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Results for “Microscopy, Scanning Tunneling”

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PubMed1992

Imaging of subunit complexes of thermophilic bacterium H(+)-ATPase with scanning tunneling microscopy.

Using a scanning tunneling microscope (STM), we observed reconstructed subunit complexes of H(+)-ATPase of a thermophilic bacterium. The measurement was carried out in air without conductive coating on the samples deposited on a highly oriented pyrolytic graphite (HOPG). The F1 subunit complex of the H(+)-ATPase, and an H(+)-ATPase whose F0 portion was embedded into liposomes prepared from soybean lecithin were imaged. Overall structural images of the subunit complex F1 were obtained: the structural dimensions of the STM images are in agreement with those deduced from conventional methods such as an transmission electron microscopy (TEM) and small-angle X-ray scattering (SAX) experimentation. Regarding the STM imaging of these samples, we discuss the advantages and disadvantages of the STM over those of conventional methods such as a TEM and SAX.

Cloning, Molecular↗

PubMed1991

An approach to imaging of living cell surface topography by scanning tunneling microscopy.

Since a scanning tunneling microscope (STM) was developed, an observation of living cell surface has been one of the final aims in the biological application of STM. By developing a new style of STM which was combined with an optical microscope and with a novel system for the centering of both images, we successfully got the STM images of living cell surface of T24 cells (human bladder cancer cell line) and CHO cells (Chinese hamster ovary fibroblast) cultured on highly oriented pyrolytic graphite under the appropriate condition (V greater than 8.0 V, I less than 0.2 nA). Unexpectedly, the living T24 cell showed a slightly uneven surface with a steep foot slope. The CHO cell showed more rough surface with steeper slope of cell foot. Although the STM system had a fine spatial resolution less than 3 nm, the profile of living cell surface covered with electrolyte was clear only when the scanning area was more than 10 microns square.

Animals↗

PubMed2005

A single molecule view of bistilbene photoisomerization on a surface using scanning tunneling microscopy.

The advent of scanning tunneling microscopy (STM) has permitted a detailed atomic view of organic molecules adsorbed on solid surfaces. In this work, we make use of the STM to provide an unprecedented direct single-molecule perspective on the cis-trans photoisomerization of stilbene molecules within ordered monolayers physisorbed on the Ag/Ge(111)-( radical3x radical3)R30 degrees surface. The STM view of the molecular structure transformation upon irradiation provides direct evidence for the generally accepted one-bond-flip mechanism proposed for the photoisomerization process. We also find that the surface environment produces a profound effect on the reaction mechanism. The reaction is observed to proceed mainly through pairs of co-isomerizing molecules situated at domain boundaries. To explain these observations, we propose a mechanism whereby excitation migrates to the domain boundary and the reaction occurs through a biexciton reaction pathway.

Journal Article↗

PubMed2006

Observation of single dinuclear metal-complex molecules using scanning tunneling microscopy.

We report a scanning tunneling microscopy (STM) investigation of a dinuclear organometallic molecule, trans-[Cl(dppe)2Ru(C[triple bond]C)6Ru(dppe)2Cl] (Ru2), absorbed on a Au(111) surface; this molecule is a potential candidate for use in molecular quantum-dot cellular automata (QCA) devices. Isolated Ru2 molecules were observed under ultra-high-vacuum conditions. Submolecular structure was clearly discernible in the STM images, with a bright feature corresponding to each of the two Ru-ligand complexes within the Ru2 molecule. Rotation and translation of the Ru2 molecules were observed to be induced by the STM tip under some tunneling conditions.

Journal Article↗

PubMed2002

Probing high-barrier pathways of surface reactions by scanning tunneling microscopy.

The ability of scanning tunneling microscopy to probe the pathways of thermally activated high-barrier surface processes is frequently limited by competing low-barrier processes that can confuse measurement of the true initial and final configuration. We introduce an approach to circumvent this difficulty by driving the surface process with nanosecond laser heating. The method is applied to determine the pathway of recombinative desorption in the H/Si(001) system. The observed configuration of dangling bonds after laser heating reveals that the desorbed hydrogen molecules are not formed on single dimers, but rather from neighboring silicon dimers via an interdimer reaction pathway.

Journal Article↗

PubMedDate not supplied

Optical characterization of probes for photon scanning tunnelling microscopy.

The photon scanning tunnelling microscope is a well-established member of the family of scanning near-field optical microscopes used for optical imaging at the subwavelength scale. The quality of the probes, typically pointed uncoated optical fibres, used is however, difficult to evaluate in a direct manner and has most often been inferred from the apparent quality of recorded optical images. Complicated near-field optical imaging characteristics, together with the possibility of topographically induced artefacts, however, has increased demands for a more reliable probe characterization technique. Here we present experimental results obtained for optical characterization of two different probes by imaging of a well-specified near-field intensity distribution at various spatial frequencies. In particular, we observe that a sharply pointed dielectric probe can be highly suitable for imaging when using p-polarized light for the illumination. We conclude that the proposed scheme can be used directly for probe characterization and, subsequently, for determination of an optical transfer function. which would allow one to deduce from an experimentally obtained image of a weakly scattering sample the field distribution existing near the sample surface in the absence of the probe.

Journal Article↗

PubMed2004

Controlled low-temperature molecular manipulation of sexiphenyl molecules on Ag111 using scanning tunneling microscopy.

A novel scanning tunneling microscope manipulation scheme for a controlled molecular transport of weakly adsorbed molecules is demonstrated. Single sexiphenyl molecules adsorbed on a Ag(111) surface at 6 K are shot towards single silver atoms by excitation with the tip. To achieve atomically straight shooting paths, an electron resonator consisting of linear standing-wave fronts is constructed. The sexiphenyl manipulation signals reveal a pi ring flipping as the molecule moves from the hcp to fcc site. Ab initio calculations show an incorporation of the Ag atom below the center of a pi ring.

Journal Article↗

PubMed1990

Scanning tunneling microscopy of the enzymes of muscle glycogenolysis.

Scanning tunneling microscopy (STM) has been used to examine the structures of the skeletal muscle enzymes phosphorylase and phosphorylase kinase. The interaction of these two proteins represents the last step in the process of signal transduction which results in muscle glycogen being converted into metabolic energy for use in muscle contraction. Phosphorylase b has a molecular weight of 97,000 and the dimer is seen by STM to have dimensions of 11 X 5.7 nm. Phosphorylase b has a tendency to form linear arrays of dimers on the graphite surface used as the support for STM imaging. Phosphorylase kinase is imaged as a butterfly-like object with lateral dimensions of 36 X 27 nm. The molecular thicknesses given by scanning tunneling microscopy for these two non-conducting molecules is significantly less than expected. The height measurement in STM is dependent not only on the surface topology of the object being imaged, but also on the electronic work function of the object compared to that of the graphite surface on which it lies. In addition to the individual proteins, a complex between phosphorylase and phosphorylase kinase has been observed by scanning tunneling microscopy.

Animals↗

PubMed2006

Identification of single-strand DNA by in situ scanning tunneling microscopy.

We report here in situ scanning tunneling microscopy imaging of hexaammineruthenium (II)/(III) (RuHex) binding to single-strand DNA oligonucleotide with 13 bases immobilized in a mixed monolayer on a single-crystal Au(111) surface. RuHex does not bind to the other component in the monolayer, mercaptohexanol. Images before and after addition of RuHex show a strong contrast increase, suggesting that single-stranded DNA is, indeed, conducting when a redox group is bound to the strand. When compared with previous results, the data also suggest that the mechanism of domain formation of the immobilized DNA is independent of the sequence.

Adsorption↗

PubMed1991

Images of 16S ribosomal RNA by scanning tunnelling microscopy.

We report the use of scanning tunnelling microscopy (STM) to study surface topographies of complex nucleic acid structures. From low-resolution STM images of uncoated 16S ribosomal RNA, we demonstrate the possibility of determining several objective parameters (molecular mass and radius of gyration) in order to characterize and identify the molecules observed. These parameters were compared with values obtained by other physical methods and the radius of gyration was found to be the most reliable. At high resolution, it was possible to measure the main dimensions of selected V-form particles more precisely than with electron microscopy. Images of the more compact form have been also obtained that show different domains in the macromolecular structure.

Escherichia coli↗

PubMed2000

A scanning tunnelling microscopy study of Clostridium pasteurianum rubredoxin.

Scanning tunnelling microscopy (STM), which can provide 'direct' and 'non-averaged' information on molecular structure in three dimensions, has been used to achieve sub-molecular resolution in a 'single molecule' of rubredoxin, an important iron-sulphur protein, at the gold (111)/water interface. The metal-ligand site [Fe(III)-Cys4] appears distinct because of an enhancement of the tunnelling current over this region compared to the surrounding protein structure.

Clostridium↗

PubMed1999

An approach to long-range electron transfer mechanisms in metalloproteins: in situ scanning tunneling microscopy with submolecular resolution.

In situ scanning tunneling microscopy (STM) of redox molecules, in aqueous solution, shows interesting analogies and differences compared with interfacial electrochemical electron transfer (ET) and ET in homogeneous solution. This is because the redox level represents a deep indentation in the tunnel barrier, with possible temporary electronic population. Particular perspectives are that both the bias voltage and the overvoltage relative to a reference electrode can be controlled, reflected in spectroscopic features when the potential variation brings the redox level to cross the Fermi levels of the substrate and tip. The blue copper protein azurin adsorbs on gold(111) via a surface disulfide group. Well resolved in situ STM images show arrays of molecules on the triangular gold(111) terraces. This points to the feasibility of in situ STM of redox metalloproteins directly in their natural aqueous medium. Each structure also shows a central brighter contrast in the constant current mode, indicative of 2- to 4-fold current enhancement compared with the peripheral parts. This supports the notion of tunneling via the redox level of the copper atom and of in situ STM as a new approach to long-range electron tunneling in metalloproteins.

Adsorption↗

PubMed1990

Scanning tunnelling microscopy in biotechnology.

The scanning tunnelling microscope (STM) is capable of atomic resolution of highly conductive materials. Whether biological molecules can be visualized to the same extent remains an open question, but remarkable progress in the past year confirms the possibility of seeing the fine structure of nucleic acids, proteins, membranes and viruses, and provides evidence that their dynamic interactions can be monitored under conditions approximating to those of the native environment.

Biotechnology↗

PubMed1989

Scanning tunnelling microscopy of Z-DNA.

Scanning tunnelling microscopy (STM) has been used to map the surface topography of inorganic materials at the atomic level, and is potentially one of the most powerful techniques for probing biomolecular structure. Recent STM studies of calf thymus DNA and poly(rA).poly(rU) have shown that the helical pitch and periodic alternation of major and minor grooves can be visualized and reliably measured. Here we present the first STM images of poly(dG-me5dC).poly(dG-me5dC) in the Z-form. Both the general appearance of the fibres and measurements of helical parameters are in good agreement with models derived from X-ray diffraction.

DNA↗

PubMed2004

Contrast reversal and shape changes of atomic adsorbates measured with scanning tunneling microscopy.

Systematic, quantitative comparisons between scanning tunneling microscopy (STM) experiments and first principles simulations of O(2 x 2)/Ru(0001) have been performed. The shape of the atomic adsorbates in the images depends strongly on the tunneling resistance and changes reversibly from circular (high resistance) to triangular (low resistance). In addition, after adsorption of oxygen on the STM tip we observe a contrast reversal on the surface, confirmed by extensive numerical simulations.

Journal Article↗

PubMed2004

Novel water overlayer growth on Pd(111) characterized with scanning tunneling microscopy and density functional theory.

Scanning tunneling microscopy (STM) images of water submonolayers on Pd(111) reveal quasiperiodic and isolated adclusters with internal structure that would ordinarily be ascribed to icelike puckered hexagonal units. However, density functional theory and STM simulations contradict this conventional picture, showing instead that the water adlayers are composed mainly of flat-lying molecules arranged in planar water hexagons. A new rule for two dimensional (2D) water growth is offered that generates the structures observed experimentally from planar hexamer units.

Journal Article↗

PubMed2006

Magnon excitation with spin-polarized scanning tunneling microscopy.

Using spin-polarized scanning tunneling microscopy, the local excitation of magnons in Fe and Co has been studied. A large cross section for magnon excitation was found for bulk Fe samples while for thin Co films on Cu(111) the cross section linearly scales with film thickness. Recording inelastic tunneling spectra with Fe coated W tips in a magnetic field, the magnonic nature of the excitation was proven. Magnon excitation could be detected without the use of a separating insulating layer opening up the possibility to directly study magnons in magnetic nanostructures via spin-polarized currents.

Journal Article↗

PubMed1992

Scanning tunnelling microscopy observations of biomolecules on layered materials.

Scanning tunnelling microscopy (STM) has been performed on the reverse transcriptases of the human immunodeficiency virus (HIV-1) and the moloney murine leukaemia virus (MuLV). The biological molecules are adsorbed on n-type semiconducting MoTe2. The p66 (66 kD) subunit of the RT of HIV-1 is imaged by STM. Both STM and processed transmission electron microscopy (TEM) data show a spherical and horseshoe-like shape of external diameter ca. 65 A, depending on the angle of observation. The STM results show a larger diameter which is related to the curvature radius of the tip of the probing needle. The RTs of HIV-1 and MuLV exhibit a circular hole of ca. 20 A diameter in accordance with structure predictions and functioning considerations. The surface-molecule interaction is discussed in terms of the electronic properties of the semiconductor surface including the influence of small defect sites at the layered crystal surface.

Dialysis↗