Calculated Scanning Tunneling Microscopy Images Research Articles

Angle dependence of the local electronic properties of the graphene/MoS2 interface determined by ab initio calculations

We present a full theoretical study of the graphene/MoS2 interface, using density functional theory (DFT) calculations and scanning tunneling microscopy (STM) simulations. In particular, we show that contrary to previous theoretical predictions, the rotation angle between the layers has no influence on the global electronic properties of the interface, providing a careful choice of lattice vectors and supercells is made, in order to avoid artificial modifications in the electronic structure. However, small modifications of the local electronic properties do appear, as revealed by the calculated STM images. This result might be exploited in nanoelectronic devices by specific local contacting.

Atomistic Origins of Surface Defects in CH3NH3PbBr3 Perovskite and Their Electronic Structures

The inherent instability of CH3NH3PbX3 remains a major technical barrier for the industrial applications of perovskite materials. Recently, the most stable surface structures of CH3NH3PbX3 have been successfully characterized by using density functional theory (DFT) calculations together with the high-resolution scanning tunneling microscopy (STM) results. The two coexisting phases of the perovskite surfaces have been ascribed to the alternate orientation of the methylammonium (MA) cations. Notably, similar surface defect images (a dark depression at the sites of X atoms) have been observed on surfaces produced with various experimental methods. As such, these defects are expected to be intrinsic to the perovskite crystals and may play an important role in the structural decomposition of perovskite materials. Understanding the nature of such defects should provide some useful information toward understanding the instability of perovskite materials. Thus, we investigate the chemical identity of the surface defects systematically with first-principles density functional theory calculations and STM simulations. The calculated STM images of the Br and Br-MA vacancies are both in good agreement with the experimental measurements. In vacuum conditions, the formation energy of Br-MA is 0.43 eV less than the Br vacancy. In the presence of solvation effects, however, the formation energy of a Br vacancy becomes 0.42 eV lower than the Br-MA vacancy. In addition, at the vacancy sites, the adsorption energies of water, oxygen, and acetonitrile molecules are significantly higher than those on the pristine surfaces. This clearly demonstrated that the structural decomposition of perovskites are much easier to start from these vacancy sites than the pristine surfaces. Combining DFT calculations and STM simulations, this work reveals the chemical identities of the intrinsic defects in the CH3NH3PbX3 perovskite crystals and their effects on the stability of perovskite materials.

Surface structures of rutile TiO2(114)

The surface structures of rutile TiO2(114) have been studied using a combination of scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. Depending on the sample preparation, the surface exhibits many complicated local nanostructures, e.g., dot-like, missing row, row-like (1 × 3), and twin dotted (2 × 2) structures. After several cycles of sputtering and high-temperature annealing, all samples exhibit triangular pyramidal structure. Microfaceted structural models, which are composed of combinations of {111} and (001) microfacets, can explain all experimental results as well as the structural variety. The calculated STM images are in good agreement with the experimental results. The decreasing density of dangling bonds, the increasing coordination number, and the evolution of non-polar structures stabilize the surface energy, which results in the microfaceted reconstructions. The formation of various nanostructures and the surface stoichiometric changes are discussed.

Surfaces of complex intermetallic compounds: insights from density functional calculations.

CONSPECTUS: Complex intermetallic compounds are a class of ordered alloys consisting of quasicrystals and other ordered compounds with large unit cells; many of them are approximant phases to quasicrystals. Quasicrystals are the limiting case where the unit cell becomes infinitely large; approximants are series of periodic structures converging to the quasicrystal. While the unique properties of quasicrystals have inspired many investigations of their surfaces, relatively little attention has been devoted to the surface properties of the approximants. In general, complex intermetallic compounds display rather irregular, often strongly corrugated surfaces, making the determination of their atomic structure a very complex and challenging task. During recent years, scanning tunneling microscopy (STM) has been used to study the surfaces of several complex intermetallic compounds. If atomic resolution can be achieved, STM permits visualization of the local atomistic surface structure. However, the interpretation of the STM images is often ambiguous and sometimes even impossible without a realistic model of the structure of the surface and the distribution of the electronic density above the surface. Here we demonstrate that ab initio density functional theory (DFT) can be used to determine the energetics and the geometric and electronic structures of the stable surfaces of complex intermetallic compounds. Calculations for surfaces with different chemical compositions can be performed in the grand canonical ensemble. Simulated cleavage experiments permit us to determine the formation of the cleavage planes requiring the lowest energy. The investigation of the adsorption of molecular species permits a comparison with temperature-programmed thermal desorption experiments. Calculated surface electronic densities of state can be compared with the results of photoelectron spectroscopy. Simulations of detailed STM images can be directly confronted with the experimental results. Detailed results are presented for two intermetallic compounds that have recently attracted much attention as active and highly selective catalysts for the semihydrogenation of alkynes to alkenes, but the identification of the catalytically active surfaces was found to be very difficult. The crystal structure of B20-type GaPd can be interpreted as the lowest order approximant of icosahedral Al-Pd-Mn quasicrystals. Among the low-index surfaces, the {100} surface shows 2-fold symmetry and the {210} surface pseudo-5-fold symmetry; for both the surface stoichiometry is identical to that of the bulk. Because the structure lacks inversion symmetry, the {111} surfaces have polar character and permit terminations of widely different chemical composition. Results for all three surfaces are presented and compared with the available experiments. The crystal structure of orthorhombic Al13Co4 is built by pentagonal clusters similar to those found in decagonal Al-Co and Al-Ni-Co quasicrystals. A simulated cleavage experiment shows that the constituent clusters remain intact upon cleavage, resulting in the formation of a highly corrugated (100) surface. The calculated STM images are found to be in very good agreement with experiment and permit in addition identification of possible surface modifications by the desorption of individual atoms. Pentagonal motifs on the {210} surface of GaPd and on the (100) surface of Al13Co4 consisting of simple- and transition-metal atoms have been identified as the catalytically active centers for the semihydrogenation of acetylene to ethylene.

Theoretical reproduction of superstructures revealed by STM on bilayer graphene

We performed density functional theory calculations and we calculated Scanning Tunneling Microscopy images (constant height mode) on twisted bilayer graphene (BLG). The STM theoretical images show the graphene structure and also superstructures. The roughness associated to the surface carbon atoms appears over a large oscillation amplitude which is in agreement with the “giant corrugation” experimentally reported by several authors. Additionally we found a strong dependence between the corrugation amplitude of the calculated images and the bias voltage considered. These results suggest that superstructures in twisted BLG have to do mainly with a redistribution of the electronic density and that deformations introduced by tip-sample mechanical interaction could be of second order.

Noninvasive embedding of single Co atoms in Ge(111)2 × 1 surfaces

We report on a combined scanning tunneling microscopy (STM) and density functional theory (DFT) based investigation of Co atoms on Ge(111)2x1 surfaces. When deposited on cold surfaces, individual Co atoms have a limited diffusivity on the atomically flat areas and apparently reside on top of the upper pi-bonded chain rows exclusively. Voltage-dependent STM imaging reveals a highly anisotropic electronic perturbation of the Ge surface surrounding these Co atoms and pronounced one-dimensional confinement along the pi-bonded chains. DFT calculations reveal that the individual Co atoms are in fact embedded in the Ge surface, where they occupy a quasi-stationary position within the big 7-member Ge ring in between the 3rd and 4th atomic Ge layer. The energy needed for the Co atoms to overcome the potential barrier for penetration in the Ge surface is provided by the kinetic energy resulting from the deposition process. DFT calculations further demonstrate that the embedded Co atoms form four covalent Co-Ge bonds, resulting in a Co4+ valence state and a 3d5 electronic configuration. Calculated STM images are in perfect agreement with the experimental atomic resolution STM images for the broad range of applied tunneling voltages.

Architecture of PTCDA molecular structures on a reconstructed InSb(001) surface

An extensive scanning tunneling microscopy (STM) study of adsorption of submonolayer coverages of PTCDA molecules on the $c(8\ifmmode\times\else\texttimes\fi{}2)$ reconstructed InSb(001) surface is presented together with ab initio density functional theory (DFT) calculations. Our DFT calculations explain the variety of adsorption sites seen on the experimental STM images. In particular, we prove that the molecules are oriented with their long axes along the [110] direction. Calculated STM images of the molecule agree well with the high-resolution STM images obtained at the temperature of 77 K. We find that molecules form four covalent bonds between edge oxygen atoms of the PTCDA and In atoms of the surface. We also study in detail their diffusion mechanism and explain their ability to form experimentally observed chains along the [110] direction.

Structurally driven magnetic state transition of biatomic Fe chains on Ir(001)

Using first-principles calculations, we demonstrate that the magnetic exchange interaction and the magnetocrystalline anisotropy of biatomic Fe chains grown in the trenches of the $(5\ifmmode\times\else\texttimes\fi{}1)$ reconstructed Ir(001) surface depend sensitively on the atomic arrangement of the Fe atoms. Two structural configurations have been considered which are suggested from recent experiments. They differ by the local symmetry and the spacing between the two strands of the biatomic Fe chain. Since both configurations are very close in total energy they may coexist in experiment. We have investigated collinear ferro- and antiferromagnetic solutions as well as a collinear state with two moments in one direction and one in the opposite direction ($\ensuremath{\uparrow}\ensuremath{\downarrow}\ensuremath{\uparrow}$-state). For the structure with a small interchain spacing, there is a strong exchange interaction between the strands and the ferromagnetic state is energetically favorable. In the structure with larger spacing, the two strands are magnetically nearly decoupled and exhibit antiferromagnetic order along the chain. In both cases, due to hybridization with the Ir substrate the exchange interaction along the chain axis is relatively small compared to free-standing biatomic iron chains. The easy magnetization axis of the Fe chains also switches with the structural configuration and is out-of-plane for the ferromagnetic chains with small spacing and along the chain axis for the antiferromagnetic chains with large spacing between the two strands. Calculated scanning tunneling microscopy images and spectra suggest the possibility to experimentally distinguish between the two structural and magnetic configurations.

Ab initioapproach to reconstructions of theInP(111)Asurface: Role of hydrogen atoms passivating surface dangling bonds

The reconstructions on $\text{InP}(111)A$ surface are systematically investigated using an ab inito--based approach, which incorporates chemical potentials in the gas phase of ${\text{P}}_{2}$ and ${\text{H}}_{2}$ molecules as functions of temperature and pressure. The calculated surface energy clarifies that the reconstruction depends on both hydrogen and phosphorous chemical potentials. The surface phase diagram as function of temperature and ${\text{P}}_{2}$ pressure without taking account of passivating H atoms reveals that the stable region for the $(2\ifmmode\times\else\texttimes\fi{}2)$ surface with In vacancy is located beyond 450--680 K depending on the pressure, consistent with the experimentally reported temperature range $(\ensuremath{\sim}670\text{ }\text{K})$. However, the stable temperature range for the $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})R30\ifmmode^\circ\else\textdegree\fi{}$ surface with P trimer (below 290--430 K) is much lower than the experimental results $(\ensuremath{\sim}530\text{ }\text{K})$. Considering a reconstruction partially passivated by H atoms, the stable region for the surface with P trimer expands toward higher temperature by $\ensuremath{\sim}200\text{ }\text{K}$ and reasonably agrees with experimentally reported temperature range. Furthermore, comparisons of the calculated scanning tunneling microscopy images for the $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})R30\ifmmode^\circ\else\textdegree\fi{}$ surface containing P trimer to the experimental data support the plausibility of the surfaces passivated by H atoms. The results obtained thus suggest a possible explanation for the appearance of the $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})R30\ifmmode^\circ\else\textdegree\fi{}$ reconstruction on $\text{InP}(111)A$ surface.

The structure of mixed H2O–OH monolayer films on Ru(0001)

Scanning tunneling microscopy (STM) and x-ray absorption spectroscopy (XAS) have been used to study the structures produced by water on Ru(0001) at temperatures above 140 K. It was found that while undissociated water layers are metastable below 140 K, heating above this temperature produces drastic transformations, whereby a fraction of the water molecules partially dissociate and form mixed H(2)O-OH structures. X-ray photoelectron spectroscopy and XAS revealed the presence of hydroxyl groups with their O-H bond essentially parallel to the surface. STM images show that the mixed H(2)O-OH structures consist of long narrow stripes aligned with the three crystallographic directions perpendicular to the close-packed atomic rows of the Ru(0001) substrate. The internal structure of the stripes is a honeycomb network of H-bonded water and hydroxyl species. We found that the metastable low temperature molecular phase can also be converted to a mixed H(2)O-OH phase through excitation by the tunneling electrons when their energy is 0.5 eV or higher above the Fermi level. Structural models based on the STM images were used for density functional theory optimizations of the stripe geometry. The optimized geometry was then utilized to calculate STM images for comparison with the experiment.

Electronic structure changes ofSi(001)−(2×1)from subsurface Mn observed by STM

The deposition of Mn atoms onto the $\mathrm{Si}(001)\text{\ensuremath{-}}(2\ifmmode\times\else\texttimes\fi{}1)$ reconstructed surface has been studied using scanning tunneling microscopy (STM) and first-principles electronic structure calculations. Room-temperature deposition of 0.1 ML (monolayer) of Mn gives rise to a disordered surface structure. After in situ annealing between 300 and $700\phantom{\rule{0.2em}{0ex}}\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$, most of the Mn is incorporated into three-dimensional manganese silicide islands, and Si dimer rows reappear in the STM images on most of the substrate surface. At the same time, rowlike structures are visible in the atomic-scale STM images. A comparison with calculated STM images provides evidence that Mn atoms are incorporated into the row structures in subsurface interstitial sites, which are the lowest-energy position for Mn on Si(001). The subsurface Mn alters the height and local density of states of the Si dimer atoms, causing them to appear $0.6\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$ higher than a neighboring Si dimer with no Mn below. This height difference that allows the detection the subsurface Mn results from a subtle interplay of geometrical and electronic effects.

Atomic and electronic structure of the cleaved6H−SiC(112¯0)surface

We present a combined cross-section scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) and ab initio simulations study of the nonpolar $(11\overline{2}0)$ cleaved surface of 6H-SiC. The experimental results show an unreconstructed surface in agreement with theory. Upon truncation, two surface bands appear inside the semiconductor band gap: one empty band localized on the Si atoms and one filled band on the C atoms. According to the STS experimental results on $n$-doped samples, the Fermi energy is pinned at the surface inside the band gap. By comparison of STM filled and empty states topographies we propose that on the fresh cleaved surface the Fermi level lies at the bottom of the Si-like band. The calculated STM images reproduce the experimental contrast of the 6H stacking sequence and its bias dependence very well.

Atomic structure of the carbon induced Si(001)–c(4×4) surface

The atomic and electronic structures of the Si(0 0 1)– c (4 × 4) surface have been studied by scanning tunneling microscopy (STM) and density functional theory (DFT). To explain the experimental bias dependent STM observations, a modified mixed ad-dimer reconstruction model is introduced. The model involves three tilted Si dimers and a carbon atom incorporated into the third subsurface layer per c (4 × 4) unit cell. The calculated STM images show a close resemblance to the experimental ones.

Surface vacancies at the fivefold icosahedral Al-Pd-Mn quasicrystal surface: A comparison ofab initiocalculated and experimental STM images

Scanning tunneling microscopy (STM) images of the fivefold surface of the icosahedral $(i)$ Al-Pd-Mn quasicrystal have been calculated using ab initio density functional methods. The STM signal is formed predominantly by the Al atoms in the surface plane. The Pd atoms are seen in the STM image as dark spots. The reason for their small contribution to the STM current is a small local density of states around the Fermi level and the localized $d$-character of the Pd states. On the other hand, the local paramagnetic density of states on Mn atoms is much higher than that on Pd atoms and therefore Mn atoms are seen in the STM images as bright spots. A direct comparison of the experimental images obtained from the STM with the ab initio calculated STM images reveals that the characteristic features of the images---the dark pentagonal holes---can also be created by surface vacancies and not only by truncated Bergman clusters as it has been supposed up to now.

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.

Spin driving reconstructions on the GaAs(001):Mn surface

The scanning tunneling microscopy (STM) experiment reveals a $2\ifmmode\times\else\texttimes\fi{}2$ surface reconstruction on GaAs(001):Mn. A comprehensive theory for spin-driven reconstructions is developed by the first-principles methods: Mn incorporation results in two structural motifs to accommodate the spin degree of freedom. Low-energy reconstructions are generally antiferromagnetic to preserve the semiconducting band gaps. The gaps, however, decrease with increasing Mn coverage, leading to metallic surfaces. At one-monolayer coverage, the transition is complete. The calculated STM images agree with experiment.

Interference between competing tunneling channels and chemical resolution of STM

In a recent scanning tunneling microscopy (STM) experiment [Appl. Phys. Lett. 71 (1997) 213], CO molecules have been distinguished from another adsorbate species on Cu(1 1 1) surface using a controlled transfer of a CO molecule to the microscope tip. With a clean tip, both adsorbates are seen as dark depressions in the STM image. Functionalizing the tip with a CO molecule inverts the contrast of the adsorbed CO, but the images of the other species remain dark. In this Letter, we calculate STM images of CO for both the tip conditions, and reproduce the contrast inversion. Interference effects between different tunneling channels explain this behaviour: the contrast inversion takes place because the currents through both the adsorbate and the tip molecule are of the same order of magnitude as the current through vacuum, but they are in an opposite phase to through vacuum tunneling.

Theoretical study on the structural phase transition of Si([formula omitted])[formula omitted]-Ag surface

We study the arrangement of Ag atoms of the Si(111)3×3-Ag surface by Monte Carlo simulations (MCS). For this purpose, an adiabatic potential for Ag atoms representing short-ranged interactions including three-body terms is proposed, and the parameters in it are derived from results of first-principles calculations. We perform MCS with this potential and show that the surface undergoes an order–disorder phase transition with respect to the arrangement of Ag atoms. The transition temperature estimated by the present MCS is consistent with results of scanning tunneling microscopy (STM) observations. Calculated STM images based on results of MCS clearly show that the observed STM images with a honeycomb pattern are well understood by the fluctuation of Ag atoms.

Resolving discrepancies between LEED and STM throughab initiocalculations: Surface and bonding of sulfur on Mo(110)

The adsorption of sulfur at 0.5 ML in both $c(2\ifmmode\times\else\texttimes\fi{}2)$ and ${[}_{1}^{2}{}_{1}^{2\ifmmode\bar\else\textasciimacron\fi{}}]$ configurations on the Mo(110) surface is studied using the density-functional, pseudopotential method with a plane-wave basis and a seven-layer slab geometry in conjunction with scanning tunneling microscopy (STM) and low-energy electron diffraction (LEED) experiments. The sulfur adatoms are placed in different possible binding sites in order to determine the most favorable adsorption site. The ${[}_{1}^{2}{}_{1}^{2\ifmmode\bar\else\textasciimacron\fi{}}]$ overlayer is more stable than the $c(2\ifmmode\times\else\texttimes\fi{}2)$ by 0.31 eV, in agreement with experiment. The greater stability of the ${[}_{1}^{2}{}_{1}^{2\ifmmode\bar\else\textasciimacron\fi{}}]$ structure is attributed to differences in metal-metal bonding. Sulfur is predicted to adsorb at a low-symmetry position near the long-bridge site; the long-bridge site is slightly less favorable in energy. Simulated STM images of the sulfur-covered surface are constructed, and found to model well the experimental images. We find that the bright areas in the calculated STM images do not necessarily correspond to the position of the sulfur atoms, which explains the difference between the LEED pattern and the experimentally observed STM images.

Atomic and electronic structure of Li-adsorbed Si(100) surfaces

We investigate the atomic and electronic structure of Li-adsorbed Si(100) surfaces through first-principles pseudopotential calculations. We find that Li adatoms interact mainly with the dangling-bond orbitals of Si dimers, however, no hydrogenlike directional bonds exist between the Li and substrate Si atoms, based on calculated scanning tunneling microscopy images. The analysis of charge densities demonstrates a large charge transfer from the Li adatom to a dangling-bond orbital of a Si dimer, which is responsible for a large decrease of work function at submonolayer coverages. The Li atoms form linear chains either by occupying the interdimer bridge sites along the dimer row direction or the dimer bridge and cave sites perpendicular to the dimer row. As Li coverage (\ensuremath{\Theta}) increases, repulsive interactions between the adatoms in the chains are also found to increase. Thus, at 1-ML Li coverage, the stable adsorptions sites are changed to either the cave and pedestal sites or the valley-bridge and pedestal sites, with all the Si dimers symmetric, resulting in a $2\ifmmode\times\else\texttimes\fi{}1$ structure. From the calculated formation energies, we find a $1\ifmmode\times\else\texttimes\fi{}1$ phase to be thermodynamically stable at $\ensuremath{\Theta}=2,$ in contrast to other alkali-metal adsorptions.