On-surface synthesis of a doubly anti-aromatic carbon allotrope.

Synthetic carbon allotropes such as graphene1, carbon nanotubes2 and fullerenes3 have revolutionized materials science and led to new technologies. Many hypothetical carbon allotropes have been discussed4, but few have been studied experimentally. Recently, unconventional synthetic strategies such as dynamic covalent chemistry5 and on-surface synthesis6 have been used to create new forms of carbon, including γ-graphyne7, fullerene polymers8, biphenylene networks9 and cyclocarbons10,11. Cyclo[N]carbons are molecular rings consisting of N carbon atoms12,13; the three that have been reported to date (N = 10, 14 and 18)10,11 are doubly aromatic, which prompts the question: is it possible to prepare doubly anti-aromatic versions? Here we report the synthesis and characterization of an anti-aromatic carbon allotrope, cyclo[16]carbon, by using tip-induced on-surface chemistry6. In addition to structural information from atomic force microscopy, we probed its electronic structure by recording orbital density maps14 with scanning tunnelling microscopy. The observation of bond-length alternation in cyclo[16]carbon confirms its double anti-aromaticity, in concordance with theory. The simple structure of C16 renders it an interesting model system for studying the limits of aromaticity, and its high reactivity makes it a promising precursor to novel carbon allotropes15.

Aromaticity Reversal Induced by Vibrations in Cyclo[16]carbon.

Aromaticity is typically regarded as an intrinsic property of a molecule, correlated with electron delocalization, stability, and other properties. Small variations in the molecular geometry usually result in small changes in aromaticity, in line with Hammond's postulate. For example, introducing bond-length alternation in benzene and square cyclobutadiene by modulating the geometry along the Kekulé vibration gradually decreases the magnitude of their ring currents, making them less aromatic and less antiaromatic, respectively. A sign change in the ring current, corresponding to a reversal of aromaticity, typically requires a gross perturbation such as electronic excitation, addition or removal of two electrons, or a dramatic change in the molecular geometry. Here, we use multireference calculations to show how movement along the Kekulé vibration, which controls bond-length alternation, induces a sudden reversal in the ring current of cyclo[16]carbon, C16. This reversal occurs when the two orthogonal π systems of C16 sustain opposing currents. These results are rationalized by a Hückel model which includes bond-length alternation, and which is combined with a minimal model accounting for orbital contributions to the ring current. Finally, we successfully describe the electronic structure of C16 with a "divide-and-conquer" approach suitable for execution on a quantum computer.

Visualization and identification of single meteoritic organic molecules by atomic force microscopy.

Using high-resolution atomic force microscopy (AFM) with CO-functionalized tips, we atomically resolved individual molecules from Murchison meteorite samples. We analyzed powdered Murchison meteorite material directly, as well as processed extracts that we prepared to facilitate characterization by AFM. From the untreated Murchison sample, we resolved very few molecules, as the sample contained mostly small molecules that could not be identified by AFM. By contrast, using a procedure based on several trituration and extraction steps with organic solvents, we isolated a fraction enriched in larger organic compounds. The treatment increased the fraction of molecules that could be resolved by AFM, allowing us to identify organic constituents and molecular moieties, such as polycyclic aromatic hydrocarbons and aliphatic chains. The AFM measurements are complemented by high-resolution mass spectrometry analysis of Murchison fractions. We provide a proof of principle that AFM can be used to image and identify individual organic molecules from meteorites and propose a method for extracting and preparing meteorite samples for their investigation by AFM. We discuss the challenges and prospects of this approach to study extraterrestrial samples based on single-molecule identification.

π-Diradical Aromatic Soot Precursors in Flames.

Soot emitted from incomplete combustion of hydrocarbon fuels contributes to global warming and causes human disease. The mechanism by which soot nanoparticles form within hydrocarbon flames is still an unsolved problem in combustion science. Mechanisms proposed to date involving purely chemical growth are limited by slow reaction rates, whereas mechanisms relying on solely physical interactions between molecules are limited by weak intermolecular interactions that are unstable at flame temperatures. Here, we show evidence for a reactive π-diradical aromatic soot precursor imaged using non-contact atomic force microscopy. Localization of π-electrons on non-hexagonal rings was found to allow for Kekulé aromatic soot precursors to possess a triplet diradical ground state. Barrierless chain reactions are shown between these reactive sites, which provide thermally stable aromatic rim-linked hydrocarbons under flame conditions. Quantum molecular dynamics simulations demonstrate physical condensation of aromatics that survive for tens of picoseconds. Bound internal rotors then enable the reactive sites to find each other and become chemically cross-linked before dissociation. These species provide a rapid, thermally stable chain reaction toward soot nanoparticle formation and could provide molecular targets for limiting the emission of these toxic combustion products.

Probing Molecular Excited States by Atomic Force Microscopy.

By employing single charge injections with an atomic force microscope, we investigated redox reactions of a molecule on a multilayer insulating film. First, we charged the molecule positively by attaching a single hole. Then we neutralized it by attaching an electron and observed three channels for the neutralization. We rationalize that the three channels correspond to transitions to the neutral ground state, to the lowest energy triplet excited states and to the lowest energy singlet excited states. By single-electron tunneling spectroscopy we measured the energy differences between the transitions obtaining triplet and singlet excited state energies. The experimental values are compared with density functional theory calculations of the excited state energies. Our results show that molecules in excited states can be prepared and that energies of optical gaps can be quantified by controlled single-charge injections. Our work demonstrates the access to, and provides insight into, ubiquitous electron-attachment processes related to excited-state transitions important in electron transfer and molecular optoelectronics phenomena on surfaces.

An on-surface Diels-Alder reaction.

The Diels-Alder reaction is one of the most popular reactions in organic chemistry. However, its use in the field of on-surface synthesis is hampered by the spatial restrictions of this cycloaddition reaction. Herein we selected a cyclic strained triyne to demonstrate an on-surface hexadehydro-Diels-Alder reaction in a single molecule. The reaction was studied in detail by means of atomic force microscopy (AFM) with CO-functionalized tips. Our results pave the way to use this iconic pericyclic reaction for on-surface synthesis, introducing the concept of atom economy in the field.

Synthesis of Cyclo[18]carbon via Debromination of C18Br6.

Cyclo[18]carbon (C18, a molecular carbon allotrope) can be synthesized by dehalogenation of a bromocyclocarbon precursor, C18Br6, in 64% yield, by atomic manipulation on a sodium chloride bilayer on Cu(111) at 5 K, and imaged by high-resolution atomic force microscopy. This method of generating C18 gives a higher yield than that reported previously from the cyclocarbon oxide C24O6. The experimental images of C18 were compared with simulated images for four theoretical model geometries, including possible bond-angle alternation: D18h cumulene, D9h polyyne, D9h cumulene, and C9h polyyne. Cumulenic structures, with (D9h) and without (D18h) bond-angle alternation, can be excluded. Polyynic structures, with (C9h) and without (D9h) bond-angle alternation, both show a good agreement with the experiment and are challenging to differentiate.

Intramolecular Coupling of Terminal Alkynes by Atom Manipulation.

Glaser-like coupling of terminal alkynes by thermal activation is extensively used in on-surface chemistry. Here we demonstrate an intramolecular version of this reaction performed by atom manipulation. We used voltage pulses from the tip to trigger a Glaser-like coupling between terminal alkyne carbons within a custom-synthesized precursor molecule adsorbed on bilayer NaCl on Cu(111). Different conformations of the precursor molecule and the product were characterized by molecular structure elucidation with atomic force microscopy and orbital density mapping with scanning tunneling microscopy, accompanied by density functional theory calculations. We revealed partially dehydrogenated intermediates, providing insight into the reaction pathway.

Revisiting Kekulene: Synthesis and Single-Molecule Imaging.

Four decades after the first (and only) reported synthesis of kekulene, this emblematic cycloarene has been obtained again through an improved route involving the construction of a key synthetic intermediate, 5,6,8,9-tetrahydrobenzo[m]tetraphene, by means of a double Diels-Alder reaction between styrene and a versatile benzodiyne synthon. Ultra-high-resolution AFM imaging of single molecules of kekulene and computational calculations provide additional support for a molecular structure with a significant degree of bond localization in accordance with the resonance structure predicted by the Clar model.

Charge-Induced Structural Changes in a Single Molecule Investigated by Atomic Force Microscopy.

Intramolecular structural relaxations occurring upon electron transfer are crucial in determining the rate of redox reactions. Here, we demonstrate that subangstrom structural changes occurring upon single-electron charging can be quantified by means of atomically resolved atomic force microscopy (AFM) for the case of single copper(II)phthalocyanine (CuPc) molecules deposited on an ultrathin NaCl film. Imaging the molecule in distinct charge states (neutral and anionic) reveals characteristic differences in the AFM contrast. In comparison to density functional theory simulations these changes in contrast can be directly related to relaxations of the molecule's geometric structure upon charging. The dominant contribution arises from a nonhomogeneous vertical relaxation of the molecule, caused by a change in the electrostatic interaction with the surface.

Exploring a Route to Cyclic Acenes by On-Surface Synthesis.

A route to generate cyclacenes by on-surface synthesis is explored. We started by synthesizing two tetraepoxycyclacenes by sequences of Diels-Alder cycloadditions. Subsequently, these molecules were deposited onto Cu(111) and scanning-tunneling-microscopy(STM)-based atom manipulation was employed to dissociate the oxygen atoms. Atomic force microscopy (AFM) with CO-functionalized tips enabled the detailed characterization of the reaction products and revealed that, at most, two oxygens per molecule could be removed. Importantly, our experimental results suggest that the generation of cyclacenes by the described route might be possible for larger epoxycyclacenes.

Atomic Force Microscopy Identifying Fuel Pyrolysis Products and Directing the Synthesis of Analytical Standards.

Here we present a new method that integrates atomic force microscopy (AFM) with analytical tools such as high-performance liquid chromatography (HPLC) with diode-array ultraviolet-visible (UV) absorbance, and mass spectrometry (MS) along with synthetic chemistry. This allows the detection, identification, and quantification of novel polycyclic aromatic hydrocarbons (PAH) in complex molecular mixtures. This multidisciplinary methodology is employed to characterize the supercritical pyrolysis products of n-decane, a model fuel. The pyrolysis experiments result in a complex mixture of both unsubstituted as well as highly methylated PAH. We demonstrate the AFM-driven discovery of a novel compound, benz[ l]indeno[1,2,3- cd]pyrene, with the chemical structure assignment serving as input for the chemical synthesis of such molecule. The synthesis is verified by AFM, and the synthesized compound is used as a reference standard in analytical measurements, establishing the first-ever unequivocal identification and quantification of this PAH as a fuel product. Moreover, the high-resolution AFM analysis detected several five- to eight-ring PAH, which represents novel fuel pyrolysis and/or combustion products. This work provides a route to develop new analytical standards by symbiotically using AFM, chemical synthesis, and modern analytical tools.

Controlled Fragmentation of Single Molecules with Atomic Force Microscopy by Employing Doubly Charged States.

By atom manipulation we performed on-surface chemical reactions of a single molecule on a multilayer insulating film using noncontact atomic force microscopy. The single-electron sensitivity of atomic force microscopy allows us to follow the addition of single electrons to the molecule and the investigation of the reaction products. By performing a novel strategy based on long-lived doubly charged states a single molecule is fragmented. The fragmentation can be reverted by again changing the charge state of the system, characterizing a reversible reaction. The experimental results in addition to density-functional theory provide insight into the charge states of the different products and reaction pathways. Similar molecular systems could be used as charge-transfer units and to induce reversible chemical reactions.

[19]Dendriphene: A 19-Ring Dendritic Nanographene.

The synthesis of a threefold symmetric nanographene with 19 cata-fused benzene rings distributed within six branches is reported. This flat dendritic starphene, which is the largest unsubstituted cata-condensed PAH that has been obtained to date, was prepared in solution by means of a palladium-catalyzed aryne cyclotrimerization reaction and it was characterized on surface by scanning probe microscopy with atomic resolution.

Atomic Force Microscopy for Molecular Structure Elucidation.

Using scanning probe microscopy techniques, at low temperatures and in ultrahigh vacuum, individual molecules adsorbed on surfaces can be probed with ultrahigh resolution to determine their structure and details of their conformation, configuration, charge states, aromaticity, and the contributions of resonance structures. Functionalizing the tip of an atomic force microscope with a CO molecule enabled atomic-resolution imaging of single molecules, and measurement of their adsorption geometry and bond-order relations. In addition, by using scanning tunneling microscopy and Kelvin probe force microscopy, the density of the molecular frontier orbitals and the electric charge distribution within molecules can be mapped. Combining these techniques yields a high-resolution tool for the identification and characterization of individual molecules. The single-molecule sensitivity and the possibility of atom manipulation to induce chemical reactions with the tip of the microscope open up unique applications in chemistry, and differentiate scanning probe microscopy from conventional methods for molecular structure elucidation. Besides being an aid for challenging cases in natural product identification, atomic force microscopy has been shown to be a powerful tool for the investigation of on-surface reactions and the characterization of radicals and molecular mixtures. Herein we review the progress that high-resolution scanning probe microscopy with functionalized tips has made for molecular structure identification and characterization, and discuss the challenges it will face in the years to come.

The Electric Field of CO Tips and Its Relevance for Atomic Force Microscopy.

Metal tips decorated with CO molecules have paved the way for an impressively high resolution in atomic force microscopy (AFM). Although Pauli repulsion and the associated CO tilting play a dominant role at short distances, experiments on polar and metallic systems show that electrostatic interactions are necessary to understand the complex contrast observed and its distance evolution. Attempts to describe those interactions in terms of a single electrostatic dipole replacing the tip have led to contradictory statements about its nature and strength. Here, we solve this puzzle with a comprehensive experimental and theoretical characterization of the AFM contrast on Cl vacancies. Our model, based on density functional theory (DFT) calculations, reproduces the complex evolution of the contrast between both the Na cation and Cl anion sites, and the positively charged vacancy as a function of tip height, and highlights the key contribution of electrostatic interactions for tip-sample distances larger than 500 pm. For smaller separations, Pauli repulsion and the associated CO tilting start to dominate the contrast. The electrostatic field of the CO-metal tip can be represented by the superposition of the fields from the metal tip and the CO molecule. The long-range behavior is defined by the metal tip that contributes the field of a dipole with its positive pole at the apex. At short-range, the CO exhibits an opposite field that prevails. The interplay of these fields, with opposite sign and rather different spatial extension, is crucial to describe the contrast evolution as a function of the tip height.

Charge-State-Dependent Diffusion of Individual Gold Adatoms on Ionic Thin NaCl Films.

It is known that individual metal atoms on insulating ionic films can occur in several different (meta)stable charge states, which can be reversibly switched in a controlled fashion. Here we show that the diffusion of gold adatoms on NaCl thin films depends critically on their charge state. Surprisingly, the anionic species has a lower diffusion barrier than the neutral one. Furthermore, for the former we observe that the diffusion atop a bilayer of NaCl is strongly influenced by the interface between NaCl and the underlying copper substrate. This effect disappears for a trilayer of NaCl. These observations open the prospect of controlling the diffusion properties of individual metal atoms on thin insulating films.

Unraveling the Molecular Structures of Asphaltenes by Atomic Force Microscopy.

Petroleum is one of the most precious and complex molecular mixtures existing. Because of its chemical complexity, the solid component of crude oil, the asphaltenes, poses an exceptional challenge for structure analysis, with tremendous economic relevance. Here, we combine atomic-resolution imaging using atomic force microscopy and molecular orbital imaging using scanning tunnelling microscopy to study more than 100 asphaltene molecules. The complexity and range of asphaltene polycyclic aromatic hydrocarbons are established in detail. Identifying molecular structures provides a foundation to understand all aspects of petroleum science from colloidal structure and interfacial interactions to petroleum thermodynamics, enabling a first-principles approach to optimize resource utilization. Particularly, the findings contribute to a long-standing debate about asphaltene molecular architecture. Our technique constitutes a paradigm shift for the analysis of complex molecular mixtures, with possible applications in molecular electronics, organic light emitting diodes, and photovoltaic devices.

The synthesis and STM/AFM imaging of 'olympicene' benzo[cd]pyrenes.

H-Benzo[cd]pyrene ('Olympicene') is a polyaromatic hydrocarbon and non-Kekulé fragment of graphene. A new synthetic method has been developed for the formation of 6H-benzo[cd]pyrene and related ketones including the first time isolation of the unstable alcohol 6H-benzo[cd]pyren-6-ol. Molecular imaging of the reaction products with scanning tunnelling microscopy (STM) and non-contact atomic force microscopy (NC-AFM) characterised the 6H-benzo[cd]pyrene as well as the previously intangible and significantly less stable 5H-benzo[cd]pyrene, the fully conjugated benzo[cd]pyrenyl radical and the ketones as oxidation products.