Single-Molecule Identification of the Isomers of a Lipidic Antibody Activator.

Molecular structural elucidation can be accomplished by different techniques, such as nuclear magnetic resonance or X-ray diffraction. However, the former does not give information about the three-dimensional atomic arrangement, and the latter needs crystallizable solid samples. An alternative is direct, real-space visualization of the molecules by cryogenic scanning tunneling microscopy (STM). This technique is usually limited to thermally robust molecules because an annealing step is required for sample deposition. A landmark development has been the coupling of STM with electrospray deposition (ESD), which smooths the process and widens the scope of the visualization technique. In this work, we present the on-surface characterization of air-, light-, and temperature-sensitive rhamnopolyene with relevance in molecular biology. Supported by theoretical calculations, we characterize two isomers of this flexible molecule, confirming the potential of the technique to inspect labile, non-crystallizable compounds.

The effect of water on gold supported chiral graphene nanoribbons: rupture of conjugation by an alternating hydrogenation pattern.

In the last few years we have observed a breakpoint in the development of graphene-derived technologies, such as liquid phase filtering and their application to electronics. In most of these cases, they imply exposure of the material to solvents and ambient moisture, either in the fabrication of the material or the final device. The present study demonstrates the sensitivity of graphene nanoribbon (GNR) zigzag edges to water, even in extremely low concentrations. We have addressed the unique reactivity of (3,1)-chiral GNR with moisture on Au(111). Water shows a reductive behaviour, hydrogenating the central carbon of the zigzag segments. By combining scanning tunnelling microscopy (STM) with simulations, we demonstrate how their reactivity reaches a thermodynamic limit when half of the unit cells are reduced, resulting in an alternating pattern of hydrogenated and pristine unit cells starting from the terminal segments. Once a quasi-perfect alternation is reached, the reaction stops regardless of the water concentration. The hydrogenated segments limit the electronic conjugation of the GNR, but the reduction can be reversed both by tip manipulation and annealing. Selective tip-induced dehydrogenation allowed the stabilization of radical states at the edges of the ribbons, while the annealing of the sample completely recovered the original, pristine GNR.

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.

On-surface synthesis of non-benzenoid conjugated polymers by selective atomic rearrangement of ethynylarenes.

Here, we report a new on-surface synthetic strategy to precisely introduce five-membered units into conjugated polymers from specifically designed precursor molecules that give rise to low-bandgap fulvalene-bridged bisanthene polymers. The selective formation of non-benzenoid units is finely controlled by the annealing parameters, which govern the initiation of atomic rearrangements that efficiently transform previously formed diethynyl bridges into fulvalene moieties. The atomically precise structures and electronic properties have been unmistakably characterized by STM, nc-AFM, and STS and the results are supported by DFT theoretical calculations. Interestingly, the fulvalene-bridged bisanthene polymers exhibit experimental narrow frontier electronic gaps of 1.2 eV on Au(111) with fully conjugated units. This on-surface synthetic strategy can potentially be extended to other conjugated polymers to tune their optoelectronic properties by integrating five-membered rings at precise sites.

Unusual Scaffold Rearrangement in Polyaromatic Hydrocarbons Driven by Concerted Action of Single Gold Atoms on a Gold Surface.

Chemical transformation of polyaromatic hydrocarbon (PAH) molecules following different reaction strategies has always been the focus of organic synthesis. In this work, we report the synthesis of a PAH molecule, formation of which consists of an unusual C-C bond cleavage accompanied by a complex π-conjugated molecular scaffold rearrangement. We demonstrate that the complex chemical transformation is steered by concerted motion of individual Au0 gold atoms on a supporting Au(111) surface. This observation underpins the importance of single-atom catalysis mediated by adatoms in on-surface synthesis as well as catalytic activity of single Au0 atoms facilitating cleavage of covalent carbon bonds.

Circumventing the stability problems of graphene nanoribbon zigzag edges.

Carbon nanostructures with zigzag edges exhibit unique properties-such as localized electronic states and spins-with exciting potential applications. Such nanostructures however are generally synthesized under vacuum because their zigzag edges are unstable under ambient conditions: a barrier that must be surmounted to achieve their scalable integration into devices for practical purposes. Here we show two chemical protection/deprotection strategies, demonstrated on labile, air-sensitive chiral graphene nanoribbons. Upon hydrogenation, the chiral graphene nanoribbons survive exposure to air, after which they are easily converted back to their original structure by annealing. We also approach the problem from another angle by synthesizing a form of the chiral graphene nanoribbons that is functionalized with ketone side groups. This oxidized form is chemically stable and can be converted to the pristine hydrocarbon form by hydrogenation and annealing. In both cases, the deprotected chiral graphene nanoribbons regain electronic properties similar to those of the pristine nanoribbons. We believe both approaches may be extended to other graphene nanoribbons and carbon-based nanostructures.

Resolving Atomic-Scale Defects in Conjugated Polymers On-Surfaces.

Atomic scale defects significantly affect the mechanical, electronic, and optical properties of π-conjugated polymers. Here, isolated atomic-scale defects are deliberately introduced into a prototypical anthracene-ethynylene π-conjugated polymer, and its local density of states is carefully examined on the atomic scale to show how individual defects modify the inherent electronic and magnetic properties of this one-dimensional systems. Scanning tunneling and atomic force microscopy experiments, supplemented with density functional theory calculations, reveal the existence of a sharp electronic resonance at the Fermi energy around certain defects, which is associated with the formation of a local magnetic moment accompanied by substantial mitigation of the mobility of charge carriers. While defects in traditionally synthesized polymers lead to arbitrary conformations, the presented results clearly reflect the preferential formation of low dimensional defects at specific polymer sites, which may introduce the possibility of engineering macroscopic defects in surface-synthesized conjugated polymers.

Atomic Scale Control and Visualization of Topological Quantum Phase Transition in π-Conjugated Polymers Driven by Their Length.

Quantum phase transitions (QPTs) driven by quantum fluctuations are transitions between distinct quantum phases of matter. At present, they are poorly understood and not readily controlled. Here, scanning tunneling microscopy (STM) and noncontact atomic force microscopy (nc-AFM) are used to explore atomic scale control over quantum phase transitions between two different topological quantum states of a well-defined π-conjugated polymer. The phase transition is driven by a pseudo Jahn-Teller effect that is activated above a certain polymer chain length. In addition, theoretical calculations indicate the presence of long-lasting coherent fluctuations between the polymer's two quantum phases near the phase transition, at finite temperature. This work thus presents a new way of exploring atomic-scale control over QPTs and indicates that emerging quantum criticality in the vicinity of a QPT can give rise to new states of organic matter.

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 Strain-Driven Synthesis of Nonalternant Non-Benzenoid Aromatic Compounds Containing Four- to Eight-Membered Rings.

The synthesis of polycyclic aromatic hydrocarbons containing various non-benzenoid rings remains a big challenge facing contemporary organic chemistry despite a considerable effort made over the last decades. Herein, we present a novel route, employing on-surface chemistry, to synthesize nonalternant polycyclic aromatic hydrocarbons containing up to four distinct kinds of non-benzenoid rings. We show that the surface-induced mechanical constraints imposed on strained helical reactants play a decisive role leading to the formation of products, energetically unfavorable in solution, with a peculiar ring current stabilizing the aromatic character of the π-conjugated system. Determination of the chemical and electronic structures of the most frequent product reveals its closed-shell character and low band gap. The present study renders a new route for the synthesis of novel nonalternant polycyclic aromatic hydrocarbons or other hydrocarbons driven by internal stress imposed by the surface not available by traditional approaches of organic chemistry in solution.

On-Surface Synthesis of One-Dimensional Coordination Polymers with Tailored Magnetic Anisotropy.

One-dimensional (1D) metalloporphyrin polymers can exhibit magnetism, depending on the central metal ion and the surrounding ligand field. The possibility of tailoring the magnetic signal in such nanostructures is highly desirable for potential spintronic devices. We present low-temperature (4.2 K) scanning tunneling microscopy and spectroscopy (LT-STM/STS) in combination with high-resolution atomic force microscopy (AFM) and a density functional theory (DFT) study of a two-step synthetic protocol to grow a robust Fe-porphyrin-based 1D polymer on-surface and to tune its magnetic properties. A thermally assisted Ullmann-like coupling reaction of Fe(III)diphenyl-bromine-porphyrin (2BrFeDPP-Cl) on Au(111) in ultra-high vacuum results in long (up to 50 nm) 1D metal-organic wires with regularly distributed magnetic and (electronically) independent porphyrins units, as confirmed by STM images. Thermally controlled C-H bond activation leads to conformational changes in the porphyrin units, which results in molecular planarization steered by 2D surface confinement, as confirmed by high-resolution AFM images. Spin-flip STS images in combination with DFT self-consistent spin-orbit coupling calculations of porphyrin units with different structural conformations reveal that the magnetic anisotropy of the triplet ground state of the central Fe ion units drops down substantially upon intramolecular rearrangements. These results point out to new opportunities for realizing and studying well-defined 1D organic magnets on surfaces and demonstrate the feasibility of tailoring their magnetic properties.

Tailoring π-conjugation and vibrational modes to steer on-surface synthesis of pentalene-bridged ladder polymers.

The development of synthetic strategies to engineer π-conjugated polymers is of paramount importance in modern chemistry and materials science. Here we introduce a synthetic protocol based on the search for specific vibrational modes through an appropriate tailoring of the π-conjugation of the precursors, in order to increase the attempt frequency of a chemical reaction. First, we design a 1D π-conjugated polymer on Au(111), which is based on bisanthene monomers linked by cumulene bridges that tune specific vibrational modes. In a second step, upon further annealing, such vibrational modes steer the twofold cyclization reaction between adjacent bisanthene moieties, which gives rise to a long pentalene-bridged conjugated ladder polymer featuring a low bandgap. In addition, high resolution atomic force microscopy allows us to identify by atomistic insights the resonance form of the polymer, thus confirming the validity of the Glidewell and Lloyd´s rules for aromaticity. This on-surface synthetic strategy may stimulate exploiting previously precluded reactions towards π-conjugated polymers with specific structures and properties.

Diradical Organic One-Dimensional Polymers Synthesized on a Metallic Surface.

We report on the synthesis and characterization of atomically precise one-dimensional diradical peripentacene polymers on a Au(111) surface. By means of high-resolution scanning probe microscopy complemented by theoretical simulations, we provide evidence of their magnetic properties, which arise from the presence of two unpaired spins at their termini. Additionally, we probe a transition of their magnetic properties related to the length of the polymer. Peripentacene dimers exhibit an antiferromagnetic (S=0) singlet ground state. They are characterized by singlet-triplet spin-flip inelastic excitations with an effective exchange coupling (Jeff ) of 2.5 meV, whereas trimers and longer peripentacene polymers reveal a paramagnetic nature and feature Kondo fingerprints at each terminus due to the unpaired spin. Our work provides access to the precise fabrication of polymers featuring diradical character which are potentially useful in carbon-based optoelectronics and spintronics.

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.

Tailoring topological order and π-conjugation to engineer quasi-metallic polymers.

Topological band theory predicts that a topological electronic phase transition between two insulators must proceed via closure of the electronic gap. Here, we use this transition to circumvent the instability of metallic phases in π-conjugated one-dimensional (1D) polymers. By means of density functional theory, tight-binding and GW calculations, we predict polymers near the topological transition from a trivial to a non-trivial quantum phase. We then use on-surface synthesis with custom-designed precursors to make polymers consisting of 1D linearly bridged acene moieties, which feature narrow bandgaps and in-gap zero-energy edge states when in the topologically non-trivial phase close to the topological transition point. We also reveal the fundamental connection between topological classes and resonant forms of 1D π-conjugated polymers.

Thermally induced intra-molecular transformation and metalation of free-base porphyrin on Au(111) surface steered by surface confinement and ad-atoms.

We investigated chemical transformations of a fluorinated free-base porphyrin, 5,10,15,20-tetrakis(4-fluorophenyl)-21,23H-porphyrin (2H-4FTPP) under a Au(111) surface confinement and including gold adatoms by using an experiment and density functional theory based first-principles calculations. Annealing of 2H-4FTPP led to cyclodehydrogenation of the molecule to a π-extended fused aromatic planar compound, 2H-4FPP, and metallation of the porphyrin ring by Au atoms to Au-4FPP complex. Noticeable lowering of bond-dissociation energies of the pyrrole's C-H bonds of the Au(111) supported molecule with respect to their values in the gas phase explained the observed on-surface planarization. Our findings also indicate that Au adatoms may catalyze cleavage of C-H/F bonds in temperature-initiated processes on Au surfaces. BDEs and explicit inclusion of Au adatoms helps to rationalize thermally induced chemical reactions on the respective surface.

Nitrous oxide as an effective AFM tip functionalization: a comparative study.

We investigate the possibility of functionalizing Au tips by N2O molecules deposited on a Au(111) surface and their further use for imaging with submolecular resolution. First, we characterize the adsorption of the N2O species on Au(111) by means of atomic force microscopy with CO-functionalized tips and density functional theory (DFT) simulations. Subsequently we devise a method of attaching a single N2O to a metal tip apex and benchmark its high-resolution imaging and spectroscopic capabilities using FePc molecules. Our results demonstrate the feasibility of high-resolution imaging. However, we find an inherent asymmetry of the N2O probe-particle adsorption on the tip apex, in contrast to a CO tip reference. These findings are consistent with DFT calculations of the N2O- and CO tip apexes.

On-Surface Synthesis of Ethynylene-Bridged Anthracene Polymers.

Engineering low-band-gap π-conjugated polymers is a growing area in basic and applied research. The main synthetic challenge lies in the solubility of the starting materials, which precludes advancements in the field. Here, we report an on-surface synthesis protocol to overcome such difficulties and produce poly(p-anthracene ethynylene) molecular wires on Au(111). To this aim, a quinoid anthracene precursor with =CBr2 moieties is deposited and annealed to 400 K, resulting in anthracene-based polymers. High-resolution nc-AFM measurements confirm the nature of the ethynylene-bridge bond between the anthracene moieties. Theoretical simulations illustrate the mechanism of the chemical reaction, highlighting three major steps: dehalogenation, diffusion of surface-stabilized carbenes, and homocoupling, which enables the formation of an ethynylene bridge. Our results introduce a novel chemical protocol to design π-conjugated polymers based on oligoacene precursors and pave new avenues for advancing the emerging field of on-surface synthesis.