High-resolution Scanning Tunneling Microscopy Research Articles

Topology selectivity of a conformationally flexible precursor through selenium doping

Conformational arrangements within nanostructures play a crucial role in shaping the overall configuration and determining the properties, for example in covalent/metal organic frameworks. In on-surface synthesis, conformational diversity often leads to uncontrollable or disordered structures. Therefore, the exploration of controlling and directing the conformational arrangements is significant in achieving desired nanoarchitectures. Herein, a conformationally flexible precursor 2,4,6-tris(3-bromophenyl)−1,3,5-triazine is employed, and a random phase consisting of C3h and Cs conformers is firstly obtained after deposition of the precursor on Cu(111) at room temperature to 365 K. At low coverage (0.01 ML) selenium doping, we achieve the selectivity of the C3h conformer and improve the nanopore structural homogeneity. The ordered two-dimensional metal organic nanostructure can be fulfilled by selenium doping from room temperature to 365 K. The formation of the conformationally flexible precursor on Cu(111) is explored through the combination of high-resolution scanning tunneling microscopy and non-contact atomic force microscopy. The regulation of energy diagrams in the absence or presence of the Se atom is revealed by density functional theory calculations. These results can enrich the on-surface synthesis toolbox of conformationally flexible precursors, for the design of complex nanoarchitectures, and for future development of engineered nanomaterials.

Ag+-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes.

Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a "hairpin" fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA-silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics.

Direct observation of a magnetic-field-induced Wigner crystal.

Wigner predicted that when the Coulomb interactions between electrons become much stronger than their kinetic energy, electrons crystallize into a closely packed lattice1. A variety of two-dimensional systems have shown evidence for Wigner crystals2-11 (WCs). However, a spontaneously formed classical or quantum WC has never been directly visualized. Neither the identification of the WC symmetry nor direct investigation of its melting has been accomplished. Here we use high-resolution scanning tunnelling microscopy measurements to directly image a magnetic-field-induced electron WC in Bernal-stacked bilayer graphene and examine its structural properties as a function of electron density, magnetic field and temperature. At high fields and the lowest temperature, we observe a triangular lattice electron WC in the lowest Landau level. The WC possesses the expected lattice constant and is robust between filling factor ν ≈ 0.13 and ν ≈ 0.38 except near fillings where it competes with fractional quantum Hall states. Increasing the density or temperature results in the melting of the WC into a liquid phase that is isotropic but has a modulated structure characterized by the Bragg wavevector of the WC. At low magnetic fields, the WC unexpectedly transitions into an anisotropic stripe phase, which has been commonly anticipated to form in higher Landau levels. Analysis of individual lattice sites shows signatures that may be related to the quantum zero-point motion of electrons in the WC lattice.

High-resolution scanning tunneling microscope and its adaptation for local thermopower measurements in 2D materials

We present the design, fabrication and discuss the performance of a new combined high-resolution Scanning Tunneling and Thermopower Microscope (STM/SThEM). We also describe the development of the electronic control, the user interface, the vacuum system, and arrangements to reduce acoustical noise and vibrations. We demonstrate the microscope’s performance with atomic-resolution topographic images of highly oriented pyrolytic graphite (HOPG) and local thermopower measurements in the semimetal Bi2Te3. Our system offers a tool to investigate the relationship between electronic structure and thermoelectric properties at the nanoscale.

Feature correlation method for image reconstruction evaluation in under-sampled scanning probe microscopy

We introduce an advanced feature-correlation approach for evaluating the accuracy of data completion in scanning probe microscopy (SPM). Our method utilizes characteristic patterns from conventional SPM images and their reconstructions via data interpolation. We develop a refined comparative evaluation algorithm based on correlation coefficients. This algorithm provides a precise assessment by effectively addressing SPM-specific distortions such as thermal drift, feedback error, and noise limitations often overlooked by traditional metrics such as peak signal-to-noise ratio and structural similarity index measure. The effectiveness of our approach is demonstrated through its application in high-resolution and extensive scanning tunneling microscopy assessments.

Design and performance of an ultrahigh vacuum spectroscopic-imaging scanning tunneling microscope with a hybrid vibration isolation system.

A spectroscopic imaging-scanning tunneling microscope (SI-STM) allows for the atomic scale visualization of the surface electronic and magnetic structure of novel quantum materials with a high energy resolution. To achieve the optimal performance, a low vibration facility is required. Here, we describe the design and performance of an ultrahigh vacuum STM system supported by a hybrid vibration isolation system that consists of a pneumatic passive and a piezoelectric active vibration isolation stage. We present the detailed vibrational noise analysis of the hybrid vibration isolation system, which shows that the vibration level can be suppressed below 10-8 m/sec/√Hz for most frequencies up to 100Hz. Combined with a rigid STM design, vibrational noise can be successfully removed from the tunneling current. We demonstrate the performance of our STM system by taking high resolution spectroscopic maps and topographic images on several quantum materials. Our results establish a new strategy to achieve an effective vibration isolation system for high-resolution STM and other scanning probe microscopies to investigate the nanoscale quantum phenomena.

Structure Discovery in Atomic Force Microscopy Imaging of Ice.

The interaction of water with surfaces is crucially important in a wide range of natural and technological settings. In particular, at low temperatures, unveiling the atomistic structure of adsorbed water clusters would provide valuable data for understanding the ice nucleation process. Using high-resolution atomic force microscopy (AFM) and scanning tunneling microscopy, several studies have demonstrated the presence of water pentamers, hexamers, and heptamers (and of their combinations) on a variety of metallic surfaces, as well as the initial stages of 2D ice growth on an insulating surface. However, in all of these cases, the observed structures were completely flat, providing a relatively straightforward path to interpretation. Here, we present high-resolution AFM measurements of several water clusters on Au(111) and Cu(111), whose understanding presents significant challenges due to both their highly 3D configuration and their large size. For each of them, we use a combination of machine learning, atomistic modeling with neural network potentials, and statistical sampling to propose an underlying atomic structure, finally comparing its AFM simulated images to the experimental ones. These results provide insights into the early phases of ice formation, which is a ubiquitous phenomenon ranging from biology to astrophysics.

New insights into the structure of the Ag(111)-p(4 × 4)-O phase: high-resolution STM and DFT study.

The atomic structure of the Ag(111)-p(4 × 4)-O phase was reexamined with scanning tunneling microscopy (STM) and density functional theory. We discovered two different phases with the same (4 × 4) periodicity and demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images. Using bias dependencies of the STM images, we have shown that the p(4 × 4) phase is highly nonuniform, with local oxygen coverage varying from 1/8 ML up to 1/2 ML.

Atomic and electronic structure of monolayer ferroelectric GeS on Cu(111)

Two-dimensional (2D) ferroelectric materials are important materials for both fundamental properties and potential applications. Especially, group Ⅳ monochalcogenide possesses highest thermoelectric performance and intrinsic ferroelectric polarization properties and can sever as a model to explore ferroelectric polarization properties. However, due to the relatively large exfoliation energy, the creation of high-quality and large-size monolayer group Ⅳ monochalcogenide is not so easy, which seriously hinders the integration of these materials into the fast-developing field of 2D materials and their heterostructures. Herein, monolayer GeS is successfully fabricated on Cu(111) substrate by molecular beam epitaxy method, and the lattice structure and the electronic band structure of monolayer GeS are systematically characterized by high-resolution scanning tunneling microscopy, low-energy electron diffraction, <i>in-situ</i> X-ray photoelectron spectroscopy, Raman spectra, and angle-resolved photoelectron spectroscopy, and density functional theory calculations. All atomically resolved STM images reveal that the obtained monolayer GeS has an orthogonal lattice structure, which consists with theoretical prediction. Meanwhile, the distinct moiré pattern formed between monolayer GeS and Cu(111) substrate also confirms the orthogonal lattice structure. In order to examine the chemical composition and valence state of as-prepared monolayer GeS, <i>in-situ</i> XPS is utilized without being exposed to air. The measured spectra of XPS core levels suggest that the valence states of Ge and S elements are identified to be +2 and –2, respectively and the atomic ratio of Ge/S is 1∶1.5, which is extremely close to the stoichiometric ratio of 1∶1 for GeS. To further corroborate the quality and lattice structure of the monolayer GeS film, <i>ex-situ</i> Raman measurements are also performed for monolayer GeS on highly oriented pyrolytic graphene (HOPG) and multilayer graphene substrate. Three well-defined typical characteristic Raman peaks of GeS are observed. Finally, <i>in-situ</i> ARPES measurement are conducted to determine the electronic band structure of monolayer GeS on Cu(111). The results demonstrate that the monolayer GeS has a nearly flat band electronic band structure, consistent with our density functional theory calculation. The realization and investigation of the monolayer GeS extend the scope of 2D ferroelectric materials and make it possible to prepare high quality and large size monolayer group Ⅳ monochalcogenides, which is beneficial to the application of this main group material to the rapidly developing 2D ferroelectric materials and heterojunction research.

Study on the Assembly of Multilayer Vanadium Phthalocyanine fabricated on a Ag<sub>2</sub> Sb Monolayer

Fabricating ordered molecular films and further tuning their assembly behavior is important for constructing organic devices with diverse performances. By using high-resolution scanning tunneling microscopy, in this work, we demonstrate that well-organized vanadyl phthalocyanine (VOPc) films can be formed <i>via</i> 'bottom-up' molecular self-assembly on a binary alloy Ag<sub>2</sub>Sb/Ag(111). The Ag<sub>2</sub>Sb monolayer is prepared by evaporating Sb atoms and followed annealing on clean Ag(111). VOPc molecules are deposited on the Ag<sub>2</sub>Sb layer <i>via</i> thermal evaporation. The molecular configuration, structural and orbital characteristics of VOPc were clearly clarified at the submolecular level. It is found that initially the ordered VOPc membrane only exhibits the O-up adsorption configuration. Its square-shaped unit cell consists of five VOPc molecules where two adsorption orientations coexist with the horizontal axis of VOPc is rotated by about 11° or 21° relative to the side of the unit cell. Due to the molecular dipole-dipole interaction, further-deposited molecules result in the assembly of the second-layered VOPc films with the O-down configuration and the square-shaped unit cell that contains only one VOPc molecule. Subsequently, due to the dipole-dipole interaction between layered molecules, following VOPc molecular layers adopt alternating O-up and O-down configurations as well as the square-shaped unit cell, similar to the case of the second layer. In addition, we found that the molecular orbitals overlap in each assembled molecular layer due to the π-π interaction which could facilitate the charge transport along the π stacking direction of VOPc. This research provides possibility to regulate the adsorption configuration and assembly behavior of functional organic molecules on metal surfaces by forming surface alloys.

Discarding metal incorporation in pyrazole macrocycles and the role of the substrate on single-layer assemblies.

Pyrazole derivatives are key in crystal engineering and liquid crystal fields and thrive in agriculture, pharmaceutical, or biomedicine industries. Such versatility relies in their supramolecular bond adaptability when forming hydrogen bonds or metal-pyrazole complexes. Interestingly, the precise structure of pyrazole-based macrocycles forming widespread porous structures is still unsolved. We bring insight into such fundamental question by studying the self-assembled structures of a bis-pyrazole derivative sublimed in ultra-high-vacuum conditions (without solvents) onto the three (111) noble metal surfaces. By means of high-resolution scanning tunneling microscopy that is validated by gas phase density functional theory calculations, we find a common hexagonal nanoporous network condensed by triple hydrogen bonds at the molecule-metal interface. Such assembly is disrupted and divergent after annealing: (i) on copper, the molecular integrity is compromised leading to structural chaos, (ii) on silver, an incommensurate new oblique structure requiring molecular deprotonation is found and, (iii) on gold, metal-organic complexes are promoted yielding irregular chain structures. Our findings confirm the critical role of these metals on the different pyrazole nanoporous structure formation, discarding their preference for metal incorporation into the connecting nodes whenever there is no solvent involved.

In Situ STM Investigations of Cu(100) and Bimetallic Ag/Cu(100) Model Catalysts for CO2 Electroreduction in Bicarbonate Solution

The electrochemical conversion of carbon dioxide (CO2RR) to valuable chemicals and fuels plays a crucial role in the sustainable energy economy as it represents a promising potential for the renewable energy storage as well as closing the carbon loop.[1,2] Thus, the design and development of a highly efficient and selective electrocatalyst for CO2RR has become a topic of great importance in recent years. Among elemental metals, copper exhibits unique catalytic behaviour to reduce CO2 towards multi-carbon products with reasonable Faradaic efficiency due to its moderate CO-binding energy.[3,4] However, the selectivity and activity of pure copper is still far away for a practical application. The integration of a secondary metal species provides a promising strategy to improve the catalytical performance of the copper catalyst. Combination with silver is particularly interesting for such bimetallic catalysts, since Ag is a highly efficient catalyst for CO2RR to CO, probably the most important intermediate in the CO2RR, and has been shown to promote the formation of multi-carbon products.[5]Here, we present in situ scanning tunnelling microscopy studies of well-defined Cu and AgCu electrodes in CO2-satured 0.1 M KHCO3, which is one of the most common electrolytes for CO2 electroreduction. For Cu(100) in the double layer potential range, coexistence of two ordered (bi)carbonate adlayer phases was observed (Fig. 1a,b, published in [6]). These adlayer phases have a highly complex structure, exhibit dynamic fluctuations, and undergo a potential dependent order-disorder transition at about 0 V vs. the reversible hydrogen electrode. Detailed density functional calculations reveal that the observed layer is composed of carbonate and water that coadsorb on the electrode surface, underlining the key role of water in the stabilization of the (bi)carbonate adlayers.[6]Upon decreasing the potential to the onset of CO2RR, the formation of Cu nanoclusters is observed on the Cu(100) surfaces by in situ STM. This surface restructuring can be assigned to the influence of CO intermediates formed in the CO2RR. Upon subsequent increase of the potential back into the double layer range, the clusters disperse, resulting in a highly disordered interface structure that contains Cu adatoms, (bi)carbonates, and further molecular adsorbates. This irreversible change of the molecular-scale electrode surface is supported by spectroscopic results.AgCu bimetallic model catalysts were prepared by electrodeposition of submonolayer Ag coverage on Cu(100) in 0.1 M H2SO4. Silver forms islands on Cu(100) with a hexagonal quasi-Ag(111) atomic lattice. After the preparation and characterization of the Ag-decorated Cu(100), the electrolyte was exchanged under potential control to 0.1 M KHCO3. The electrolyte exchange results in the distinct restructuring on the surface in the double layer potential range, in which the islands develop a strongly anisotropic shape. In addition, appearance of new islands and a reduced surface mobility are observed. Furthermore, in contrast to the Ag-free Cu(100), high-resolution STM images show a disordered molecular adlayer.Our results demonstrate the pronounced role of adsorbed (bi)carbonate at the catalyst/electrolyte interface and its impact on the surface morphology and dynamics already at potentials in the double layer regime. These adsorbate-induced structural changes need to be considered for a fundamental understanding and rational design of electrocatalysts for CO2RR.The Authors gratefully acknowledge financial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via SPP 2080, project no. 327886311.

Remote regulation on the hydration sites of adenine molecules via derivatization

Hydration, as a ubiquitous and vital phenomenon in nature, has attracted great attention in the field of surface science concerning the fundamental interactions between water and organic molecules. However, the role of functional group derivatization is still elusive in terms of its potential impact on hydration. By the combination of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, the hydration of 9mA molecules was realized on Au(111) in real space, forming 9mA–H2O–9mA structures. In comparison with the hydration of adenine molecules, methyl derivatization is experimentally found to remotely regulate the hydration sites from the imidazole ring to the pyrimidine ring and is further theoretically revealed to allow intramolecular electron redistribution and, therefore, steer the priority of the hydration sites. These results provide sub-molecular understandings of the relationship between derivatization and hydration, which would shed light on the regulation of hydration processes in chemically and biologically related systems.

Effect of immersion time on the structural order of the self-assembled monolayers of terphenylthiols on the gold surface: Coexistence of different molecular adlayer phases

By the example of terphenylthiolate (TPT) films on Au(111), we show by using a high-resolution scanning tunneling microscope (STM) that a long immersion time at room temperature results in the formation of distinct polymorphism. At least three different structural phases namely, α, β, and γ are found to coexist on the gold surface. Two of these phases (α and β) have not been previously detected in the STM images obtained for TPT monolayers prepared for shorter exposure times. The α phase is characterized by the commensurate (4×25)R9.7° structure, with an area per molecule of 34.7 Å2. Whereas the structure of the β phase can be described either by a semi-rectangular (25×213)R7°unit cell or an oblique (25×217)R23° unit cell with a molecular footprint of 33.4 Å2. The third γ phase can be assigned either as a (2×8)or (23×2)structure with a molecular area of 28.8 Å2. The γ phase was found to contain a high-density of translational domains. Unlike shorter immersion times, our results showed that prolonged exposure of the gold substrate to a TPT thiol solution (190 h) leads to the formation of loosely packed monolayers where molecules are largely tilted downward away from surface normal, contrasting with the fully saturated monolayers in which the (23×3)R30°superstructure with an average areal molecular density of 21.6 Å2 was observed in previous studies but, unexpectedly, it is absent in our current results.

Epitaxial growth of Si thin films with hexagonal close-packed structures on metal substrates.

We have studied the epitaxial growth of Si thin films on the Cd(0001) surface using low-temperature scanning tunneling microscopy. When deposited at low temperatures (100K), Si atoms form dendritic islands with triangular shapes, indicating the existence of anisotropic edge diffusion in the process of Si film growth. After annealing to elevated temperatures, the triangular dendritic Si islands become hexagonal compact islands. Moreover, the 2D Si islands located on two different substrate terraces exhibit different heights due to the influence of quantum-well states in Cd(0001) films. Based on high-resolution scanning tunneling microscopy images, it is observed that the first, second, and third Si layers show the pseudomorphic 1 × 1 structure. In particular, the first and second layer islands reveal the opposite triangles, indicating the hexagonal close-packed stacking of Si atoms. These results provide important information for the growth of pristine Si films on metal substrates and the understanding of Si-metal interaction.

The role of halogens in Au–S bond cleavage for energy-differentiated catalysis at the single-bond limit

The transformation from one compound to another involves the breaking and formation of chemical bonds at the single-bond level, especially during catalytic reactions that are of great significance in broad fields such as energy conversion, environmental science, life science and chemical synthesis. The study of the reaction process at the single-bond limit is the key to understanding the catalytic reaction mechanism and further rationally designing catalysts. Here, we develop a method to monitor the catalytic process from the perspective of the single-bond energy using high-resolution scanning tunneling microscopy single-molecule junctions. Experimental and theoretical studies consistently reveal that the attack of a halogen atom on an Au atom can reduce the breaking energy of Au−S bonds, thereby accelerating the bond cleavage reaction and shortening the plateau length during the single-molecule junction breaking. Furthermore, the distinction in catalytic activity between different halogen atoms can be compared as well. This study establishes the intrinsic relationship among the reaction activation energy, the chemical bond breaking energy and the single-molecule junction breaking process, strengthening our mastery of catalytic reactions towards precise chemistry.

Direct Observation of Twin van der Waals Molecular Chains.

The van der Waals (vdW) assemblies are the most common structures of materials. However, direct mapping of intermolecular electron clouds of a vdW assembly has never been obtained, even though the intramolecular electron clouds were visualized by atomic-resolution techniques. In this report, we unprecedentedly mapped the intermolecular electron cloud of the assemblies of ethanol molecules via ethyl groups with high-resolution atomic force microscopy and scanning tunneling microscopy at 5 K, leading to the first visualization of vdW molecular chains, in which ethanol molecules assemble into twin vdW molecular chains in a reverse parallel configuration on the Ag(111) plane. Furthermore, spontaneous order-disorder transitions in the chain were dynamically observed, suggesting its unusual properties different from those of 2D vdW materials. These findings provide an "eye" to see the atomic world of vdW materials.

On-surface synthesis of Au–C4 and Au–O4 alternately arranged organometallic coordination networks via selective aromatic C–H bond activation

Selective activation of the C–H bond of aromatic hydrocarbons is significant in synthetic chemistry. However, achieving oriented C–H activation remains challenging due to the poor selectivity of aromatic C–H bonds. Herein, we successfully constructed alternately arranged Au–C4 and Au–O4 organometallic coordination networks through selective aromatic C–H bond activation on Au(111) substrate. The stepwise reaction process of the 5, 12-dibromopyrene 3,4,9, 10-tetracarboxylic dianhydride precursor is monitored by high-resolution scanning tunneling microscopy. Our results show that the gold atoms in C–Au–C organometallic chains play a crucial role in promoting the selective ortho C–H bonds activation and forming Au–C4 coordination structure, which is further demonstrated by a comparative experiment of PTCDA precursor on Au(111). Furthermore, our experiment of 2Br-PTCDA precursor on Cu(111) substrate confirms that copper atoms in C–Cu–C organometallic chains can also assist the formation of Cu–C4 coordination structure. Our results reveal the vital effect of organometallic coordination on selective C–H bond activation of reactants, which holds promising implications for controllable on-surface synthesis.

Growth and characterization of Bi(110)/CrTe2 heterostructures: Exploring interplay between magnetism and topology

The interplay between topology and magnetism is vital for realizing exotic quantum phenomena, significant examples including quantum anomalous Hall effect, axion insulators, and high-order topological states. These states host great potential for future applications in high-speed and low-consumption electronic devices. Despite being extensively investigated, practical platforms are still scarce. In this work, with molecular beam epitaxy (MBE), we provide the first experimental report on high-quality Bi(110)/CrTe2 magnetic heterostructure. By employing in-situ high-resolution scanning tunneling microscopy, we are able to examine the interaction between magnetism and topology. There is a potential edge state at an energy level above the Fermi level, but no edge states observed near the Fermi level The absence of high-order topological corner states near E F highlights the importance of lattice matching and interface engineering in designing high-order topological states. Our study provides key insights into the interplay between two-dimensional magnetic and topological materials and offers an important dimension for engineering magnetic topological states.

Visualizing Chiral Interactions in Carbohydrates Adsorbed on Au(111) by High-Resolution STM Imaging.

Carbohydrates are the most abundant organic material on Earth and the structural "material of choice" in many living systems. Nevertheless, design and engineering of synthetic carbohydrate materials presently lag behind that for protein and nucleic acids. Bottom-up engineering of carbohydrate materials demands an atomic-level understanding of their molecular structures and interactions in condensed phases. Here, high-resolution scanning tunneling microscopy (STM) is used to visualize at submolecular resolution the three-dimensional structure of cellulose oligomers assembled on Au(1111) and the interactions that drive their assembly. The STM imaging, supported by ab initio calculations, reveals the orientation of all glycosidic bonds and pyranose rings in the oligomers, as well as details of intermolecular interactions between the oligomers. By comparing the assembly of D- and L-oligomers, these interactions are shown to be enantioselective, capable of driving spontaneous enantioseparation of cellulose chains from its unnatural enantiomer and promoting the formation of engineered carbohydrate assemblies in the condensed phases.