The ability to control the transition from a two-dimensional (2D) monolayer to the three-dimensional (3D) molecular structure in the growth of organic layers on surfaces is essential for the production of functional thin films and devices. This has, however, proved to be extremely challenging, starting from the currently limited ability to attain a molecular scale characterization of this transition. Here, through innovative application of low-dose electron diffraction and aberration-corrected transmission electron microscopy (acTEM), combined with scanning tunneling microscopy (STM), we reveal the structural changes occurring as film thickness is increased from monolayer to tens of nanometers for supramolecular assembly of two prototypical benzenecarboxylic acids – terephthalic acid (TPA) and trimesic acid (TMA) – on graphene. The intermolecular hydrogen bonding in these molecules is similar and both form well-ordered monolayers on graphene, but their structural transitions with film thickness are very different. While the structure of TPA thin films varies continuously towards the 3D lattice, TMA retains its planar monolayer structure up to a critical thickness, after which a transition to a polycrystalline film occurs. These distinctive structural evolutions can be rationalized in terms of the topological differences in the 3D crystallography of the two molecules. The templated 2D structure of TPA can smoothly map to its 3D structure through continuous molecular tilting within the unit cell, whilst the 3D structure of TMA is topologically distinct from its 2D form, so that only an abrupt transition is possible. The concept of topological protection of the 2D structure gives a new tool for the molecular design of nanostructured films.

Self-assembly of three related molecules – terephthalic acid and its hydroxylated analogues – at liquid/solid interfaces (graphite/heptanoic acid and graphite/1-phenyloctane) has been studied using a combination of scanning tunnelling microscopy and molecular mechanics and molecular dynamics calculations. Brickwork-like patterns typical for terephthalic acid self-assembly have been observed for all three molecules. However, several differences became apparent: (i) formation or lack of adsorbed monolayers (self-assembled monolayers formed in all systems, with one notable exception of terephthalic acid at the graphite/1-phenyloctane interface where no adsorption was observed), (ii) the size of adsorbate islands (large islands at the interface with heptanoic acid and smaller ones at the interface with 1-phenyloctane), and (iii) polymorphism of the hydroxylated terephthalic acids’ monolayers, dependent on the molecular structure and/or solvent. To rationalise this behaviour, molecular mechanics and molecular dynamics calculations have been performed, to analyse the three key aspects of the energetics of self-assembly: intermolecular, substrate–adsorbate and solvent–solute interactions. These energetic characteristics of self-assembly were brought together in a Born–Haber cycle, to obtain the overall energy effects of formation of self-assembled monolayers at these liquid/solid interfaces.

We have synthesised osmium nanoparticles of defined size (1.5–50 nm) on a B- and S-doped turbostratic graphitic structure by electron-beam irradiation of an organometallic osmium complex encapsulated in self-spreading polymer micelles, and characterised them by transmission electron microscopy (TEM), high-resolution TEM (HRTEM), and atomic force microscopy (AFM) on the same grid. Oxidation of the osmium nanoparticles after exposure to air was detected by X-ray photoelectron spectroscopy (XPS).

The unique electronic properties and functional tunability of polycyclic aromatic hydrocarbons have recently fostered high hopes for their use in flexible, green, portable, and cheap technologies. Most applications require the deposition of thin molecular films onto conductive electrodes. The growth of the first few molecular layers represents a crucial step in the device fabrication since it determines the structure of the molecular film and the energy level alignment of the metal–organic interface. Here, we explore the formation of this interface by analyzing the interplay between reversible molecule–substrate charge transfer, yielding intermolecular repulsion, and van der Waals attractions in driving the molecular assembly. Using a series of ad hoc designed molecules to balance the two effects, we combine scanning tunnelling microscopy with atomistic simulations to study the self-assembly behavior. Our systematic analysis identifies a growth mode characterized by anomalous coarsening that we anticipate to occur in a wide class of metal–organic interfaces and which should thus be considered as integral part of the self-assembly process when depositing a molecule on a conducting surface.Keywords: charge transfer; interfacial dipoles; metal−organic interfaces; polycyclic aromatic hydrocarbons; self-assembly at surfaces;

The interaction of a de novo synthesised ester with single crystal metal surfaces has been investigated as a model system for the heterogeneous hydrogenolysis of esters. Scanning tunnelling microscopy measurements show dissociative adsorption at room temperature on Cu(110) but no significant reaction on Au(111). The dissociative pathway has been identified by comparing with possible fragment species, demonstrating that the ester cleavage occurs along the RCH(CH3)–OC(O)R bond.

•Surface morphology of MnSi thin films grown by solid-phase epitaxy on Si(111)-7 × 7•STM and DFT investigation by systematically changing the amount of deposited Mn•New 3 × 3 surface reconstruction identified and atomic model based on DFT proposedThe surface morphology of MnSi thin films grown on Si(111)-7 × 7 substrates was investigated by systematically changing the amount of deposited Mn. A new 3 × 3 surface reconstruction was found at the very initial growth stages, whose atomic configuration was analyzed both experimentally and theoretically. At a coverage of 0.1 monolayers, the formation of nanometer-sized MnSi islands was observed in coexistence with Mn nanoclusters that fit within the 7 × 7 half unit cell. With increasing Mn deposition, the MnSi islands grow, develop extended flat tops and eventually coalesce into an atomically flat film with a high corrugated 3×3 reconstruction punctuated by several holes. The successive film growth mode is characterized by the formation of MnSi quadlayers with a low corrugated 3×3 reconstruction.

Supramolecular nanostructures with tunable dimensionalities are fabricated by deposition of benzene–carboxylic acids on the Cu(110) surface. By tailoring the number and position of the functional moieties, the structure of the final molecular assemblies can be rationally modified ranging from isolated one-dimensional chains to compact two-dimensional islands. Molecular units are chosen that can assemble through metal–organic and electrostatic interactions. The hierarchy between these intermolecular forces guarantees that a primary organization level, constituted by metal–organic polymeric chains, is developed by all molecular units while the secondary interchain interactions can be arbitrarily adjusted. Scanning tunneling microscopy, density functional theory calculations, and kinetic Monte Carlo simulations are used to characterize and rationalize the experimental findings.

The possibility of modifying the intermolecular interactions of absorbed benzene-carboxylic acids from coordination to hydrogen bonding by changing their surface coverage is demonstrated through a combination of scanning tunnelling microscopy, X-ray photoemission spectroscopy and density functional theory calculations.

The influence of the density of metallic atoms on the formation of supramolecular structures onto Si surface alloys is investigated by scanning tunneling microscopy. Terephthalic acid (TPA) adsorption experiments are performed on the Si(111) α- and β-(3×3)-Bi surfaces. Although both surfaces have the same unit cell with Bi atoms incorporated into the Si substrate, they show a completely different behavior in respect to the formation of the supramolecular arrays. TPA molecules do not build any regular structure and adsorb randomly on the α surface but self-assemble into ordered and extended layers on the β surface. This demonstrates that the absence of dangling bonds in metal-Si surface alloys is not a sufficient condition for supramolecular self-assembly but that the surface density of metallic atoms is a further essential parameter.Highlights► Deposition of terephthalic acid on Si(111)-(3 × 3)-Bi surface alloys. ► Random adsorption on the Si(111) α-(3 × 3)-Bi surface. ► Supramolecular arrays on the Si(111) β-(3 × 3)-surface. ► Importance of high surface density of metallic atoms in the formation of ordered molecular arrays.

We report on the formation of chiral domains self-assembled from terephthalic acid (TPA) and iron on a Cu(110) surface. Using scanning tunnelling microscopy, we observe that the supramolecular structures are organized on successive hierarchical levels. Chirality develops only at the latest assembly step, with the primary TPA constituents and the secondary diiron−terephthalate metal−organic complexes being mirror symmetric. The driving forces for the generation of these high-order chiral architectures are identified as competing coordination bonding within the metal−organic complexes and hydrogen bonding among them. The emergence of extended metal−organic networks is hindered by the incommensurability with the substrate.

Terephthalic acid (TPA) deposited on Si(111)-7 × 7, Si(111)--Ag and Ag(111) has been studied as a model system to understand how much passivated semiconductor surfaces differ from semiconductor and metal surfaces in respect of supramolecular self assembly. By scanning tunneling microscopy it is found that TPA molecules do not form any ordered supramolecular structure on the pristine semiconductor surface, due to a strong molecule–substrate interaction. On the contrary, TPA has a weaker interaction with Si(111)--Ag, leading to the formation of an ordered supramolecular layer stabilized by carboxyl hydrogen bonds. These structures are very similar to the supramolecular layer of TPA formed on Ag(111), indicating that the two substrates behave similarly for what concerns the adsorption of functional organic molecules. However, the deposition of Fe on the TPA layers on Si(111)--Ag does not induce the formation of two-dimensional metal–organic frameworks which, on the contrary, readily develop on Ag(111). Possible origins of this difference are discussed.

The interaction of a de novo synthesised ester with single crystal metal surfaces has been investigated as a model system for the heterogeneous hydrogenolysis of esters. Scanning tunnelling microscopy measurements show dissociative adsorption at room temperature on Cu(110) but no significant reaction on Au(111). The dissociative pathway has been identified by comparing with possible fragment species, demonstrating that the ester cleavage occurs along the RCH(CH3)–OC(O)R bond.

Terephthalic acid (TPA) deposited on Si(111)-7 × 7, Si(111)--Ag and Ag(111) has been studied as a model system to understand how much passivated semiconductor surfaces differ from semiconductor and metal surfaces in respect of supramolecular self assembly. By scanning tunneling microscopy it is found that TPA molecules do not form any ordered supramolecular structure on the pristine semiconductor surface, due to a strong molecule–substrate interaction. On the contrary, TPA has a weaker interaction with Si(111)--Ag, leading to the formation of an ordered supramolecular layer stabilized by carboxyl hydrogen bonds. These structures are very similar to the supramolecular layer of TPA formed on Ag(111), indicating that the two substrates behave similarly for what concerns the adsorption of functional organic molecules. However, the deposition of Fe on the TPA layers on Si(111)--Ag does not induce the formation of two-dimensional metal–organic frameworks which, on the contrary, readily develop on Ag(111). Possible origins of this difference are discussed.

The possibility of modifying the intermolecular interactions of absorbed benzene-carboxylic acids from coordination to hydrogen bonding by changing their surface coverage is demonstrated through a combination of scanning tunnelling microscopy, X-ray photoemission spectroscopy and density functional theory calculations.

We have synthesised osmium nanoparticles of defined size (1.5–50 nm) on a B- and S-doped turbostratic graphitic structure by electron-beam irradiation of an organometallic osmium complex encapsulated in self-spreading polymer micelles, and characterised them by transmission electron microscopy (TEM), high-resolution TEM (HRTEM), and atomic force microscopy (AFM) on the same grid. Oxidation of the osmium nanoparticles after exposure to air was detected by X-ray photoelectron spectroscopy (XPS).