Analysis Of Scanning Tunneling Microscopy Images Research Articles

Classification of adsorbates in scanning tunneling microscopy images of Fe3O4(111) surfaces exposed to water and carbon monoxide

Understanding the structure of catalyst surfaces with adsorbed molecules is key to improving catalyst design. Scanning tunneling microscopy (STM) allows the observation of adsorption states and sites and provides insights into diffusion and desorption processes; however, the presence of multiple types of molecules on the surface presents challenges such as the identification of species and verification of reaction progress, particularly at room temperature or higher. In this study, we develop a protocol for the height classification analysis of STM images using the Watershed algorithm. This method is applied to a system involving the co-adsorption of H2O and CO on the Fe3O4(111) surface, which represents the beginning of the water-gas shift reaction. Water molecules and dissociated OH species were identified in STM images of the Fe3O4(111) surface following the adsorption of water. Furthermore, gradual changes in the types of surface species were observed upon exposure of the surface to CO, indicating reaction progression. Our observations suggest that CO may react with molecular water rather than with dissociated OH on Fe sites. Despite its simplicity, the height classification analysis effectively identifies changes in the adsorbates on the catalyst surface. This method can be extended to other catalyst surfaces with adsorbed gasses.

Deciphering Alloy Composition in Superconducting Single-Layer FeSe1-xSx on SrTiO3(001) Substrates by Machine Learning of STM/S Data.

Scanning tunneling microscopy (STM) is a powerful technique for imaging atomic structure and inferring information on local elemental composition, chemical bonding, and electronic excitations. However, a plain visual analysis of STM images can be challenging for such determination in multicomponent alloys, particularly beyond the diluted limit due to chemical disorder and electronic inhomogeneity. One viable solution is to use machine learning to analyze STM data and identify hidden patterns and correlations. Here, we apply this approach to determine the Se/S concentration in superconducting single-layer FeSe1-xSx alloys epitaxially grown on SrTiO3(001) substrates via molecular beam epitaxy. First, the K-means clustering method is applied to identify defect-related dI/dV tunneling spectra taken by current imaging tunneling spectroscopy. Then, the Se/S ratio is calculated by analyzing the remaining spectra based on the singular value decomposition method. Such analysis provides an efficient and reliable determination of alloy composition and further reveals the correlations of nanoscale chemical inhomogeneity to superconductivity in single-layer iron chalcogenide films.

In Situ Imaging and Computational Modeling Reveal That Thiophene Complexation with Co(II)porphyrin/Graphite Is Highly Cooperative

Scanning tunneling microscopy (STM) was employed to quantitively investigate in situ binding of 3-phenyl thiophene (PhTh) to Co(II)octaethyl porphyrin (CoOEP) supported on highly ordered pyrolytic graphite (HOPG) in fluid solution. To our knowledge, this is the first single-molecule level study of a complexation reaction between a metalloporphyrin and a sulfur base at the solution/solid interface and one of the few examples of thiophene coordination with a d7 transition metal. Real-time imaging experiments revealed that PhTh binds reversibly to HOPG-supported CoOEP at room temperature. The coordination process increases with increasing PhTh concentration. The nearest-neighbor analysis of STM images indicates that the complexation reaction is cooperative. Because PhTh does not bind to CoOEP in solution, the STM results strongly suggest that the presence of HOPG is crucial to observe ligand binding and cooperativity in this system. Periodic plane-wave density functional theory (DFT) computations corroborate that PhTh has low binding affinity toward CoOEP in solution but predict that the ligand can adsorb to CoOEP/HOPG through coordination with S atoms or interact through noncovalent π–π bonding with the porphyrin chromophore. Three possible structures were considered, and DFT theory was used to calculate binding energies and free energies. In solution and on the HOPG surface both a π–π configuration and a η1(S) configuration have similar computed energies. The η1(S) structure shows the largest stabilization in going from the vapor to adsorbed on HOPG. We also show that statistical analysis of nearest neighbors is more sensitive to cooperative binding than is fitting with the Temkin or Langmuir isotherm. The implication is that isotherm fitting alone is insufficient for identifying cooperative binding on surfaces.

Identification of a nitrogen vacancy in GaN by scanning probe microscopy

Gallium nitride (GaN) is a material with important applications in optoelectronics, wireless communications, and power electronics. Devices for such applications are normally made with GaN single-crystal wafers. Yet an infinitesimal amount of atomic defects in these single crystals considerably hinders the electronic performance of GaN. One kind of atomic defect in GaN crystals that has been theoretically predicted but eludes direct experimental observation is nitrogen (N) vacancies. Here, we unambiguously identify a single N vacancy on a cleaved $m$-plane surface of GaN by direct visualization in real space with scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The presence of a vacancy is established by AFM imaging and force spectroscopy measurements. The identification is accomplished by the analysis of STM images, tunneling current spectroscopy, and comparison with the outcomes from the quantification of band bending near the surface, current calculations, and first-principles simulations. All this information provides insight into the electronic perturbation of a single N vacancy at the surface band structure of GaN. Our results provide further understanding of the effect that point defects have on GaN, and will hopefully contribute to tune the behavior of this technologically relevant material in electronic devices.

NH3 adsorption on anatase-TiO2(101).

The adsorption of ammonia on anatase TiO2 is of fundamental importance for several catalytic applications of TiO2 and for probing acid-base interactions. Utilizing high-resolution scanning tunneling microscopy (STM), synchrotron X-ray photoelectron spectroscopy, temperature-programmed desorption (TPD), and density functional theory (DFT), we identify the adsorption mode and quantify the adsorption strength on the anatase TiO2(101) surface. It was found that ammonia adsorbs non-dissociatively as NH3 on regular five-fold coordinated titanium surface sites (5f-Ti) with an estimated exothermic adsorption energy of 1.2 eV for an isolated ammonia molecule. For higher adsorbate coverages, the adsorption energy progressively shifts to smaller values, due to repulsive intermolecular interactions. The repulsive adsorbate-adsorbate interactions are quantified using DFT and autocorrelation analysis of STM images, which both showed a repulsive energy of ∼50 meV for nearest neighbor sites and a lowering in binding energy for an ammonia molecule in a full monolayer of 0.28 eV, which is in agreement with TPD spectra.

Investigation of the atomic and electronic structures of highly ordered two-dimensional germanium on Au(111)

Low energy electron diffraction (LEED), scanning tunneling microscopy (STM), and photoelectron spectroscopy have been used to study an ordered structure formed by Ge atoms deposited onto the Au(111) surface. Based on a careful analysis of STM images and LEED patterns, we propose a new unit cell for the atomic structure of the Ge layer. Core level data indicate that some Ge atoms diffuse into the Au(111) crystal during annealing after deposition at room temperature. This is further corroborated by angle resolved photoelectron spectroscopy measured for different amounts of Ge remaining after sputtering and annealing. The results of the ARPES study clearly exclude the interpretation, in the literature, of a parabolic band as part of a Dirac cone of germanene.

Analysis of STM images with pure and CO-functionalized tips: A first-principles and experimental study

We describe a first principles method to calculate scanning tunneling microscopy (STM) images, and compare the results to well-characterized experiments combining STM with atomic force microscopy (AFM). The theory is based on density functional theory (DFT) with a localized basis set, where the wave functions in the vacuum gap are computed by propagating the localized-basis wave functions into the gap using a real-space grid. Constant-height STM images are computed using Bardeen's approximation method, including averaging over the reciprocal space. We consider copper adatoms and single CO molecules adsorbed on Cu(111), scanned with a single-atom copper tip with and without CO functionalization. The calculated images agree with state-of-the-art experiments, where the atomic structure of the tip apex is determined by AFM. The comparison further allows for detailed interpretation of the STM images.

Adjusting island density and morphology of the SrTiO3(110)-(4 × 1) surface: Pulsed laser deposition combined with scanning tunneling microscopy

The first stages of homoepitaxial growth of the (4×1) reconstructed surface of SrTiO3(110) are probed by a combination of pulsed laser deposition (PLD) with in-situ reflection high energy electron diffraction (RHEED) and scanning tunneling microscopy (STM). Considerations of interfacing high-pressure PLD growth with ultra-high-vacuum surface characterization methods are discussed, and the experimental setup and procedures are described in detail. The relation between RHEED intensity oscillations and ideal layer-by-layer growth is confirmed by analysis of STM images acquired after deposition of sub-monolayer amounts of SrTiO3. For a quantitative agreement between RHEED and STM results one has to take into account two interfaces: the steps at the circumference of islands, as well as the borders between two different reconstruction phases on the islands themselves. Analysis of STM images acquired after one single laser shot reveals an exponential decrease of the island density with increasing substrate temperature. This behavior is also directly visible from the temperature dependence of the relaxation times of the RHEED intensity. Moreover, the aspect ratio of islands changes considerably with temperature. The growth mode depends on the laser pulse repetition rate, and can be tuned from predominantly layer-by-layer to the step-flow growth regime.

Understanding domain symmetry in vanadium oxide phthalocyanine monolayers on Au (111)

Understanding the growth of organic semiconductors on solid surfaces is of key importance for the field of organic electronics. Non planar phthalocyanines have shown great promise in organic photovoltaic (OPV) applications, but little of the fundamental surface characterization to understand their structure and properties has been performed. Acquiring a deeper understanding of the molecule/substrate interaction in small molecule systems is a vital step in controlling structure/property relationships. Here we characterize the vanadium oxide phthalocyanine (VOPc)/Au (111) surface using a combination of low energy electron diffraction (LEED) and scanning tunneling microscopy (STM), obtaining complex diffraction patterns which can be understood using two dimensional fast Fourier transform (2D-FFT) analysis of STM images. These measurements reveal coexistence of three symmetrically equivalent in-plane orientations with respect to the substrate, each of which is imaged simultaneously within a single area. Combining scanning probe and diffraction measurements allows symmetrically related domains to be visualized and structurally analyzed, providing fundamental information useful for the structural engineering of non-planar phthalocyanine interfaces.

Growth of Bi on Cu(111): Alloying and dealloying transitions

We report on the observation of surface alloying and dealloying transitions during the submonolayer growth of Bi on the Cu(111) surface. In-situ scanning tunneling microscopy (STM) analysis reveals that at low coverage, and for quasi thermodynamical equilibrium, embedded Bi atoms are randomly distributed within the first Cu layer. Near the ideal coverage of 1/3, we observe an ordered BiCu2 substitutional surface alloy. Between 1/3 and 1/2 monolayer a dealloying process takes place where the surface alloy coexists with two different domains of dense Bi overlayer. In order to understand the mechanisms behind this process, the ordered alloy has been used as a template for subsequent Bi adsorption. An apparently etched surface develops during deposition and using STM image analysis, we propose that this growth mode is accompanied by a large Bi and Cu atoms redistribution inside the surface alloy.

Hydrogen bonding network of truxenone on a graphite surface studied with scanning tunneling microscopy and theoretical computation

The self-assembly of truxenone on highly oriented pyrolytical graphite (HOPG) was investigated with scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. Truxenone assembled into a dense hexagonal adlayer with large and near-perfect domains on the graphite surface. Two types of topography image of truxenone were observed in experiments. DFT modeling indicates the center-hole image represents the contour of the lowest unoccupied molecular orbital (LUMO) of truxenone while the propeller-like image is more complicated and can't be assigned simply to an individual molecular orbital. Truxenone trimer was proposed as the basic unit of the adlayer through analysis of STM images and molecular structure. The optimized structure of the truxenone trimer by DFT calculation revealed that the hydrogen bonding network exists in the adlayer, which is responsible for the excellent stability and perfect domains of the whole assembly. In addition, the preferred adsorption site of truxenone on graphite was determined on the basis of DFT calculations and STM images. The results are of significance in supramolecular engineering by self-assembly and device fabrication based on truxenone and its derivatives.

Growth Process of Silicon on the Si(111) .RAD.3*.RAD.3-Ag Surface at Room Temperature

The growth process of silicon on the Si(111)√3×√3-Ag surface (here after √3Ag surface) has been studied by scanning tunneling microscopy (STM). Islands of one bilayer thickness with infinite form and triangular geometry are observed for 0.32 ML(ML:1 ML=7.8×1014/cm2) deposition of silicon on the √3Ag surface. The orientation of two dimensional islands with triangular geometry is the same as that of unfaulted half unit of the Si(111)7×7 structure (here after 7×7 structure). The surface structure of the Si islands is characterized as the √3 structure by analysis of STM images of the island. It is believed that Ag atoms segregate on the deposited silicon islands and the island surfaces become the √3Ag structure. In comparison with densities of the islands on the 7×7 and the √3Ag surfaces, it is concluded that the diffusion coefficient of Si atoms on the √3Ag surface is about 60 times larger than that of Si atoms on the 7×7 surface. The value of the diffusion coefficient is independence on deposition rates. We also discuss a possibility of the Schwoebel effect on the √3Ag surface for Si atoms because populations of the islands at step edges of upper terraces are higher than those at lower step edges. [DOI: 10.1380/ejssnt.2009.763]

Adsorption Behavior of Iron Phthalocyanine on Au(111) Surface at Submonolayer Coverage

Adsorption behavior of iron(II) phthalocyanine (FePc) on Au(111) surface at submonolayer coverage has been investigated using low-temperature scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. At the initial adsorption stage, FePc molecules prefer to adsorb on terrace dispersedly as isolated adsorbates because of the stronger molecule−substrate interaction than the lateral intermolecular interaction. Two different configurations of FePc on Au(111) surface are resolved on the basis of STM image analysis and are further identified by DFT calculations. When increasing molecule coverage, the intermolecular interaction becomes more important. The FePc molecules assemble to dimers, trimers, and short chains and even peculiar porous hexamers with two configurations. At a saturated coverage, highly ordered FePc monolayer with only one configuration of FePc is observed. The results indicate that the adsorption behavior of FePc on Au(111) is governed by a coverage-dependent compet...

Single Molecule Observations of the Adsorption Sites of Methyl Isocyanide on Pt(111) by Low-Temperature Scanning Tunneling Microscopy

Scanning tunneling microscopy (STM) has been used to directly investigate the local structure of methyl isocyanide (CNCH3) adsorbed on Pt(111). At low coverages, CNCH3 is preferentially adsorbed at on-top sites, in agreement with earlier deductions based on vibrational spectroscopy. When dosed at low coverages at 50 K, the molecules tend to adsorb near other CNCH3 molecules with preferred distances of a and a, where a = 2.78 A is the lattice constant of Pt. Annealing the surface to 120 K, however, results in a more uniform separation of the molecules. At higher coverages, the CNCH3 molecules are observed to occupy both on-top and two-fold bridge sites. On the basis of STM image analysis, CNCH3 forms an ordered layer of (2 x 3) periodicity at 0.33 ML. Additional details on the structures of CNCH3 adsorbed at the on-top and two-fold bridge sites are provided by density functional theory (DFT) calculations. At a coverage that saturates the first layer (0.33 ML), the occupation ratio for the on-top and two-fold bridge bonded CNCH3 is 1:1, which is consistent with the results obtained from the combined use of experimental reflection absorption infrared spectroscopy (RAIRS) data and DFT calculations.

Image Contrast Analysis of STM Images of Self‐Assembled Dioctadecyl Chalcogenides on Graphite at the Liquid–Solid Interface

The structures of self-assembled monolayers of dioctadecyl selenide (CH3(CH2)17)2Se and dioctadecyl telluride (CH3(CH2)17)2Te, as well as dioctadecyl ether (CH3(CH2)17)2O and dioctadecyl sulfide (CH3(CH2)17)2S, on graphite at the liquid-solid interface were systematically investigated by scanning tunneling microscopy (STM). Both dioctadecyl selenide and telluride formed monolayer structures in which the tilt angle between the molecular axis of the alkyl chain and the lamellae axis was 90 degrees , while dioctadecyl ether assembled with a tilt angle of 60 degrees . Dioctadecyl sulfide was found to make two different self-assembled structures having tilt angles of 60 and 90 degrees . When selenide was embedded in ether compounds in mixed self-assembled monolayers, the alkyl chains of the selenide became blurred, implying that the alkyl chains in the monolayers were unstable. This is in contrast with the structure of co-adsorbed monolayers of the ether and sulfide compounds, where the images of all alkyl chains had high spatial resolution. For the co-adsorbed monolayers, the image contrast of chalcogen atoms was normalized compared with that of alkyl chains of the ether compound in the same image frame. The normalized image contrast was found to be independent of the measurement conditions involving tip shapes, having the following trend, Te>Se>S>C>O. The difference in the normalized image contrast among chalcogen atoms are discussed based on fundamental parameters like polarizability and atomic radii.

Theoretical study on the temperature-induced structural transition of the Si(1 1 3) surface

The temperature-induced structural transition of the Si(1 1 3) surface is investigated by ab initio calculations. In this study, it is found that the room-temperature phase and the high-temperature phase have the 3 × 2 interstitial structure and the 3 × 1 interstitial structure, respectively. The existence of the 3 × 2 and 3 × 1 interstitial structures is supported by the analysis of scanning tunneling microscopy (STM) images and the calculation of surface core level shifts using final state pseudopotential theory. The theoretical STM images of interstitial structures are in good agreement with the STM images suggested by experiments. The analysis of STM images provides an insight into the characteristics of domain boundaries observed frequently in experiments. It is also found that the domain boundary can be formed by local 3 × 1 interstitial structures on the 3 × 2 interstitial surface. The theoretical analysis of the surface core level shifts reveals that the surface core levels in experiment originate from the interstitial structures. The lowest values in the surface core level shifts are found to be associated with the 2p core level shifts of the interstitial atoms.

Structural and statistical analysis of Yb/Si(1 1 1) and Eu/Si(1 1 1) reconstructions

We have performed the structural and statistical analysis of Yb/Si(1 1 1) and Eu/Si(1 1 1) surfaces in the submonolayer regime utilizing low-energy electron diffraction and scanning tunneling microscopy (STM). The almost identical series of one-dimensional chain structures (e.g., 3 × 2/3 × 1, 5 × 1, 7 × 1, 9 × 1, and 2 × 1 phases) are found in order of increasing metal coverage for both adsorbed systems, however, only the Eu/Si system reveals the ‘√3’-like reconstruction before the 2 × 1 endpoint phase. The atomic models of chain structures are proposed and discussed. In particular, our results suggest the odd-order n×1 ( n=5,7,9,…) intermediate reconstructions to incorporate the Seiwatz chains and honeycomb chains with the proportion of m:1, where m= n−1 2 −1 . The statistical analysis of STM images is carried out to examine the correlation of atomic rows on Eu/Si and Yb/Si surfaces. It is found that Eu stabilizes more ordered row configuration compared to Yb, which can be explained in terms of indirect electronic interaction of atomic chains or/and different magnetic properties of adsorbed species.

Adsorption structure of 1,3-butadiene on Pd(1 1 0)

Adsorption structure of 1,3-butadiene chemisorbed on Pd(1 1 0) has been studied by high resolution electron energy loss spectroscopy (HREELS), near edge X-ray absorption fine structure (NEXAFS), and scanning tunneling microscopy (STM). The HREELS and NEXAFS results revealed that 1,3-butadiene is adsorbed with π-bond and the molecular plane is parallel to the surface, in which the C–C single bond in 1,3-butadiene on Pd(1 1 0) is aligned toward [1 1 ̄ 0] . The adsorption site and geometry were determined on the basis of the STM image analysis.

(10×2) strained reconstruction induced by oxygen adsorption on the Rh(110) surface

Oxygen adsorption on the (1×2) missing row reconstructed Rh(110) surface has been studied by means of low-energy electron diffraction (LEED), x-ray photoelectron spectroscopy (XPS), and scanning tunneling microscopy (STM). Starting from the already known (2×2)p2mg oxygen overlayer in which the substrate is (1×2) reconstructed, further oxygen has been dosed at room and lower temperatures. Upon heating, additional substrate reconstruction takes place and the surface forms a new structure with (10×2) periodicity and high local oxygen coverage. Oxygen 1s XPS measurements show a binding energy shift from 530.25 eV in the (2×2)p2mg to 529.75 eV in the (10×2) layer. Analysis of STM images reveals that in the (10×2) layer, the rhodium close-packed rows are strained and segmented in the [11̄0] direction. On the basis of the experimental results, models for the (10×2) structure and its formation process are proposed and compared with “pseudo-oxide” structures.

Voltammetric anodic stripping of silver from platinum electrodes consisting of an array of nm-sized voids

Abstract Silver voltammetric anodic stripping from stabilized rough platinum electrodes in 1 M H2SO4+co Ag2SO4 (5×10−4 M≤co≤10−3 M) and 1 M H2SO4 aqueous solutions, at 298 K, was investigated. The topography of these electrodes was determined by scanning tunneling microscopy (STM). The roughness factor, R, was varied from 10 to 71. The analysis of STM images showed that the rough structure consists of an array of nm-sized protrusions and voids as a columnar structured surface. For each value of R, the average size and volume of voids were determined. The voltammetric features of silver anodic stripping depend on R and the electrodeposited silver charge, QAg. The value of QAg(vs), the saturation value of QAg for voids, was estimated. The anodic stripping of underpotential deposited silver occurs in the potential range where oxygen electroadsorption on platinum takes place. By using data derived from STM imaging and equations that have been derived for the voltammetric anodic stripping reactions, in which the reactant is confined to nm-sized voids, the voltammetric behaviour of the system can be reproduced reasonably.