Highly Selective On-Surface Ring-Opening of Aromatic Azulene Moiety.

Controllable ring-opening of polycyclic aromatic hydrocarbons plays a crucial role in various chemical and biological processes. However, breaking down aromatic covalent C-C bonds is exceptionally challenging due to their high stability and strong aromaticity. This study presents a seminal report on the precise and highly selective on-surface ring-opening of the seven-membered ring within the aromatic azulene moieties under mild conditions. The chemical structures of the resulting products were identified using bond-resolved scanning probe microscopy. Furthermore, through density functional theory calculations, we uncovered the mechanism behind the ring-opening process and elucidated its chemical driving force. The key to achieving this ring-opening process lies in manipulating the local aromaticity of the aromatic azulene moiety through strain-induced internal ring rearrangement and cyclodehydrogenation. By precisely controlling these factors, we successfully triggered the desired ring-opening reaction. Our findings not only provide valuable insights into the ring-opening process of polycyclic aromatic hydrocarbons but also open up new possibilities for the manipulation and reconstruction of these important chemical structures.

Molecular sensitised probe for amino acid recognition within peptide sequences.

The combination of low-temperature scanning tunnelling microscopy with a mass-selective electro-spray ion-beam deposition established the investigation of large biomolecules at nanometer and sub-nanometer scale. Due to complex architecture and conformational freedom, however, the chemical identification of building blocks of these biopolymers often relies on the presence of markers, extensive simulations, or is not possible at all. Here, we present a molecular probe-sensitisation approach addressing the identification of a specific amino acid within different peptides. A selective intermolecular interaction between the sensitiser attached at the tip-apex and the target amino acid on the surface induces an enhanced tunnelling conductance of one specific spectral feature, which can be mapped in spectroscopic imaging. Density functional theory calculations suggest a mechanism that relies on conformational changes of the sensitiser that are accompanied by local charge redistributions in the tunnelling junction, which, in turn, lower the tunnelling barrier at that specific part of the peptide.

Coverage-modulated halogen bond geometry transformation in supramolecular assemblies.

Halogen bonding (HB) has emerged as a promising route for designing supramolecular assemblies due to its directional nature and versatility in modifying interactions through the choice of halogens and molecular entities. Despite this, methods for tuning these interactions on surfaces, particularly in terms of directionality, are limited. In this study, we present a strategy for tuning the directionality of self-assembly processes in homomolecular organic compounds on inert metal surfaces. A variety of halogen-halogen geometries can promote highly-extended one-dimensional or two-dimensional self-assembly depending on the molecular coverage. Our results indicate that under lower molecular coverage conditions, robust one-dimensional (1D) structures promote the self-assembly of halogen-bonded molecules on Au(111). At certain coverage, a transformation from type-I to synthon halogen bonding is observed, leading to an extended hexagonal pattern of molecular assembly. The atomistic details of the structures are experimentally studied using high-resolution atomic force microscopy and supported by first-principle calculations. We employed DFT to evaluate the interplay between electrostatics and dispersion forces driving both type-I and synthon assemblies. The results reveal a halogen-bond geometry transformation induced by a subtle balance of molecule-molecule interaction. Finally, we investigate the capability of the halogen-bonded supramolecular assembly to periodically confine electronic quantum states and single atoms. Our findings demonstrate the versatility of sigma-bonding in regulating molecular assembly and provide new insights for tailoring functional molecular structures on an inert metal substrate.

Structural Expansion of Cyclohepta[def]fluorene towards Azulene-Embedded Non-Benzenoid Nanographenes.

Non-benzenoid non-alternant nanographenes (NGs) have attracted increasing attention on account of their distinct electronic and structural features in comparison to their isomeric benzenoid counterparts. In this work, we present a series of unprecedented azulene-embedded NGs on Au(111) during the attempted synthesis of cyclohepta[def]fluorene-based high-spin non-Kekulé structure. Comprehensive scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM) evidence the structures and conformations of these unexpected products. The dynamics of the precursor bearing 9-(2,6-dimethylphenyl)anthracene and dihydro-dibenzo-cyclohepta[def]fluorene units and its reaction products on the surface are analyzed by density functional theory (DFT) and molecular dynamics (MD) simulations. Our study sheds light on the fundamental understanding of precursor design for the fabrication of π-extended non-benzenoid NGs on a metal surface.

Electronic Self-Passivation of Single Vacancy in Black Phosphorus via Ionization.

We report that monoelemental black phosphorus presents a new electronic self-passivation scheme of single vacancy (SV). By means of low-temperature scanning tunneling microscopy and noncontact atomic force microscopy, we demonstrate that the local reconstruction and ionization of SV into negatively charged SV^{-} leads to the passivation of dangling bonds and, thus, the quenching of in-gap states, which can be achieved by mild thermal annealing or STM tip manipulation. SV exhibits a strong and symmetric Friedel oscillation (FO) pattern, while SV^{-} shows an asymmetric FO pattern with local perturbation amplitude reduced by one order of magnitude and a faster decay rate. The enhanced passivation by forming SV^{-} can be attributed to its weak dipolelike perturbation, consistent with density-functional theory numerical calculations. Therefore, self-passivated SV^{-} is electrically benign and acts as a much weaker scattering center, which may hold the key to further enhance the charge mobility of black phosphorus and its analogs.

On-Surface Synthesis of a Dicationic Diazahexabenzocoronene Derivative on the Au(111) Surface.

The atomically precise control over the size, shape and structure of nanographenes (NGs) or the introduction of heteroatom dopants into their sp2 -carbon lattice confer them valuable electronic, optical and magnetic properties. Herein, we report on the design and synthesis of a hexabenzocoronene derivative embedded with graphitic nitrogen in its honeycomb lattice, achieved via on-surface assisted cyclodehydrogenation on the Au(111) surface. Combined scanning tunnelling microscopy/spectroscopy and non-contact atomic force microscopy investigations unveil the chemical and electronic structures of the obtained dicationic NG. Kelvin probe force microscopy measurements reveal a considerable variation of the local contact potential difference toward lower values with respect to the gold surface, indicative of its positive net charge. Altogether, we introduce the concept of cationic nitrogen doping of NGs on surfaces, opening new avenues for the design of novel carbon nanostructures.

On-Surface Hydrogenation of Buckybowls: From Curved Aromatic Molecules to Planar Non-Kekulé Aromatic Hydrocarbons.

Functionalization of surfaces with derivatives of Buckminsterfullerene fragment molecules seems to be a promising approach toward bottom-up fabrication of carbon nanotube modified electrode surfaces. The modification of a Cu(100) surface with molecules of the buckybowl pentaindenocorannulene has been studied by means of scanning tunneling microscopy, carbon monoxide-modified noncontact atomic force microscopy, time-of-flight secondary mass spectrometry, and quantum chemical calculations. Two different adsorbate modes are identified, in which the majority is oriented such that the bowl cavity points away from the surface and the convex side is partially immersed into a four-atom vacancy in the Cu(100) surface. A minority is oriented such that the convex side points away from the surface with the five benzo tabs oriented basically parallel to the surface. Thermal annealing leads to hydrogenation and planarization of the molecules in two steps under specific C-C bond cleavage. The benzo tabs of the convex side up species serve as a hydrogen source. The final product has an open-shell electron structure that is quenched on the surface.

Steering alkyne homocoupling with on-surface synthesized metal-organic complexes.

We report a multi-step on-surface synthesis strategy. The first step consists in the surface-supported synthesis of metal-organic complexes, which are subsequently used to steer on-surface alkyne coupling reactions. In addition, we analyze and compare the electronic properties of the different coupling motifs obtained.

Multiscale Analysis of Phase Transformations in Self-Assembled Layers of 4,4'-Biphenyl Dicarboxylic Acid on the Ag(001) Surface.

Understanding the nucleation and growth kinetics of thin films is a prerequisite for their large-scale utilization in devices. For self-assembled molecular phases near thermodynamic equilibrium the nucleation-growth kinetic models are still not developed. Here, we employ real-time low-energy electron microscopy (LEEM) to visualize a phase transformation induced by the carboxylation of 4,4'-biphenyl dicarboxylic acid on Ag(001) under ultra-high-vacuum conditions. The initial (α) and transformed (ß) molecular phases are characterized in detail by X-ray photoemission spectroscopy, single-domain low-energy electron diffraction, room-temperature scanning tunneling microscopy, noncontact atomic force microscopy, and density functional theory calculations. The phase transformation is shown to exhibit a rich variety of phenomena, including Ostwald ripening of the α domains, burst nucleation of the ß domains outside the α phase, remote dissolution of the α domains by nearby ß domains, and a structural change from disorder to order. We show that all phenomena are well described by a general growth-conversion-growth (GCG) model. Here, the two-dimensional gas of admolecules has a dual role: it mediates mass transport between the molecular islands and hosts a slow deprotonation reaction. Further, we conclude that burst nucleation is consistent with a combination of rather weak intermolecular bonding and the onset of an additional weak many-body attractive interaction when a molecule is surrounded by its nearest neighbors. In addition, we conclude that Ostwald ripening and remote dissolution are essentially the same phenomenon, where a more stable structure grows at the expense of a kinetically formed, less stable entity via transport through the 2D gas. The proposed GCG model is validated through kinetic Monte Carlo (kMC) simulations.

Strain-Induced Isomerization in One-Dimensional Metal-Organic Chains.

The ability to use mechanical strain to steer chemical reactions creates completely new opportunities for solution- and solid-phase synthesis of functional molecules and materials. However, this strategy is not readily applied in the bottom-up on-surface synthesis of well-defined nanostructures. We report an internal strain-induced skeletal rearrangement of one-dimensional (1D) metal-organic chains (MOCs) via a concurrent atom shift and bond cleavage on Cu(111) at room temperature. The process involves Cu-catalyzed debromination of organic monomers to generate 1,5-dimethylnaphthalene diradicals that coordinate to Cu adatoms, forming MOCs with both homochiral and heterochiral naphthalene backbone arrangements. Bond-resolved non-contact atomic force microscopy imaging combined with density functional theory calculations showed that the relief of substrate-induced internal strain drives the skeletal rearrangement of MOCs via 1,3-H shifts and shift of Cu adatoms that enable migration of the monomer backbone toward an energetically favorable registry with the Cu(111) substrate. Our findings on this strain-induced structural rearrangement in 1D systems will enrich the toolbox for on-surface synthesis of novel functional materials and quantum nanostructures.

Controlling the stereospecific bonding motif of Au-thiolate links.

Over the last decades, organosulfur compounds at the interface of noble metals have proved to be extremely versatile systems for both fundamental and applied research. However, the anchoring of thiols to gold remained an object of controversy for a long time. The RS-Au-SR linkage, in particular, is a robust bonding configuration that displays interesting properties. It is generated spontaneously at room temperature and can be used for the production of extended molecular nanostructures. In this work we explore the behavior of 1,4-bis(4-mercaptophenyl)benzene (BMB) on the Au(111) surface, which results in the formation of 2D crystalline metal-organic assemblies stabilized by this type of Au-thiolate bonds. We show how to control the thiolate's stereospecific bonding motif and thereby choose whether to form ordered arrays of Au3BMB3 units with embedded triangular nanopores or linearly stacked metal-organic chains. The former turn out to be thermodynamically favored structures and display confinement of the underneath Au(111) surface state. The electronic properties of single molecules as well as of the 2D crystalline self-assemblies have been characterized both on the metal-organic backbone and inside the associated pores.

Atomic-scale defects and electronic properties of a transferred synthesized MoS2 monolayer.

MoS2 monolayer samples were synthesized on a SiO2/Si wafer and transferred to Ir(111) for nano-scale characterization. The samples were extensively characterized during every step of the transfer process, and MoS2 on the final substrate was examined down to the atomic level by scanning tunneling microscopy (STM). The procedures conducted yielded high-quality monolayer MoS2 of milimeter-scale size with an average defect density of 2 × 1013 cm-2. The lift-off from the growth substrate was followed by a release of the tensile strain, visible in a widening of the optical band gap measured by photoluminescence. Subsequent transfer to the Ir(111) surface led to a strong drop of this optical signal but without further shifts of characteristic peaks. The electronic band gap was measured by scanning tunneling spectroscopy (STS), revealing n-doping and lateral nano-scale variations. The combined use of STM imaging and density functional theory (DFT) calculations allows us to identify the most recurring point-like defects as S vacancies.