-molecular vibration modes through detailed analysis of HREELS spectra, and (iv) parametrization of the intermolecular interaction via pair potential calculation.

The Orientation of Silver Surfaces Drives the Reactivity and the Selectivity in Homo-Coupling Reactions.

Original reaction pathways can be explored in the on-surface synthesis approach where small aromatic precursors are confined to the surface of single crystal metals. The bis-indanedione molecule reacted with itself on silver surfaces in different ways, through a Knoevenagel reaction or an oxidative coupling, leading to the formation of a variety of new molecular compounds and covalently-linked 1D or 2D networks. Noteworthy, original reaction products were obtained that cannot be synthesized in traditional solvent-based chemistry. The lowest activation temperature for the homo-coupling reactions was found on the Ag(111) surface. The Ag(110) was highly selective in terms of coupling reaction type, while on Ag(100) the temperature could finely control the selectivity. The on-surface synthesis approach is shown here to be particularly efficient to produce original compounds in mild conditions, using activation temperatures as low as 200 °C. The different structures were characterized by scanning tunnelling microscopy (STM) together with X-ray photoelectron emission spectroscopy (XPS) and high-resolution electron energy loss spectroscopy (HREELS).

On-surface synthesis of aligned functional nanoribbons monitored by scanning tunnelling microscopy and vibrational spectroscopy.

In the blooming field of on-surface synthesis, molecular building blocks are designed to self-assemble and covalently couple directly on a well-defined surface, thus allowing the exploration of unusual reaction pathways and the production of specific compounds in mild conditions. Here we report on the creation of functionalized organic nanoribbons on the Ag(110) surface. C-H bond activation and homo-coupling of the precursors is achieved upon thermal activation. The anisotropic substrate acts as an efficient template fostering the alignment of the nanoribbons, up to the full monolayer regime. The length of the nanoribbons can be sequentially increased by controlling the annealing temperature, from dimers to a maximum length of about 10 nm, limited by epitaxial stress. The different structures are characterized by room-temperature scanning tunnelling microscopy. Distinct signatures of the covalent coupling are measured with high-resolution electron energy loss spectroscopy, as supported by density functional theory calculations.

Thermodynamic balance of perylene self-assembly on Ag(110).

We present a room temperature STM study of perylene adsorption on Ag(110) at the monolayer coverage regime. We found that structure and symmetry of the perylene monolayer are settled by thermodynamic balance of the three factors: (i) the ability of perylene molecules to recognize specific adsorption sites on the (110) lattice, (ii) the intermolecular interaction, and (iii) the accommodation of thermal motion of the molecules. The moderate strength of the site recognition and the intermolecular interaction, of the same order of magnitude as kT ∼ 25 meV, represents a key feature of the thermodynamic balance. It bestows to this system the unique quality to form the quasi-liquid monolayer of epitaxial as well as self-assembling character. The perylene monolayer accommodates the short-range motion of the molecules instead of quenching it. It precludes the formation of possible solid nuclei and maintains common registry of the included molecules. The surface registry of the quasi-liquid phase is provided by locking of a structure-related fraction of the perylene molecules into specific adsorption sites of the (110) lattice favorable in terms of intermolecular interaction.

Self-assembly of decoupled borazines on metal surfaces: the role of the peripheral groups.

Two borazine derivatives have been synthesised to investigate their self-assembly behaviour on Au(111) and Cu(111) surfaces by scanning tunnelling microscopy (STM) and theoretical simulations. Both borazines form extended 2D networks upon adsorption on both substrates at room temperature. Whereas the more compact triphenyl borazine 1 arranges into close-packed ordered molecular islands with an extremely low density of defects on both substrates, the tris(phenyl-4-phenylethynyl) derivative 2 assembles into porous molecular networks due to its longer lateral substituents. For both species, the steric hindrance between the phenyl and mesityl substituents results in an effective decoupling of the central borazine core from the surface. For borazine 1, this is enough to weaken the molecule-substrate interaction, so that the assemblies are only driven by attractive van der Waals intermolecular forces. For the longer and more flexible borazine 2, a stronger molecule-substrate interaction becomes possible through its peripheral substituents on the more reactive copper surface.

"Magic" surface clustering of borazines driven by repulsive intermolecular forces.

It's a kind of magic: Hydroxy pentaaryl borazine molecules self-assemble into small clusters (see structure) on Cu(111) surfaces, whereas with symmetric hexaaryl borazine molecules large islands are obtained. Simulations indicate that the observed "magic" cluster sizes result from long-range repulsive Coulomb forces arising from the deprotonation of the B-OH groups of the hydroxy pentaaryl borazine.

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.

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.

Global and local expression of chirality in serine on the Cu{110} surface.

Establishing a molecular-level understanding of enantioselectivity and chiral resolution at the organic-inorganic interfaces is a key challenge in the field of heterogeneous catalysis. As a model system, we investigate the adsorption geometry of serine on Cu{110} using a combination of low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The chirality of enantiopure chemisorbed layers, where serine is in its deprotonated (anionic) state, is expressed at three levels: (i) the molecules form dimers whose orientation with respect to the substrate depends on the molecular chirality, (ii) dimers of L- and D-enantiomers aggregate into superstructures with chiral (-1 ∓2; 4 0) lattices, respectively, which are mirror images of each other, and (iii) small islands have elongated shapes with the dominant direction depending on the chirality of the molecules. Dimer and superlattice formation can be explained in terms of intra- and interdimer bonds involving carboxylate, amino, and ß-OH groups. The stability of the layers increases with the size of ordered islands. In racemic mixtures, we observe chiral resolution into small ordered enantiopure islands, which appears to be driven by the formation of homochiral dimer subunits and the directionality of interdimer hydrogen bonds. These islands show the same enantiospecific elongated shapes those as in low-coverage enantiopure layers.

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.

Self-assembly of hydrogen-bonded chains of molecular landers.

One-dimensional chains of a specially designed lander molecule with di-carboxyl imide functional moieties, enabling complementary intermolecular hydrogen bonding, have been self-assembled under ultra high vacuum conditions on a Au(111) surface and characterized by scanning tunneling microscopy.

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.