Use Of Scanning Tunneling Microscopy Research Articles

Structural evolution of the conformational ensembles in peptide fibrillar aggregates

Exploring the folding structures and intermolecular recognitions of proteins in their assemblies is essential for revealing the mechanisms of amyloid fibrillar aggregation. However, the molecular-level description of protein structural changes with aggregation progression is challenging due to the heterogeneity of assembled structures. Here we report the use of scanning tunneling microscopy (STM), which is competent in analyzing the highly heterogeneous structures with submolecular resolution, to probe the structures of human islet amyloid polypeptide (hIAPP) assemblies at the different time points of hIAPP fibrillation. The conformational substate ensembles of the β-strands formed by hIAPP as well as the interpeptide interactions are found to change with time in the growth and plateau phases. Detailed analyses of the distribution probability of interpeptide interactions at the different time points manifest that the enthalpic contribution to the structural conversions of β-sheet fibrillation becomes more significant. Our single-molecular level studies highlight the dynamic nature of protein structures within a β-sheet-assembled fibril.

Single-molecule visualization determines conformational substate ensembles in β-sheet–rich peptide fibrils

An understanding of protein conformational ensembles is essential for revealing the underlying mechanisms of interpeptide recognition and association. However, experimentally resolving multiple simultaneously existing conformational substates remains challenging. Here, we report the use of scanning tunneling microscopy (STM) to analyze the conformational substate ensembles of β sheet peptides with a submolecular resolution (in-plane <2.6 Å). We observed ensembles of more than 10 conformational substates (with free energy fluctuations between several k B T s) in peptide homoassemblies of keratin (KRT) and amyloidal peptides (−5Aβ42 and TDP-43 341–357). Furthermore, STM reveals a change in the conformational ensemble of peptide mutants, which is correlated with the macroscopic properties of peptide assemblies. Our results demonstrate that the STM-based single-molecule imaging can capture a thorough picture of the conformational substates with which to build an energetic landscape of interconformational interactions and can rapidly screen conformational ensembles, which can complement conventional characterization techniques.

Experimental Insights into Conformational Ensembles of Assembled β-Sheet Peptides.

Deciphering the conformations and interactions of peptides in their assemblies offers a basis for guiding the rational design of peptide-assembled materials. Here we report the use of scanning tunneling microscopy (STM), a single-molecule imaging method with a submolecular resolution, to distinguish 18 types of coexisting conformational substates of the β-strand of the 8-37 segment of human islet amyloid polypeptide (hIAPP 8-37). We analyzed the pairwise peptide-peptide interactions in the hIAPP 8-37 assembly and found 82 interconformation interactions within a free energy difference of 3.40 kBT. Besides hIAPP 8-37, this STM method validates the existence of multiple conformations of other β-sheet peptide assemblies, including mutated hIAPP 8-37 and amyloid-β 42. Overall, the results reported in this work provide single-molecule experimental insights into the conformational ensemble and interpeptide interactions in the β-sheet peptide assembly.

Spontaneous doping of the basal plane of MoS2 single layers through oxygen substitution under ambient conditions.

The chemical inertness of the defect-free basal plane confers environmental stability to MoS2 single layers, but it also limits their chemical versatility and catalytic activity. The stability of pristine MoS2 basal plane against oxidation under ambient conditions is a widely accepted assumption however, here we report single-atom-level structural investigations that reveal that oxygen atoms spontaneously incorporate into the basal plane of MoS2 single layers during ambient exposure. The use of scanning tunnelling microscopy reveals a slow oxygen-substitution reaction, during which individual sulfur atoms are replaced one by one by oxygen, giving rise to solid-solution-type 2D MoS2-xOx crystals. Oxygen substitution sites present all over the basal plane act as single-atom reaction centres, substantially increasing the catalytic activity of the entire MoS2 basal plane for the electrochemical H2 evolution reaction.

All-electronic Nanosecond-resolved Scanning Tunneling Microscopy: Facilitating the Investigation of Single Dopant Charge Dynamics.

The miniaturization of semiconductor devices to scales where small numbers of dopants can control device properties requires the development of new techniques capable of characterizing their dynamics. Investigating single dopants requires sub-nanometer spatial resolution, which motivates the use of scanning tunneling microscopy (STM). However, conventional STM is limited to millisecond temporal resolution. Several methods have been developed to overcome this shortcoming, including all-electronic time-resolved STM, which is used in this study to examine dopant dynamics in silicon with nanosecond resolution. The methods presented here are widely accessible and allow for local measurement of a wide variety of dynamics at the atomic scale. A novel time-resolved scanning tunneling spectroscopy technique is presented and used to efficiently search for dynamics.

All-electronic Nanosecond-resolved Scanning Tunneling Microscopy: Facilitating the Investigation of Single Dopant Charge Dynamics

The miniaturization of semiconductor devices to scales where small numbers of dopants can control device properties requires the development of new techniques capable of characterizing their dynamics. Investigating single dopants requires sub-nanometer spatial resolution, which motivates the use of scanning tunneling microscopy (STM). However, conventional STM is limited to millisecond temporal resolution. Several methods have been developed to overcome this shortcoming, including all-electronic time-resolved STM, which is used in this study to examine dopant dynamics in silicon with nanosecond resolution. The methods presented here are widely accessible and allow for local measurement of a wide variety of dynamics at the atomic scale. A novel time-resolved scanning tunneling spectroscopy technique is presented and used to efficiently search for dynamics.

Imaging electrostatically confined Dirac fermions in graphene quantum dots

Electrostatic confinement of charge carriers in graphene is governed by Klein tunneling, a relativistic quantum process in which particle-hole transmutation leads to unusual anisotropic transmission at pn junction boundaries. Reflection and transmission at these novel potential barriers should affect the quantum interference of electronic wavefunctions near these boundaries. Here we report the use of scanning tunneling microscopy (STM) to map the electronic structure of Dirac fermions confined by circular graphene pn junctions. These effective quantum dots were fabricated using a new technique involving local manipulation of defect charge within the insulating substrate beneath a graphene monolayer. Inside such graphene quantum dots we observe energy levels corresponding to quasi-bound states and we spatially visualize the quantum interference patterns of confined electrons. Dirac fermions outside these quantum dots exhibit Friedel oscillation-like behavior. Bolstered with a theoretical model describing relativistic particles in a harmonic oscillator potential, our findings yield new insight into the spatial behavior of electrostatically confined Dirac fermions.

Synthesis, Tailoring and Characterization of V2O5-Cathodes for High Performance Li+-, Na+- and Mg2+-Ion Batteries

Battery technology based electric energy storage devices are inevitable on the way to electromobility and the widespread application of renewable energies like wind- or solar-power.1 Until now, Li+-ion batteries represent the state of art technology meeting best the demands of high energy- and power-densities. However issues related to high costs and safety still require improvement. 2,3 One strategy to tackle those issues is to replace the costly Li-metal by other, more abundant metals, such as Na or Mg.4 Due to the different ionic, electronic and chemical properties of Li+-, Na+- and Mg2+-ions, not every Li+-ion host material is suitable for the other ions. One exception is V2O5, which recently was successfully used as high voltage cathode for Na+- and Mg2+-ion intercalation.5,6 Similar to the research on Li-ion battery electrode materials, where people pursue the strategy of electrode nanostructuring in order to increase the rate capability and hence the power density, a wide variety of synthesis techniques was applied to obtain nano-V2O5, including top-down and bottom-up techniques.7 In this work, V2O5-nanofibres were synthesized by ultrasonication and electrochemical deposition. Anodization of vanadium metal yielded V2O5-nanotubes, while hydrothermal synthesis results in hollow V2O5-nanospheres. In order to characterize and specify the different electrode morphologies and performances, electrochemical, spectroscopic and microscopic techniques were applied (see Figure 1). In addition, fundamental studies on V2O5 and its interaction with Li+-, Na+- and Mg2+-ions were conducted making use of Scanning Tunneling Microscopy (STM) and the Electrochemical Quartz Crystal Microbalance technique (EQCM). Figure 1. SEM images of (a) hollow V2O5-nanospheres, (b) electrodeposited V2O5 and (c) ultrasonicated V2O5 1B. Dunn, H. Kamath, J.-M. Tarascon, Science, 334 (2011) 928 2M. Armand, J.-M. Tarascon, Nature, 451 (2008) 652 3J. B. Goodenough, J. Solid State Electrochem., 16 (2012) 2019 4J. O. Besenhard, M. Winter, ChemPhysChem, 3 (2002) 155 5G. Gershinsky, H. D. Yoo, Y. Gofer, D. Aurbach, Langmuir, 29 (2013) 10964 6D. W. Su, S. X. Dou, G. X. Wang, J. Mater. Chem., 2 (2014) 11185 7A. S. Arico, P.Bruce, B. Scrosati, J.-M. Tarascon, W. van Schalkwijk, Nature, 4 (2005) 366 Figure 1

Stoichiometry engineering of ternary oxide ultrathin films:BaxTi2O3on Au(111)

Ternary oxide ${\mathrm{Ba}}_{x}{\mathrm{Ti}}_{2}{\mathrm{O}}_{3}$ ultrathin films on Au(111) substrates $(x\ensuremath{\le}2/3)$ have been studied using a joint experimental and theoretical approach, including the use of scanning tunneling microscopy (STM), first principles calculations, and Monte Carlo simulations. The films are created by first covering the Au(111) substrate with a ${\mathrm{Ti}}_{2}{\mathrm{O}}_{3}\phantom{\rule{0.28em}{0ex}}(2\ifmmode\times\else\texttimes\fi{}2)$ honeycomb (HC) network and then evaporating low concentrations of Ba atoms onto this film. STM imaging shows that the Ba atoms adsorb individually in the hollow sites of the HC network. Depending on the Ba coverage $x$, which ranges from 0 to 2/3, two ordered phases can be identified at $x=1/3$ and $x=2/3$. A disordered labyrinthlike phase is observed for values of $x$ between 1/3 and 2/3. Theoretical modeling shows that the structural character of these films is driven by the charge transfer that occurs between the electropositive Ba atoms and the electronegative ${\mathrm{Ti}}_{2}{\mathrm{O}}_{3}$/Au substrate. This results in a number of calculated effects including an increase in the film rumpling and a reduction of the film work function with increasing $x$. The evolution of the structure of the thin films as a function of Ba coverage can be described by a lattice gas model with first-, second-, and third-neighbor Ba-Ba repulsive interactions. The range of the dipolar interactions is a key factor in understanding the behavior of Ba ordering. The structural and electronic flexibility, which can be engineered through stoichiometry, temperature, or support control, makes these ultrathin films promising materials for applications related to adsorption or reactivity, or as template supports for the growth of size-selected clusters.

Characterization of PTCDA nanocrystals on Ge(0 0 1):H-(2 × 1) surfaces

We analyze self-assembled nanocrystals of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) molecules on hydrogen passivated Ge(001) surfaces with use of scanning tunneling microscopy (STM) and spectroscopy (STS). At 0.7ML coverage, 2.1nm high, elongated, hexagonal islands inclined at 37° with respect to the substrate row are mostly observed. By measuring the differential tunneling conductance, we observe an effect of electronic decoupling of the nanocrystals due to the introduced passivating layer. Finally, we shortly discuss the stability of the islands and their interaction with the scanning probe in the ultra-high vacuum environment.

Thermal evolution of the morphology of Ni/Ge(111)-c(2 × 8) surface

Abstract The thermal evolution of the interface formed by room temperature (RT) deposition of Ni atoms (coverage 0.1, 0.5, 1.2 ML) onto a Ge(111)-c(2 × 8) surface has been studied with the use of scanning tunneling microscopy (STM). Atomically resolved STM images revealed that, at RT, the boundaries between the different c(2 × 8) domains acted as nucleation sites for Ni atoms. After annealing the surface with deposited material at 473 to 673 K the formation of nano-sized islands of NixGey compounds was observed. In addition, the occurrence of ring-like structures was recorded. Based on the dual-polarity images the latter were assigned to Ni atoms adsorbed on Ge adatoms.

Strong interaction between graphene edge and metal revealed by scanning tunneling microscopy

Abstract The interaction between a graphene edge and the underlying metal is investigated through the use of scanning tunneling microscopy (STM) and density functional theory (DFT) calculations and found to influence the geometrical structure of the graphene edge and its electronic properties. STM study reveals that graphene nanoislands grow on a Pt(1 1 1) surface with the considerable bending of the graphene at the edge arising from the strong graphene-edge–Pt-substrate interactions. Periodic ripples along the graphene edge due to both the strong interaction and the lattice mismatch with the underlying metal were seen. DFT calculations confirm such significant bending and also reproduce the periodic ripples along the graphene edge. The highly distorted edge geometry causes strain-induced pseudo-magnetic fields, which are manifested as Landau levels in the scanning tunneling spectroscopy. The electronic properties of the graphene edge are thus concluded to be strongly influenced by the curvature rather than the localized states along the zigzag edge as was previously predicted.

Unusual ultra-low-frequency fluctuations in freestanding graphene.

Intrinsic ripples in freestanding graphene have been exceedingly difficult to study. Individual ripple geometry was recently imaged using scanning tunnelling microscopy, but these measurements are limited to static configurations. Thermally-activated flexural phonon modes should generate dynamic changes in curvature. Here we show how to track the vertical movement of a one-square-angstrom region of freestanding graphene using scanning tunnelling microscopy, thereby allowing measurement of the out-of-plane time trajectory and fluctuations over long time periods. We also present a model from elasticity theory to explain the very-low-frequency oscillations. Unexpectedly, we sometimes detect a sudden colossal jump, which we interpret as due to mirror buckling. This innovative technique provides a much needed atomic-scale probe for the time-dependent behaviours of intrinsic ripples. The discovery of this novel progenitor represents a fundamental advance in the use of scanning tunnelling microscopy, which together with the application of a thermal load provides a low-frequency nano-resonator.

Theoretical modelling of Jahn-Teller distorted C60 anions on a surface

Through the use of scanning tunnelling microscopy (STM), it is possible to directly observe the molecular orbitals associated with a particular molecule. For the charged ions of the C60 fullerene, the interpretation of these experimental images has an additional complication due to the inherent presence of the Jahn-Teller (JT) effect. In this work, the influence of the JT effect on STM images is examined. We also include interactions between the molecule and both the surface substrate on which it rests, and, when present within a monolayer, the nearest neighbours. Simple symmetry arguments are used to explain the effects of these external interactions on the energy of the different JT wells relating to molecular distortions of D3d, D5d, and D2h symmetry. We first investigate the C−60 monoanion, and then, through the construction of multi-electron states, move on to consider anions with higher charges. It is found that for high symmetry orientations of the molecule on the surface, the wells that are degenerate in the absence of external interactions split into equal energy subgroups, with the grouping dependent on the orientation of the molecule. Hückel molecular orbital theory is then used to investigate the effect this has on STM images. We show that when dynamic JT effects are considered, the images are always formed from some linear combination of the squares of the individual single electron molecular orbitals that make up the lowest unoccupied molecular orbital of the neutral molecule.

STM studies of epitaxial graphene

Abstract

Correlations between the catalytic activity of heteropoly acids and the special features of their tunneling spectra

The electronic-vibrational spectra of phosphomolybdic acid, a classic heteropoly acid with a Keggin anion, were measured in an ultrahigh vacuum with the use of scanning tunneling microscopy. The dependences of the resonance characteristics of the spectra, so-called negative differential resistances (NDRs), on the vacuum gap, the polarity of applied voltage, and the direction of tunnel current were determined. A new mechanism of the formation of NDRs was proposed based on the quantum effect of the localization of the electronic states of multicenter systems in strong electric fields. The character of correlations between NDRs and the catalytic properties of heteropoly acid catalysts was established.

Additive Perturbed Molecular Assembly in Two-Dimensional Crystals: Differentiating Kinetic and Thermodynamic Pathways

During attempts to produce novel two-dimensional cocrystals by coadsorbing components in a binary mixture, the formation of a metastable form was observed in analogy to the phenomenon of additive-induced polymorph formation reported in three-dimensional crystallization. Mechanistic insights into this phenomenon were gained through the use of scanning tunneling microscopy and several adsorbate/additive combinations. One additive plays a critical role in forming a disordered assembly through a process that is primarily kinetic whereas another additive thermodynamically stabilized an intermediate form, resulting in interrupting a phase transformation to a more stable form. These additive effects elucidate one of the potential pathways to kinetically isolate a metastable polymorph formed during cocrystallization in three-dimensional crystallization.

Dimerization of Nitrosobenzene Derivatives on an Au(111) Surface

In this study, we have investigated the ability of C-nitrosobenzenes to dimerize on an Au(111) surface and form ordered self-assembled bilayers (SABs). Use of scanning tunneling microscopy (STM) revealed that nitrosobenzene derivatives are able to form both well-ordered monolayers (SAMs) and bilayers (SABs). High-resolution STM images showed that within SAM regions molecules are arranged into hexagonal structures. Moiré-type superstructure with a periodicity of 1.5 nm was observed, indicating a 3√3 × 3√3 molecular arrangement. Molecularly resolved STM images showed that within bilayers molecules are also arranged into hexagonally ordered structures at intermolecular spacing of ∼0.4 nm. Furthermore, it was observed that the second layer is better ordered than the first one, probably because of the softer background. Use of atomic force microscopy (AFM), through measured height differences between monolayers and bilayers, further confirmed the formation of SABs. The results of the present study demonstrate that nitrosobenzenes represent convenient molecular models that can be used for systematic design and study of bilayers on metal surfaces. Besides the previously known properties of C-nitroso compounds to form dimers in crystals, here we have found a new situation under which these molecules dimerize, which is, in principle, a 2D crystallization.

Nano-Molecular Junctions on STM Tips

We present a technique for metal-organic-metal junctions, which contain ten or fewer conjugated molecules between each of such junction, and the investigations of the I–V response of these junctions. The junctions are made by self assembling thiolated molecules onto gold coated tips for use in scanning tunneling microscopy. We show that this easy technique probes the qualitative properties of the molecules. Current-voltage characteristics of a Tour wire and a new molecular rectifier are presented.

Nano-Molecular Junctions on STM Tips

Abstract We present a technique for metal-organic-metal junctions, which contain ten or fewer conjugated molecules between each of such junction, and the investigations of the I–V response of these junctions. The junctions are made by self assembling thiolated molecules onto gold coated tips for use in scanning tunneling microscopy. We show that this easy technique probes the qualitative properties of the molecules. Current-voltage characteristics of a Tour wire and a new molecular rectifier are presented.