Simulated Scanning Tunneling Microscopy Research Articles

Assembling phosphorene flexagons for 2D electron-density-guided nanopatterning and nanofabrication.

To build upon the rich structural diversity in the ever-increasing polymorphic phases of two-dimensional phosphorene, we propose different assembly methods (namely, the "bottom-up" and "top-down" approaches) that involve four commonly reported parent phases (i.e. the α-, β-, γ-, and δ-phosphorene) in combination with the lately reported remarkably low-energy one-dimensional defects in α-phosphorene. In doing so, we generate various periodically repeated phosphorene patterns in these so-called phosphorene flexagons and present their local electron density (via simulated scanning tunneling microscopy (STM) images). These interesting electron density patterns seen in the flexagons (mimicking symmetry patterns that one may typically see in a kaleidoscope) may assist as potential 2D templates where electron-density-guided nanopatterning and nanofabrication in complex organized nanoarchitectures are important.

Towards a quantitative description of tunneling conductance of superconductors: Application to LiFeAs

Since the discovery of iron-based superconductors, a number of theories have been put forward to explain the qualitative origin of pairing, but there have been few attempts to make quantitative, material-specific comparisons to experimental results. The spin-fluctuation theory of electronic pairing, based on first-principles electronic structure calculations, makes predictions for the superconducting gap. Within the same framework, the surface wave functions may also be calculated, allowing, e.g., for detailed comparisons between theoretical results and measured scanning tunneling topographs and spectra. Here we present such a comparison between theory and experiment on the Fe-based superconductor LiFeAs. Results for the homogeneous surface as well as impurity states are presented as a benchmark test of the theory. For the homogeneous system, we argue that the maxima of topographic image intensity may be located at positions above either the As or Li atoms, depending on tip height and the setpoint current of the measurement. We further report the experimental observation of transitions between As and Li-registered lattices as functions of both tip height and setpoint bias, in agreement with this prediction. Next, we give a detailed comparison between the simulated scanning tunneling microscopy images of transition-metal defects with experiment. Finally, we discuss possible extensions of the current framework to obtain a theory with true predictive power for scanning tunneling microscopy in Fe-based systems.

Oxygen vacancy induced surface stabilization: (110) terminated magnetite

Scanning tunneling microscopy (STM) measurements of the (110) surface of magnetite showed the coexistence of two reconstructions: the known $(1\ifmmode\times\else\texttimes\fi{}3)$ row reconstruction and a surprising atomic structure of high complexity which occupies a small fraction of the surface. Oxygen vacancies on the ${\mathrm{Fe}}_{3}{\mathrm{O}}_{4}$(110) B-terminated surface have previously been determined to be the most energetically favorable surface termination of those considered [Li et al., Surf. Sci. 601, 876 (2007)]. However, this study only investigated oxygen vacancies which were threefold coordinated. Here, first principles calculations indicate that twofold coordinated oxygen represents the most energetically stable oxygen vacancy on the B-terminated (110) surface of magnetite. STM simulations reveal that the structure that occupies a small fraction of the surface corresponds to this energetically favorable B-terminated ${\mathrm{Fe}}_{3}{\mathrm{O}}_{4}$(110) surface. The oxygen vacancies form an ordered array: Along the $[\overline{1}10]$ direction, every second twofold coordinated oxygen atom is vacant, and vacancies are separated by 6 \AA{}. In adjacent twofold coordinated oxygen rows, the vacancies are shifted in the $[\overline{1}10]$ direction by 3 \AA{}. Density functional theory calculations of the spin density distributions indicate that surface and subsurface octahedrally coordinated iron atoms are charge ordered. The charge ordering and existence of oxygen vacancies act to reduce the surface charge. However, other polarity compensation mechanisms may be at play to stabilize the surface.

Molecular Dissociation on the SiC(0001) 3×3 Surface.

In the framework of density functional theory, the adsorption of the halogenated polycyclic aromatic hydrocarbon 2,11-diiodohexabenzocoronene (HBC-I2 ) on the SiC(0001) 3×3 surface has been investigated. Nondissociative and dissociative molecular adsorption is considered, and simulated scanning tunneling microscopy (STM) images are compared with the corresponding experimental observations. Calculations show that dissociative adsorption is favorable and reveal the crucial importance of the extended flat carbon core on molecule-surface interactions in dissociative adsorption; the iodine atom-surface interaction is of minor importance. Indeed, removing iodine atoms does not significantly affect the STM images of the central part of the molecule. This study shows that the dissociation of large halogenated polycyclic aromatic hydrocarbon molecules can occur on the SiC surface. This opens up interesting perspectives in the chemical reactivity and functionalization of wide band gap semiconductors.

Electronic structure of 2H-NbSe2 single-layers in the CDW state

A density functional theory study of NbSe2 single-layers in the normal non-modulated and the 3 × 3 CDW states is reported. We show that, in the single layer, the CDW barely affects the Fermi surface of the system, thus ruling out a nesting mechanism as the driving force for the modulation. The CDW stabilizes levels lying around 1.35 eV below the Fermi level within the Se-based valence band but having a substantial Nb–Nb bonding character. The absence of interlayer interactions leads to the suppression of the pancake-like portion of the bulk Fermi surface in the single-layer. We perform scanning tunneling microscopy simulations and find that the images noticeably change with the sign and magnitude of the voltage bias. The atomic corrugation of the Se sublayer induced by the modulation plays a primary role in leading to these images, but the electronic reorganization also has an important contribution. The analysis of the variation of these images with the bias voltage does not support a Fermi surface nesting mechanism for the CDW. It is also shown that underlying graphene layers (present in some of the recent experimental work) do not modify the conduction band, but do affect the shape of the valence band of NbSe2 single-layers. The relevance of these results in understanding recent physical measurements for NbSe2 single-layers is discussed.

Density functional theory study of interaction of graphene with hypoxanthine, xanthine, and uric acid

ABSTRACTHypoxanthine (HX), xanthine (XA), and uric acid (UA) are important molecules in human beings. However, the physics underlying the interaction between these molecules and carbon nanomaterials is still unclear. In this study, we theoretically anlaysed the interaction of the graphene with HX, XA, and UA via the LDA, Perdew–Burke–Ernzerhof, and a second version of van der Waals (vdW)–DF2 exchange–correlation functionals of density functional theory. It was observed that these molecules could be adsorbed on the surface of the graphene steadily. The adsorption energies of these molecules on the graphene for the same site in vdW–DF2 functional show the following ordering: UA > XA > HX, the adsorption distances the following ordering: UA < XA < HX. The mechanism of this stable adsorption was revealed to be π–π and O–π interactions between these molecules and the graphene. Simulated scanning tunnelling microscopy (STM) images of HX, XA, and UA on the surface of the graphene layer as application, HX can be distinguished from XA and UA via the STM technique as a result of the interaction between the graphene and these molecules. The findings of this study provide a theoretical reference in the development and design of highly accurate biodevices and biosensors.

Fe(II)Ti(IV)O3 mixed oxide monolayer at rutile TiO2(011): Structures and reactivities

Mixed-metal oxide monolayer grown at an oxide support is of great potential in applications like heterogeneous catalysis. In this work, the experimentally obtained ordered mixed FeTiO3 oxide monolayer supported by rutile TiO2(011) surface has been carefully studied with density functional theory calculations. The genetic algorithm based optimization scheme has been employed to improve the searching capacity for possible structures, and a well ordered mixed Fe(II)Ti(IV)O3 monolayer oxide structure much more stable than the one proposed previously has been successfully located. The new surface structure consists of uniformly distributed Ti and Fe cations in the ratio of 2:1. The simulated Scanning Tunneling Microscopy image based on this model is well consistent with the experimental one. Our calculations have shown that the O vacancy formation energy is rather high at the surface. We have also studied the adsorption of O2 and CO at the exposed Fe sites on the surface as well as their reactions. The adsorption energies of O2 are generally higher than those of CO. The catalytic cycle of CO oxidation following an Eley-Rideal type mechanism has been located for CO to react with surface adsorbed O2 and O.

Water adsorption on the LaMnO3 surface.

Studying the adsorption of water on the metallic LaMnO3 surface can provide insight into this complicated surface-adsorbate interaction. Using density functional theory, we investigated the adsorption of a water monomer, dimer, trimer, and a monolayer on the surface. The electronic structure of ground state configurations is explored using analysis of density of states, charge density, and crystal orbital overlap populations. We found that the interaction between the surface and water molecules is stronger than hydrogen bonding between molecules, which facilitates wetting of the surface. Adsorbed water molecules form very strong hydrogen bonds, with substantially shifted OH stretch modes. For the monolayer of adsorbed water, a hint of a bilayer is observed with a height separation of only 0.2 A. However, simulated scanning tunneling microscopy images and vibrational spectra suggest a significant difference between the two layers due to intermolecular bonding and interaction with the substrate.

Magnetic properties of intrinsic vacancies on the GaN $$(10\bar 10)$$ surface: a density-functional-theory study

We report density functional theory calculations on the vacancy-induced magnetic properties of the wurzite GaN\((10\bar 10)\) surface. Among various intrinsic vacancies on the surface, we focus on the monatomic Ga and N vacancies. We have found two stable geometries of a surface Ga vacancy and one stable geometry of a surface N vacancy. Two stable surface Ga vacancy structures are shown to have magnetic moments of 3 μB, which is the same as for the bulk Ga vacancy. Differently from the bulk N vacancy carrying null magnetic moment, the monatomic surface N vacancy has a finite magnetic moment of 1 μB. These results support the experimental claim that the roomtemperature ferromagnetism observed in inorganic nanoparticles is due to surface vacancies and their complexes. We also present simulated scanning tunneling microscope images for comparison with those obtained in future experimental studies.

Effects of strain on carbon donors and acceptors in hexagonal boron nitride monolayers

We present first-principles density functional calculations that clarify the electronic properties of carbon defects in hexagonal boron nitride $(h$-BN) monolayers under biaxially applied strains. We find that strain can control the ionization energies of both donor and acceptor states. Furthermore, we also find that strain can lead to the dramatic change in conduction channel properties of donor states due to the interchange of the conduction-band-minimum state with the nearly-free-electron state. We also report the simulated scanning tunneling microscopy (STM) images of carbon defects in $h$-BN monolayers for experimental identification of those defects. We show that the STM images strongly reflect distinctive spatial distributions of local density of states around carbon defects depending on the substitution sites and thereby they could be identified by using STM experiments.

Organics on oxidic metal surfaces: a first-principles DFT study of PMDA and ODA fragments on the pristine and mildly oxidized surfaces of Cu(111).

Metal-organic hybrid materials are ubiquitous and a fundamental understanding of the hybrid-interface is key for the development of these hybrid material systems. In this work, using first-principles density-functional theory (including van der Waals (vdW) corrections), we study the fundamental physico-chemical properties of the molecular fragments of pyromellitic dianhydride oxydianiline (PMDA-ODA) on pristine Cu(111), as well as oxidic p4:O/Cu(111) in order to investigate the effect of mild oxidation of the metal substrate on PMDA-ODA adsorption. Firstly, we report the most favorable adsorption geometries amongst the various surface models and correlate the adsorption behavior with the electronic structure of the molecular fragments and the substrate layer. PMDA adsorbs weakly on both the clean and mildly oxidized copper surface via vdW forces while ODA adsorbs much stronger with a significant charge transfer between the substrates. Here, the oxidic layer is found to reduce the adsorption strength of both fragments and in particular, the ODA molecule interacts with the substrate via additional hydrogen bonding. Finally, our simulated scanning tunneling microscopy (STM) images suggest possible orientations of PMDA and ODA on clean and oxidic Cu surfaces to guide future experiments.

Purely substitutional nitrogen on graphene/Pt(111) unveiled by STM and first principles calculations.

Nitrogen doping of graphene can be an efficient way of tuning its pristine electronic properties. Several techniques have been used to introduce nitrogen atoms on graphene layers. The main problem in most of them is the formation of a variety of C-N species that produce different electronic and structural changes on the 2D layer. Here we report on a method to obtain purely substitutional nitrogen on graphene on Pt(111) surfaces. A detailed experimental study performed in situ, under ultra-high vacuum conditions with scanning tunneling microscopy (STM), low energy electron diffraction (LEED) and Auger electron spectroscopy (AES) of the different steps on the preparation of the sample, has allowed us to gain insight into the optimal parameters for this growth method, that combines ion bombardment and annealing. This experimental work is complemented by first-principles calculations and STM simulations that provide the variation of the projected density of states due to both the metallic substrate and the nitrogen atoms. These calculations enlighten the experimental findings and prove that the species found are graphitic nitrogen. This easy and effective technique leads to the possibility of playing with the amount of dopants and the metallic substrate to obtain the desired doping of the graphene layer.

Theoretical study of the interactions of a graphene-on-Ni(111) composite with dopamine

ABSTRACTThe physics underlying the interactions between nanomaterials and biomolecules is largely unexplored. In this study, we modelled the interactions of a graphene-on-Ni(111) nanocomposite with dopamine, an important biomolecule with crucial physiological functions in the human brain and body, using density functional theory methods. Stable adsorption of the dopamine molecule was observed on the surface of the graphene-on-Ni(111) composite. The adsorption mechanism was revealed to involve both charge and π–π interactions between the dopamine and graphene when they are in close proximity. Simulated scanning tunnelling microscopy images of dopamine on the surface of the graphene-on-Ni(111) composite, as an application of this nanomaterial, could distinguish one side of the G2 conformation of dopamine from the other conformations as a result of their interactions. Therefore, the graphene-on-Ni(111) composite is expected to have potential as a nanomaterial for detecting single biomolecules. The findings of this study will provide a significant contribution to the fields of nanomaterials and biotechnology, including the development of highly accurate biodevices and biosensors.

Periodic arrays of intercalated atoms in twisted bilayer graphene: Anab initioinvestigation

We have performed an \it {ab initio} investigation of transition metals (TMs = Mo, Ru, Co, and Pt) embedded in twisted bilayer graphene (tBG) layers. Our total energy results reveal that, triggered by the misalignment between the graphene layers, Mo and Ru atoms may form a quasi-periodic (triangular) array of intercalated atoms. In contrast, the formation of those structures is not expected for the other TMs, Co and Pt atoms. The net magnetic moment (m) of Mo and Ru atoms may be quenched upon intercalation, depending on the stacking region (AA or AB). For instance, we find a magnetic moment of 0.3 $\mu_{\rm B}$ (1.8 $\mu_{\rm B}$) for Ru atoms intercalated between the AA (AB) regions of the stacked twisted layers. Through simulated scanning tunneling microscopy (STM) images, we verify that the presence of intercalated TMs can be identified by the formation of bright (hexagonal) spots lying on the graphene surface.

Defects in Phosphorene

Defects are inevitably present in materials and always can affect their properties. Here, first-principles calculations are performed to systematically study the stability, structural and electronic properties of ten kinds of point defects in semiconducting phosphorene, including the Stone-Wales (SW-1 and SW-2) defect, single (SV59 and SV5566) and double vacancy (DV585-1, DV585-2, DV555777-1, DV555777-2, DV555777-3 and DV4104) defects. We find that these defects are all much easily created in phosphorene with higher areal density compared with graphene and silicene. They are easy distinguish each other and correlate with their defective atomic structures with simulated scanning tunneling microscopy images at positive bias. The SW, DV585-1, DV555777 and DV4104 defects have little effect on phosphorene's electronic properties and defective phosphorene monolayers still show semiconducting with similar band gap values to perfect phosphorene. The SV59 and DV585-2 defects can introduce unoccupied localized states into phosphorene's fundamental band gap. Specifically, the SV59 and 5566 defects can induce hole doping in phosphorene, and only the stable SV59 defect can result in local magnetic moments in phosphorene different from all other defects.

Structural, electronic and magnetic properties of Mn3N2(0 0 1) surfaces

Spin-polarized first-principles total energy calculations have been performed to study the structural, electronic and magnetic properties of Mn3N2(001) surfaces. It is found that three surface terminations are energetically stable, in agreement with previous scanning tunneling microscopy experiments that have found three different electronic contrasts in their images. It is also found that in all three cases, the topmost layer has a MnN stoichiometry. Density of states calculations show a metallic behavior for all the stable structures with the most important contribution close to the Fermi level coming from the Mn-d orbitals. Our Tersoff–Hamann scanning tunneling microscopy simulations are in good agreement with previous experimental results.

Chemically modified STM tips for atomic-resolution imaging of ultrathin NaCl films

Cl-functionalized scanning tunneling microscopy (STM) tips are fabricated by modifying a tungsten STM tip in situ on islands of ultrathin NaCl(100) films on Au(111) surfaces. The functionalized tips are used to achieve clear atomicresolution imaging of NaCl(100) islands. In comparison with bare metal tips, the chemically modified tips yield drastically enhanced spatial resolution as well as contrast reversal in STM topographs, implying that Na atoms, rather than Cl atoms, are imaged as protrusions. STM simulations based on a Green’s function formalism reveal that the experimentally observed contrast reversal in the STM topographs is due to the highly localized character of the Cl-pz states at the tip apex. An additional remarkable characteristic of the modified tips is that in dI/dV maps, a Na atom appears as a ring with a diameter that depends crucially on the tip-sample distance.

Suppressing band gap of MoS2 by the incorporation of four- and eight-membered rings

A stable planar allotrope of MoS2, formed by introducing four- and eight-membered rings into its hexagonal network (H468), is identified to be a narrow direct-band-gap semiconductor by first principle calculations, which is remarkably different from the large band gap semiconductor of conventional MoS2 and also the zero band gap allotrope consisting of four- and eight-membered rings (H48) only. The medium-sized direct band gap indicates that H468 would find applications in nanoelectronics and near-infrared optoelectronic devices. Furthermore, the distinctive simulated scanning tunneling microscope images under positive and negative biases might be a unique characteristic for the experimental identification of such an allotrope of MoS2.

Chen's derivative rule revisited: Role of tip-orbital interference in STM

On the occasion of its 25th anniversary, we revise Chen's derivative rule for electron tunneling [C. J. Chen, Phys. Rev. B 42, 8841 (1990)] for the purpose of computationally efficient simulations of scanning tunneling microscopy (STM) based on first-principles electronic structure data. The revised model allows the weighting of tunneling matrix elements of different tip-orbital characters by an arbitrary energy-independent choice or based on energy-dependent weighting coefficients obtained by an expansion of the tip single-electron wave functions/density of states projected onto the tip-apex atom. Tip-orbital interference in the STM junction is included in the model by construction and can be analyzed quantitatively. As a further advantage, arbitrary tip geometrical orientations are included in the revised model by rotating the coordinate system of the tip apex using Euler angles and redefining the weighting coefficients of the tunneling matrix elements. We demonstrate the reliability of the model by applying it to two functionalized surfaces of recent interest where quantum interference effects play an important role in the STM imaging process: N-doped graphene and a magnetic ${\mathrm{Mn}}_{2}\mathrm{H}$ complex on the Ag(111) surface. We find that the proposed tunneling model is 25 times faster than the Bardeen method concerning computational time, while maintaining good agreement. Our results show that the electronic structure of the tip has a considerable effect on STM images, and the Tersoff-Hamann model does not always provide sufficient results in view of quantum interference effects. For both studied surfaces, we highlight the importance of interference between $s$ and ${p}_{z}$ tip orbitals that can cause a significant contrast change in the STM images. Our method, thus, provides a fast and reliable tool for calculating STM images based on Chen's derivative rule, taking into account the electronic structure and local geometry of the tip apex.

Simulated scanning tunneling microscopy images of few-layer phosphorus capped by graphene and hexagonal boron nitride monolayers

Elemental phosphorous is believed to have several stable allotropes that are energetically nearly degenerate, but chemically reactive. These structures may be capped by monolayers of hexagonal boron nitride $(h\ensuremath{-}\mathrm{BN})$ or graphene to prevent chemical degradation under ambient conditions. We perform ab initio density functional calculations to simulate scanning tunneling microscopy (STM) images of different layered allotropes of phosphorus and study the effect of the capping layers on these images. At scanning energies within its intrinsic conduction gap, protective monolayers of insulating $h\ensuremath{-}\mathrm{BN}$ allow to distinguish between the different structural phases of phosphorus underneath due to the electronic hybridization with orbitals from the upmost phosphorus atoms: $h\ensuremath{-}\mathrm{BN}$ capping monolayers thus provide a promising route to tell few-layer phosphorus allotropes from one another with local probes.