High-resolution Scanning Tunneling Microscopy Research Articles

Real-space evidence of Watson-Crick and Hoogsteen adenine-uracil base pairs on Au(111).

From the interplay of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, we show the real-space evidence of the formation of Watson-Crick and Hoogsteen adenine-uracil base pairs on an Au(111) surface with the employment of base derivatives, and further investigate the relative stability of the two types of adenine-uracil base pairs.

Moiré superlattices and 2D electronic properties of graphite/MoS2 heterostructures

Heterostructures of graphite/MoS2 display a wide range of lattice registry due to rotational alignment and/or lattice mismatch. Using high resolution scanning tunneling microscopy and spectroscopy (STM/STS) we investigated electronic properties of these heterostructures and observed changes in the bandgap as a function of the twist angle between the layers. Green's function based electronic structure calculations were carried out in order to shed light on the mechanism underlying the observed bandgap changes. Indirect coupling between the pz orbitals of the substrate Carbon atoms and the dz2 orbitals of the MoS2 layers (mediated by the pz orbitals of the bottom S layers) is found to be responsible for changes in the valence-band edge. Simple stacking of van der Waals materials with diverse properties have the potential to enable the fabrication of novel materials and device structures with tailored electronic properties.

On-Surface Synthesis of Adenine Oligomers via Ullmann Reaction.

Despite the fact that DNA bases have been well-studied on surface, the on-surface synthesis of one-dimensional DNA analogs through in situ reactions is still an interesting topic to be investigated. Herein, from the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we have delicately designed a halogenated derivative of adenine as precursor to realize the combination of DNA bases and Ullmann reaction, and then successfully synthesized adenine oligomers on Au(111) via Ullmann coupling. This model system provides a possible bottom-up strategy of fabricating adenine oligomers on surface, which may further give access to man-made DNA strands with multiple bases.

Quasi-Layer-by-Layer Growth of Pentacene on HOPG and Au Surfaces

High-resolution scanning tunneling microscopy (STM) is a promising method for characterizing organic semiconductors to obtain a deep understanding of organic semiconductor physics. However, organic films on conductive single-crystal substrates, which are required for STM, usually present different growth behaviors than the films on inert substrates such as SiO2. Here, we reported a simple modification method for modulating the organic semiconductor film growth on the highly oriented pyrolytic graphite (HOPG) and Au(111) substrates and investigated the detailed morphology evolution. Self-assembled monolayers (SAMs) fabricated from vacuum deposition and solution processing were introduced on these conductive substrates. Pentacene, a prototypical organic semiconductor, presented quasi-layer-by-layer growth on HOPG or Au(111) sufaces modified with solution-processed alkane monolayer. The pentacene film resembled the upright packing and terraced morphology but with larger grain size than that of thin-film phas...

Influence of CH···N Interaction in the Self-Assembly of an Oligo(isoquinolyne-ethynylyne) Molecule with Distinct Conformational States.

Molecular conformational flexibility can play an important role in supramolecular self-assembly on surfaces, affecting not least chiral molecular assemblies. To explicitly and systematically investigate the role of molecular conformational flexibility in surface self-assembly, we synthesized a three-bit conformational switch where each of three switching units on the molecules can assume one of two distinct binary positions on the surface. The molecules are designed to promote C-H···N type hydrogen bonds between the switching units. While supramolecular self-assembly based on strong hydrogen-bonding interactions has been widely explored, less is known about the role of such weaker directional interactions for surface self-assembly. The synthesized molecules consist of three nitrogen-containing isoquinoline (IQ) bits connected by ethynylene spokes and terminated by tert-butyl (tBu) groups. Using high-resolution scanning tunnelling microscopy, we investigate the self-assembly of the IQ-tBu molecules on a Au(111) surface under ultrahigh-vacuum conditions. The molecules form extended domains of brick-wall structure where the molecular backbones are packed regularly but without selection of specific molecular conformations. However, statistical analysis of the extended network demonstrates alignment/correlation for the orientations of the switching units indicating specific interactions. The primary interaction motifs in the structure are quantified from DFT calculations, showing that the brick-wall structure is indeed stabilized by two types of weak C-H···N bonds, involving either aromatic hydrogens on the IQ groups or nonaromatic hydrogens on the tBu groups. Analysis of the C-H···N interactions in the brick-wall structure explains the observed distribution and alignment of molecular conformations as well as the overall organization of the molecular surface structures.

Role of π-Radicals in the Spin Connectivity of Clusters and Networks of Tb Double-Decker Single Molecule Magnets.

When single molecule magnets (SMMs) self-assemble into 2D networks on a surface, they interact via the π-electrons of their ligands. This interaction is relevant to the quantum entanglement between molecular qubits, a key issue in quantum computing. Here, we examine the role played by the unpaired radical electron in the top ligand of Tb double-decker SMMs by comparing the spectroscopic features of isolated and 2D assembled entities on surfaces. High-resolution scanning tunneling microscopy (STM) is used to evidence experimentally the Kondo resonance of the unpaired radical spins in clusters and islands and its quenching due to up-pairing at orbital overlaps. The presence or the absence of the Kondo feature in the dI/dV maps turns out to be a good measure of the lateral interaction between molecules in 2D networks. In a 2D cluster of molecules, the π-orbital lobes that are linked through the orbital overlap show paired-up electron wave function (one singly occupied molecular orbital (SOMO) with spin-up and the other with spin-down) and therefore do not experience the Kondo resonance in the experiment. As a result, small clusters built by STM-assisted manipulation of molecules show alternating Kondo features of quantum mechanical origin, from the monomer to the dimer and the trimer. On the other hand, when the TbPc2 molecular clusters grow larger and form extended domains, a geometric rearrangement occurs, leading to the quenching of the Kondo signal on one lobe out of two. The even distribution of overlapping (SOMO) lobes on the perimeter of the molecule is induced by the square symmetry of the semi-infinite lattice and clearly distinguishes the lattice from the clusters.

A new recipe for preparing oxidized TiO2(1 1 0) surfaces: An STM study

Using high-resolution scanning tunneling microscopy (STM), we have studied the oxidation of rutile TiO2(1 1 0)–(1 × 1) surfaces with Had species at room temperature. We followed the evolution of various stable species as function of the O2 exposure, and the nature of the ultimately dominating species in the Ti troughs is described. When O2 saturation was accomplished using a glass-capillary array doser, we found that on-top O (Oot) adatoms are the predominant surface species. In contrast, when O2 was supplied via backfilling of the chamber the predominant surface species are tentatively assigned to terminal OH groups. We argue that unintended reactions with the chamber walls have a strong influence on the formed surface species, explaining scattered results in the literature. On the basis of our STM data we propose an alternative, easy way of preparing oxidized TiO2(1 1 0) surfaces with Oot adatoms (o-TiO2). It is certain that o-TiO2(1 1 0) surfaces prepared according to this recipe do not have any residual surface O vacancies. This contradicts the situation when oxidizing reduced TiO2(1 1 0) surfaces with O vacancies, where some O vacancies persist.

Focus on microscopy, imaging, and nanotechnology

Focus on microscopy, imaging, and nanotechnology

Comment on “Different STM images of the superstructure on a clean Si(133)-6 × 2 surface” (JETP Letters 105, 477 (2017))

In the recent paper by Teys [JETP Letters 105 (8), 477-483 (2017)], an atomic model for the Si(331) reconstructed surface (hereby referred to as T-model) was proposed on the basis of high-resolution scanning tunneling microscopy (STM) images. While detailing the virtues against previous and abandoned models, the author avoids any reference to the rather distinct 8P-model advocated few weeks earlier by Zhachuk and Teys [R. Zhachuk, S. Teys, Phys. Rev. B 95, 041412 (2017)], casting doubts to his own work. Formulated that way, findings from Ref. [JETP Letters 105 (8), 477-483 (2017)] leave readers of JETP Letters with a partial and confusing view of the problem, and above all, leaves the observations open to ambiguous interpretation. The 8P-model is also based on STM measurements, and unlike the T-model, passed through the scrutiny of first-principles calculations. The present comment reconciles Ref. [JETP Letters 105 (8), 477-483 (2017)] with the literature by supplementing the discussion with a missing and critical account on the stability and electronic structure of the T- versus 8P-models of Si(331).

Functional group selective STM Imaging in self-assembled monolayers: Benzeneselenol on Au(111)

Benzeneselenol (PSe) self-assembled monolayers (SAMs) formed on Au(111) substrate by the immersion procedure with an immersion time of 24h and 4 weeks were studied by high-resolution scanning tunneling microscopy (STM). The short molecular rows, which have been previously attributed to irregular translational domains, were found to be regularly repeated within a single domain in the SAMs fabricated upon the immersion for 4 weeks, forming adlayer structure with a very large unit cell. This structure could be assigned as a (27×5) superlattice (α phase) containing 36 molecules in the oblique unit cell. This phase coexisted with a different phase having a commensurate (83×4) superstructure (β phase) containing 28 protrusions per rectangular unit cell. Analysis of the STM images suggested that each PSe molecule in the β phase was imaged not as one but as a pair of protrusions, which were attributed to the benzene ring and the selenium headgroup of the PSe molecule. At the given molecular length, the spacing between the protrusions defined the molecular tilt, allowing us to derive the orientation of the SAM constituents directly from the STM image.

On-Surface Formation of Cumulene by Dehalogenative Homocoupling of Alkenyl gem-Dibromides.

The on-surface activation of carbon-halogen groups is an efficient route to produce radicals for constructing various hydrocarbons and carbon nanostructures. To date, the employed halide precursors have only one halogen attached to a carbon atom. It is thus of interest to study the effect of attaching more than one halogen atom to a carbon atom with the aim of producing multiple unpaired electrons. By introducing an alkenyl gem-dibromide, cumulene products were fabricated on a Au(111) surface by dehalogenative homocoupling reactions. The reaction products and pathways were unambiguously characterized by a combination of high-resolution scanning tunneling microscopy and non-contact atomic force microscopy measurements together with density functional calculations. This study further supplements the database of on-surface synthesis strategies and provides a facile manner for incorporation of more complicated carbon scaffolds into surface nanostructures.

Parity breaking in a double atomic chain system

In one-dimensional electron systems, cooperative effects are expected to cause very specific electronic instabilities. Atomic nanowires, formed via self-organized growth on semiconductor surfaces, represent viable physical realizations for the study of such fascinating one-dimensional quantum states. The system in the focus of this work, Si(553)-Au, is created by Au adsorption on a stepped silicon substrate. It features two different chain types, interspersed with each other: Au chains on the terraces, and Si step edges that are subject to the formation of spin chains. By combining high-resolution scanning tunneling microscopy and local tunneling spectroscopy, the authors reveal the complex interplay between the two distinct wire architectures. The interaction is effectively ``one-way'' in that the Si step edges respond to the Au chains, but not vice versa. As a consequence, the symmetry of the system is lowered as the parity of the Si chains is broken. This fundamental effect creates two different configurations of chains with opposite directionality.

Dynamics, Stability, and Adsorption States of Water on Oxidized RuO2(110)

Identifying and understanding how excess oxygen atoms affect the adsorption of water on metal oxides is crucial for their use in water splitting. Here, by means of high-resolution scanning tunneling microscopy and density-functional calculations, we show that excess oxygen atoms on the stoichiometric RuO2(110) significantly change the clustering, conformation, and deprotonation equilibrium of adsorbed water. We considered two reactive scenarios during which the stoichiometric surface was exposed (i) first to oxygen, followed by water, and (ii) first to water, followed by oxygen. In both cases, the [OH-OH] complex on Ru rows is the dominant species, showing a significant difference from water-only adsorption on the stoichiometric surface in which the [OH-H2O] species is found to be prevalent. Surface reactivity at almost full O coverage is also addressed; there we show that site selectivity of the surface for H adsorption and dissociation of H2O is hindered, notwithstanding the increase of the dynamic motion of both species. We found that the work function of RuO2 can serve as a descriptor for the reactivity of this surface to water and its constituents.

Nanoscale Dehydrogenation Observed by Tip-Enhanced Raman Spectroscopy

This study shows evidence of nanoscale dehydrogenation occurring during tip-enhanced Raman spectroscopy (TERS) measurements. The near-field TERS spectra obtained locally on a self-assembled monolayer of 2,13-bis(aldehyde)[7]thiaheterohelicene molecules showed vibrational frequencies in good agreement with that predicted by density functional theory calculations, except for the L-mode at ∼2000 cm–1, which is ascribed to a C≡C triple bond, implying that the benzene rings had been dehydrogenated during the experiments. Using peak analysis, incorporated with the molecular adsorption orientation deduced from high-resolution STM imaging, we conclude that one side benzene ring protruding upward was dehydrogenated as a result of pyrolysis, with the Ag tip serving as both local heat source and catalyst.

Learning surface molecular structures via machine vision

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

Supramolecular Corrals on Surfaces Resulting from Aromatic Interactions of Nonplanar Triazoles.

Interaction forces between aromatic moieties, often referred to as π-π interactions, are an important element in stabilizing complex supramolecular structures. For supramolecular self-assembly occurring on surfaces, where aromatic moieties are typically forced to adsorb coplanar with the surface, the possible role of intermolecular aromatic interactions is much less explored. Here, we report on unusual, ring-shaped supramolecular corral surface structures resulting from adsorption of a molecule with nonplanar structure, allowing for intermolecular aromatic interactions. The discrete corral structures are observed using high-resolution scanning tunneling microscopy, and the energetic driving forces for their formation are elucidated using density functional theory calculations and Monte Carlo simulations. The individual corrals involve between 11 and 18 molecules bound through triazole moieties to a ring-shaped ensemble of bridge site positions on (111) surfaces of copper, silver, or gold. The curvature required to form the corrals is identified to result from the angle dependence of aromatic interactions between molecular phenanthrene moieties. The study provides detailed quantitative insights into triazole-surface and aromatic interactions and illustrates how they may be used to drive surface supramolecular self-assembly.

High-resolution electrochemical STM of redox metalloproteins

Electrochemical studies of redox active metalloproteins have become an increasingly fruitful area of study in recent years, particularly with the single-molecule resolution capability of electrochemical scanning tunnelling microscopy (EC-STM) which provides both imaging and current-voltage spectroscopy under bipotentiostatic control. In this review, some of the most exciting advances in recent years are outlined, and directions for future research are considered.

Zn vacancies creation via (2 × 2) surface reconstruction

Zinc vacancies have been incorporated in ZnO via (2 × 2) surface reconstruction during the epitaxy growth. Evolution of in situ reflection high-energy electron diffraction (RHEED) patterns indicate Zn-polar surface (2 × 2) reconstruction was realized under extreme O-rich conditions. Atom sized triangular pits and islands were presented by the high resolution scanning tunneling microscopy (STM) images, which stand for a single Zn vacancy per (2 × 2) surface unit cell. The neutral acceptor-bound exciton (A0,X), peak located at 3.344 eV, and red luminescence (RL), maximum emission intensity at ~1.76 eV, which related to Zn vacancy, have been studied by variable-temperature/power steady-state photoluminescence (PL) spectroscopy.

Synthesis of borophene nanoribbons on Ag(110) surface

We present the successful synthesis of single-atom-thick borophene nanoribbons (BNRs) by self-assembly of boron on Ag(110) surface. The scanning tunneling microscopy (STM) studies reveal high quality BNRs: all the ribbons are along the [-110] direction of Ag(110), and can run across the steps on the surface. The width of ribbons is distributed in a narrow range around 10.3 nm. High resolution STM images revealed four ordered surface structures in BNRs. Combined with DFT calculations, we found that all the four structures of boron nanoribbons consist of the boron chains with different width, separated by hexagonal hole arrays. The successful synthesis of BNRs enriches the low dimensional allotrope of boron and may promote further applications of borophene

Symmetry forbidden morphologies and domain boundaries in nanoscale graphene islands

The synthesis of graphene nanoislands with tailored quantum properties requires an atomic control of the morphology and crystal structure. As one reduces their size down to the nanometer scale, domain boundary and edge energetics, as well as nucleation and growth mechanisms impose different stability and kinetic landscape from that at the microscale. This offers the possibility to synthesize structures that are exclusive to the nanoscale, but also calls for fundamental growth studies in order to control them.By employing high-resolution scanning tunneling microscopy we elucidate the atomic stacking configurations, domain boundaries, and edge structure of graphene nanoislands grown on Ni(1 1 1) by CVD and post-annealed at different temperatures. We find a non-conventional multistep mechanism that separates the thermal regimes for growth, edge reconstruction, and final stacking configuration, leading to nanoisland morphologies that are incompatible with their stacking symmetry. Whole islands shift their stacking configuration during cooling down, and others present continuous transitions at the edges. A statistical analysis of the domain structures obtained at different annealing temperatures reveals how polycrystalline, ill-defined structures heal into shape-selected islands of a single predominant stacking. The high crystallinity and the control on morphology and edge structure makes these graphene nanoislands ideal for their application in optoelectronics and spintronics.