Theoretical Scanning Tunneling Microscopy Images Research Articles

Theoretical study of ethyl alcohol adsorbed on a germanium (100) surface

AbstractThe chemical reaction of ethyl alcohol on a germanium surface was investigated through density functional theory analysis. The most stable product containing the HOGeGeCH2CH3 linkage was formed via OC‐dissociative adsorption. Kinetic studies revealed that the OH‐dissociative reaction pathways have relatively low activation barriers and may, respectively, occur at room temperature. Configurationally, the oxygen atom of the ethoxy fragment was bonded to the germanium atom, and the ethyl group was oriented either perpendicular or parallel to the germanium surface. The two configurations had similar adsorption energies and activation barriers. Further reaction of the dissociated hydrogen with a nearby electron‐rich germanium atom passivated the dangling bond. Theoretical scanning tunneling microscopy images simulated based on the OH‐dissociative adsorption revealed a better agreement with the experimentally observed adsorption features than those of other possible structures.

Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation

Abstract By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moire patterns observed in theoretical STM images.

Imaging Molecular Orbitals of PTCDA on Graphene on Pt(111): Electronic Structure by STM and First-Principles Calculations

The adsorption and growth of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) on graphene monolayers epitaxially grown on Pt(111) surfaces is studied by a combination of experimental scanning tunneling microscopy (STM) and spectroscopy (STS) measurements and first-principles density functional theory (DFT) calculations. For submonolayer coverage, until the completion of the first layer, PTCDA molecules form a well-ordered herringbone structure with molecules lying flat on the graphene surface weakly coupled to the Pt(111) substrate. High-resolution STM imaging at different sample biases has allowed the identification of intramolecular features that can be related to the original PTCDA frontier orbitals. Theoretical STM calculations, based on local-orbital DFT, have been carried out on the full PTCDA/graphene/Pt(111) system. The comparison of theoretical and experimental STM images has allowed us to ascribe the origin of intramolecular features to the highest occupied and lowest unoccupied molecular o...

Charge Localization in Isolated Mixed-Valence Complexes: An STM and Theoretical Study

{Cp*(dppe)Fe(C≡C-)}(2)(1,3-C(6)H(4)) is studied both as a neutral molecule, Fe(II)-Fe(II), and as a mixed-valence complex, Fe(II)-Fe(III). Scanning tunneling microscopy (STM) is used to image these species at 77 K under ultrahigh-vacuum conditions. The neutral molecule Fe(II)-Fe(II) has a symmetric, "dumbbell" appearance in STM images, while the mixed-valence complex Fe(II)-Fe(III) demonstrates an asymmetric, bright-dim double-dot structure. This asymmetry results from localization of the electron to one of the iron-ligand centers, a result which is confirmed through comparison to theoretical STM images calculated using constrained density-functional theory (CDFT). The observation of charge localization in mixed-valence complexes outside of the solution environment opens up new avenues for the control and patterning of charge on surfaces, with potential applications in smart materials and molecular electronic devices.

Scanning Tunneling Microscopy Simulations of Nitrogen- and Boron-Doped Graphene and Single-Walled Carbon Nanotubes

We report on studies of electronic properties and scanning tunneling microscopy (STM) of the most common configurations of nitrogen- or boron-doped graphene and carbon nanotubes using density functional theory. Charge transfer, shift of the Fermi level, and localized electronic states are analyzed as a function of the doping configurations and concentrations. The theoretical STM images show common fingerprints for the same doping type for graphene, and metallic or semiconducting nanotubes. In particular, nitrogen is not imaged in contrast to boron. STM patterns are mainly shaped by local density of states of the carbon atoms close to the defect. STM images are not strongly dependent on the bias voltage when scanning the defect directly. However, the scanning of the defect-free side of the tube displays a perturbation compared to the pristine tube depending on the applied bias.

Structure and energetics ofSi(111)−(5×2)-Au

We propose a new structural model for the Si(111)-(5x2)-Au reconstruction. The model incorporates a new experimental value of 0.6 monolayer for the coverage of gold atoms, equivalent to six gold atoms per 5x2 cell. Five main theoretical results, obtained from first-principles total-energy calculations, support the model. (1) In the presence of silicon adatoms the periodicity of the gold rows spontaneously doubles, in agreement with experiment. (2) The dependence of the surface energy on the adatom coverage indicates that a uniformly covered phase is unstable and will phase-separate into empty and covered regions, as observed experimentally. (3) Theoretical scanning tunneling microscopy images are in excellent agreement with experiment. (4) The calculated band structure is consistent with angle-resolved photoemission spectra; analysis of their correspondence allows the straightforward assignment of observed surface states to specific atoms. (5) The calculated activation barrier for diffusion of silicon adatoms along the row direction is in excellent agreement with the experimentally measured barrier.

First-principles study of oxidized Nb(1 0 0) surface structures

The atomic positions of the oxygen-induced c(2×2)-O, (3×1)-O and (4×1)-O surface structures on Nb(100) are determined by first-principles electronic structure calculations within the density functional theory comparing experimentally observed scanning tunneling microscopy (STM) images. STM images of these surfaces are calculated on the basis of the theory of Tersoff and Hamann. The theoretical and experimental STM images of the oxygen-chemisorbed c(2×2)-O structural model agree well. However, only the oxide-covered (3×1)-O and (4×1)-O structural models with two layers of NbO and contraction of the unit length along longitudinal 〈100〉 direction by 10% result in the theoretical STM images that agree with the experimental ones.

Atomic and electronic properties of furan on the Si(0 0 1)-(2 × 2) surface

The atomic and electronic properties of the adsorption of furan (C 4H 4O) molecule on the Si(1 0 0)-(2 × 2) surface have been studied using ab initio calculations based on pseudopotential and density functional theory. We have considered two possible chemisorption mechanisms: (i) [4 + 2] and (ii) [2 + 2] cycloaddition reactions. We have found that the [4 + 2] interaction mechanism was energetically more favorable than the [2 + 2] mechanism, by about 0.2 eV/molecule. The average angle between the C C double bond and Si(1 0 0) surface normal was found to be 22°, which is somewhat smaller than the experimental value of 28°, but somewhat bigger than other theoretical value of 19°. The electronic band structure, chemical bonds, and theoretical scanning tunneling microscopy images have also been calculated. We have determined a total of six surface states (one unoccupied and five occupied) in the fundamental band gap. Our results are seen to be in good agreement with the recent near edge X-ray absorption fine structure and high resolution photoemission spectroscopy data.

Comparative study of the adsorption and dissociation of vinylacetic acid and acrylic acid on silicon (001)

In this work, we employ the state of the art pseudopotential method, within a generalized gradient approximation to the density functional theory, to investigate the adsorption process of acrylic acid (AAc) and vinylacetic acid (VAA) on the silicon surface. Our total energy calculations support the proposed experimental process, as it indicates that the chemisorption of the molecule is as follows: The gas phase VAA (AAc) adsorbs molecularly to the electrophilic surface Si atom and then dissociates into ${\mathrm{H}}_{2}\mathrm{C}\mathrm{C}\mathrm{H}\mathrm{C}\mathrm{O}\mathrm{O}$ and H, bonded to the electrophilic and nucleophilic surface silicon dimer atoms, respectively. The activation energy for both processes correspond to thermal activations that are smaller than the usual growth temperature. In addition, the electronic structure, calculated vibrational modes, and theoretical scanning tunneling microscopy images are discussed, with a view to contribute to further experimental investigations.

Study of intercalated Ti atom in tetrahedral or octahedral sites of titanium disulfide (001) surfaces: Theoretical scanning tunneling microscopy images

We have performed ab initio linear combination of atomic orbitals-density functional theory calculations on biperiodic supercells to model the electronic and geometrical involvements of Ti intercalated atom in either octahedral or tetrahedral sites of the (001) TiS2 surfaces. For each type of defect, both the relaxed atomic structure and the electronic properties of the defect states were carefully analyzed. For the titanium atom in the van der Waals gap, the partial filling of the conduction band is in agreement with the metallic behavior reported by experimental studies and the last filled states in the bottom of the conduction band--mainly developed on titanium 3d orbitals--permit us to explain the dark defects observed on the scanning tunneling microscopy image of the (001) TiS2 surfaces. On the other hand, the intercalated titanium atom in the tetrahedral site which is just below the top sulfur atom plane governs the electronic density detected by the tip. It permits us to explain the triangular defect with a clear maximum of intensity in its center and dark sides.

Electronic and structural properties of Ti vacancies on the (001) surface of TiS2: Theoretical scanning tunneling microscopy images

Various defects--either bright or dark triangular defects--are observed on the (001) titanium disulfide surface by ultrahigh vacuum scanning tunneling microscopy. The experimental interpretations of the images available in the literature suggest that a fraction of Ti atoms could be displaced from the octahedral site they occupied to vacant sites of the crystal structure, leading to more or less correlated defects. In this paper, the authors have performed ab initio periodic linear combination of atomic orbitals-generalized gradient approximation (LCAO-GGA) calculations on (5x5) and (4x4) biperiodic supercells to model the electronic and geometrical involvements of Ti vacancy. The relaxed atomic structures of each system and the wave-function character of the defect states are carefully analyzed before the theoretical scanning tunneling microscopy images are generated within the Tersoff-Hamann approximation. The relaxed structure of the Ti vacancy shows an inward movement of the neighboring sulfur atoms at the surface. However, the occupied electronic states of the vacancy at the Fermi level are mainly developed on the atomic orbitals of the first sulfur neighbors at the surface, leading to bright triangular zones on the simulated image.

Theoretical STM images of alkaline-earth metal adsorbed Si(1 1 1)3 × 2 surfaces

We have performed total-energy calculations to study theoretical scanning tunneling microscopy (STM) images of the Si(1 1 1)3 × 2 surfaces induced by the adsorption of alkaline-earth metals (AEMs). Previously, in a series of works on Ba/Si(1 1 1) system, we have found that the observed Si(1 1 1)3 × 1–Ba LEED phase indeed has a 3 × 2 periodicity with a Ba coverage of 1/6 ML and the HCC substrate structure. Based on results of the Ba case, we proposed that the HCC structure is also adopted for other AEM atoms, which was confirmed by our recent work. In this paper, we mainly report the STM simulations for different AEM systems to compare with existing experimental data. We discuss the difference in the detailed STM images for different AEM adsorbates. Especially, the difference in filled-state images between Mg and other AEM atoms is attributed to the strong Mg–Si interaction.

Atomic geometry and theoretical scanning tunneling microscopy images of K chains on InAs(110)

We have performed total-energy density-functional calculations using ab initio pseudopotentials to investigate the atomic geometry and scanning tunneling microscopy (STM) of K adsorbed on the InAs(110) surface. We have identified the most favorable adsorption geometry formed by K adatoms occupying two almost degenerate adsorption sites. Based on this structure, we have simulated the STM images showing asymmetric and zigzag chain along the [11¯0] direction for both negative and positive sample biases. The calculated STM images agree with the recent STM observation.

Acetonitrile adsorption on Si(001)

In this work we employ the state of the art pseudopotential method, within a generalized gradient approximation to the density-functional theory, to investigate the adsorption process of acetonitrile on the silicon surface. Our first-principles calculations indicate that ${\text{CH}}_{3}\text{CN}$ adsorb via a $[2+2]$ cycloaddition reaction through the $\mathrm{C}\mathrm{N}$ group ($\text{di}\text{\ensuremath{-}}{\ensuremath{\sigma}}_{\text{CN}}$ model) with an adsorption energy around $37\phantom{\rule{0.3em}{0ex}}\text{kcal}∕\mathrm{mol}$. Although the$\text{di}\text{\ensuremath{-}}{\ensuremath{\sigma}}_{\text{CN}}$ model is found to be the most probable adsorbed structure from the energetic point of view, we have also found that the adsorption via the $\text{Si}\text{\ensuremath{-}}\mathrm{N}$ dative bond (${\text{Si-N}}_{dat}$ model) is also possible. Based in our energetic analysis, and in the spectroscopy data by Bournel and co-workers, we suggest the existence of a mixed domain surface composed by both the $\text{di}\ensuremath{-}{\ensuremath{\sigma}}_{\text{CN}}$ and ${\text{Si-N}}_{dat}$ adsorbates, although the existence of the latter structure is disregarded by the core level shift analysis by Tao and co-workers. Possible reasons for the contrast between available data are addressed. We present theoretical scanning tunneling microscopy images of the possible adsorbed systems and suggest that this experimental procedure could possibly identify the existence of the proposed mixed domain structure. In addition, the electronic structure and surface states for both the $\text{di}\text{\ensuremath{-}}{\ensuremath{\sigma}}_{\text{CN}}$ and ${\text{Si-N}}_{dat}$ models are discussed in detail.

Adsorption of 3-pyrroline on Si(100) from first principles.

The chemisorption of 3-pyrroline (C(4)H(7)N) on Si(100) is studied from first principles. Three different structures can be realized for which, depending on the temperature, the chemisorption process is facile (for two of them it is essentially barrierless); among these configurations the most favored one, from a thermodynamical point of view, is a dissociated structure obtained through an exothermic reaction characterized by the formation of a N-Si bond and a H-Si bond in which the H atom is detached from the molecule. Several other chemisorption structures are possible which, however, require overcoming a significant energy barrier and often breaking multiple bonds. A number of reaction paths going from one stable structure to another have been investigated. We have also generated, for the two basic adsorption structures, theoretical scanning tunneling microscopy images which could facilitate the interpretation of experimental measurements, and we propose a possible reaction mechanism for nitrogen incorporation.

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.

Adsorption of methylchloride on Si(100) from first principles

The chemisorption of methylchloride (CH3Cl) on Si(100) is studied from first principles. We find that, among a number of possible adsorption configurations, the lowest-energy structure is one in which the methylchloride molecule is dissociated into CH3 and Cl fragments which are bound to the two Si atoms of the same surface dimer. Our calculations show that dissociative chemisorption of methylchloride on Si(100) may proceed along different reaction paths characterized by different energy barriers that the system must overcome: some dissociation processes are mediated by a molecular precursor state and, at least in one case, we find that the dissociation process is nonactivated, in agreement with recent experimental findings. We have also generated, for many possible adsorption structures, theoretical scanning tunneling microscopy images which could facilitate the interpretation of experimental measurements.

Atomic structure and theoretical scanning tunneling microscopy images of Li zigzag chains on the GaAs(110) surface

We have investigated the Li/GaAs(110) surface by combining the low-energy electron diffraction (LEED) and the ab initio pseudopotential calculations. The potential energy surface for the single atomic adsorption shows the existence of two inequivalent adsorption sites. At 0.5 monolayer coverage of Li, a well defined $1\ifmmode\times\else\texttimes\fi{}2$ LEED pattern is observed. The atomic structure at this coverage is characterized by Li zigzag chains running in the $[11\ifmmode\bar\else\textasciimacron\fi{}0]$ direction. This structure is stabilized by electron transfer from the Li adatoms to the dangling bonds of certain surface Ga atoms. The simulated scanning tunneling microscopy images show linear (asymmetric zigzag) chains along the $[11\ifmmode\bar\else\textasciimacron\fi{}0]$ direction for positive (negative) sample biases.

A theoretical study of C 2H 2 adsorption on the Ge( [formula omitted]) surface

Using a first-principles pseudopotential technique, we have investigated the adsorption of C 2H 2 on the Ge(0 0 1) surface. We have found that, at low temperatures, the di-σ bond configuration is the most stable structure from the energetic point of view. According to our calculations, it is not possible to conclude if C 2H 2 adsorbs preferentially on alternate or adjacent dimer sites. The di-σ adsorbed system is characterized by symmetric and slightly elongated Ge–Ge dimers, and by a symmetric C–C bond with length close to the double carbon bond length of the ethylene molecule. Our total energy calculations suggest that other meta-stable configurations, like the 1,2-hydrogen transfer model, are also possible. This behaviour was also observed for the silicon based system. In addition, we present theoretical scanning tunneling microscopy images and calculated vibrational modes for the adsorbed system with a view to contribute to further experimental investigations.

Energetics and bias-dependent scanning tunneling microscopy images of Si ad-dimers on Ge(001)

We report an ab initio study of the energetics and scanning tunneling microscopy (STM) images of Si ad-dimers on Ge(001) and energetics of Ge ad-dimers on Si(001). As in the case of Si dimers on Si(001), we find for both systems that the D dimer configuration, lying between the substrate dimer rows and parallel to them, is highest in energy. Conversely, recent STM experiments for Si ad-dimers on Ge(001) deduce the D configuration to be most stable. Our theoretical STM images for this system find that both the D and C configurations (the latter also between the rows) have similar STM images for the experimental voltages. We propose an experimental test (low-bias STM imaging) which would unambiguously distinguish between the D and C configurations.