Simulated Scanning Tunneling Microscopy Research Articles

Stability, tunneling characteristics and thermoelectric properties of TeSe2 allotropes

The waste heat management becomes very important with increasing energy demand and limited fossil resources. Here, we demonstrate thermoelectric performance of allotropic TeSe2. Based on the first-principle calculations, we confirm the energetic and kinetic stability of five TeSe2 allotropes. We predict δ-TeSe2 as a new direct band gap semiconductor having 1.60 eV direct band gap. All the TeSe2 allotropes exhibit band gap in UV–Vis region. The structural phases are clearly distinguished using simulated scanning tunneling microscopy. The room temperature Seeback coefficient is maximum of 4 mV/K for δ-TeSe2. We show that room temperature thermoelectric figure of merit (ZT) can reach up to 3.1 with p-type doping in δ-TeSe2. Moreover, temperature and chemical potential tuning extends the thermoelectric performance of TeSe2 allotropes. We strongly believe that our study is compelling from an experimental perspective and holds a key towards fabrication of thermoelectric devices based on TeSe2.

Doping in the two-dimensional limit: p/n -type defects in monolayer ZnO

The thickness limit is utilized to investigate the doping physics in ZnO, i.e., monolayer (ML) ZnO. First-principles study demonstrates that the $p/n$-type defects in ML ZnO still have doping asymmetry. Among the doping defect models widely studied in bulk ZnO, ${\mathrm{Li}}_{\text{Zn}}$ and ${\mathrm{Ga}}_{\text{Zn}}$ with ionization energies of 0.86 and 0.82 eV are the optimal $p$- and $n$-type doping defects in ML ZnO, respectively. Their ionization energies are comparable with those of relatively shallow defects in other ML semiconductors. However, the ${\mathrm{Li}}_{\text{Zn}}$ acceptor faces a severe issue in that ${\mathrm{Li}}_{\text{Zn}}$ is the metastable structure and will transform into the most stable Jahn-Teller-distorted structure (${\mathrm{Li}}_{\text{Zn}}^{\text{JT}}$) with increasing its ionization energy to 1.53 eV. Furthermore, our scanning tunneling microscopy simulations show even a little structural distortion of the doping defects can be easily detected with the appropriate positive bias voltage on a sample of ML ZnO. The present study reveals the $p/n$-type defects' properties in ML ZnO and offers a way to understand and directly identify defect behaviors in wide-band-gap semiconductors in their two-dimensional limit form.

C-doping anisotropy effects on borophene electronic transport

The electronic transport anisotropy for different C-doped borophene polymorphs (β 12 and χ 3) was investigated theoretically combining density functional theory and non-equilibrium Green’s function. The energetic stability analysis reveals that B atoms replaced by C is more energetically favorable for χ 3 phase. We also verify a directional character of the electronic band structure on C-doped borophene for both phases. Simulated scanning tunneling microscopy and also total density of charge confirm the directional character of the bonds. The zero bias transmission for β 12 phase at E − E F = 0 shows that C-doping induces a local current confinement along the lines of doped sites. The I–V curves show that C-doping leads to an anisotropy amplification in the β 12 than in the χ 3. The possibility of confining the electronic current at an specific region of the C-doped systems, along with the different adsorption features of the doped sites, poses them as promising candidates to highly sensitive and selective gas sensors.

Electron beam analysis induces Cl vacancy defects in a NaCl thin film

This work reports on the electron-induced modification of NaCl thin film grown on Ag(110). We show using low energy electron diffraction that electron beam bombardment leads to desorption and formation of Cl vacancy defects on NaCl surface. The topographic structure of these defects is studied using scanning tunneling microscopy (STM) showing the Cl defects as depressions on the NaCl surface. Most of the observed defects are mono-atomic vacancies and are located on flat NaCl terraces. Auger electron spectroscopy confirms the effect of electron exposure on NaCl thin films showing Cl atoms desorption from the surface. Using density functional theory taken into account the van der Waals dispersion interactions, we confirm the observed experimental STM measurements with STM simulation. Furthermore, comparing the adsorption of defect free NaCl and defective NaCl monolayer on Ag(110) surfaces, we found an increase of the adhesion energy and the charge transfer between the NaCl film and the substrate due to the Cl vacancy. In details, the adhesion energy increases between the NaCl film and the metallic Ag substrate from 30.4 meV Å−2 for the NaCl film without Cl vacancy and from 39.5 meV Å−2 for NaCl film with a single Cl vacancy. The charge transfer from the NaCl film to the Ag substrate is enhanced when the vacancy is created, from 0.63e− to 1.25e−.

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.

DFT, NBO, HOMO-LUMO, NCI, stability, Fukui function and hole – Electron analyses of tolcapone

Parkinson’s disease is a neurodegenerative disorder that damages the nervous system. The treatment of this disease is carried using tolcapone as a drug combination with Levodopa. Tolcapone is investigated by the B3LYP/6-311G method by using DFT calculations. HOMO-LUMO results and fingerprint analysis reveal that it is a hard, stable molecule with hydrogen bond donor and acceptor system. According to NBO analysis, the presence of hydrogen bond, conjugation of double bonds, and CT nature enhances the stability. Fukui function analysis suggests that this molecule is more prone to nucleophilic attack. Multiwfn 3.8 is used to interpret the following results. NCI interaction study reveals that it is having steric effect, Van der Waals force, and hydrogen bond. Hole-electron interaction studies reveal that S1, S5, and S6 undergo a charge transfer excitation. The simulated Scanning Tunneling Microscope (STM) analysis shows that the tunneling current is located at C12 and H26.

Electronic Properties and Scanning Tunneling Microscopy Simulation of MoS2 Nanosheets by Using Density Functional Theory

The ab-initio Density Functional Theory (DFT) approach is used to study the electronic properties of bulk and layered MoS2 nanosheets. For the layered structures mono, bi, tri, tetra and penta layered structure is used. The direct to indirect transition of bandgap is observed as the number of layers is increasing. This transition of bandgap is attributed to the van der Waals interlayer interaction between two layers of MoS2 nanosheets. The indirect bandgap in the bulk MoS2 is found to be 0.94 eV, whereas for a single layered nanosheet is found to be direct bandgap with the value of 1.83 eV. To confirm the surface termination and understand the surface morphology of MoS2 the scanning tunneling microscopy (STM) simulation is performed in constant height mode. It is found that the detection of surface atoms via STM depends on the tip atom of the STM.
 Dhaka Univ. J. Sci. 69(1): 53-57, 2021 (January)

Surface structures of magnetostrictive D03-Fe3Ga(0 0 1)

First-principles total energy calculations and scanning tunneling microscopy experiments were performed to study the surface reconstruction of the magnetostrictive Fe3Ga alloy. The inverse magnetostrictive behavior was evaluated in the bulk by compressing and stretching its lattice parameter, showing an increase in magnetic moments as strain increases. Surface analysis demonstrates two thermodynamically stable surfaces, the (1 × 1) and (3 × 1). The (1 × 1) is an ideal FeGa terminated surface, whereas the (3 × 1) is also FeGa terminated but it has a first-layer Fe atom substituted by a Ga atom every three unit-cells, forming a row-like surface structure. Tersoff–Hamann scanning tunneling microscopy simulations were obtained and compared with experimental results. We found good agreement between theory and experiment, in which the distance between rows is ~12.3 Å. Theoretical findings suggest that the substrate-induced strain may increase the stability of the (3 × 1) reconstruction. Analysis of the magnetic moments in the reconstructions showed that their behavior is affected by a surface effect, as well as by the inverse magnetostriction of the structure. A good understanding of the FeGa surface reconstructions is an important step towards further improvements in magnetic storage devices and sensors.

Determination of rutile transition metal oxide (110) surface terminations by scanning tunneling microscopy contrast reversal

The surfaces of rutile transition-metal oxides $({\mathrm{TMO}}_{2})$ are widely investigated for catalysis, photoelectrochemical solar cells, memristors, and supercapacitors, but their structures have remained controversial. Here we employ density functional theory to predict that a universal behavior of metallic ${\mathrm{TMO}}_{2}$ surfaces, i.e., the stoichiometric ${\mathrm{TMO}}_{2}$ surfaces, exhibit a contrast reversal in simulated scanning tunneling microscopy (STM) images at different scanning biases. The predictions are verified by experimental STM imaging of ${\mathrm{RuO}}_{2}(110)$ surfaces and this feature is shown to enable accurate determinations of the ${\mathrm{TMO}}_{2}(110)$ surface structures under various conditions. This work provides different insights into the electronic properties of ${\mathrm{TMO}}_{2}(110)$ surfaces and offers an effective method to directly map the surface structure and point defects using bias-dependent STM.

Interlayer magnetism in Fe3−xGeTe2

Fe$_{3-x}$GeTe$_2$ is a layered van der Waals magnetic material with a relatively high ordering temperature and large anisotropy. While most studies have concluded the interlayer ordering to be ferromagnetic, there have also been reports of interlayer antiferromagnetism in Fe$_{3-x}$GeTe$_2$. Here, we investigate the interlayer magnetic ordering by neutron diffraction experiments, scanning tunneling microscopy (STM) and spin-polarized STM measurements, density functional theory plus U calculations and STM simulations. We conclude that the layers of Fe$_{3-x}$GeTe$_2$ are coupled ferromagnetically and that in order to capture the magnetic and electronic properties of Fe$_{3-x}$GeTe$_2$ within density functional theory, Hubbard U corrections need to be taken into account.

Surface structure of 1,4-benzenedithiol on Au(111)

The structure of self-assembled monolayers of 1,4-benzene dithiol (1,4-BDT) oligomers on Au(111) has been investigated using scanning tunneling microscopy (STM) measurements in ultrahigh vacuum combined with density function theory (DFT) calculations. The dominant adsorption geometry of 1,4-BDT oligomer chains involves an Au adatom linker forming a complex with two trans anchoring groups, resulting in a zigzag structure. STM measurements show preferential growth from step edges where gold adatoms can be extracted to form the oligomers. Ladder-like structures involving two parallel oligomer chains are observed at medium coverages, suggesting a stabilizing interaction between neighboring chains and reduced mobility following oligomerization. At high-coverages, the gold surface is covered with close-packed domains of oligomers. DFT STM simulations were performed using the Tersoff-Hamann method in order to elucidate structures observed in STM measurements.

Two-dimensional Si–Ge monolayers: Stabilities, structures, and electronic properties

Si–Ge monolayers (SiGeMLs) with different elementary proportions x (0 < x < 1) were systematically studied for the first time using ab initio calculations in this work. The structural stabilities of the Si1 − xGexML with different symmetries were investigated using phonon spectra, and an infinite miscibility between Si and Ge elements was revealed in 2D honeycomb structures. The simulated scanning tunneling microscope images and Raman and infrared active modes of the Si1 − xGexML were then obtained for structural characterizations. Interestingly, the study of electronic properties revealed previously unreported oscillatory nonlinear dependence of bandgap values on the elementary proportion x in the Si1 − xGexML, which suggests an alternative way for tuning the bandgaps of 2D materials. Additionally, low effective masses (0.008 m0–0.021 m0) of the carriers in the semiconducting Si1 − xGexML were found, which have the potential for high-speed applications. Considering the advantage of their compatibility with current Si-based technology and the trend of miniature electronic devices, the Si1 − xGexML with stable structures and excellent properties would be important for 2D applications based on group IV materials.

A full picture of intrinsic defects induced self-activation of elastic potential fluctuation within monolayered metal chalcogenide

Pursuing the precise structural identification of functional two-dimensional (2D) layered metal chalcogenides (LMCs) are key factors dominating the origins of the unique electronic and ferroelectric properties. However, the complicated phase change of In2Se3 and their high sensitivity towards the intrinsic defects still require the advanced technology to identify the origins of the inhomogeneous charge distribution induced in-plane and out-of-plane ferroelectricity. Herein, we have presented comprehensive theoretical research to reveal the simulated scanning tunneling microscope (STM) images as a toolbox for the experimental results to distinguish the structural features. Moreover, the corresponding electron-phonon behaviors of α-In2Se3 with major intrinsic defects provide pivotal references to explain the unique in-plane and out-of-plane electronic and ferroelectric properties in different applications, which is crucial for optimizing the growth of ultrathin 2D LMCs materials for future electronic devices.

Hydrogen inserted into the Si(100)-2 × 1-H surface: a first-principles study.

Hydrogen can be inserted into Si(100)-2 × 1-H during surface preparation or during the hydrogen desorption lithography used to create atomic-scale devices. Here, a hydrogen atom inserted into a hydrogen monolayer on the Si(100)-2 × 1 surface has been studied using density functional theory. Hydrogen-induced defects were considered in their neutral, negative, and positive charge states. It was found that hydrogen forms a dihydride unit on the surface in the most stable neutral and negative charge states. Hydrogen located in the groove between dimer rows is also one of the most stable negative charge states. In the positive charge state, hydrogen forms a three-center bond inside a Si dimer, Si-H-Si, similar to the bulk case. A comparison of simulated scanning tunneling microscopy (STM) images with the experimental data available in the literature showed that neutral and negatively charged hydrogen-induced defects were already observed in experiments. The results reveal that the H atom inserted into a hydrogen monolayer on the Si(100)-2 × 1 surface can lead to the formation of a positively or negatively charged defect. It is shown that H atoms in the considered configurations can play a role in various surface reactions.

Enhanced sensitivity of band gap engineered phosphorene towards NH3 and NO2 toxic gases

Band gap tuning is an efficient approach to modify the sensing ability of phosphorene. Herein, density functional theory (DFT) calculations have been performed to investigate the effect of various group elements (III-VI) doping in phosphorene sheet for NH3 and NO2 gas sensing ability. The presence of NH3 and NO2 gas molecules on doped phosphorene nanosheet is found to alter the structural network, electronic properties hence leading to a better sensing and selectivity of the doped nanosheet. B doped phosphorene showed maximum adsorption of −2.64 eV and −3.70 eV towards the NH3 and NO2 gas molecules respectively. NH3 adsorption on C, Si and S-doped phosphorene causes direct to indirect band gap transition while NO2 adsorption shows indirect band gap for pristine and S-doped phosphorene. Simulated scanning tunneling microscopy (STM) images showed different structural phases after gas adsorption due to electronic hybridization with orbitals from the upmost phosphorous atoms and the gas molecule. After gas adsorption, some flat bands are observed and localized states appear near the Fermi level, which are readily accessible at low bias voltages, thereby indicating the improved sensory functionality of doped phosphorene.

Structural evolution and the role of native defects in subnanometer MoS nanowires

We carried out first-principles calculations based on density functional theory aiming to understand the structural evolution along the stretching process and the impact of native defects in metallic subnanometer MoS nanowires (NWs). By pulling the pristine NWs quasistatically, we investigate the full structural evolution along the stretching process until the nanowire breaking point, obtaining a maximum applied stress (force) of $\ensuremath{\approx}18.9$ GPa (7.1 nN). On the other hand, since the existence of intrinsic defects is likely to occur in these samples, we show that under S-rich conditions a sulfur antisite is found to be the energetically most stable defect, and under Mo-rich conditions a sulfur vacancy has the lowest formation energy. Our results also reveal that these defects present local reconstruction that can be clearly identified by the simulated scanning tunneling microscopy images. Furthermore, through a detailed analysis of the electronic structure, we verify that with the exception of the Mo interstitial and S antisite, all defects preserve the metallic behavior of the MoS nanowires.

Adsorption geometries and interface electronic structure of C60 on Si(100)2 × 1 reconstruction surface

The adsorption geometries and interface electronic structure of C60 adsorbed on the Si(100)2 × 1 reconstruction surface have been investigated. Twelve adsorption geometries with different adsorption sites and molecular orientations are taken into account. The adsorption energy calculations discover more favorable adsorption geometries of a single C60 molecule. Simulated scanning tunneling microscope (STM) images distinctly show the intramolecular features, which depend only on the molecule orientation. Charge density difference (CDD) analysis and surface work function calculations confirm the negative charge transfers from Si(100)2 × 1 substrate to C60. The orbital hybridization and chemical bonding of interface C and Si atoms are clarified by density of states (DOS) and partial DOS (PDOS) analysis.

Modeling the Kondo effect of a magnetic atom adsorbed on graphene

The Kondo effect due to a magnetic atom adsorbed on graphene is investigated using two theoretical approaches, including the non-equilibrium Green’s function method within the slave-boson mean-field approximation and a newly developed tight-binding (TB) model with an effectively infinite Hubbard U term. Both methods reveal the presence of a Kondo peak in the local density of state (LDOS) of graphene near the Fermi level. A sharp Kondo peak is only observed in the odd-neighboring C sites of the C atom directly below the magnetic atom placed in top position. The peak intensity is found to decay quickly with respect to the distance between the C site and the magnetic atom. A theoretical model of scanning tunneling microscopy (STM) of graphene is presented as a means to identify the manifestation of the Kondo effect via direct topographic STM measurements. STM simulations show that in the proximity of the magnetic atom, only the C atoms of one sublattice are visible at low bias potential and thus a triangular lattice can be seen, in agreement with recent experiments. Further away from the magnetic atom, the Kondo effect dies down and eventually both sublattices are visible, leading to the recovery of the hexagonal lattice. This work not only provides a new TB method to study the Kondo effect in graphene, but also presents both scanning tunneling spectroscopy and microscopy fingerprints of the Kondo effect to facilitate its experimental verification.