Noncontact Atomic Force Microscopy Research Articles

Noncontact Atomic Force Microscopy for Studying Biomolecules in Liquids

Noncontact Atomic Force Microscopy for Studying Biomolecules in Liquids

Highly Selective On-Surface Dehydrogenative Aromatization of n-Hexyl to Phenyl Substituents.

Dehydrogenative aromatization of alkyl substituents represents a powerful approach to aryl-substituted functional molecules. However, the inertness of alkyl groups and the need for harsh reaction conditions accompanied by low product selectivity hamper its widespread applications. Here, we demonstrate the highly selective on-surface thermal aromatization of n-hexyl substituents on polycyclic aromatic hydrocarbons (PAHs) to their phenyl-substituted analogues under mild conditions. After depositing two representative precursor molecules, n-hexyl-substituted hexaphenylbenzene (HPB-Hex) and bianthryl octacarboxylic tetraimide (BATI-Hex), onto a pre-heated Au(111) substrate, dehydroaromatization of the peripheral n-hexyl groups into phenyl rings occurs, following the planarization of hexaphenylbenzene and bianthryl core. This process involves sequential intramolecular C-C bond rotations, dehydrogenation, and cyclodehydrogenation reactions, yielding phenyl-substituted hexabenzocoronene (HBC-Ph) and bisanthene octacarboxylic tetraimides (BSTI-Ph). The reaction sequences were monitored using scanning tunneling microscopy (STM) and bond-resolved non-contact atomic force microscopy (nc-AFM), offering structural proof of both intermediates and final products. These experimental techniques were complemented by density functional theory (DFT) simulations, which facilitated the detection of crucial steps in the conversion of n-hexyl to phenyl groups. Moreover, the effect of alkyl aromatization on the electronic properties of the newly formed aromatic hydrocarbons was elucidated using scanning tunneling spectroscopy (STS).

Room-temperature selective cyclodehydrogenation on Au(111) via radical addition of open-shell resonance structures

Cyclodehydrogenation is an important ring-formation reaction that can directly produce planar-conjugated carbon-based nanomaterials from nonplanar molecules. However, inherently high C–H bond energy necessitates a high temperature during dehydrogenation, and the ubiquity of C − H bonds in molecules and small differences in their bond energies hinder the selectivity of dehydrogenation. Here, we report a room-temperature cyclodehydrogenation reaction on Au(111) via radical addition of open-shell resonance structures and demonstrate that radical addition significantly decreases cyclodehydrogenation temperature and further improves the chemoselectivity of dehydrogenation. Using scanning tunneling microscopy and non-contact atomic force microscopy, we visualize the cascade reaction process involved in cyclodehydrogenation and determine atomic structures and molecular orbitals of the planar acetylene-linked oxa-nanographene products. The nonplanar intermediates observed during progression annealing, combined with density functional theory calculations, suggest that room-temperature cyclodehydrogenation involves the formation of transient radicals, intramolecular radical addition, and hydrogen elimination; and that the high chemoselectivity of cyclodehydrogenation arises from the reversibility and different thermodynamics of radical addition step.

Atomically resolved imaging of the conformations and adsorption geometries of individual β-cyclodextrins with non-contact AFM

Glycans, consisting of covalently linked sugar units, are a major class of biopolymers essential to all known living organisms. To better understand their biological functions and further applications in fields from biomedicine to materials science, detailed knowledge of their structure is essential. However, due to the extraordinary complexity and conformational flexibility of glycans, state-of-the-art glycan analysis methods often fail to provide structural information with atomic precision. Here, we combine electrospray deposition in ultra-high vacuum with non-contact atomic force microscopy and theoretical calculations to unravel the structure of β-cyclodextrin, a cyclic glucose oligomer, with atomic-scale detail. Our results, established on the single-molecule level, reveal the different adsorption geometries and conformations of β-cyclodextrin. The position of individual hydroxy groups and the location of the stabilizing intramolecular H-bonds are deduced from atomically resolved images, enabling the unambiguous assignment of the molecular structure and demonstrating the potential of the method for glycan analysis.

Real-space investigation of polarons in hematite Fe2O3.

In polarizable materials, electronic charge carriers interact with the surrounding ions, leading to quasiparticle behavior. The resulting polarons play a central role in many materials properties including electrical transport, interaction with light, surface reactivity, and magnetoresistance, and polarons are typically investigated indirectly through these macroscopic characteristics. Here, noncontact atomic force microscopy (nc-AFM) is used to directly image polarons in Fe2O3 at the single quasiparticle limit. A combination of Kelvin probe force microscopy (KPFM) and kinetic Monte Carlo (KMC) simulations shows that the mobility of electron polarons can be markedly increased by Ti doping. Density functional theory (DFT) calculations indicate that a transition from polaronic to metastable free-carrier states can play a key role in migration of electron polarons. In contrast, hole polarons are significantly less mobile, and their hopping is hampered further by trapping centers.

Advancements in π-Magnetism and Precision Engineering of Carbon-Based Nanostructures.

The emergence of π-magnetism in low-dimensional carbon-based nanostructures, such as nanographenes (NGs), has captured significant attention due to their unique properties and potential applications in spintronics and quantum technologies. Recent advancements in on-surface synthesis under ultra-high vacuum conditions have enabled the atomically precise engineering of these nanostructures, effectively overcoming the challenges posed by their inherent strong chemical reactivity. This review highlights the essential concepts and synthesis methods used in studying NGs. It also outlines the remarkable progress made in understanding and controlling their magnetic properties. Advanced characterization techniques, such as scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM), have been instrumental in visualizing and manipulating these nanostructures, which highlighting their critical role in the field. The review underscores the versatility of carbon-based π-magnetic materials and their potential for integration into next-generation electronic devices. It also outlines future research directions aimed at optimizing their synthesis and exploring applications in cutting-edge technologies.

Recent Progress of Imaging Chemical Bonds by Scanning Probe Microscopy: A Review.

In the past decades, the invention of scanning probe microscopy (SPM) as the versatile surface-based characterization of organic molecules has triggered significant interest throughout multidisciplinary fields. In particular, the bond-resolved imaging acquired by SPM techniques has extended its fundamental function of not only unraveling the chemical structure but also allowing us to resolve the structure-property relationship. Here, we present a systematical review on the history of chemical bonds imaged by means of noncontact atomic force microscopy (nc-AFM) and bond-resolved scanning tunneling microscopy (BR-STM) techniques. We first summarize the advancement of real-space imaging of covalent bonds and the investigation of intermolecular noncovalent bonds. Beyond the bond imaging, we also highlight the applications of the bond-resolved SPM techniques such as on-surface synthesis, the determination of the reaction pathway, the identification of molecular configurations and unknown products, and the generation of artificial molecules created via tip manipulation. Lastly, we discuss the current status of SPM techniques and highlight several key technical challenges that must be solved in the coming years. In comparison to the existing reviews, this work invokes researchers from surface science, chemistry, condensed matter physics, and theoretical physics to uncover the bond-resolved SPM technique as an emerging tool in exploiting the molecule/surface system and their future applications.

Solution Versus On-Surface Synthesis of Peripherally Oxygen-Annulated Porphyrins through C-O Bond Formation.

This study investigates the synthesis of tetra- and octa-O-fused porphyrinoids employing an oxidative O-annulation approach through C-H activation. Despite encountering challenges such as overoxidation and instability in conventional solution protocols, successful synthesis was achieved on Au(111) surfaces under ultra-high vacuum (UHV) conditions. X-ray photoelectron spectroscopy, scanning tunneling microscopy, and non-contact atomic force microscopy elucidated the preferential formation of pyran moieties via C-O bond formation and subsequent self-assembly driven by C-H⋅⋅⋅O interactions. Furthermore, the O-annulation process was found to reduce the HOMO-LUMO gap by lifting the HOMO energy level, with the effect rising upon increasing the number of embedded O-atoms.

Stable Au(111) Hexagonal Reconstruction Induced by Perchlorinated Nanographene Molecules.

Surface reconstructions play a crucial role in surface science because of their influence on the adsorption and arrangement of molecules or nanoparticles. On the Au(111) surface, the herringbone reconstruction presents favorable anchoring at the elbow sites, where the highest reactivity is found. In this work, we deposited large organic perchlorinated molecules on a Au(111) surface via high-vacuum electrospray deposition. With noncontact atomic force microscopy measurements at room temperature, we studied the molecular structures formed on the surface before and after annealing at different temperatures. We found that a supramolecular layer is formed and that a hexagonal reconstruction of the Au(111) surface is induced. After high-temperature annealing, the molecules are removed, but the hexagonal Au(111) surface reconstruction is preserved. With the hexagonal Au(111) surface reconstruction, a periodic lattice of anchoring sites is formed.

Controlling friction energy dissipation by ultrafast interlayer electron-phonon coupling in WS2/graphene heterostructures

Electrons and phonons are regarded as the microscopic carriers of friction energy dissipation and their coupling is a typical dissipation mode. However, due to the lack of ultrafast detection technic, the friction mechanism about electron-phonon coupling remains unexplained. Here, using high resolution non-contact atomic force microscopy and ultrafast pump-probe spectroscopy, we find that interlayer electron-phonon coupling dissipation channel in WS2/graphene heterostructures can be enhanced by defects and the electron-phonon scattering time is accelerated from 0.62ps to 0.27ps. The enhanced electron-phonon coupling leads to significant energy dissipation. We further quantitatively model the friction with dissipation rate to control the friction energy dissipation by ultrafast interlayer electron-phonon coupling. This work provides a new way to understand the mechanism of electron-phonon coupling in friction.

On-Surface Stepwise Double Dehydrogenation for the Formation of a para-Quinodimethane-Containing Undecacene Isomer.

The on-surface synthesis of an isomer of undecacene, bearing two four-membered rings and two para-quinodimethane moieties, starting from a tetramethyl-substituted diepoxy precursor, is presented. The transformation implies a thermal double deoxygenation followed by a stepwise double dehydrogenation reaction on the Au(111) surface, locally induced by inelastic tunneling electrons. This results in the transformation of para-dimethylbenzene moieties into non-aromatic para-quinodimethanes. The structures and electronic properties of the intermediate and final products are investigated at the single molecule level with high spatial resolution, using both scanning tunneling microscopy/spectroscopy and non-contact atomic force microscopy. The experimental results are supported by density functional theory calculations.

Characterization of strongly coupled quartz tuning fork sensors for precision force measurement in atomic force microscopy

Miniaturized quartz tuning forks (QTFs) have been adopted as force sensors for non-contact atomic force microscopy (AFM). However, the coupled oscillation behaviors of the QTF prongs are not well understood, preventing quantitative measurement of the nanoscale tip-sample interaction forces. This article presents a lumped model that accurately delineates the coupled mechanical oscillations of QTF prongs, establishing rigorous relationships between experimental observables and tip-sample interaction forces. The first-order resonance spectra of a commercial QTF were fully characterized by correlating its piezoelectric response with the actual mechanical oscillation measured with a Fabry-Pérot interferometer. In order to uniquely determine the modeling parameters (i.e., the effective masses, spring constants, and damping constants), the experimental results were compared with the lumped model predictions while masses were added to one prong. The results reveal that the QTF’s center of mass is highly damped, preventing the observation of a symmetric resonance mode. In addition, the mass loading experiment demonstrates that the mechanical oscillations of the QTF prongs are strongly coupled, accounting for 59% (84%) of the effective stiffness at the in-plane (out-of-plane), antisymmetric resonance mode. We believe that the obtained QTF characterization results will pave the way for quantitative measurements of non-contact interaction forces in QTF-based AFM platforms, significantly improving the precision and reliability of nanoscale force measurements.

Stoichiometric reconstruction of the Al2O3(0001) surface.

Macroscopic properties of materials stem from fundamental atomic-scale details, yet for insulators, resolving surface structures remains a challenge. We imaged the basal (0001) plane of α-aluminum oxide (α-Al2O3) using noncontact atomic force microscopy with an atomically defined tip apex. The surface formed a complex ([Formula: see text] × [Formula: see text])R±9° reconstruction. The lateral positions of the individual oxygen and aluminum surface atoms come directly from experiment; we determined with computational modeling how these connect to the underlying crystal bulk. Before the restructuring, the surface Al atoms assume an unfavorable, threefold planar coordination; the reconstruction allows a rehybridization with subsurface O that leads to a substantial energy gain. The reconstructed surface remains stoichiometric, Al2O3.

Synthesis of Hexabenzocoronene-Cored Graphdiyne Nanosheets through Dehydrogenative Coupling on Au(111) Surface.

Thermally-induced dehydrogenative coupling of polyphenylenes on metal surfaces is an important technique to synthesize -conjugated carbon nanostructures with atomic precision. However, this protocol has rarely been utilized to fabricate structurally defined carbon nanosheets composed of sp- and sp2-hybridized carbon atoms. Here, we present the synthesis of butadiyne-linked hexabenzocoronenes (HBCs) on Au(111) surfaces as core-expanded graphdiynes. The reaction started from hexa(4-ethylphenyl)benzene, which undergoes dehydrogenation toward hexa(4-vinylphenyl)benzene, followed by planarization to hexabenzocoronene, coupling between the vinyl groups, and further dehydrogenation. In addition to butadiyne linkages, benzene groups were also found as another type of linker. The reaction sequences were monitored by scanning tunneling microscopy and bond-resolved non-contact atomic force microscopy, which disclose the structures of intermediates and final products. In combination with density functional theory simulations, the key steps from ethyl substituents to butadiyne and benzene linkers were elucidated. This is a new on-surface synthesis of core-expanded graphdiynes with unprecedented electronic properties.

Effect of ion-specific water structures at metal surfaces on hydrogen production

Water structures at electrolyte/electrode interfaces play a crucial role in determining the selectivity and kinetics of electrochemical reactions. Despite extensive experimental and theoretical efforts, atomic-level details of ion-specific water structures on metal surfaces remain unclear. Here we show, using scanning tunneling microscopy and noncontact atomic force microscopy, that we can visualize water layers containing alkali metal cations on a charged Au(111) surface with atomic resolution. Our results reveal that Li+ cations are elevated from the surface, facilitating the formation of an ice-like water layer between the Li+ cations and the surface. In contrast, K+ and Cs+ cations are in direct contact with the surface. We observe that the water network structure transitions from a hexagonal arrangement with Li+ to a distorted hydrogen-bonding configuration with Cs+. These observations are consistent with surface-enhanced infrared absorption spectroscopy data and suggest that alkali metal cations significantly impact hydrogen evolution reaction kinetics and efficiency. Our findings provide insights into ion-specific water structures on metal surfaces and underscore the critical role of spectator ions in electrochemical processes.

Low defect density in MoS2 monolayers grown on Au(111) by metal-organic chemical vapor deposition

Monolayers of transition metal dichalcogenides (TMDs) possess high potential for applications in novel electronic and optoelectronic devices and therefore the development of methods for their scalable growth is of high importance. Among different suggested approaches, metal-organic chemical vapor deposition (MOCVD) is the most promising one for technological applications because of its lower growth temperature compared to the most other methods, e.g., conventional chemical vapor or atomic layer deposition (CVD, ALD). Here we demonstrate for the first time the epitaxial growth of MoS2 monolayers on Au(111) by MOCVD at 450 °C. We confirm the high quality of the grown TMD monolayers down to the atomic scale using several complementary methods. These include Raman spectroscopy, non-contact atomic force microscopy (nc-AFM), X-ray photoelectron spectroscopy and scanning tunneling microscopy (STM). The topographic corrugation of the MoS2 monolayer on Au(111), revealed in a moiré structure, was measured as ≈20 pm by nc-AFM. The estimated defect density calculated from STM images of the as-grown MoS2 monolayers is in the order of 1012 vacancies/cm2. The defects are mainly caused by single sulfur vacancies. Our approach is a step forward towards the technologically relevant growth of high-quality, large-area TMD monolayers.

Signal generation in dynamic interferometric displacement detection.

Laser interferometry is a well-established and widely used technique for precise displacement measurements. In a non-contact atomic force microscope (NC-AFM), it facilitates the force measurement by recording the periodic displacement of an oscillating microcantilever. To understand signal generation in a NC-AFM-based Michelson-type interferometer, we evaluate the non-linear response of the interferometer to the harmonic displacement of the cantilever in the time domain. As the interferometer signal is limited in amplitude because of the spatial periodicity of the interferometer light field, an increasing cantilever oscillation amplitude creates an output signal with an increasingly complex temporal structure. By the fit of a model to the measured time-domain signal, all parameters governing the interferometric displacement signal can precisely be determined. It is demonstrated, that such an analysis specifically allows for the calibration of the cantilever oscillation amplitude with 2% accuracy.

Advancing scanning probe microscopy simulations: A decade of development in probe-particle models

The Probe-Particle Model combine theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article we present the latest version of the Probe-Particle Model implemented in the open-source ppafm package, highlighting substantial advancements in accuracy, computational performance, and user-friendliness. To demonstrate this we provide a comprehensive review of approaches for simulating non-contact Atomic Force Microscopy. They vary in complexity from simple Lennard-Jones potential to the latest full density-based model. We compared those approaches with ab initio calculated references, showcasing their respective merits. All parts of the ppafm package have undergone acceleration by 1-2 orders of magnitude using OpenMP and OpenCL technologies. The updated package includes an interactive graphical user interface and seamless integration into the Python ecosystem via pip, facilitating advanced scripting and interoperability with other software. This adaptability positions ppafm as an ideal tool for high-throughput applications, including the training of machine learning models for the automatic recovery of atomic structures from nc-AFM measurements. We envision significant potential for this application in future single-molecule analysis, synthesis, and advancements in surface science in general. Additionally, we discuss simulations of other sub-molecular scanning-probe imaging techniques, such as bond-resolved scanning tunneling microscopy and kelvin probe force microscopy, all built on the robust foundation of the Probe-Particle Model. Altogether this demonstrates the broad impact of the model across diverse domains of on-surface science and molecular chemistry.

Single Atom Platforms on Surfaces: A Step Towards Future Catalysts

Single (metal) atoms (SAs) have attracted great attention in virtue of their intriguing physical and chemical properties, representing a fertile playground for fundamental studies of electronic, magnetic and chemical phenomena. Placing SAs on clean, crystalline and atomically flat substrates allows the study of their properties and functions via the whole plethora of surface science tools, offering direct access to their features with ultimate resolution. Moreover, the isolated metal atoms exhibit peculiar properties and tend to behave similarly to reactive centres in solution or gas phase, bridging homogeneous and heterogeneous catalysis. In these regards, atomically dispersed metal catalysts (ADCs) have recently received great attention [1, 2]. However, they suffer some intrinsic bottlenecks such as a poor tunability and limited maximum density.Here we show the successful achievement of single atom platforms (SAPs), where SAs are coordinated to atomically precise organic templates, confined to a two dimensional surface. The templates are obtained via the on-surface synthesis (OSS) of carefully designed molecular precursors, and consist of carbon-based, covalent polymers equipped with side moieties that act as coordination sites. These groups capture metal atoms that are deposited on the substrate in a post-synthetic step, and together form active site with rich potential applications. Conceptually, the obtained SAP offers rich tunability prospects by varying not only the substrate and the SA, but also the organic ligand. Its shape and composition (e.g. heteroatoms, functional groups, strain, etc.) will influence the properties of the SA and enable their fine tuning. Moreover, the versatility of the OSS strategy offers a wide plethora of possible architectures, allowing also the precise modification of the SA density.We have characterized each stage of the SAP preparation via high-resolution scanning tunnelling microscopy (STM) and noncontact atomic force microscopy (nc-AFM) with functionalized tips [3]. The trapping and conversion ability of these well-defined active sites towards CO and CO2 was then studied. Our investigation allows the direct visualization of reactants and binding motifs with unprecedented resolution, and opens new avenues for the study of chemical reactions localized at the active sites of our SAP.[1] Wang, A.; Li, J.; Zhang, T. Heterogeneous Single-Atom Catalysis. Nature Reviews Chemistry 2018, 2 (6), 65–81.[2] Hannagan, R. T.; Giannakakis, G.; Flytzani-Stephanopoulos, M.; Sykes, E. C. H. Single-Atom Alloy Catalysis. Chem. Rev. 2020, 120 (21), 12044–12088.[3] Gross, L.; Mohn, F.; Moll, N.; Liljeroth, P.; Meyer, G. The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy. Science 2009, 325 (5944), 1110–1114. Figure 1. Single atom platform concept. Sketch of surface-adsorbed single atoms (orange dots) and of a single atom platform. Here, the organic part is represented by 1D polymers adsorbed on a surface, and the single atoms decorate the coordination sites (U-shaped motifs). Figure 1

On-Surface Synthesis of 2D Radical Frameworks

The design of atom thick two-dimensional (2D) frameworks by on-surface synthesis has recently contributed to the development of advanced materials with high control over their structural, electronic, optical and magnetic properties. Countless 2D frameworks, with a large variety of applications, can be synthesized made of purely organic molecules (covalent organic and supramolecular frameworks) or combining both metals and organic molecules (metalorganic frameworks). Here, we focus on the design and synthesis of radical 2D frameworks, composed of open-shell nanographenes equipped with azaindole units, on an Au(111) surface. Interestingly, the deposition of transition metal atoms on such frameworks allow the tuning of their magnetic properties, expanding their possible applications. The structural, electronic and magnetic characterization of the frameworks was performed by scanning tunneling microscopy/spectroscopy (STM/STS) and non-contact atomic force microscopy, and supported by density functional theory (DFT) calculations. Additionally, the magnetic characterization was complemented by nickelocene-functionalized tips investigations, which act as a magnetic sensor that unveils the magnetism of the frameworks at the single molecule level.