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PubMed1992

Scanning tunneling microscopy of biological macromolecular structures coated with a conducting film.

We have studied the capability of scanning tunneling microscopy (STM) to reveal the three-dimensional structure of biological macromolecular structures that have been rendered conductive by metal-coating. The sample preparation used has been derived from a well established method in transmission electron microscopy (TEM). It includes adsorption, freezing and dehydration by vacuum-sublimation, followed by metal-shadowing of the specimen. As an alternative to adsorption and coating, fluid biomaterials can be replaced by conductive freeze-fracture replica. We give an introduction into the sample preparation of metal-coated specimens and discuss how each step can affect the structural preservation and thereby the quality of the data. Some aspects of the data acquisition and the quantitative evaluation of STM data are shown. Possible contributions of STM in the biological macromolecular research are pointed out.

Animals↗
PubMed2000

Scanning tunneling microscopy: a unique tool in the study of chirality, dynamics, and reactivity in physisorbed organic monolayers.

Scanning tunneling microscopy (STM) is applied to study organic monolayers, physisorbed at the liquid-graphite interface. Due to the very local nature of the probing, the structure of these adlayers has been imaged with very high detail. The high resolution allowed us to investigate the effect of molecular chirality on the monolayer formation and provided a unique way to study chemical reactions at the liquid-graphite interface. Making use of a fast scanning mode, dynamic processes in these adlayers have been visualized.

Absorption↗
PubMed1996

Scanning tunneling microscopy study of cytochrome P450 2B4 incorporated in proteoliposomes.

In the present paper, the application of scanning tunneling microscopy in cytochrome P450s membrane topology is discussed. The method enables visualization of heme location in the lipid-bilayer-incorporated protein. It is supposed that the membrane-bound cytochrome P450 on the tunneling microscope substrate should behave as 'molecular diode'. A model explaining the liposome and the proteoliposome images observed is proposed.

Animals↗
PubMed2006

Electronic and geometric properties of Au nanoparticles on Highly Ordered Pyrolytic Graphite (HOPG) studied using X-ray Photoelectron Spectroscopy (XPS) and Scanning Tunneling Microscopy (STM).

Au nanoparticles grown on mildly sputtered Highly Ordered Pyrolytic Graphite (HOPG) surfaces were studied using Scanning Tunneling Microscopy (STM) and X-ray Photoelectron Spectroscopy (XPS). The results were compared with those of Ag nanoparticles on the same substrate. By varying the defect densities of HOPG and the Au coverages, one can create Au nanoparticles in various sizes. At high Au coverages, the structures of the Au films significantly deviate from the ideal truncated octahedral form: the existence of many steps between different Au atomic layers can be observed, most likely due to a high activation barrier of the diffusion of Au atoms across the step edges. This implies that the particle growth at room temperature is strongly limited by kinetic factors. Hexagonal shapes of Au structures could be identified, indicating preferential growth of Au nanostructures along the (111) direction normal to the surface. In the case of Au, XPS studies reveal a weaker core level shift with decreasing particle size compared to the 3d level in similarly sized Ag particles. Also taking into account the Auger analysis of the Ag particles, the core level shifts of the metal nanoparticles on HOPG can be understood in terms of the metal/substrate charge transfer. Ag is (partially) positively charged, whereas Au negatively charged on HOPG. It is demonstrated that XPS can be a useful tool to study metal-support interactions, which plays an important role for heterogeneous catalysis, for example.

Electrochemistry↗
PubMed2002

A scanning tunneling microscopy (STM) investigation of complex formation between cytochrome P450(cam) and putidaredoxin.

We have previously reported the scanning tunnelling microscopy (STM) imaging under buffer of the heme monooxygenase cytochrome P450(cam) from Pseudomonas putida [Faraday Discuss. 116 (2000) 1]. We describe here the adsorption and STM imaging under buffer of complexes of a mutant of cytochrome P450(cam), K344C, and wild-type putidaredoxin (Pdx) on gold(111). The images of Pdx on its own on gold(111) are not uniform, presumably due to multiple orientations of protein adsorption because of the presence of five or more cysteines on the protein surface. STM imaging of a 1:1 mixture of P450(cam)-K344C/Pdx showed a regular array of pairs of different-sized proteins 20-25 A apart arranged in rows across the gold(111) surface which we attribute to the P450(cam)/Pdx complex. The images of the pairs are more regular than those of Pdx on its own, probably as a result of complex formation with P450(cam) partly overcoming the heterogeneity of Pdx adsorption. As far as we are aware this is the first report of STM imaging of a protein/protein complex, and the first direct observation of P450(cam)/Pdx complex formation which is a key step in the catalytic cycle of P450(cam) catalysis. The redox centers of the two proteins are ca. 20 A apart, too far for rapid intracomplex electron transfer. Whether the observed complex is competent for electron transfer or physiologically relevant is not known, and further work is in progress to elucidate the protein-protein interaction.

Camphor 5-Monooxygenase↗
PubMed1993

A scanning tunnelling microscopy study of the formation and chemical activation of step defects on the basal plane of pyrolytic graphite.

Scanning tunnelling microscopy is used to monitor etching of the basal plane of highly orientated pyrolytic graphite by ozone, oxygen and nitric acid. These treatments are seen to produce numerous single and multilayer step defects. Subsequent modification of the graphite sheet edges flanking these cavities by cyanuric chloride, TiCl4 and other reagents is shown to activate the edges, thereby making them capable of covalently binding various molecules.

Acrylates↗
PubMed2005

Scanning tunneling microscopy investigation of the structure of methanethiolate on Ag(111).

Scanning tunneling microscopy (STM) has been used to investigate the structure of the ordered methanethiolate overlayer formed on Ag(111) by reaction at room temperature with dimethyl disulfide. High-resolution images show an ordered structure with three inequivalent atomic-scale protrusions within each ( radical7 x radical7)R19 degrees surface unit mesh which can be reconciled with methanethiolate species on a regular lateral submesh, similar to that proposed in the multilayer ( radical7 x radical7)R19 degrees -S sulfide phase previously reported. STM imaging during dynamic dosing also provides evidence for a significant change in the outermost layer Ag atom density, consistent with a reconstructed surface model. Possible models for this reconstruction are presented and discussed in the light of available information.

Journal Article↗
PubMed2002

Dislocation emission around nanoindentations on a (001) fcc metal surface studied by scanning tunneling microscopy and atomistic simulations.

We present a combined study by scanning tunneling microscopy and atomistic simulations of the emission of dissociated dislocation loops by nanoindentation on a (001) fcc surface. The latter consist of two stacking-fault ribbons bounded by Shockley partials and a stair-rod dislocation. These dissociated loops, which intersect the surface, are shown to originate from loops of interstitial character emitted along the <110> directions and are usually located at hundreds of angstroms away from the indentation point. Simulations reproduce the nucleation and glide of these dislocation loops.

Journal Article↗
PubMed1994

Scanning tunneling microscopy of insulators and biological specimens based on lateral conductivity of ultrathin water films.

Scanning tunneling microscopy is based on the flow of an electrical current and thus cannot be used to directly image insulating material. It has been found, however, that a very thin film of water (about one monolayer) adsorbed to a surface exhibits a surprisingly high conductivity that is sufficient to allow scanning tunneling microscope imaging at currents below 1 picoampere. Hydrophilic insulators, such as glass and mica, can thus be imaged in humid air. The same is true for biological specimens deposited on such surfaces, as demonstrated by the scanning tunneling microscope imaging of plasmid DNA on mica.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1992

Electrostatic spraying of DNA molecules for investigation by scanning tunneling microscopy.

We have investigated electrostatic spraying of DNA onto gold surfaces as an alternative sample-preparation technique for STM studies. Preliminary results show that a higher distribution of isolated strands as well as well ordered aggregates can be obtained with this technique when compared with electrodeposition or drop evaporation. In many places, the well ordered aggregates were found to cleave in a direction perpendicular to their length after repeated scanning in the same direction.

DNA↗
PubMed2001

Scanning tunneling microscopy with chemically modified tips: discrimination of porphyrin centers based on metal coordination and hydrogen bond interactions.

STM gold tips chemically modified with 4-mercaptopyridine (4MP) were found capable of discriminating zinc(II) 5,15-bis(4-octadecyloxyphenyl)porphyrin (Por-Zn) from its metal-free porphyrin (Por-2H) and nickel(II) complexes (Por-Ni) in the mixed monolayers of these compounds, spontaneously formed at the solution/graphite interface. The porphyrin centers in STM images observed with 4MP-modified tips exhibited bright spots, while those measured with unmodified tips exhibited the porphyrin centers as dark depressions. The centers of Por-Zn were brighter than those of Por-2H and Por-Ni, thereby allowing the discrimination of Por-Zn from Por-2H or Por-Ni in mixed monolayers. The changes in the contrasts of porphyrin centers of Por-2H and Por-Zn/ Por-Ni were explained by facilitated electron tunneling due to hydrogen bond and metal coordination interactions, respectively, between porphyrin centers and the pyridyl group of 4MP on the tip.

Hydrogen Bonding↗
PubMed2006

Scanning tunneling microscopy of ethylated Si(111) surfaces prepared by a chlorination/alkylation process.

Scanning tunneling microscopy (STM) and computational modeling have been used to study the structure of ethyl-terminated Si(111) surfaces. The ethyl-terminated surface was prepared by treating the H-terminated Si(111) surface with PCl5 to form a Cl-terminated Si(111) surface with subsequent exposure to C(2)H(5)MgCl in tetrahydrofuran to produce an alkylated Si(111) surface. The STM data at 77 K revealed local, close-packed, and relatively ordered regions with a nearest-neighbor spacing of 0.38 nm as well as disordered regions. The average spot density corresponded to approximately 85% of the density of Si atop sites on an unreconstructed Si(111) surface. Molecular dynamics simulations of a Si(111) surface randomly populated with ethyl groups to a total coverage of approximately 80% confirmed that the ethyl-terminated Si(111) surface, in theory, can assume reasonable packing arrangements to accommodate such a high surface coverage, which could be produced by an exoergic surface functionalization route such as the two-step chlorination/alkylation process. Hence, it is possible to consistently interpret the STM data within a model suggested by recent X-ray photoelectron spectroscopic data and infrared absorption data, which indicate that the two-step halogenation/alkylation method can provide a relatively high coverage of ethyl groups on Si(111) surfaces.

Journal Article↗