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PubMed2006

Scanning tunneling microscopy and scanning tunneling spectroscopy studies of planar and nonplanar naphthalocyanine on graphite (0001). Part 2: tip-sample distance-dependent I-V spectroscopy.

Tip-sample distance-dependent current-voltage tunneling spectroscopy on monolayers of base-free naphthalocyanine (Nc), a planar molecule, and tin-naphthalocyanine (SnNc), a nonplanar molecule, has been studied on a freshly cleaved highly oriented pyrolytic graphite (HOPG) surface using a variable-temperature STM at 50 K under ultra-high vacuum conditions. The current-voltage curves show an unsymmetrical diode-like nature especially at large tip-sample distances in both cases. Normalized differential conductivity of all spectra has been considered for further analysis. The ionization and electron affinity levels are compared with the single-molecule local density of states (LDOS) near the Fermi energy using a theoretical calculation for Nc and SnNc. A tip-sample distance-dependent highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap shrinking is observed in the case of Nc, in which the filled levels of the molecules are pinned while the unfilled levels near the Fermi energy are shifting toward lower energy. In contrast, there is no such HOMO-LUMO gap shrinking in the case of the SnNc decreasing tip-sample distance. However, a subsequent increase in the tunneling current was observed by almost 1 order of magnitude compared with Nc. A model is proposed to explain this phenomenon where the Nc-graphite interface is considered as a pure capacitive interface.

Journal Article↗
PubMed1989

Images of single-stranded nucleic acids by scanning tunnelling microscopy.

The scanning tunnelling microscope has the potential to resolve the structure of biological molecules with atomic detail. Progress has been made in the imaging of dried, unshadowed double helices of DNA4-7 and in recording images of DNA under water. Also, images of unshadowed complexes of DNA with the RecA protein from Escherichia coli indicate that this technique may not be restricted to thin biological samples. Here we present images of polydeoxyadenylate molecules aligned in parallel, with their bases lying flat on a surface of highly oriented pyrolytic graphite and with their charged phosphodiester backbones protruding upwards. Based on these images, a molecular model has been built which suggests the presence of a hydrogen bond that could stabilize the parallel alignment. Our micrographs demonstrate the potential application of scanning tunnelling microscopy in structural studies of nucleic acids and provide evidence that it could be used to sequence DNA.

Adsorption↗
PubMed2005

Supramolecular structures of coronene and alkane acids at the Au(111)-solution interface: a scanning tunneling microscopy study.

Scanning tunneling microscopy (STM) is utilized to study the solution-solid interface formed between Au(111) and solutions of coronene in hexanoic, heptanoic, and octanoic acids. In all three cases adsorbed coronene is observed and lays flat on the metal surface. Heptanoic and hexanoic acid solutions produce a hexagonal symmetry monolayer. For the heptanoic and hexanoic cases, dipole-image dipole interactions and H bonding stabilize a surface structure in which 12 acid molecules surround each coronene and produce a coronene spacing of 1.45 nm. In the case of octanoic acid as solvent, the incorporation of the solvent into the monolayer is not as strongly favored. The coronene spacing can range from close-packed (1.2 nm) with no solvent presumed present in the monolayer, to 1.50 nm with up to 12 solvent molecules surrounding each coronene. The close-packed regions have hexagonal symmetry, as do those with the largest (1.5 nm) spacing. Heptanoic acid solutions give the clearest STM images and are associated with the most stable two-component monolayer. The present paper demonstrates that non-covalent interactions at the solution-metal interface can lead to complex multicomponent monolayer structures.

Journal Article↗
PubMed2005

Direct observation of geometrical phase transitions in mesoscopic superconductors by scanning tunneling microscopy.

Using scanning tunneling microscopy, we mapped the distribution of the local density of states in a single crystal superconductor heterostructure with an array of submicron normal metal islands. We observe the coexistence of strongly interacting multiquanta vortex lattice with interstitial Abrikosov vortices. The newly formed composite magnetic flux structure undergoes a series of phase transitions between different topological configuration states. The vortex configuration states are strongly dependent on the number of flux quanta and the nanoscale confinement architecture of the mesoscopic superconductor. Here, we present images of vortex phase transitions due to confinement effects when the number of magnetic flux quanta in the system changes. The vortex dynamics in these systems could serve as a model for behavior of confined many-body systems when the number of particles changes.

Journal Article↗
PubMedDate not supplied

Combined atomic force microscopy and scanning tunneling microscopy imaging of cross-sectioned GaN light-emitting diodes.

Cross-sectional scanning tunneling microscopy (STM) was combined with atomic force microscopy (AFM) over the same area to characterize a cross-sectioned GaN light emitting diode. Because GaN is typically grown on a non-native substrate and also forms a wurtzite crystal structure, a cryogenic cleaving technique was developed to generate smooth surfaces. The depletion region surrounding the p-n junction was clearly identified using STM. Furthermore, by imaging under multiple sample biases, distinctions between the n-doped and p-doped GaN could be made.

Journal Article↗
PubMedDate not supplied

Characterization of reflection scanning near-field optical microscopy and scanning tunnelling optical microscopy/photon scanning tunnelling microscopy working in preliminary approach constant height scanning mode.

The resolution in near-field images is currently determined by the visual inspection of recorded images. One of the major questions in near-field optical microscopy is 'what resolution can be reached, the tip-to-sample distance being known?' This knowledge is critical when choosing the scanning step and the distance between the tip and the sample, in a preliminary scan. This preliminary scan is often the only way to detect the interesting parts of the sample, with limited risk of tip crash and topographical artefacts. The method proposed here needs two scans of the same area, of the same sample, in constant height mode, recorded at two tip-to-sample distances. The pseudotransfer function is the ratio of the Fourier transform of these two data maps. This function enables the evaluation of the limit of resolution. Theoretical considerations are introduced to assess the method.

Journal Article↗
PubMed1994

Atomic force microscopy and scanning tunnelling microscopy: refining techniques for studying biomolecules.

The scanning tunnelling microscope and the atomic force microscope offer the prospect of real-time, nanometre-scale imaging of biomolecules and biosurfaces under physiological environments. Much effort is therefore being made to establish these techniques as routine biophysical tools. The considerable recent progress that has been made in biotechnological applications is reviewed, highlighting specific examples of the applications of this new and exciting method of analysis.

Biological Products↗
PubMed1994

A study of lignin formation at the molecular level by scanning tunneling microscopy.

A scanning tunneling microscope (STM) was used to observe the temporal formation and organization of dehydrogenative polymer (DHP) synthesized from coniferyl alcohol. The images obtained elucidate this structure for the first time. The structure of DHP, as seen from STM images, shows long-range order. It appears that DHP consists of building units or modules assembled into larger assemblies called supermodules. Supermodules are interconnected into the overall lattice-like polymer structure with or without spherical regions. One module consists of about 20 monomers, while the supermodule contains about 500 monomers. Calculated molecular weights for modules and supermodules agree with DHP molecular weight distribution peaks. Samples prepared at two different pH values, 6.4 and 7.6, have the same characteristics. The results presented demonstrate that the process of lignification, even in in vitro conditions, is highly ordered, and as such contribute to our understanding of the structure of lignin, a significant constitutive and functional element of cell walls.

Hydrogen-Ion Concentration↗
PubMed1990

Atomic-scale imaging of DNA using scanning tunnelling microscopy.

The scanning tunnelling microscope (STM) has been used to visualize DNA under water, under oil and in air. Images of single-stranded DNA have shown that submolecular resolution is possible. Here we describe atomic-resolution imaging of duplex DNA. Topographic STM images of uncoated duplex DNA on a graphite substrate obtained in ultra-high vacuum are presented that show double-helical structure, base pairs, and atomic-scale substructure. Experimental STM profiles show excellent correlation with atomic contours of the van der Waals surface of A-form DNA derived from X-ray crystallography. A comparison of variations in the barrier to quantum mechanical tunnelling (barrier-height) with atomic-scale topography shows correlation over the phosphate-sugar backbone but anticorrelation over the base pairs. This relationship may be due to the different chemical characteristics of parts of the molecule. Further investigation of this phenomenon should lead to a better understanding of the physics of imaging adsorbates with the STM and may prove useful in sequencing DNA. The improved resolution compared with previously published STM images of DNA may be attributable to ultra-high vacuum, high data-pixel density, slow scan rate, a fortuitously clean and sharp tip and/or a relatively dilute and extremely clean sample solution. This work demonstrates the potential of the STM for characterization of large biomolecular structures, but additional development will be required to make such high resolution imaging of DNA and other large molecules routine.

Animals↗
PubMed2004

Oriented immobilization of Pseudomonas putida putidaredoxin at a gold (111)-buffer interface: a real time scanning tunnelling microscopy study.

A scanning tunnelling microscopy study of adsorption of wild-type Pseudomonas putida putidaredoxin at a gold (111)-buffer interface has been made in real time. Reversible adsorption has been observed reflecting weak interaction of the wild-type protein with a gold (111) electrode. A genetically engineered mutant, C73S-D58C, which contains a surface thiol, has been used for 'immobilization' and 'orientated adsorption' on the gold surface. The implication of such orientated immobilization in development of a bio-electrode surface has been predicted.

Adsorption↗
PubMed1998

Single-molecule high-resolution structure and electron conduction of photosystem II from scanning tunneling microscopy and spectroscopy.

Scanning tunneling microscopy (STM) and spectroscopy (STS) were used to obtain the first direct high resolution ( approximately 0.3 nm) images of single isolated Photosystem II (PS II) molecules, and to determine the supramolecular organization of oxygen-evolving PS II core complexes and PS II membrane fragments including the identification, assignment, location and dimensions of the polypeptide units. Our results predict a unique structural model which we then compare with alternative models. We show that the combination of quasi-constant-height mode STM operation, STS and suitable choice of sample-substrate preparations can be used to enable investigation of the structure and function of single PS II particles under normal thermodynamic and hydration conditions without the requirement and complications of ordered PS II arrays or crystals. STS was also used to characterize single-molecule electron conduction and tunneling mechanisms in PS II including the semiconduction and photoconduction behavior of the reaction center and photoexcitation effects in the light-harvesting complex LHC II.

Electron Transport↗
PubMed2004

High-resolution scanning tunneling microscopy for molecules.

Scanning tunneling microscopy (STM) can detect individual molecular configuration with its high spatial resolution ability, but some intrinsical and extrinsic factors result in the complexities of STM imaging of single molecules. By combining STM experimental work and theoretical simulation with the local density approximation based on Bardeen perturbation method, we have explored the atomic-scale configuration of the following molecular systems: C(60) molecules adsorbed on Si(111)-(7x7); alkanethiol self-assembly monolayers on Au(111); C(60) molecule imaged by STM tip adsorbed with another C(60) molecule; O(2) molecule adsorbed on Ag(110) and CO molecule adsorbed on Cu(111) imaged by CO chemically modified STM tip. Some related problems including: molecule-substrate interactions, STM imaging mechanism, chemically modified STM tip, etc., are discussed.

Journal Article↗
PubMed2005

Role of the anion in the underpotential deposition of cadmium on a Rh(111) electrode: probed by voltammetry and in situ scanning tunneling microscopy.

In situ scanning tunneling microscopy (STM) and cyclic voltammetry (CV) were employed to examine the underpotential deposition (UPD) of cadmium on a rhodium(111) electrode in sulfuric and hydrochloric acids. The (bi)sulfate and chloride anions in the electrolytes played a main role in controlling the number and arrangement of Cd adatoms. Deposition of Cd along with hydrogen adsorption occurred near 0.1 V (vs reversible hydrogen electrode) in either 0.05 M H2SO4 or 0.1 M HCl containing 1 mM Cd(ClO4)2. These coupled processes resulted in an erroneous coverage of Cd adatoms. The process of Cd deposition shifted positively to 0.3 V and thus separated from that of hydrogen in 0.05 M H2SO4 containing 0.5 M Cd2+. The amount of charge (80 microC/cm2) for Cd deposition in 0.5 M Cd2+ implied a coverage of 0.17 for the Cd adatoms, which agreed with in situ STM results. Regardless of [Cd2+], in situ STM imaging revealed a highly ordered Rh(111)-(6 x 6)-6Cd + HSO4- or SO42- structure in sulfuric acid,. In hydrochloric acid, in situ STM discerned a (2 x 2)-Cd + Cl structure at potentials where Cd deposition commenced. STM atomic resolution showed roughly one-quarter of a monolayer of Cd adatoms were deposited, ca. 50% more than in sulfuric acid. Dynamic in situ STM imaging showed potential dependent, reversible transformations between the (6 x 6) Cd adlattices and (square root 3 x square root 7)-(bi)sulfate structure, and between (2 x 2) and (square root 7 x square root 7)R19.1 degrees -Cl structures. The fact that different Cd structures observed in H2SO4 and HCl entailed the involvement of anions in Cd deposition, i.e. (bi)sulfate and chloride anions were codeposited with Cd adatoms on Rh(111).

Journal Article↗
PubMed2004

Elucidation of the deposition processes and spatial structures of alkanethiol and arylthiol molecules adsorbed on Pt111 electrodes with in situ scanning tunneling microscopy.

In situ scanning tunneling microscopy (STM) was used to examine the spatial structures of n-alkane thiols (1-hexanethiol, 1-nonanethiol, and 1-octahexanethiol) and arylthiols (benzenethiol and 4-hydroxybenzenethiol) adsorbed on well-ordered Pt111 electrodes in 0.1 M HClO4. The electrochemical potential and molecular flux were found to be the dominant factors in determining the growth mechanisms, final coverages, and spatial structures of these organic adlayers. Depending on the concentrations of the thiols, deposition of self-assembled monolayers (SAMs) followed either the nucleation-and-growth mechanism or the random fill-in mechanism. Low and high thiol concentrations respectively produced two ordered structures, (2 x 2) and (square root of 3 x square root of 3)R30 degrees , between 0.05 and 0.3 V. On average, an ordered domain spanned 500 A when the SAMs were made at 0.15 V, but this dimension shrank substantially once the potential was raised above 0.3 V. This potential-induced order-to-disorder phase transition resulted from a continuous deposition of thiols, preferentially at domain boundaries of (square root of 3 x square root of 3 x )R30 degrees arrays. All molecular adlayers were completely disordered by 0.6 V, and this restructuring event was irreversible with potential modulation. Since all thiols were arranged in a manner similar to that adopted by sulfur adatoms (Sung et al. J. Am. Chem. Soc. 1997, 119, 194), it is likely that they were adsorbed mainly through their sulfur headgroups in a tilted configuration, irrespective of the coverage. Both the sulfur and phenyl groups of benzenethiol admolecules gave rise to features with different corrugation heights in the molecular-resolution STM images. All thiols were adsorbed strongly enough that they remained intact at a potential as negative as -1.0 V in 0.1 M KOH.

Journal Article↗
PubMed2006

Detailed studies of molecular conductance using atomic resolution scanning tunneling microscopy.

Atomically resolved scanning tunneling microscopy and spectroscopy (STM/STS) have been used to carefully examine the relationship between molecular conductivity and the adsorption state of various organic molecules on silicon surfaces. We show that the particular configuration of styrene and cyclopentene molecules on silicon affects the conductivity of the molecules. Detailed correlation of STM images with point specific current-voltage spectroscopy reveal that observed negative peaks are due to random configuration changes driven by inelastically scattered electrons and not due to tuned alignment of molecule and electrode levels. These random processes, which include molecular rearrangement, desorption, and/or decomposition occur with increasing frequency at larger voltage and current settings.

Journal Article↗
PubMed1991

Application of scanning tunneling microscopy to structural biology.

Scanning tunneling microscopy offers the possibility of visualizing biological molecules in conditions similar to those in vivo with molecular resolution. Images of DNA and various proteins have been obtained, but insufficient conductivity through, and inhomogeneous and unstable adsorption of the biomolecules continue to prevent reliable imaging. Applying a metal coating to samples, to separate the conductivity and deposition problems has yielded satisfactory deposition procedures in various laboratories, but extension of this protocol to high resolution imaging of macromolecules has yet to be demonstrated. In this paper we present a review of the main results obtained in our laboratory, which illustrate the main problems encountered by investigators attempting to image metal-coated and uncoated biological specimens.

DNA↗
PubMed2005

Structural investigation of zeolite-templated, ordered microporous carbon by scanning tunneling microscopy and Raman spectroscopy.

Scanning tunneling microscopy (STM) and Raman spectroscopy have been employed for a detailed structural characterization of an ordered microporous carbon synthesized in the nanochannels of zeolite Y by a templating approach. The carbon exhibited an exceptionally high adsorption capacity together with a long-range structural organization on the nanometer scale. As revealed by STM, this material exhibited both terrace-like and periodic (approximately 1.4 nm) stripe-like nanostructures. The vertical separation between contiguous terraces was measured to be also about 1.4 nm and was thus coincident with the structural periodicity deduced by X-ray diffraction. The terraces of the carbon material were shown to consist of arrays of approximately 1 nm wide carbon clusters. The carbon clusters displayed only a limited degree of local order within the terraces but not long-range periodicity. Likewise, STM indicated that the micropore structure of this carbon originated from the large number of voids that separate adjacent clusters, being morphologically very different from that commonly found in activated carbons. The range of void sizes measured by STM (0.8-2.3 nm) was in complete agreement with the pore size distribution determined from nitrogen adsorption measurements. The origin of the nanostructural features observed for this microporous carbon was discussed on the basis of the surface structure of the zeolite Y template. Finally, Raman spectroscopy provided evidence that the carbon clusters were made up of nanographenes with a curved topology.

Carbon↗