Simulated Scanning Tunneling Microscopy Research Articles

Physical Fingerprints of the 2O-tαP Phase in Phosphorene Stacking.

The 2O-tαP phase is a bilayer phosphorene stacking twisted by ∼70.5° standing out from all the potential candidates predicted by our previous work. Here, by linear response theory, we directly verified that the 2O-tαP phase preserves the intrinsic features of phonon spectrum of the existing AB phase, reflecting a stable thermodynamic behavior. Then we provided three distinct fingerprints to help finding this new phase: upon comparison to the existing shifting bilayer phosphorene, the in-plane elastic constants showed a much weaker anisotropic response, providing a characteristic mechanical criterion; the calculated Raman spectrum revealed forthe low frequency rang thelayer-breathing modeand theout-of-plane twisted mode, L-A1 and L-A2, both of which together stabilize the twisted structure; in particular, thesimulated scanning tunneling microscope image presented recognizable cross stripes, which should withstand an examination of exfoliated bilayer and few-layer black phosphorus.

Multi-scale approach to first-principles electron transport beyond 100 nm.

Multi-scale computational approaches are important for studies of novel, low-dimensional electronic devices since they are able to capture the different length-scales involved in the device operation, and at the same time describe critical parts such as surfaces, defects, interfaces, gates, and applied bias, on a atomistic, quantum-chemical level. Here we present a multi-scale method which enables calculations of electronic currents in two-dimensional devices larger than 100 nm2, where multiple perturbed regions described by density functional theory (DFT) are embedded into an extended unperturbed region described by a DFT-parametrized tight-binding model. We explain the details of the method, provide examples, and point out the main challenges regarding its practical implementation. Finally we apply it to study current propagation in pristine, defected and nanoporous graphene devices, injected by chemically accurate contacts simulating scanning tunneling microscopy probes.

First-principles computational design of unknown flat arsenene epitaxially grown on copper substrate

Two-dimensional materials play essential roles in utilizing surface reactions, such as catalysts, adsorption and separation of chemicals. Especially, group-V mono-elemental materials are highlighted for transistors, optoelectronic devices, and mechanical sensors. Here, we identify unknown honeycomb-type arsenene epitaxially grown on copper substrate using first-principles density functional theory calculations. Key materials properties of lattice mismatch, thermodynamic stability, and surface transport properties are evaluated to verify the feasibility of the structural formation. Furthermore, ab-initio molecular dynamic simulations and scanning tunneling microscopy simulations clearly describe the mechanism of the initial nucleation and growth process. Electronic structure-level calculations characterize a strong covalency between each As atom pair. Our approach combining electronic structure calculations and thermodynamic/kinetic property predictions can be useful for quick screening and plausible design of new low-dimensional materials, which can efficiently functionalize emerging surface systems.

Toward interactive scanning tunneling microscopy simulations of large-scale molecular systems in real time

We have developed a simulation tool in which structural or chemical modifications of an adsorbed molecular layer can be interactively performed, and where structural relaxation and nearly real-time evaluation of a scanning tunneling microscopy (STM) image are considered. This approach is built from an optimized integration of the atomic superposition and electron delocalization molecular orbital theory (ASED-MO) to which a van der Waals correction term is added in conjunction with a non-linear optimization algorithm based on the Broyden-Fletcher-Goldfarb-Shanno method. This integrated approach provides reliable optimized geometries for adsorbed species on metallic surfaces in a reasonable time. Although we performed a major revision of the ASED-MO parameters, the proposed computational approach can accurately reproduce the geometries of a various amount of covalent molecules and weakly bonded complexes contained in two well-defined datasets. More importantly, the relaxation of adsorbed species on a metal surface leads to molecular geometries in good agreement with experimental and Density Functional Theory results. From this, the electronic structure obtained from ASED-MO is used to compute the STM image of the system nearly in real-time using the Tersoff-Hamann formalism. We developed a parallelization strategy that uses Graphics Processing Units to reduce the computing time of STM simulation by a factor of 30. Such improvements allow one to simulate STM images of large supramolecular arrangements and to investigate the influence of realistic local chemical or structural defects on metal surfaces.

Lattice Mismatch Drives Spatial Modulation of Corannulene Tilt on Ag(111)

We investigated the adsorption of corannulene (C20H10) on the Ag(111) surface by experimental and simulated scanning tunneling microscopy (STM), X-ray photoemission (XPS), and near-edge X-ray absorption fine structure (NEXAFS). Structural optimizations of the adsorbed molecules were performed by density functional theory (DFT) and the core excited spectra evaluated within the transition-potential approach. Corannulene is physisorbed in a bowl-up orientation displaying a very high mobility (diffusing) and dynamics (tilting and spinning) at room temperature. At the monolayer saturation coverage, molecules order into a close-compact phase with an average intermolecular spacing of ∼10.5 ± 0.3 A. The lattice mismatch drives a long wavelength structural modulation of the molecular rows, which, however, could not be identified with a specific superlattice periodicity. DFT calculations indicate that the structural and spectroscopic properties are intermediate between those predicted for the limiting cases of an o...

Forces and electronic transport in a contact formed by a graphene tip and a defective MoS2 monolayer: a theoretical study

A theoretical study of a graphene-like tip used in atomic force microscopy (AFM) is presented. Based on first principles simulations, we proved the low reactivity of this kind of tip, using a MoS2 monolayer as the testing sample. Our simulations show that the tip–MoS2 interaction is mediated through weak van der Waals forces. Even on the defective monolayer, the interaction is reduced by one order of magnitude with respect to the values obtained using a highly reactive metallic tip. On the pristine monolayer, the S atoms were imaged for large distances together with the substitutional defects which should be observed as brighter spots in non-contact AFM measurements. This result is in contradiction with previous simulations performed with Cu or Si tips where the metallic defects were imaged for much larger distances than the S atoms. For shorter distances, the Mo sites will be brighter even though a vacancy is formed. On the other hand, the largest conductance value is obtained over the defect formed by two Mo atoms occupying a S divacancy when the half-occupied py-states of the graphene-like tip find a better coupling with d-orbitals of the highest substitutional atom. Due to the weak interaction, no conductance plateau is formed in any of the sites. A great advantage of this tip lies in the absence of atomic transfer between the tip and the sample leading to a more stable AFM measurement. Finally, and as previously shown, we confirm the atomic resolution in a scanning tunneling microscopy simulation using this graphene-based tip.

Imaging Catalytic Activation of CO2 on Cu2O (110): A First-Principles Study.

Balancing global energy needs against increasing greenhouse gas emissions requires new methods for efficient CO2 reduction. While photoreduction of CO2 is promising, the rational design of photocatalysts hinges on precise characterization of the surface catalytic reactions. Cu2O is a promising next-generation photocatalyst, but the atomic-scale description of the interaction between CO2 and the Cu2O surface is largely unknown, and detailed experimental measures are lacking. In this study, density-functional theory (DFT) calculations have been performed to identify the Cu2O (110) surface stoichiometry that favors CO2 reduction. To facilitate interpretation of scanning tunneling microscopy (STM) and X-ray absorption near-edge structures (XANES) measurements, which are useful for characterizing catalytic reactions, we present simulations based on DFT-derived surface morphologies with various adsorbate types. STM and XANES simulations were performed using the Tersoff-Hamann approximation and Bethe-Salpeter equation (BSE) approach, respectively. The results provide guidance for observation of CO2 reduction reaction on, and rational surface engineering of, Cu2O (110). They also demonstrate the effectiveness of computational image and spectroscopy modeling as a predictive tool for surface catalysis characterization.

Characterization of point defects in monolayer arsenene

Topological defects that are inevitably found in 2D materials can dramatically affect their properties. Using density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) method, the structural, thermodynamic, electronic and magnetic properties of six types of typical point defects in arsenene, i.e. the Stone-Wales defect, single and double vacancies and adatoms, were systemically studied. It was found that these defects were all more easily generated in arsenene with lower formation energies than those with graphene and silicene. Stone-Wales defects can be transformed from pristine arsenene by overcoming a barrier of 2.19 eV and single vacancy defects tend to coalesce into double vacancy defects by diffusion. However, a type of adatom defect does not exhibit kinetic stability at room temperature. In addition, SV defects and another type of adatom defect can remarkably affect the electronic and magnetic properties of arsenene, e.g. they can introduce localized states near the Fermi level, as well as a strongly local magnetic moment due to dangling bond and unpaired electron. Furthermore, the simulated scanning tunneling microscopy (STM) and Raman spectroscopy were computed and the types of point defects can be fully characterized by correlating the STM images and Raman spectra to the defective atomistic structures. The results provide significant insights to the effect of defects in arsenene for potential applications, as well as identifications of two helpful tools (STM and Raman spectroscopy) to distinguish the type of defects in arsenene for future experiments.

Symmetrical metallic and magnetic edge states of nanoribbon from semiconductive monolayer PtS2

Transition metal dichalcogenides (TMD) MoS2 or graphene could be designed to metallic nanoribbons, which always have only one edge show metallic properties due to symmetric protection. In present work, a nanoribbon with two parallel metallic and magnetic edges was designed from a noble TMD PtS2 by employing first-principles calculations based on density functional theory (DFT). Edge energy, bonding charge density, band structure, density of states (DOS) and simulated scanning tunneling microscopy (STM) of four possible edge states of monolayer semiconductive PtS2 were systematically studied. Detailed calculations show that only Pt-terminated edge state among four edge states was relatively stable, metallic and magnetic. Those metallic and magnetic properties mainly contributed from 5d orbits of Pt atoms located at edges. What's more, two of those central symmetric edges coexist in one zigzag nanoribbon, which providing two atomic metallic wires thus may have promising application for the realization of quantum effects, such as Aharanov–Bohm effect and atomic power transmission lines in single nanoribbon.

Hybridization induced metallic and magnetic edge states in noble transition-metal-dichalcogenides of PtX2(X = S, Se) nanoribbons

The semiconducting transition metal dichalcogenide (TMD) 2H-MoS2 zigzag nanoribbon has two different edges, and only one edge shows metallic properties due to symmetric protection. In the present work, a nanoribbon with two parallel metallic and magnetic edges was designed from a noble TMD 1T-PtX2 (X = S, Se) by employing first-principles calculations based on density functional theory (DFT). The band structure, density of states (DOS), and simulated scanning tunneling microscopy (STM) of three possible zigzag edge states of monolayer semiconducting PtX2 were systematically studied. Detailed calculations showed that the Pt-terminated edge state among the three zigzag edge states was metallic. The Pt-terminated edge state designed from monolayer PtS2 showed both metallic and magnetic properties. These metallic and magnetic properties were mainly contributed to by the hybridization of the 5d orbitals of Pt atoms and the 3p orbitals of S atoms located at the edges. However, hybridization of the 5d orbitals of Pt atoms and the 4p orbitals of Se atoms located at the edges does not bring magnetic properties to the zigzag metallic PtSe2 nanoribbon. The interesting electronic and magnetic properties of 1T-PtX2 nanoribbons indicate that they may have promising applications as zigzag nanoribbons in spin electronics and photovoltaic cells.

Influence of Cu adatoms on the molecular assembly of 4,4'-bipyridine on Cu(111).

The formation of highly organized structures based on two ligands with pyridyl functionalities, 4,4'-bipyridine (BPY) and 1,4-di(4,4''-pyridyl) benzene (BPYB), and Cu adatoms on the Cu(111) surface has been studied with low temperature and variable temperature scanning tunneling microscopy (STM) and first-principles calculations. We show that the formation of a highly organized adlayer built from adatom-molecule and molecule-molecule units strongly depends on the number of mobile Cu atoms on the surface. While a high concentration of Cu adatoms (high adatom/BPY ratio, ≥1) leads systematically to the formation of organometallic nanolines, their absence (low adatom/BPY ratio, ≈0) gives a compact self-assembled molecular network, and more specifically hydrogen-bond networks (HBN) with BPY molecules organized in a T-shaped fashion. Alternatively, an intermediate concentration of Cu adatoms (0 < adatom/BPY < 1) allows the formation of a well-organized and compact structure where both organometallic and HBN components coexist. Although STM images cannot clearly reveal the presence of Cu adatoms within the organometallic moiety, the bonding of BPY to a single or two Cu adatoms can be clearly identified by scanning tunneling spectroscopy (STS), and is supported by Density Functional Theory (DFT) results. Additional STM simulations suggest that the relative position of the Cu adatom with respect to the organic ligands just above has a significant impact on its detection by STM. This study exemplifies the prominent role of metallic adatoms on the formation of a complex organometallic network and should open more rational practices to optimize the formation of these supramolecular networks.

Hybrid image potential states in molecular overlayers on graphene

The structural and electronic properties of naphthalene adsorbed on graphene are studied from first principles using the van der Waals density functional method. It is shown that naphthalene molecules are stabilized by forming a superstructure with the periodicity of $(2\sqrt{3}\ifmmode\times\else\texttimes\fi{}2\sqrt{3})$ and a tilted molecular adsorption geometry on graphene, in good agreement with the scanning tunneling microscopy (STM) experiments on highly oriented pyrolytic graphite. Our results predict that image potential states (IPSs) are induced by intermolecular interaction on the naphthalene overlayer, hybridizing with the IPSs derived from graphene. The resultant hybrid IPSs are characterized by anisotropic effective mass reflecting the molecular structure of naphthalene. By means of STM simulations, we reveal that one of the hybrid IPSs manifests itself as an oval protrusion distinguishable from naphthalene molecular orbitals, which identifies the origin of an experimental STM image previously attributed to the lowest unoccupied molecular orbital of naphthalene.

First-Principle Study of the Electronic Structure and Stability of Reconstructed AgInSe2 (112) Polar Surfaces

Chalcopyrite AgInSe2 (AIS) is a candidate material for alloying with Cu(In,Ga)Se2 (CIGS) to increase the band gap and potentially enhance the efficiency of CIGS thin-film photovoltaic materials. As Cu depletion at the heterojunction of CIGS photovoltaic cells plays an important role in its high efficiency, the stoichiometry, stability, and electronic structure of AIS surfaces are a matter of interest. In this work, hybrid density functional theory was implemented to study the (112) polar surface of AIS. We found that, similar to the corresponding CIS surface, as-cleaved AIS (112) surfaces are reconstructed by Ag vacancies or Ag-on-In antisites depending on the thermodynamic environment. The former is found to be more favorable under most typical growth conditions. Moreover, unlike CIS, the fluctuations in the position of the AIS valence band are small for the Ag vacancy reconstruction, but can increase if antisite reconstructions are present. Simulated scanning tunneling microscopy topographs are compared to those obtained from the experiment. Our findings suggest that alloying Ag into CIGS can potentially reduce electron–hole recombination at defects, leading to improved device performance.

Spin polarization and magnetic characteristics at C6H6/Co2MnSi(001) spinterface.

Organic materials with mechanical flexibility, low cost, chemical engineering, and long spin lifetime attract considerable attention for building spintronic devices. Here, a C6H6/Co2MnSi(001) spinterface is investigated by first-principles calculations and spin-polarized scanning tunneling microscopy simulations. Several high symmetry adsorption sites are discussed, together with two possible surface terminations of Co2MnSi(001). An inversion of the spin polarization is induced near EF even in the case of an external electric field, indicating that C6H6 can act as a spin filter to exploit the spin injection efficiency in organic spintronic devices. Unlike previous studies on molecule/ferromagnet interfaces, this inversion is closely related to the electronic structure of the atoms in the subsurface layer of Co2MnSi according to the orbital symmetry analysis. Furthermore, the magnetic moment and magnetic anisotropic energy (MAE) in the outermost Co2MnSi layer are studied. Particularly, in the most stable configuration, the sign of MAE is inversed due to hybridization between C p and Co dz2 orbitals, which suggests that a greater modification on MAE can be achieved by the use of a highly chemically reactive organic molecule. These findings improve the study on the engineering of magnetic properties at molecule/ferromagnetic interfaces through a single π-conjugated organic molecule.

Indium coverage of the Si(111)- 7×3 -In surface

The indium coverage of the Si(111)-$\sqrt{7}\ifmmode\times\else\texttimes\fi{}\sqrt{3}$-In surface is investigated by means of x-ray photoelectron spectroscopy and first-principles density functional theory calculations. Both experimental and theoretical results indicate that the In coverage is a double layer rather than a single layer. Moreover, the atomic structure of the Si(111)-$\sqrt{7}\ifmmode\times\else\texttimes\fi{}\sqrt{3}$-In surface is discussed by comparing experimental with simulated scanning tunneling microscopy (STM) images and scanning tunneling spectra with the calculated density of states. Our structural assignment agrees with previous studies, except for the interpretation of experimental STM images.

Thermo-controllable self-assembled structures of single-layer 4, 4″-diamino-p-terphenyl molecules on Au (110)**Project supported by the National Natural Science Foundation of China (Grant Nos. 61390501, 61471337, 61622116, and 51325204), the National Key Scientific Instrument and Equipment Development Project of China (Grant No. 2013YQ1203451), the CAS Hundred Talents Program, the Transregional Collaborative Research Center TRR 61 (Grant No. 21661132006), and the National Supercomputing

Here we report the thermo-controllable self-assembled structures of single-layer 4, 4″-diamino-p-terphenyl (DAT) molecules on Au (110), which are investigated by scanning tunneling microscopy (STM) combined with density functional theory (DFT) based calculations. With the deposition of monolayer DAT molecules on Au (110) and subsequent annealing at 100 °C, all DAT molecules adsorb on a (1 × 5) reconstructed surface with a ladder-like structure. After annealing the sample at about 200 °C, STM images show three distinct domains, including DAT molecules on a (1 × 3) reconstructed surface, dehydrogenated molecules with two hydrogen atoms detached from one amino group (−2H-DAT) on a (1 × 5) reconstructed surface and dehydrogenated molecules with four hydrogen atoms detached from two amino groups (–4H-DAT) on a (1 × 3) reconstructed surface through N–Au bonds. Furthermore, after annealing the sample to 350 °C, STM image shows only one self-assembled structure with −4H-DAT molecules on a (1 × 3) reconstructed surface. Relative STM simulations of different self-assembled structures show excellent agreements with the experimental STM images at different annealing temperatures. Further DFT calculations on the dehydrogenation process of DAT molecule prove that the dehydrogenation barrier on a (1 × 5) reconstructed surface is lower than that on (1 × 3) one, which demonstrate the experimental results that the formation temperature of a (1 × 3) reconstructed surface is higher than that of a (1 × 5) one.

Electronic properties of a graphene/periodic porous graphene heterostructure

Recently, two-dimensional van der Waals materials such as graphene and hexagonal boron nitride have attracted interest as research topics. The two-dimensional material of polyphenylene superhoneycomb network (PSN) is similarly interesting because it is a type of periodic porous graphene. In this paper, we report a first-principles study of the geometric and electronic properties of vertical heterostructures comprising graphene and PSN. AA, AA′, and AB stacking configurations of a graphene sheet on a PSN sheet produce band gaps of 63, 16, and 3 meV, respectively. We also determine the relationships between the band gap and the interlayer distance between the graphene and PSN sheets. Finally, we present computationally simulated scanning tunneling microscopy images, which indicate the local electronic structures of the surfaces of the graphene and PSN sides.

MoTe2 is a good match for GeI by preserving quantum spin Hall phase

Quantum spin Hall (QSH) insulator is a new class of materials that is quickly becoming mainstream in condensed-matter physics. The main obstacle for the development of QSH insulators is that their strong interactions with substrates make them difficult to study experimentally. In this study, using density functional theory, we discovered that MoTe2 is a good match for a GeI monolayer. The thermal stability of a van der Waals GeI/MoTe2 heterosheet was examined via molecular-dynamics simulations. Simulated scanning tunneling microscopy revealed that the GeI monolayer perfectly preserves the bulked honeycomb structure of MoTe2. The GeI on MoTe2 was confirmed to maintain its topological band structure with a sizable indirect bulk bandgap of 0.24 eV by directly calculating the spin Chern number to be −1. As expected, the electron mobility of the GeI is enhanced by MoTe2 substrate restriction. According to deformation-potential theory with the effective-mass approximation, the electron mobility of GeI/MoTe2 was estimated as 372.7 cm2·s−1·V−1 at 300 K, which is 20 times higher than that of freestanding GeI. Our research shows that traditional substrates always destroy the topological states and hinder the electron transport in QSH insulators, and pave way for the further realization and utilization of QSH insulators at room temperature. Open image in new window

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.

Periodic DFT+U investigation of the bulk and surface properties of marcasite (FeS2).

Marcasite FeS2 and its surface properties have been investigated by Hubbard-corrected Density Functional Theory (DFT+U) calculations. The calculated structural parameters, interatomic bond distances, elastic constants and electronic properties of the bulk mineral were determined and compared with earlier theoretical reports and experimental data where available. We have also investigated the relative stabilities, interlayer spacing relaxations, work functions, and electronic structures of the {010}, {101}, {110} and {130} surfaces under dehydrated and hydrated conditions. Using the calculated surface energies, we have derived the equilibrium crystal shape of marcasite from a Wulff construction. The {101} and {010} surfaces dominate the marcasite crystallite surface area under both dehydrated and hydrated conditions, in agreement with their relative stabilities compared to the other surfaces. The simulated scanning tunneling microscopy (STM) images of the {101} and {010} facets are also presented, for comparison with future experiments.