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Scanning tunneling microscopy of a wheat seed storage protein reveals details of an unusual supersecondary structure.

Scanning tunneling microscopy has been used to demonstrate that a spiral structure based on beta-reverse turns is adopted by the repeat sequences present in a group of wheat gluten proteins. This structure is similar to the beta-spiral formed by a synthetic polypentapeptide based on a repeat sequence present in elastin. Wheat gluten and elastin are both elastomeric and it is possible that the spiral structure contributes to this property.

Journal Article↗

Adsorption structures of benzene on a Si(5 5 12)-2x1 surface: a combined scanning tunneling microscopy and theoretical study.

In the first ever attempt to study the adsorption of organic molecules on high-index Si surfaces, we investigated the adsorption of benzene on Si(5 5 12)-(2x1) by using variable-low-temperature scanning tunneling microscopy and density-functional theory (DFT) calculations. Several distinct adsorption structures of the benzene molecule were found. In one structure, the benzene molecule binds to two adatoms between the dimers of D3 and D2 units in a tilted butterfly configuration. This structure is produced by the formation of di-sigma bonds with the substrate and of two C[Double Bond]C double bonds in the benzene molecule. In another structure, the molecule adsorbs on honeycomb chains with a low adsorption energy because of strain effects. Our DFT calculations predict that the adsorption energies of benzene are 1.03-1.20 eV on the adatoms and 0.22 eV on the honeycomb chains.

Adsorption↗

Scanning tunnelling microscopy of collagen I reveals filament bundles to be arranged in a left-handed helix.

Collagen I is the most abundant protein found in the body. Its quaternary structure has been extensively characterised and consists of filaments arranged into bundles. In this study we used scanning tunnelling microscopy to image the collagen I filaments and fibrils directly. The images suggested that filaments are arranged into a left-handed helical structure with a periodicity of about 10nm. Such a structure potentially adds increased tensile strength to the collagen fibrils.

Animals↗

Scanning tunneling microscopy of sulfur and benzenethiol chemisorbed on Ru(0001) in 0.1 M HClO4.

In situ scanning tunneling microscopy (STM) combined with linear sweep voltammetry was used to examine spatial structures of sulfur adatoms (SA) and benzenethiol (BT) molecules adsorbed on an ordered Ru(0001) electrode in 0.1 M HClO4. The Ru(0001) surface, prepared by mechanical polishing and electrochemical reduction at -1.5 V (vs RHE) in 0.1 M HClO4, contained atomically flat terraces with an average width of 20 nm. Cyclic voltammograms obtained with an as-prepared Ru(0001) electrode in 0.1 M HClO4 showed characteristics nearly identical to those of Ru(0001) treated in high vacuum. High-quality STM images were obtained for SA and BT to determine their spatial structures as a function of potential. The structure of the SA adlayer changed from (2 x mean square root of 3)rect to domain walls to (mean square root of 7 x mean square root of 7)R19.1 degrees and then to disordered as the potential was scanned from 0.3 to 0.6 V. In contrast, molecules of BT were arranged in (2 x mean square root of 3)rect between 0.1 and 0.4 V, while they were disordered at all other potentials. Adsorption of BT molecules was predominantly through the sulfur headgroup. Sulfur adatoms and adsorbed BT molecules were stable against anodic polarization up to 1.0 V (vs RHE). These two species were adsorbed so strongly that their desorption did not occur even at the onset potential for the reduction of water in 0.1 M KOH.

Journal Article↗

Self-assembly of [Et,Et]-bacteriochlorophyll cF on highly oriented pyrolytic graphite revealed by scanning tunneling microscopy.

The chlorosomal light-harvesting antennae of green phototrophic bacteria consist of large supramolecular aggregates of bacteriochlorophyll c (BChl c). The supramolecular structure of (3(1)-R/S)-BChl c on highly oriented pyrolytic graphite (HOPG) and molybdenum disulfide (MoS2) has been investigated by scanning tunneling microscopy (STM). On MoS2, we observed single BChl c molecules, dimers or tetramers, depending on the polarity of the solvent. On HOPG, we observed extensive self-assembly of the dimers and tetramers. We propose C=O...H-O...Mg bonding networks for the observed dimer chains, in agreement with former ultraviolet-visible and infrared spectroscopic work. The BChl c moieties in the tetramers are probably linked by four C=O...H-O hydrogen bonds to form a circle and further stabilized by Mg...O-H bondings to underlying BChl c layers. The tetramers form highly ordered, distinct chains and extended two-dimensional networks. We investigated semisynthetic chlorins for comparison by STM but observed that only BChl c self-assembles to well-structured large aggregates on HOPG. The results on the synthetic chlorins support our structure proposition.

Bacterial Proteins↗

Monolayer assemblies of a de novo designed 4-alpha-helix bundle carboprotein and its sulfur anchor fragment on Au(111) surfaces addressed by voltammetry and in situ scanning tunneling microscopy.

Mapping and control of proteins and oligonucleotides on metallic and nonmetallic surfaces are important in many respects. Electrochemical techniques based on single-crystal electrodes and scanning probe microscopies directly in aqueous solution (in situ SPM) have recently opened perspectives for such mapping at a resolution that approaches the single-molecule level. De novo design of model proteins has evolved in parallel and holds promise for testing and controlling protein folding and for new tailored protein structural motifs. In this report we combine these two strategies. We present a scheme for the synthesis of a new 4-alpha-helix bundle carboprotein built on a galactopyranoside derivative with a thiol anchor aglycon suitable for surface immobilization on gold. The carboprotein with thiol anchor in monomeric and dimeric (disulfide) form, the thiol anchor alone, and a sulfur-free 4-alpha-helix bundle carboprotein without thiol anchor have been prepared and investigated for comparison. Cyclic and differential pulse voltammetry (DPV) of the proteins show desorption peaks around -750 mV (SCE), whereas the thiol anchor desorption peak is at -685 mV. The peaks are by far the highest for thiol monomeric 4-alpha-helix bundle carboprotein and the thiol anchor. This pattern is supported by capacitance data. The DPV and capacitance data for the thiolated 4-alpha-helix bundle carboproteins and the thiol anchor hold a strong Faradaic reductive desorption component as supported by X-ray photoelectron spectroscopy. The desorption peak of the sulfur-free 4-alpha-helix bundle carboprotein, however, also points to a capacitive component. In situ scanning tunneling microscopy (in situ STM) of the thiol anchor discloses an adlayer with small domains and single molecules ordered in pin-striped supramolecular structures. In situ STM of thiolated 4-alpha-helix bundle carboprotein monomer shows a dense monolayer in a broad potential range on the positive side of the desorption potential. The coverage decreases close to this potential and single-molecule structures become apparent. The in situ STM contrast is also strengthened, indicative of a new redox-based tunneling mechanism. The data overall suggest that single-molecule mapping of natural and synthetic proteins on well-characterized surfaces by electrochemistry and in situ STM is within reach.

Amino Acid Sequence↗

Scanning tunneling microscopy and spectroscopy of donor-acceptor-donor triads at the liquid/solid interface.

By means of scanning tunneling microscopy (STM), the self-assembly of two organic donor-acceptor-donor triads (donor=oligo(p-phenylene vinylene) (OPV); acceptor=perylene diimide (PDI)) and their mixtures has been investigated at the liquid/solid interface. Both triads differ in the nature of the substituents and, therefore, in the redox properties of the central perylene diimide unit (H or Cl). Thanks to the submolecular resolution, the distinct electronic properties of the units, within a triad and between the two triads, are reflected by the relative STM contrast in the bias-dependent imaging experiments. Moreover, scanning tunneling spectroscopy reveals an inverse rectifying behavior of the OPV and H-substituted PDI units, which is discussed in the framework of quasi-resonant tunneling. A striking difference is observed for the Cl-substituted triad.

Journal Article↗

Determination of surface topography of biological specimens at high resolution by scanning tunnelling microscopy.

Although techniques are available for the determination of the three-dimensional structure of biological specimens, for example scanning electron microscopy, they all have some serious drawback, such as low resolution, the requirement for crystals or for the sample to be analysed in a high vacuum. In an attempt to develop a technique for high-resolution three-dimensional structure analysis of non-crystalline biological material, we have tested the applicability of scanning tunnelling microscopy (STM), a method that has been used successfully in the analysis of metal and semiconductor surface structures. We report here that scanning tunnelling electron microscopy can be used to determine the surface topography of biological specimens at atmospheric pressure and room temperature, giving a vertical resolution of the order of 1 A. Our results show that quantum mechanical tunnelling of electrons through biological material is possible provided that the specimen is deposited on a conducting surface.

Atmospheric Pressure↗

Atomic-scale scanning tunneling microscopy study of plasma-oxidized ultrahigh-modulus carbon fiber surfaces.

In the present work, scanning tunneling microscopy (STM) was employed to study the surface modification of ultrahigh modulus carbon fibers at the atomic level by oxygen plasma. As detected by STM, the distinctive feature of the fresh, untreated surface was the general presence of atomic-scale arrangements in different degrees of order (from atomic-sized spots without a clearly ordered disposition to triangular patterns identical to those typical of perfect graphite). Following fiber exposure to the plasma, the STM images showed evidence of the abstraction of carbon atoms from random locations on the fiber surface, giving rise to the development of defects (i.e., structural disorder), which in turn were the places where oxygen could be introduced during and after the plasma etching. It was observed that the most effective treatments in terms of extent of surface structural modification (disordering) and uniform introduction of oxygen were those carried out for just a few ( approximately 3) minutes. Considerably shorter exposures failed to provide a homogeneous modification and many locations on the fiber surface remained unaltered, retaining their original atomic-scale order, whereas longer treatments did not bring about further structural changes to the surface and only led to fiber consumption. These results are consistent with previous X-ray photoelectron spectroscopy measurements on these fibers and provide an atomic-level understanding of the saturation effect observed in the surface oxygen concentration of this and other types of carbon fibers with plasma oxidation. Such understanding may also prove helpful for the accurate control and optimization of fiber-matrix interaction in composite materials.

Journal Article↗

Solid-state quantum computer based on scanning tunneling microscopy.

We propose a solid-state nuclear-spin quantum computer based on application of scanning tunneling microscopy (STM) and well-developed silicon technology. It requires the measurement of tunneling-current modulation caused by the Larmor precession of a single electron spin. Our envisioned STM quantum computer would operate at the high magnetic field (approximately 10 T) and at low temperature approximately 1 K.

Journal Article↗

Scanning tunneling microscopy and surface simulation of zinc-blende GaN(001) intrinsic 4x reconstruction: linear gallium tetramers?

Scanning tunneling microscopy images confirm electron diffraction studies that the zinc-blende GaN(001)-4x reconstruction consists of rows aligned along [110] with a spacing along [110] of 4a. Dual-bias imaging shows a 180 degree shift of the corrugation maximum position between the profiles of empty and occupied states, in agreement with surface simulations based on the 4 x 1 linear tetramer model of Neugebauer et al. [Phys. Rev. Lett. 80, 3097 (1998)]. Electronic structure calculations predict a surface band gap of 1.1 eV, close to the measured value of 1.14 eV and the previously predicted value (1.2 eV). Despite the successes of this model, high-resolution images reveal an unexpected 3x periodicity (not seen in diffraction) along the [110] row direction, indicating the need for a 4 x 3 model, and putting into question the existence of linear Ga tetramers.

Journal Article↗

Chiral recognition in dimerization of adsorbed cysteine observed by scanning tunnelling microscopy.

Stereochemistry plays a central role in controlling molecular recognition and interaction: the chemical and biological properties of molecules depend not only on the nature of their constituent atoms but also on how these atoms are positioned in space. Chiral specificity is consequently fundamental in chemical biology and pharmacology and has accordingly been widely studied. Advances in scanning probe microscopies now make it possible to probe chiral phenomena at surfaces at the molecular level. These methods have been used to determine the chirality of adsorbed molecules, and to provide direct evidence for chiral discrimination in molecular interactions and the spontaneous resolution of adsorbates into extended enantiomerically pure overlayers. Here we report scanning tunnelling microscopy studies of cysteine adsorbed to a (110) gold surface, which show that molecular pairs formed from a racemic mixture of this naturally occurring amino acid are exclusively homochiral, and that their binding to the gold surface is associated with local surface restructuring. Density-functional theory calculations indicate that the chiral specificity of the dimer formation process is driven by the optimization of three bonds on each cysteine molecule. These findings thus provide a clear molecular-level illustration of the well known three-point contact model for chiral recognition in a simple bimolecular system.

Cysteine↗

Spin-polarized scanning tunneling microscopy: insight into magnetism from nanostructures to atomic scale spin structures.

The system of Fe on W(001) is investigated using spin-integrated as well as spin-resolved scanning tunneling microscopy (STM). This study ranges from three-dimensional Fe islands down to the Fe monolayer and different growth modes are observed related to the preparation temperature. With scanning tunneling spectroscopy (STS), a layer-dependent electronic structure is observed that can easily be used to assign the local coverage to the investigated sample areas. Spin-resolved measurements of the ferromagnetic layers in the pseudomorphic regime immediately reveal the fourfold magnetic in-plane anisotropy. A direct comparison of the observed arrangement of the domains of the exposed layers shows a rotation of the easy axis from the fourth to the third monolayer and a collinear magnetic alignment of third and second monolayer. This is confirmed by the quantitative analysis of the layer-resolved intensities of differential tunneling conductance. The first monolayer does not show a magnetic component parallel to the surface but has a perpendicular anisotropy. For this layer, measurements with an applied magnetic field prove a c(2x2) antiferromagnetic structure, i.e., a checkerboard arrangement of spins.

Anisotropy↗

Probing charge transport at the single-molecule level on silicon by using cryogenic ultra-high vacuum scanning tunneling microscopy.

A cryogenic variable-temperature ultra-high vacuum scanning tunneling microscope is used for measuring the electrical properties of isolated cyclopentene molecules adsorbed to the degenerately p-type Si(100)-2x1 surface at a temperature of 80 K. Current-voltage curves taken under these conditions show negative differential resistance at positive sample bias, in agreement with previous observations at room temperature. Because of the enhanced stability of the scanning tunneling microscope at cryogenic temperatures, repeated measurements can be routinely taken over the same molecule. Taking advantage of this improved stability, we show that current-voltage curves on isolated cyclopentene molecules are reproducible and possess negligible hysteresis for a given tip-molecule distance. On the other hand, subsequent measurements with variable tip position show that the negative differential resistance voltage increases with increasing tip-molecule distance. By using a one-dimensional capacitive equivalent circuit and a resonant tunneling model, this behavior can be quantitatively explained, thus providing insight into the electrostatic potential distribution across a semiconductor-molecule-vacuum-metal tunnel junction. This model also provides a quantitative estimate for the alignment of the highest occupied molecular orbital of cyclopentene with respect to the Fermi level of the silicon substrate, thus suggesting that this experimental approach can be used for performing chemical spectroscopy at the single-molecule level on semiconductor surfaces. Overall, these results serve as the basis for a series of design rules that can be applied to silicon-based molecular electronic devices.

Electron Transport↗

Coated silica tips for use in high-pressure, high-temperature, scanning tunneling microscopy.

A novel application of coated silica tips for use in high-pressure, high-temperature, scanning tunneling microscopy is introduced. Thermal drift is reduced in the Z-direction due to the low thermal expansion of silica. Virtually, any conducting material that can be evaporated or sputtered can be used as a tip material. Experimental results are shown for tips sputter coated with platinum, along with images obtained.

Journal Article↗

Dissociation mechanism of 2-propanol on a Si(111)-(7x7) surface studied by scanning tunneling microscopy.

Adsorption of 2-propanol, (CH3)2CHOH, on a Si(111)-7x7 surface was studied by scanning tunneling microscopy. (CH3)2CHOH adsorbs equally on the faulted and unfaulted half unit cells by forming Si-OCH(CH3)2 and Si-H on an adatom and rest atom pair. Si-OCH(CH3)2 is consecutively increased in each half unit cell, and the adsorption is saturated when every half unit cell has three Si-OCH(CH3)2, which corresponds to 0.5 of the adatom coverage. The sticking probability for the dissociation of (CH3)2CHOH is independent of the adatom coverage from 0 to 0.4, but it depends on coverage at higher than 0.4. By counting the darkened adatoms, Si-OCH(CH3)2 on the center adatom (m) and that on the corner adatom (n), it was found the m/n ratio is ca. 4 for the first dissociation of (CH3)2CHOH in virgin half unit cell, but it becomes ca. 1.9 and 1.8 when two and three Si-OCH(CH3)2 are contained in a half unit cell. This result reveals that the dissociation probability of (CH3)2CHOH at the adatom-rest atom pair site is influenced by the nearest Si-OCH(CH3)2 in the half unit cell.

Journal Article↗

Hydrogen adatoms on TiO2(110)-(1x1) characterized by scanning tunneling microscopy and electron stimulated desorption

Hydrogen atoms adsorbed on TiO2(110)-(1x1) surfaces have been characterized by scanning tunneling microscopy (STM) combined with electron stimulated desorption (ESD) technique. Certain amounts of H atoms are unexpectedly found on the TiO2 surfaces annealed at 900 K. Two forms of adsorption were discriminated in STM images from the different sensitivity to ESD and tentatively assigned to hydroxyl-type (O-H) and hydride-type (Ti-H) species.

Journal Article↗

Scanning tunnelling microscopy and dynamic contact angle studies of the effects of partial denaturation on immunoassay solid phase antibody.

A range of partial denaturation antibody pre-treatments that affect immunoassay performance have been evaluated. Monoclonal anti-ferritin antibody was either partially denatured by heat, urea or pH pre-treatment or left untreated and then passively adsorbed to polystyrene microtiter wells. The adsorption characteristics and functionality of the different surfaces produced have been evaluated by dynamic contact angle (DCA) analysis and scanning tunnelling microscopy (STM) imaging respectively. The DCA data show that the effect of partial denaturation is to change the wetting characteristics of the antibody surfaces, while, in addition, STM imaging reveals marked effects seen in the aggregation properties of the denatured antibodies.

Adsorption↗