Simulated Scanning Tunneling Microscopy Images Research Articles

Data-Driven Structure Recognition of Scanning Tunneling Microscopy Images in a Case of Iron Carbide.

Scanning tunneling microscopy (STM) serves as a critical tool for high-resolution surface imaging, yet deciphering the atomic structures from STM images on multielement surfaces, such as oxides and carbides, remains a challenging task that heavily relies on the expertise and intuition of researchers. In this study, we introduce a data-driven method for rapid structural recognition from STM images. This method involves extracting structural features, filtering through a structural database, and matching with simulated STM images and surface energy analyses, thereby providing researchers with several of the most probable structures. We demonstrate the capabilities of this technique using our previously reported iron carbide grown on an Fe(110) crystal. By proposing a candidate structure set and establishing a comprehensive database linking STM images to corresponding structures and surface energies, we selected 6 out of more than 10 000 possible surfaces. On the basis of these 6 recommendations, researchers can conveniently determine the real surface structures. Our work provides an efficient tool for the structure recognition of STM images to construct surface structures, potentially serving as a universal auxiliary tool for STM structural analysis.

Provably Trainable Rotationally Equivariant Quantum Machine Learning

Exploiting the power of quantum computation to realize superior machine learning algorithms has been a major research focus of recent years, but the prospects of quantum machine learning (QML) remain dampened by considerable technical challenges. A particularly significant issue is that generic QML models suffer from so-called barren plateaus in their training landscapes—large regions where cost function gradients vanish exponentially in the number of qubits employed, rendering large models effectively untrainable. A leading strategy for combating this effect is to build problem-specific models that take into account the symmetries of their data in order to focus on a smaller, relevant subset of Hilbert space. In this work, we introduce a family of rotationally equivariant QML models built upon the quantum Fourier transform, and leverage recent insights from the Lie-algebraic study of QML models to prove that (a subset of) our models do not exhibit barren plateaus. In addition to our analytical results we numerically test our rotationally equivariant models on a dataset of simulated scanning tunneling microscope images of phosphorus impurities in silicon, where rotational symmetry naturally arises, and find that they dramatically outperform their generic counterparts in practice. Published by the American Physical Society 2024

Self-assembled oligomeric structures of an asymmetric molecular linker; 4-isocyanophenyl disulfide on Au(111)

Para-substituted benzenes, such as 1,4-benzene dithiol and 1,4-phenyl diisocyanide, have been observed to oligomerize on the Au(111) surface by incorporating gold adatoms extracted from the substrate. This work investigates if oligomerization occurs for an analogous but asymmetric linker, 4-isocyanophenyl disulfide (ICPD) on Au(111). This molecule is comprised of both disulfide and isocyanide terminal groups attached to the phenyl ring. The resulting surface structures formed on Au(111) following exposure to ICPD are studied using scanning tunneling microscopy (STM). 1,4-isocyanophenyl thiolate (ICPT), formed through scission of ICPD’s disulfide bond, was also found to oligomerize on the surface, and potential oligomer structures and binding geometries are proposed with the aid of density functional theory (DFT) calculations, along with simulated STM images of the resulting structures. It is observed in this work that ICPT forms oligomeric structures that cover large sections of the substrate and appear to create etch pits resulting from gold atom extraction. Numerous potential binding geometries are investigated based on the distances between substrate gold atom adsorption sites compared to the monomer length. Selected structural candidates were optimized using DFT and were used to generate simulated STM images using the Tersoff–Hamann method to compare with experiment. It has been shown previously that the isocyanide- and thiol-connected oligomers conduct electrons, suggesting the possibility that the asymmetric oligomers found here might form the basis for fabricating molecular diodes.

Br-Vacancies Induced Variable Ranging Hopping Conduction in High-Order Topological Insulator Bi4Br4.

The defects have a remarkable influence on the electronic structures and the electric transport behaviors of the matter, providing the additional means to engineering their physical properties. In this work, a comprehensive study on the effect of Br-vacancies on the electronic structures and transport behaviors in the high-order topological insulator Bi4Br4 is performed by the combined techniques of the scanning tunneling microscopy (STM), angle-resolved photoemission spectroscopy (ARPES), and physical properties measurement system along with the first-principle calculations. The STM results show the defects on the cleaved surface of a single crystal and reveal that the defects are correlated to the Br-vacancies with the support of the simulated STM images. The role of the Br-vacancies in the modulation of the band structures has been identified by ARPES spectra and the calculated energy-momentum dispersion. The relationship between the Br-vacancies and the semiconducting-like transport behaviors at low temperature has been established, implying a Mott variable ranging hopping conduction in Bi4Br4. The work not only resolves the unclear transport behaviors in this matter, but also paves a way to modulate the electric conduction path by the defects engineering.

First-principles simulations of scanning tunneling microscopy images exhibiting anomalous dot patterns on armchair-edged graphene nanoribbons

To interpret our recent scanning tunneling microscopy (STM) experiment of nanographene sheets, in which the existence of rectangularlike lattices is confirmed, we conducted first-principles calculations of both simple and wrinkled armchair-edged graphene nanoribbons (AGNRs). We focused on the origin of this unique lattice and simulated STM images in the occupied band for the above-mentioned ribbons with different widths. Combined with the band structures of AGNRs, we investigated the features of electron distribution in detail under various magnitudes of applied sample biases (−1 to −0.05 V). In contrast to the well-known hexagonal structure of graphene at a large bias of −1 V, a rectangularlike lattice emerges in the STM images of AGNRs with specific widths when they are generated solely by electronic states occupying the valence band maximum. Furthermore, we find that a wrinkle in graphene parallel to the edges in AGNR significantly affects the STM images of a neighboring flat graphene region, even when its height is only several angstroms. By comparing the partial density of states of the wrinkle with flat graphene, we discussed the role of a wrinkle in functionalizing graphene sheets. Published by the American Physical Society 2024

Automated Generation and Analysis of Molecular Images Using Generative Artificial Intelligence Models.

The development of scanning probe microscopy (SPM) has enabled unprecedented scientific discoveries through high-resolution imaging. Simulations and theoretical analysis of SPM images are equally important as obtaining experimental images since their comparisons provide fruitful understandings of the structures and physical properties of the investigated systems. So far, SPM image simulations are conventionally based on quantum mechanical theories, which can take several days in tasks of large-scale systems. Here, we have developed a scanning tunneling microscopy (STM) molecular image simulation and analysis framework based on a generative adversarial model, CycleGAN. It allows efficient translations between STM data and molecular models. Our CycleGAN-based framework introduces an approach for high-fidelity STM image simulation, outperforming traditional quantum mechanical methods in efficiency and accuracy. We envision that the integration of generative networks and high-resolution molecular imaging opens avenues in materials discovery relying on SPM technologies.

A high density nanopore 3-triangulene kagome lattice.

Nanopore-containing two-dimensional materials have been explored for a wide range of applications including filtration, sensing, catalysis, energy storage and conversion. Triangulenes have recently been experimentally synthesized in a variety of sizes. In this regard, using these systems as building blocks, we theoretically examined 3-triangulene kagome crystals with inherent holes of ∼12 Å diameter and a greater density array of nanopores (≥1013 cm-2) compared to conventional 2D systems. The energetic, electronic, and transport properties of pristine and B/N-doped 3-triangulene kagome crystals were evaluated through a combination of density functional theory and non-equilibrium Green's function method. The simulated scanning tunneling microscopy images clearly capture electronic perturbation around the doped sites, which can be used to distinguish the pristine system from the doped systems. The viability of precisely controlling the band structure and transport properties by changing the type and concentration of doping atoms is demonstrated. The findings presented herein can potentially widen the applicability of these systems that combine unique electronic properties and intrinsically high-density pores, which can pave the way for the next generation of nanopore-based devices.

Nano-protrusions in intercalated graphite: understanding the structural and electronic effects through DFT.

Complex phenomena characterize the intercalation of ions inside stratified crystals. Their comprehension is crucial in view of exploiting the intercalation mechanism to change the transport properties of the crystal or obtaining a fine control of crystal delamination. In particular, the relationship between the concentration and nature of intercalated ions and surface structural modifications of the host stratified crystal is still under debate. Here, we discuss a theoretical effort to provide a rationale for some structural changes observed on the highly oriented pyrolytic graphite (HOPG) surface after electrochemical treatment in perchloric and sulphuric acid solutions. The formation of the so-called nano-protrusions on the basal plane of intercalated graphite was previously observed with scanning tunneling microscopy (STM). In this work, we employed both STM and density functional theory (DFT) simulations to elucidate the physical and chemical mechanisms driving the emergence of these nano-protrusions. The DFT results show that, in a bilayer graphene system, the presence of a single ion can generate a nano-protrusion with 2.49 Å height and 21.27 Å width. In the deformed area, the C-C bond length is stretched by about 2.5% more than the normal graphene bond. These values are of the same dimensional scale as those reported in previous STM experimental results.25 However, the simulated STM images obtained by increasing the amount of intercalated ions per area suggest that the presence of more than one ion is needed for the deformation of the uppermost graphite layer during the early stages of intercalation. In contrast, in a multilayer graphene system, no significant surface deformation is detected when ions are intercalated between the third and fourth layers. Charge analysis indicates an altered distribution of the charges as a consequence of the intercalation. The charge transfer from graphene layers to the intercalated ions results in a surface layer more prone to oxidation.

Structural Characterization of Boron Sheets beyond the Monolayer and Implication for Experimental Synthesis and Identification.

The successful synthesis of quasi-freestanding bilayer borophene has aroused much attention for its superior physical properties and holds great promise for future electronic devices. Herein, we comprehensively explore six boron sheets beyond the monolayer and structurally characterize them via various methods using first-principles calculations for experimental references. On the basis of atomic models of borophenes, simulated scanning tunneling microscope (STM) images show different morphologies at different bias voltages and are explained by the partial densities of states and the height differences in the vertical direction. Simulated transmission electron microscope images further probe the internal atomic arrangement of boron sheets and compensate for the shortcomings of STM images to better distinguish different phases of boron sheets. The interlayer coupling strength is stronger in bilayer borophenes than in the three-layer system via the electron localization function and Mulliken bond population. In addition, simulated X-ray diffraction and infrared spectra show different characteristic peaks and corresponding vibrational modes to further characterize these boron sheets. These theoretical results can decrease the prime cost and provide vital guidance for the experimental synthesis and identification of boron sheets beyond the monolayer.

Vacancies and Stone–Wales defects in twisted bilayer graphene – A comparative theoretical study

The combination of miss-alignment and point defects on the electronic structure of bilayer graphene can lead to special properties, which deserve a theoretical investigation, since they are scarcely studied up to now. Although most graphene layers are nominally free of defects, they can be introduced in a simple way to achieve the desired properties. By performing density functional theory calculations implemented in two different computational approaches (SIESTA and QuantumEspresso) and a tight-binding hybrid method (DFTB+), we analyze the effects of single vacancies and Stone-Wale defects on the electronic structure of Twisted Bilayer Graphene (tBLG). Our results show that both kinds of defects can induce flat bands near the Fermi energy of tBLG, even for rotation angles quite larger than the well-known magic angles associated with the superconductivity of these systems. Additionally, with the aim to provide a theoretical background to identify defects on tBLG during experimental characterization, we simulate scanning tunneling microscopy (STM) images of these systems. As expected, such simulated STM images are dramatically influenced by the van Hove Singularities associated to the flat bands induced by defects. The results of our theoretical study may have an influence on the targeted introduction of defects in tBLG for the future design of tBLG with particular properties for some technological applications.

Mechanism of Stoichiometrically Governed Titanium Oxide Brownian Tree Formation on Stepped Au(111)

Previously observed formation of substoichiometric titanium oxide dendritic structures across terraces of Au(111) is computationally studied and shown to follow the classical fractal formation mechanism of diffusion-limited aggregation (DLA). Globally optimized gas-phase oxide cluster structures are sampled in a variety of landing formations on gold surfaces and shown to favor isomers driving polymerization to Brownian tree fractal structures. Mobility of Ti3O5 monomers is shown to be extremely high, with diffusion barriers of 0.21 eV or less. Through bonding stabilization, polymerization of these monomers is energetically favorable and irreversible on the 111 terrace but geometrically impossible to propagate along the step edge. Simulated scanning tunneling microscopy (STM) images show strong similarity to experiment. By contrast, observation of Ti3O6 aggregating as wires along step edges is explained by the affinity of oxygen to step edges and statistical arguments for aggregation entropy at the step, in addition to low barriers for monomer diffusion and polymerization.

A General Framework of Scanning Tunneling Microscopy Based on Bardeen's Approximation for Isolated Molecules.

Scanning tunneling microscopy (STM) is one of the most popular techniques for precise characterization. Yet, its current theoretical implementation is often based on the periodic boundary condition with the Tersoff-Hamann approximation, which is inefficient to explore the tip states other than the s-wave and to treat properly the charged molecules that are ubiquitous in chemistry. In this work, we establish a general theoretical framework for STM image simulations, which is based on the Bardeen's approximation and utilizes the boundary condition of the cluster model. We develop an analytic algorithm for the precise evaluation of the transfer Hamiltonian matrix, addressing correctly the asymptotic behaviors of the tip states. Numerical results demonstrate that the molecular images under different STM tip states and mapping modes can be quantitatively simulated in the present framework, which paves the avenue for the conclusive investigation of the ground state electronic structures for either neutral or charged molecules.

Topological defects and their induced metallicity in monolayer semiconducting γ-phase group IV monochalcogenides

γ-Phase group IV monochalcogenides (γ-MX), predicted to be stable with semiconducting characteristics, have been synthesized by chemical vapor deposition but showing metallicity. The ubiquitous topological defects introduced during the growth process could bring about key influences on the electronic behaviors, but their structures and properties remain unexplored. Taking monolayer γ-GeSe as an example, first-principles calculations were performed to investigate the structural, thermodynamic, and electronic properties of dislocation cores (DCs) and grain boundaries (GBs). Various derivative DCs emerge depending on different arrangements of atoms. The calculated low-energy DCs are then used to determine preferential structures of GBs versus tilt angle, with special attention paid to the whole family of 60° twin GBs, showing distinct hexagons or Ge—Ge bonds. Furthermore, electronic structures are calculated for thermodynamically favored 21.8° with closely packed dislocations and 60° twin GBs. Most of them show a strong resonance between the bulk and dislocation states, rendering the systems metallic, while some display semiconducting behaviors with reduced band gap. These electronic properties are universal for other γ-MXs. The simulated scanning tunneling microscopy images show characteristic fingerprints to help identify their existence in practice. Our results show that topological defects in γ-MX with versatile properties should be carefully engineered for their potential applications.

Hydrogen-Induced Restructuring of a Cu(100) Electrode in Electroreduction Conditions

The rearrangement of Cu surfaces under electrochemical conditions is known to play a key role in the surface activation for major electrocatalytic reactions. Despite the extensive experimental insights into such rearrangements, from surface-sensitive spectroscopy and microscopy, the spatial and temporal resolution of these methods is insufficient to provide an atomistic picture of the electrochemical interface. Theoretical characterization has also been challenged by the diversity of restructuring configurations, surface stoichiometry, adsorbate configurations, and the effect of the electrode potential. Here, atomistic insight into the restructuring of the electrochemical interface is gained from first principles. Cu(100) restructuring under varying applied potentials and adsorbate coverages is studied by grand canonical density functional theory and global optimization techniques, as well as ab initio molecular dynamics and mechanistic calculations. We show that electroreduction conditions cause the formation of a shifted-row reconstruction on Cu(100), induced by hydrogen adsorption. The reconstruction is initiated at 1/6 ML H coverage, when the Cu-H bonding sufficiently weakens the Cu-Cu bonds between the top- and sublayer, and further stabilized at 1/3 ML when H adsorbates fill all the created 3-fold hollow sites. The simulated scanning tunneling microscopy (STM) images of the calculated reconstructed interfaces agree with experimental in situ STM. However, compared to the thermodynamic prediction, the onsets of reconstruction events in the experiment occur at more negative applied voltages. This is attributed to kinetic effects in restructuring, which we describe via different statistical models, to produce the potential- and pH-dependent surface stability diagram. This manuscript provides rich atomistic insight into surface restructuring in electroreduction conditions, which is required for the understanding and design of Cu-based materials for electrocatalytic processes. It also offers the methodology to study the problem of in situ electrode reconstruction.

Higher-indexed Moiré patterns and surface states of MoTe2/graphene heterostructure grown by molecular beam epitaxy

Stabilization of the 2H phase of MoTe2 during molecular beam epitaxy (MBE) growth on graphene terminated 6H-SiC(0001) is highly desirable in order to take advantage of its promising properties in electronic applications. By properly adjusting the conditions, direct growth of the highly crystalline 2H phase of MoTe2 has been achieved. In such van der Waals heterostructure, the atomically-clean interface between graphene and MoTe2 permits the electronic coupling between the adjacent layers and the emergence of a high variety of Moiré patterns. In this paper, we investigate a single layer of 2H-MoTe2 grown on graphene by MBE and we present scanning tunneling microscopy (STM) investigations combined with density functional theory (DFT) calculations and simulations of STM images. Our results show that the STM images of the MoTe2/graphene heterostructure surprisingly amplify the otherwise weak Moiré potential modulations leading to the appearance of unique higher-indexed Moiré patterns. These patterns are unusually rich with many Fourier-overtones and show a remarkable variety of different applied bias voltages, revealing the complex electronic features of the heterostructure.

Topological Defects Induced High-Spin Quartet State in Truxene-Based Molecular Graphenoids

Topological Defects Induced High-Spin Quartet State in Truxene-Based Molecular Graphenoids

Simulation of STM Images of Hematite α-Fe2O3(0001) Surfaces: Dependence on Distance and Bias

Experimental scanning tunneling microscopy (STM) images of the hematite (0001) surface exhibit long-range superstructures formed by coexisting domains consisting of different terminations (α, β, γ) of the α-Fe2O3(0001) surface. In this work extensive simulations of STM images of different terminations of hematite (0001) surfaces are performed and compared with measured ones in order to identify the nature of the superstructure unit meshes. Based on DFT calculations of α-Fe2O3(0001) surfaces, the STM images are simulated using Chen’s derivative rules approach. Different bias voltages and tip–sample distances as well as the role of the tip type are considered and discussed. For some terminations an extreme dependence of the simulated image on the distance and bias voltage is found. The difference between simulations of metal and insulator/semiconductor surfaces is discussed. The condition of simultaneous agreement between simulation and experiment for all terminations within a narrow STM parameter range leads to the assignment of the α, β and γ terminations to the ferryl, Fe-Fe–O3– or Fe–O3–Fe–, and O3–Fe–Fe– terminations, respectively.

Density Functional Theory Study of Ethylene Carbonate Adsorption on the (0001) Surface of Aluminum Oxide α-Al2O3.

Surface coating is one of the techniques used to improve the electrochemical performance and enhance the resistance against decomposition of cathode materials in lithium-ion batteries. Despite several experimental studies addressing the surface coating of secondary Li-ion batteries using α-Al2O3, the reactivity of the material toward the electrolyte components is not yet fully understood. Here, we have employed calculations based on the density functional theory to investigate the adsorption of the organic solvent ethylene carbonate (EC) on the major α-Al2O3(0001) surface. During adsorption of a single EC molecule, it was found that it prefers to bind parallel to the surface through its carboxyl oxygen. As the surface coverage (θ) was increased up to a monolayer, we observed larger adsorption energies per EC molecule (Eads/NEC) for parallel interactions and a reduction for perpendicular interactions. We also noted that increasing the surface coverage with both parallel and perpendicularly interacting EC molecules led to a decrease of the surface free energies and hence increased stability of the α-Al2O3(0001) surface. Despite the larger Eads/NEC observed when the molecule was placed parallel to the surface, minimal charge transfer was calculated for single EC interactions and at higher surface coverages. The simulated scanning tunneling microscopy images are also presented for a clean corundum α-Al2O3 surface and after adsorption with different coverages of parallel and perpendicularly placed EC molecules.

Theoretical study on adsorption and reaction of polymeric formic acid on the Cu(111) surface

We investigate the polymeric adsorption of formic acid (HCOOH) on the Cu(111) surface by means of density functional theory. We present structural models for the polymeric form of HCOOH on Cu(111) and characterize their stability, electronic, and vibrational properties. Based on the energetics and dynamics, as well as simulated scanning tunneling microscopy and atomic force microscopy images, we propose that the $\ensuremath{\alpha}$ polymorph is likely to be formed on the Cu(111) surface and can explain the experimental findings. We also study the initial step of the catalytic dehydrogenation of HCOOH and find that the O-H bond dissociation at the edge of the polymer is facilitated, rather than that forming hydrogen bonding, agreeing well with the experiments.

Catalytic Conversion of CO and H2 into Hydrocarbons on the Cobalt Co(111) Surface: Implications for the Fischer–Tropsch Process

The Fischer–Tropsch (FT) process consists of the reaction of a synthesis gas (syngas) mixture containing carbon monoxide (CO) and hydrogen (H2), which are polymerized into liquid hydrocarbon chains, often using a cobalt catalyst, although the mechanistic pathway is not yet fully understood. Here, we have employed unrestricted density functional theory calculations with a Hubbard Hamiltonian and long-range dispersion corrections [DFT+U−D3−(BJ)] to investigate the reaction of syngas and the selectivity toward the hydrocarbons formed on the cobalt Co(111) surface. The single CO and dissociated H2 molecules prefer to adsorb at two different types of trigonal surface sites, and we discuss how the interatomic distances, fundamental vibrational modes, charge transfers, surface-free energies, and work functions are modified by the adsorbates. The coadsorption of the syngas molecules in close proximity provides enough energy for the system to cross the saddle points on the minimum energy pathway (MEP), leading to the catalytic hydrogenolysis of the C–O bond. The adsorbed CO, alongside the intermediates CH and OH, are further stabilized when the ratio of equilibrium coverage (C) is CH/CCO,CH,OH > 6:1 under the temperature conditions required for the FT process. We propose several mechanistic pathways to account for the formation of ethane (C2H6), as a model for long-chain hydrocarbons, as well as methane (CH4) which is an undesirable product. The MEPs for these processes show that the coupling of the C–C bond followed by hydrogenation is the most favorable process, which takes precedence over the production of CH4. The termination reaction suggests that water (H2O) remains weakly physisorbed to the surface, allowing the reutilization of its catalytic site. The simulated fundamental vibrational frequencies and scanning tunneling microscopy images of the surface-bound intermediates are in agreement with the available experimental data. Our findings are important in the interpretation of the elementary steps of the FT process on the Co(111) surface.