Combustion-generated soot particles can have significant impact on climate, environment and human health. Thus, understanding the processes governing the formation of soot particles in combustion is a topic of ongoing research. In this study, high-resolution atomic force microscopy (AFM) was used for direct imaging of the building blocks forming the particles in the early stages of soot formation. Incipient soot particles were collected right after the particle nucleation zone of a slightly sooting ethylene/air laminar premixed flame at atmospheric pressure and analyzed by AFM after a rapid sublimation procedure. Our data shed light on one of the most complex and still debated aspect on soot formation, i.e., the nucleation process. The molecular constituents of the initial particles have been individually analyzed in detail in their chemical/structural characteristics. Our data demonstrate the large complexity/variety of the aromatic compounds which are the building blocks of the initial soot particles. Nevertheless, some fundamental and specific characteristics have been clearly ascertained. These include a significant presence of penta-rings as opposed to the purely benzenoid aromatic compounds and the noticeable presence of aliphatic side-chains. In addition, there were indications for the presence of persistent π radicals. Incipient soot was also investigated by Raman spectroscopy, the results of which agreed in terms of chemical and structural composition of the particles with those obtained by AFM.

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.

AbstractMit der Rastersondenmikroskopie kann man auf einer Oberfläche adsorbierte Moleküle individuell und mit hoher Auflösung untersuchen. Die Technik, die bei tiefen Temperaturen und im Ultrahochvakuum durchgeführt wird, liefert Informationen über Struktur, Konfiguration, Ladungszustand, Aromatizität und die Beteiligung von Resonanzstrukturen. Durch Funktionalisierung der Spitze eines Rasterkraftmikroskops mit einem CO‐Molekül können Einzelmoleküle mit atomarer Auflösung abgebildet werden, ihre Adsorptionsgeometrie kann gemessen und die Bindungsordnungen im Molekül können bestimmt werden. Mit der Rastertunnelmikroskopie und der Kelvinsondenkraftmikroskopie kann man zudem die Elektronendichte der molekularen Grenzorbitale bzw. die Ladungsverteilung innerhalb des Moleküls kartieren. In Kombination ergeben diese Methoden ein hochauflösendes Verfahren zur Identifizierung und Charakterisierung von Einzelmolekülen. Die Empfindlichkeit auf Einzelmoleküle sowie die Option, durch Manipulation von Atomen mit der Spitze des Mikroskops chemische Reaktionen auszulösen, eröffnen einzigartige chemische Anwendungsmöglichkeiten und heben die Rastersondenmikroskopie von den klassischen Methoden zur molekularen Strukturaufklärung heraus. Somit kann die Rasterkraftmikroskopie nicht nur bei der Identifizierung von schwer zu bestimmenden Naturstoffen helfen, sondern sie ist auch ein leistungsstarkes und besonders gut geeignetes Instrument, um Oberflächenreaktionen zu untersuchen und Radikale und molekulare Mischungen zu charakterisieren. In diesem Aufsatz zeigen wir auf, welche Entwicklung die hochauflösende Rastersondenmikroskopie mit funktionalisierter Spitze bei der molekularen Strukturaufklärung und ‐charakterisierung in den vergangenen Jahren genommen hat, und erörtern die Herausforderungen der kommenden Jahre.

In this chapter, we illustrate the great potential of combining organic synthesis with atomic resolution AFM and STM to address relevant and classic issues in chemistry, by summarizing selected examples in which we were involved in recent years. As case studies, the long-standing chemical challenges covered here include the experimental discrimination of bond orders in single molecules, the characterization of extremely insoluble compounds such as nanographenes, the analysis of the individual components of complex mixtures, and the on-surface generation and identification of highly reactive molecules and intermediates.

Sequential tunneling of electrons through a single chlorine vacancy on a multilayer NaCl film on Cu(100) in the junction of a non-contact atomic force microscope with a conductive tip can lead to a negative damping of the cantilever. The characteristic features in the damping signal as a function of NaCl-layer thickness, tip position and tip-sample bias can be explained in a simple rate-equation model for the sequential tunneling process through the double-barrier tunnel junction. The first barrier results from the vacuum gap between tip and vacancy and its tunneling rate is tuned by the tip position and the applied bias. The second barrier results from the NaCl film and its tunneling rate is governed by the film's thickness. The current-induced damping is strongest if the two tunneling rates through each of the barriers individually are both comparable to the cantilever's oscillation frequency. The damping signal can be employed for detecting subfemtoampere tunneling currents and furthermore, maps of the damping signal can be used to inspect the mesoscopic tip shape. The observed and described current-induced damping should be a common phenomenon in non-contact atomic force microscopy for double-barrier tunnel junction geometries. (C) 2018 Published by Elsevier B.V.

Dissolved organic carbon (DOC) is the largest pool of exchangeable organic carbon in the ocean. However, less than 10% of DOC has been molecularly characterized in the deep ocean to understand DOC's recalcitrance. Here we analyze the radiocarbon (C-14) depleted, and presumably refractory, low molecular weight (LMW) DOC from the North Central Pacific using atomic force microscopy to produce the first atomic-resolution images of individual LMW DOC molecules. We evaluate surface and deep LMW DOC chemical structures in the context of their relative persistence and recalcitrance. Atomic force microscopy resolved planar structures with features similar to polycyclic aromatic compounds and carboxylic-rich alicyclic structures with less than five aromatic carbon rings. These compounds comprise 8% and 20% of the measurable molecules investigated in the surface and deep, respectively. Resolving the structures of individual DOC molecules represents a step forward in molecular characterization of DOC and in understanding its long-term stability. Plain Language Summary The marine dissolved organic carbon (DOC) reservoir is similar in size to that of atmospheric carbon dioxide and plays an important role in the ocean carbon cycle. DOC comprises a vast mixture of diverse molecules, the majority of which remain structurally uncharacterized. Identification of DOC molecular structures will aid our understanding of DOC cycling. Here, we present the first images of individual DOC molecules using atomic force microscopy. We compare images of low molecular weight DOC molecules extracted from samples collected at different depths in the North Central Pacific. Our results help unravel the molecular architecture, formation processes, and cycling of marine DOC in the ocean. This work demonstrates that atomic force microscopy can facilitate structure determination in oceanic mixtures and provide an additional complimentary toolbox for analytical techniques in geophysical relevant environments.

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.

Si dangling bonds at the interface of quasi-free-standing monolayer graphene (QFMLG) are known to act as scattering centers that can severely affect carrier mobility. Herein, we investigate the atomic and electronic structure of Si dangling bonds in QFMLG using low-temperature scanning tunneling microscopy/spectroscopy (STM/STS), atomic force microscopy (AFM), and density functional theory (DFT) calculations. Two types of defects with different contrast were observed on a flat graphene terrace by STM and AFM; in particular, their STM contrast varied with the bias voltage. Moreover, these defects showed characteristic STS peaks at different energies, 1.1 and 1.4 eV. The comparison of the experimental data with the DFT calculations indicates that the defects with STS peak energies of 1.1 and 1.4 eV consist of clusters of three and four Si dangling bonds, respectively. The relevance of the present results for the optimization of graphene synthesis is discussed.

Rearrangements that change the connectivity of a carbon skeleton are often useful in synthesis, but it can be difficult to follow their mechanisms. Scanning probe microscopy can be used to manipulate a skeletal rearrangement at the single-molecule level, while monitoring the geometry of reactants, intermediates and final products with atomic resolution. We studied the reductive rearrangement of 1,1-dibromo alkenes to polyynes on a NaCl surface at 5 K, a reaction that resembles the Fritsch–Buttenberg–Wiechell rearrangement. Voltage pulses were used to cleave one C–Br bond, forming a radical, then to cleave the remaining C•–Br bond, triggering the rearrangement. These experiments provide structural insight into the bromo-vinyl radical intermediates, showing that the C=C•–Br unit is nonlinear. Long polyynes, up to the octayne Ph–(C≡C)8–Ph, have been prepared in this way. The control of skeletal rearrangements opens a new window on carbon-rich materials and extends the toolbox for molecular synthesis by atom manipulation. Atomic manipulation was used to control the reductive rearrangement of 1,1-dibromo alkenes to acetylenes on a NaCl surface at 5 K, and the stages of the reaction were visualized with atomic resolution using AFM. Polyynes ranging from triyne to octayne were prepared in this way, and STM was used to map their frontier orbitals and determine their transport gaps.

Antiaromatic and open-shell molecules are attractive because of their distinct electronic and magnetic behaviour. However, their increased reactivity creates a challenge for probing their properties. Here, we describe the on-surface and in-solution generation and characterisation of a highly reactive antiaromatic molecule: indeno[1,2-b]fluorene (IF). In solution, we generated IF by KI-induced dehalogenation of a dibromo-substituted precursor molecule and found that IF survives for minutes at ambient conditions. Using atom manipulation at low temperatures we generated IF on Cu(111) and on bilayer NaCl. On these surfaces, we characterised IF by bond-order analysis using non-contact atomic force microscopy with CO-functionalised tips and by orbital imaging using scanning tunnelling microscopy. We found that the closed-shell configuration and antiaromatic character predicted for gas-phase IF are preserved on the NaCl film. On Cu(111), we observed significant bond-order reorganisation within the s-indacene moiety because of chemisorption, highlighting the importance of molecule surface interactions on the π-electron distribution.

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.

Intermolecular single-electron transfer on electrically insulating films is a key process in molecular electronics 1 – 4 and an important example of a redox reaction 5 , 6 . Electron-transfer rates in molecular systems depend on a few fundamental parameters, such as interadsorbate distance, temperature and, in particular, the Marcus reorganization energy 7 . This crucial parameter is the energy gain that results from the distortion of the equilibrium nuclear geometry in the molecule and its environment on charging 8 , 9 . The substrate, especially ionic films 10 , can have an important influence on the reorganization energy 11 , 12 . Reorganization energies are measured in electrochemistry 13 as well as with optical 14 , 15 and photoemission spectroscopies 16 , 17 , but not at the single-molecule limit and nor on insulating surfaces. Atomic force microscopy (AFM), with single-charge sensitivity 18 – 22 , atomic-scale spatial resolution 20 and operable on insulating films, overcomes these challenges. Here, we investigate redox reactions of single naphthalocyanine (NPc) molecules on multilayered NaCl films. Employing the atomic force microscope as an ultralow current meter allows us to measure the differential conductance related to transitions between two charge states in both directions. Thereby, the reorganization energy of NPc on NaCl is determined as (0.8 ± 0.2) eV, and density functional theory (DFT) calculations provide the atomistic picture of the nuclear relaxations on charging. Our approach presents a route to perform tunnelling spectroscopy of single adsorbates on insulating substrates and provides insight into single-electron intermolecular transport.

Heavy oil molecular mixtures were investigated on the basis of single molecules resolved by atomic force microscopy. The eight different samples analyzed include asphaltenes and other heavy oil fractions of different geographic/geologic origin and processing steps applied. The collected AFM data of individual molecules provide information about the molecular geometry, aromaticity, the content of nonhexagonal rings, typical types and locations of heterocycles, occurrence, length and connectivity of alkyl side chains, and ratio of archipelago- vs island-type architectures. Common and distinguishing structural motifs for the different samples could be identified. The measured size distributions and the degree of unsaturation by scanning probe microscopy is consistent with mass spectrometry data presented herein. The results obtained reveal the complexity, properties and specifics of heavy oil fractions with implications for upstream oil production and downstream oil processing. Moreover, the identified molecular structures form a basis for modeling geochemical oil formation processes.

Using combined low temperature scanning tunneling microscopy and atomic force microscopy (AFM), we demonstrate hydrogen passivation of individual, selected dangling bonds (DBs) on a hydrogen-passivated Si(100)-2 × 1 surface (H–Si) by atom manipulation. This method allows erasing of DBs and thus provides a promising scheme for error-correction in hydrogen lithography. Both Si-terminated tips (Si tips) for hydrogen desorption and H-terminated tips (H tips) for hydrogen passivation are created by deliberate contact to the H–Si surface and are assigned by their characteristic contrast in AFM. DB passivation is achieved by transferring the H atom that is at the apex of an H tip to the DB, reestablishing a locally defect-free H–Si surface.

We describe the generation of a meta-aryne at low temperature (T = 5 K) using atomic manipulation on Cu(111) and on bilayer NaCl on Cu(111). We observe different voltage thresholds for dehalogenation of the precursor and different reaction products depending on the substrate surface. The chemical structure is resolved by atomic force microscopy with CO-terminated tips, revealing the radical positions and confirming a diradical rather than an anti-Bredt olefin structure for this meta-aryne on NaCl.