Characterizing aliphatic moieties in hydrocarbons with atomic force microscopy

Role of π-Radical Localization on Thermally Stable Cross-Links Between Polycyclic Aromatic Hydrocarbons

The thermal stability of cross-links between polycyclic aromatic hydrocarbons (PAHs) is critical for understanding the formation of soot pollutants, graphite, and carbon blacks. Recently, a variety of different π-radicals have been directly imaged and suggested to enable thermally stable bonding; however, a systematic study of reactivity has been lacking. In this work, we use density functional theory to study the reactivity of PAH π-radicals. The Mulliken spin densities are initially used to categorize the different classes of localization, and the bond energy is computed to determine the degree of localization required for thermal stability. The results showed that the bond energies of PAHs are strongly correlated with the calculated spin densities, but bond energies do not exist with the bond lengths due to significant rearrangement and steric effects during bond formation. A threshold for π-radical localization is suggested that will be stable in combustion and pyrolysis environments of ρMα ≥ 0.5. Finally, the formation of multicenter bonds between localized and delocalized π-radicals was investigated using the nudge elastic band (NEB) scan, and it was found that only delocalized π-radicals provided local energy minima. These results show that the localization of π-radicals is critical for the formation of thermally stable single-center bonds between aromatic radicals.

Portraits of Soot Molecules Reveal Pathways to Large Aromatics, Five-/Seven-Membered Rings, and Inception through π-Radical Localization

Incipient soot early in the flame was studied by high-resolution atomic force microscopy and scanning tunneling microscopy to resolve the atomic structure and orbital densities of single soot molecules prepared on bilayer NaCl on Cu(111). We resolved extended catacondensed and pentagonal-ring linked (pentalinked) species indicating how small aromatics cross-link and cyclodehydrogenate to form moderately sized aromatics. In addition, we resolved embedded pentagonal and heptagonal rings in flame aromatics. These nonhexagonal rings suggest simultaneous growth through aromatic cross-linking/cyclodehydrogenation and hydrogen abstraction acetylene addition. Moreover, we observed three classes of open-shell π-radical species. First, radicals with an unpaired π-electron delocalized along the molecule's perimeter. Second, molecules with partially localized π-electrons at zigzag edges of a π-radical. Third, molecules with strong localization of a π-electron at pentagonal- and methylene-type sites. The third class consists of π-radicals localized enough to enable thermally stable bonds, as well as multiradical species such as diradicals in the open-shell triplet state. These π-diradicals can rapidly cluster through barrierless chain reactions enhanced by van der Waals interactions. These results improve our understanding of soot formation and the products formed by combustion and could provide insights for cleaner combustion and the production of hydrogen without CO₂ emissions.

Usage of the Y-Rule and the Effect of the Occurrence of Heteroatoms (N, S) on the Frontier Molecular Orbitals Gap of Polycyclic Aromatic Hydrocarbons (PAHs), and Asphaltene-PAHs

The understanding of the molecular- and colloidal-structure of asphaltenes has seen a major progress; however, there are still issues that require answer. One of them is the location of the heteroatoms in the polycyclic aromatic hydrocarbon (PAH) fused aromatic ring (FAR) region of asphaltenes. Therefore, the effect on the frontier molecular orbitals (HOMO-LUMO) energy-gap due to the addition of a heteroatom (N or S) to PAHs, which are candidates of the PAH region in asphaltenes, has been systematically analyzed by placing S or N in various sites of the PAH molecule. The S is introduced as a thiophenic ring in a bay region, while the N is introduced as a pyridinic-N, which are prevalent forms in the asphaltene-PAH. 174 PAHs are studied with five fused aromatic rings (5FAR) to 10FAR. The π-electron allocation in resonant π-sextets and isolated double bonds is obtained using the Y-rule. The frontier orbitals optical transition is calculated with the ZINDO/S method. Within a FAR family an increment of π-sextets produces and increase of the HOMO-LUMO energy-gap. There is a linear relationship between the Y-rule mapping (percentage of fraction of π-sextet bond divided by nFAR) and the HOMO-LUMO energy-gap. In addition, the effect on the frontier orbitals energy-gap and on the π-electronic allocation due to the presence of N and S is negligible; therefore, to reach conclusions related to the asphaltene-PAH based on conclusions reached for PAH systems, with no heteroatoms, is a reasonable approach.

Preparation and characterization of non-aromatic ether self-assemblies on a HOPG surface

On-surface self-assemblies of aromatic organic molecules have been widely investigated, but the characterization of analogous self-assemblies consisting of fully sp³-hybridized molecules remains challenging. The possible on-surface orientations of alkyl molecules not exclusively comprised of long alkyl chains are difficult to distinguish because of their inherently low symmetry and non-planar nature. Here, we present a detailed study of diamondoid ethers, structurally rigid and fully saturated molecules, which form uniform 2D monolayers on a highly oriented pyrolytic graphite (HOPG) surface. Using scanning tunneling microscopy, various computational tools, and x-ray structural analysis, we identified the most favorable on-surface orientations of these rigid ethers and accounted for the forces driving the self-organization process. The influence of the oxygen atom and London dispersion interactions were found to be responsible for the formation of the observed highly ordered 2D ether assemblies. Our findings provide insight into the on-surface properties and behavior of non-aromatic organic compounds and broaden our understanding of the phenomena characteristic of monolayers consisting of non-planar molecules.

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.

Direct transformation of n-alkane into all-trans conjugated polyene via cascade dehydrogenation

Selective C(sp³) −H activation is of fundamental importance in processing alkane feedstocks to produce high-value-added chemical products. By virtue of an on-surface synthesis strategy, we report selective cascade dehydrogenation of n-alkane molecules under surface constraints, which yields monodispersed all-trans conjugated polyenes with unprecedented length controllability. We are also able to demonstrate the generality of this concept for alkyl-substituted molecules with programmable lengths and diverse functionalities, and more importantly its promising potential in molecular wiring.

Model Asphaltenes Adsorbed onto Methyl- and COOH-Terminated SAMs on Gold

Petroleum asphaltenes are surface-active compounds found in crude oils, and their interactions with surfaces and interfaces have huge implications for many facets of reservoir exploitation, including production, transportation, and oil-water separation. The asphaltene fraction in oil, found in the highest boiling-point range, is composed of many different molecules that vary in size, functionality, and polarity. Studies done on asphaltene fractions have suggested that they interact via polyaromatic and heteroaromatic ring structures and functional groups containing nitrogen, sulfur, and oxygen. However, isolating a single pure chemical structure of asphaltene in abundance is challenging and often not possible, which impairs the molecular-level study of asphaltenes of various architectures on surfaces. Thus, to further the molecular fundamental understanding, we chose to use functionalized model asphaltenes (AcChol-Th, AcChol-Ph, and 1,6-DiEtPy[Bu-Carb]) and model self-assembled monolayer (SAM) surfaces with precisely known chemical structures, whereby the hydrophobicity of the model surface is controlled. We applied solutions of asphaltenes to these SAM surfaces and then analyzed them with surface-sensitive techniques of near-edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectroscopy (XPS). We observe no adsorption of asphaltenes to the hydrophobic surface. On the hydrophilic surface, AcChol-Ph penetrates into the SAM with a preferential orientation parallel to the surface; AcChol-Th adsorbs in a similar manner, and 1,6-DiEtPy[Bu-Carb] binds the surface with a bent binding geometry. Overall, this study demonstrates the need for studying pure and fractionated asphaltenes at the molecular level, as even within a family of asphaltene congeners, very different surface interactions can occur.

Deciphering structure and aggregation in asphaltenes: hypothesis-driven design and development of synthetic model compounds

Asphaltenes comprise the heaviest and least understood fraction of crude petroleum. The asphaltenes are a diverse and complex mixture of organic and organometallic molecules in which most of the molecular constituents are tightly aggregated into more complicated suprastructures. The bulk properties of asphaltenes arise from a broad range of polycyclic aromatics, heteroatoms, and polar functional groups. Despite much analytical effort, the precise molecular architectures of the material remain unresolved. To understand asphaltene characteristics and reactivity, the field has turned to synthetic model compounds that mirror asphaltene structure, aggregation behavior, and thermal chemistry, including the nucleation of coke. Historically, molecular asphaltene modeling was limited to commercial compounds, offering little illumination and few opportunities for hypothesis-driven research. More recently, however, rational molecular design and modern organic synthesis have started to impact this area. This review provides an overview of commercially available model compounds but is principally focused on the design and synthesis of structurally advanced and appropriately functionalized compounds to mimic the physical and chemical behavior of asphaltenes. Efforts to model asphaltene aggregation are briefly discussed, and a prognosis for the field is offered. A referenced tabulation of the synthetic compounds reported to date is provided.

Unveiling Adatoms in On-Surface Reactions: Combining Scanning Probe Microscopy with van't Hoff Plots

Scanning probe microscopy has become an essential tool to not only study pristine surfaces but also on-surface reactions and molecular self-assembly. Nonetheless, due to inherent limitations, some atoms or (parts of) molecules are either not imaged or cannot be unambiguously identified. Herein, we discuss the arrangement of two different nonplanar molecular assemblies of para-hexaphenyl-dicarbonitrile (Ph₆(CN)₂) on Au(111) based on a combined theoretical and experimental approach. For deposition of Ph₆(CN)₂ on Au(111) kept at room temperature, a rhombic nanoporous network stabilized by a combination of hydrogen bonding and antiparallel dipolar coupling is formed. Annealing at 575 K resulted in an irreversible thermal transformation into a hexagonal nanoporous network stabilized by native gold adatoms. However, the Au adatoms could neither be unequivocally identified by scanning tunneling microscopy nor by noncontact atomic force microscopy. By combining van't Hoff plots derived from our scanning probe images with our density functional theory calculations, we were able to confirm the presence of the elusive Au adatoms in the hexagonal molecular network.

On-Surface Synthesis and Molecular Engineering of Carbon-Based Nanoarchitectures

On-surface synthesis via covalent coupling of adsorbed precursor molecules on metal surfaces has emerged as a promising strategy for the design and fabrication of novel organic nanoarchitectures with unique properties and potential applications in nanoelectronics, optoelectronics, spintronics, catalysis, etc. Surface-chemistry-driven molecular engineering (i.e., bond cleavage, linkage, and rearrangement) by means of thermal activation, light irradiation, and tip manipulation plays critical roles in various on-surface synthetic processes, as exemplified by the work from the Ernst group in a prior issue of ACS Nano. In this Perspective, we highlight recent advances in and discuss the outlook for on-surface syntheses and molecular engineering of carbon-based nanoarchitectures.

The Role of Methyl Groups in the Early Stage of Thermal Polymerization of Polycyclic Aromatic Hydrocarbons Revealed by Molecular Imaging

The initial thermal reactions of aromatic hydrocarbons are relevant to many industrial applications. However, tracking the growing number of heavy polycyclic aromatic hydrocarbon (PAH) products is extremely challenging because many reactions are unfolding in parallel from a mixture of molecules. Herein, we studied the reactions of 2,7-dimethylpyrene (DMPY) to decipher the roles of methyl substituents during mild thermal treatment. We found that the presence of methyl substituents is key for reducing the thermal severity required to initiate chemical reactions in natural molecular mixtures. A complex mixture of thermal products including monomers, dimers, and trimers was characterized by NMR, mass spectrometry, and noncontact atomic force microscopy (nc-AFM). A wide range of structural transformations including methyl transfer and polymerization reactions were identified. A detailed mechanistic understanding on the roles of H radicals during the polymerization of polycyclic aromatic hydrocarbons was obtained.

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.

On-Surface Intramolecular Reactions

In the past decade, on-surface chemistry has provided fascinating concepts for the construction of covalently bonded molecular nanostructures and the exploration of new synthetic pathways that may be different from chemical synthesis in solution. Although the intermolecular reaction of precursor molecules may lead to the formation of the desired low-dimensional molecular architectures, it remains challenging to realize defect-free syntheses over large areas. Recently, intramolecular on-surface reactions have attracted increasing attention because they offer promising ways to synthesize functional organic molecules, especially those with extended conjugated π-systems. In this Perspective, we summarize the recent achievements in the field of on-surface intramolecular reactions and discuss future prospects.

Asphaltene Adsorption on Functionalized Solids

Asphaltenes, heavy aromatic components of crude oil, are known to adsorb on surfaces and can lead to pipe clogging or hinder oil recovery. Because of their multicomponent structure, the details of their interactions with surfaces are complex. We investigate the effect of the physicochemical properties of the substrate on the extent and mechanism of this adsorption. Using wetting measurements, we relate the initial kinetics of deposition to the interfacial energy of the surface. We then quantify the long-term adsorption dynamics using a quartz crystal microbalance and ellipsometry. Finally, we investigate the mechanism and morphology of adsorption with force spectroscopy measurements as a function of surface chemistry. We determine different adsorption regimes differing in orientation, packing density, and initial kinetics on different substrate functionalizations. Specifically, we find that alkane substrates delay the initial monolayer formation, fluorinated surfaces exhibit fast adsorption but low bonding strength, and hydroxyl substrates lead to a different adsorption orientation and a high packing density of the asphaltene layer.

Elucidating the Geometric Substitution of Petroporphyrins by Spectroscopic Analysis and Atomic Force Microscopy Molecular Imaging

Determination of the molecular structures of petroporphyrins has been crucial to understand the diagenetic pathways and maturation of petroleum. However, these studies have been hampered by their structural complexity and the challenges associated with their isolation. In comparison to the skeletal macrocyclic structures, much less is known about the substitutions, which are more sensitive to the maturation and diagenesis pathways. While these isolated vanadyl petroporphyrins largely consist of etioporphyrin and deoxophylloerythroetioporphyrin as expected, surprisingly, we find evidence that one or a few β hydrogens are present in petroporphyrins of low carbon numbers using a combination of ultraviolet-visible spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry, and non-contact atomic force microscopy. Petroporphyrins with β hydrogens were not anticipated on the basis of their biological precursors. The data support dealkylation under catagenesis but not transalkylation or random alkylation of the β and meso positions, despite the fact that more complex porphyrin structures are formed.

Molecular Identification, Bond Order Discrimination, and Apparent Intermolecular Features in Atomic Force Microscopy Studied with a Charge Density Based Method

We introduce an efficient method to simulate high-resolution atomic force microscopy (HR-AFM) images with CO probes. Our model explicitly takes into account the charge densities of the sample and the probe for the calculation of the short-range (SR) interaction and retains ab initio accuracy with only two parameters, that are essentially universal, independent of the number of chemical species and the complexity of the bonding topology. The application to molecular images shows a strong dependence on the stoichiometry and bonding configuration that precludes the chemical identification of individual atoms based on local force-distance curves. However, we have identified features in the 2D images and 3D force maps that reflect the highly anisotropic spatial decay of the molecular charge density and provide a way toward molecular identification. The model treats SR and electrostatics interactions on an equal footing and correctly pinpoints the Pauli repulsion as the underlying interaction responsible for the bond order discrimination in C60. Finally, we settle the controversy regarding the origin of the intermolecular features, discarding the effect of the charge redistribution associated with the H bonds, and linking them with the overlap of the wave functions of the atoms that constitute the bond. This overlap creates saddle regions in the potential energy landscape that are sensed by the probe.

Assigning the absolute configuration of single aliphatic molecules by visual inspection

Deciphering absolute configuration of a single molecule by direct visual inspection is the next step in compound identification, with far-reaching implications for medicinal chemistry, pharmacology, and natural product synthesis. We demonstrate the feasibility of this approach utilizing low temperature atomic force microscopy (AFM) with a CO-functionalized tip to determine the absolute configuration and orientation of a single, adsorbed [123]tetramantane molecule, the smallest chiral diamondoid. We differentiate between single enantiomers on Cu(111) by direct visual inspection, and furthermore identify molecular dimers and molecular clusters. The experimental results are confirmed by a computational study that allowed quantification of the corresponding intermolecular interactions. The unique toolset of absolute configuration determination combined with AFM tip manipulation opens a route for studying molecular nucleation, including chirality-driven assembly or reaction mechanisms.

Prototypical Organic-Oxide Interface: Intramolecular Resolution of Sexiphenyl on In2O3(111)

The performance of an organic semiconductor device is critically determined by the geometric alignment, orientation, and ordering of the organic molecules. Although an organic multilayer eventually adopts the crystal structure of the organic material, the alignment and configuration at the interface with the substrate/electrode material are essential for charge injection into the organic layer. This work focuses on the prototypical organic semiconductor para-sexiphenyl (6P) adsorbed on In2O3(111), the thermodynamically most stable surface of the material that the most common transparent conducting oxide, indium tin oxide, is based on. The onset of nucleation and formation of the first monolayer are followed with atomically resolved scanning tunneling microscopy and noncontact atomic force microscopy (nc-AFM). Annealing to 200 °C provides sufficient thermal energy for the molecules to orient themselves along the high-symmetry directions of the surface, leading to a single adsorption site. The AFM data suggests an essentially planar adsorption geometry. With increasing coverage, the 6P molecules first form a loose network with a poor long-range order. Eventually, the molecules reorient into an ordered monolayer. This first monolayer has a densely packed, well-ordered (2 × 1) structure with one 6P per In2O3(111) substrate unit cell, that is, a molecular density of 5.64 × 1013 cm-2.

Electrospray deposition of structurally complex molecules revealed by atomic force microscopy

Advances in organic chemistry allow the synthesis of large, complex and highly functionalized organic molecules having potential applications in optoelectronics, molecular electronics and organic solar cells. Their integration into devices as individual components or highly ordered thin-films is of paramount importance to address these future prospects. However, conventional sublimation techniques in vacuum are usually not applicable since large organic compounds are often non-volatile and decompose upon heating. Here, we prove by atomic force microscopy and scanning tunneling microscopy, the structural integrity of complex organic molecules deposited onto an Au(111) surface using electrospray ionisation deposition. High resolution AFM measurements with CO-terminated tips unambiguously reveal their successful transfer from solution to the gold surface in ultra-high vacuum without degradation of their chemical structures. Furthermore, the formation of molecular structures from small islands to large and highly-ordered self-assemblies of those fragile molecules is demonstrated, confirming the use of electrospray ionisation to promote also on-surface polymerization reactions of highly functionalized organic compounds, biological molecules or molecular magnets.

High resolution SPM imaging of organic molecules with functionalized tips

One of the most remarkable and exciting achievements in the field of scanning probe microscopy (SPM) in the last years is the unprecedented sub-molecular resolution of both atomic and electronic structures of single molecules deposited on solid state surfaces. Despite its youth, the technique has already brought many new possibilities to perform different kinds of measurements, which cannot be accomplished by other techniques. This opens new perspectives in advanced characterization of physical and chemical processes and properties of molecular structures on surfaces. Here, we discuss the history and recent progress of the high resolution imaging with a functionalized probe by means of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and inelastic electron tunneling spectroscopy (IETS). We describe the mechanisms responsible for the high-resolution AFM, STM and IETS-STM contrast. The complexity of this technique requires new theoretical approaches, where a relaxation of the functionalized probe is considered. We emphasise the similarities of the mechanism driving high-resolution SPM with other imaging methods. We also summarise briefly significant achievements and progress in different branches. Finally we provide brief perspectives and remaining challenges of the further refinement of these high-resolution methods.