Scanning probe microscopy characterization of gold-chemisorbed poplar plastocyanin mutants

Two poplar plastocyanin mutants adsorbed onto gold electrodes have been characterized at single molecule level by scanning probe microscopy. Immobilization of the two redox metalloprotein mutants on Au(1 1 1) surface was achieved by either a disulphide bridge (PCSS) or a single thiol (PCSH), both the anchoring groups having been introduced by site-directed mutagenesis. Scanning tunneling microscopy (STM) and atomic force microscopy (AFM) analysis gives evidence of a stable and robust binding of both mutants to gold. The lateral dimensions, as estimated by STM, and the height above the gold substrate, as evaluated by AFM, of the two mutants well agree with crystallographic sizes. A narrower height distribution is observed for PCSS compared to PCSH, corresponding to a more homogeneous orientation of the former mutant adsorbed onto gold. Major differences between the mutants are observed by electrochemical STM. In particular, the image contrast of adsorbed PCSS is affected by tuning the external electrochemical potential to the redox levels of the mutant, consistent with some involvement of copper active site in the tunneling process. On the contrary, no contrast variation is observed in electrochemical STM of adsorbed PCSH. Moreover, scanning tunneling spectroscopy experiments reveal asymmetric I–V characteristics for single PCSS proteins, reminiscent of a rectifying-like behaviour, whereas an almost symmetric I–V relation is observed for PCSH.     

Investigations of C60 molecules deposited on Si(111) by noncontact atomic force microscopy

We demonstrated the high resolution imaging of the organic molecules using noncontact atomic force microscopy in ultrahigh vacuum. The sample was C₆₀ molecules deposited on the Si(111)-7×7 reconstructed surface. When the thickness of the C₆₀ film was submonolayer, we could image some isolated C₆₀ molecules and the reconstructed Si surface simultaneously. However, the imaging was highly unstable not only because of the large structure but also due to the large difference between the interaction forces on the molecules and on the Si surface. On the other hand, when the thickness of the C₆₀ molecules was almost monolayer, individual molecules could be stably imaged.     

Adsorption and valence electronic states of nitric oxide on metal surfaces

Among fundamental diatomic molecules, the adsorption of carbon monoxide (CO) and nitric oxide (NO) on metal surfaces has been a subject of intensive research in the surface science community, partly owing to its relevance to heterogeneous catalysis used for environmental control. Compared to the rather well-defined adsorption mechanism of CO, that of NO is less understood because the adsorption results in much more complex reactions. The complexity is ascribed to the open-shell structure of valence electrons, making the molecule readily interact with the metal surface itself as well as with co-adsorbed molecules. Furthermore, the interaction crucially depends on the local structure of the surface. Therefore, to elucidate the interaction at the molecular scale, it is essential to study the valence state as well as the bonding geometry for individual NO molecules placed in a well-defined environment on the surface. Scanning tunneling microscopy (STM) is suitable for this purpose. In this review, we summarize the knowledge about the interaction of NO with metal surfaces, mainly focused on the valence electronic states, followed by recent studies using STM and atomic force microscopy (AFM) at the level of individual molecules.     

Si(1 1 1)-H(1 × 1): A mirror for atoms characterized by AFM, STM, He and H2 diffraction

AFM, STM and diffraction of He and H₂ have been used to assess Si(1 1 1)-H(1 × 1) surfaces for their potential as mirrors for matter-waves. The H-passivated samples are produced by wet-chemical methods and delivered to a different laboratory for diffraction measurements. We show that the surface is flat and homogenous over lateral scales of microns and that absolute He and H₂ reflectivities of the order of ∼3% are obtained, even after 20 h storage under Ar and several days’ storage in UHV. These characteristics allow the use of Si(1 1 1)-H(1 × 1) as a highly reflective mirror for atoms and molecules, with application in a future He microscope or focused hydrogen nano-lithography system.     

STM images from diamond surfaces: steps towards comparisons of experiment and theory

Stable clean and hydrogenated diamond (100) and (111) surface reconstructions found by density functional molecular dynamics (DFMD) are characterized in their surface electronic properties. For sufficiently large surface slab supercells we have calculated the spatially resolved charge densities of the highest occupied surface states at constant height, which are compared with recently obtained images from scanning tunneling microscopy. The calculated charge-density distributions represent signatures of the considered surfaces which might be used to understand and to classify as-grown diamond surfaces.     

STM study of l-serine adsorption on Cu(0 0 1)

The adsorption of l-serine on Cu(0 0 1) surface at 310 K was studied by scanning tunneling microscope (STM). l-serine molecules on the Cu(0 0 1) initially formed a domain of thick lines with a order structure along the direction on the terraces regardless of the coverage of serine. The thick lines were partly replaced by thin line along the direction, and completely disappeared in 2 h. It is considered that in these structures hydrogen bonds involved in hydroxymethyl group between adsorbates play some role in addition to intermolecular hydrogen bond between a hydrogen atom of amino group and an oxygen atom of carboxy group for alanine adsorption.     

STM/STS observation of ferrocene derivative adduct to C60 on HOPG

The C₆₀ONCFn cycloadduct (Fn=ferrocene) was prepared in the reaction between C₆₀ and ferrocene oxime, the ferrocene derivative was bound to C₆₀ at the 6–6 bond by a heterocyclic oxygen–nitrogen–carbon ring; the compound was stable in air. The compound dissolved in dichloroethane was deposited on HOPG and observed by UHV STM/STS methods. The molecules of C₆₀ONCFn formed several-microns-long straight chains with clearly visible adducted groups pointing to one side of the chain. The STM/STS observations are discussed within the terms of semiempirical quantum chemical molecular modeling.     

Interpretation of orientational contrast in STM images of GaAs(1 1 0) cleavage surface

The electronic structure of GaAs(1 1 0) surface is analyzed using Density Functional Theory (DFT-GGA) in atomic orbital basis (LCAO). The surface orbitals and the corresponding local density of electronic states (LDOS) are calculated for purposes of interpreting STM images. We show how local atomic orbitals of surface atoms are related to tunneling channels for electrons in STM imaging. A destructive interference between orbitals of two neighbouring atoms increases the contrast between the two atoms, and this is reflected in directionality of STM patterns of GaAs(1 1 0) surfaces. We also discuss how the basic formalism of Tersoff-Hamann approach to STM simulation can be reformulated to reveal the role of phase difference between tunneling channels.     

Immobilization of protein molecules on step-controlled sapphire surfaces

We have studied effects of surface morphology on immobilization of protein molecules using step-controlled sapphire surfaces. Preferential adsorption of avidin molecules on the step edges was observed on the single-stepped sapphire surface. A randomly-stepped sapphire surface was found to be suitable for high-density immobilization of protein molecules. These results indicate atomic scale structures of the substrate surface influence the adsorption efficiency of the proteins. By using an atomic force microscopy (AFM) equipped with a biotin-modified cantilever, we have confirmed that the immobilized avidin molecules on the substrates keep their biological activity. This means that the ligand-receptor interaction can be detected using the phase image mode of a standard AFM.     

AFM and SEM characterization of non-toxic vanadium-free Ti alloys used as biomaterials

In this work, three titanium alloys have been studied by means of atomic force microscopy (AFM) and scanning electron microscopy (SEM) to determine their surface topography. The alloys investigated were Ti–6Al–7Nb, Ti–13Nb–13Zr, and Ti–15Zr–4Nb, with no presence of the toxic element V, and with a possible use as biomaterials for osteoarticular prostheses. These alloys were studied at room temperature and also after a thermal treatment at 750 °C during 24 h, which produces a protective surface oxide layer. The aim of the present work is to compare the surface structure and morphology of the alloys, both as-received and after the oxide layer was formed at elevated temperature.     

Ab-initio calculations and STM observations on tetrapyridyl and Fe(II)-tetrapyridyl-porphyrin molecules on Ag(1 1 1)

We modelled the adsorption of tetra-pyridyl-porphyrin (TPyP) and Fe(II)-tetra-pyridyl- porphyrin (Fe-TPyP) molecules on Ag(1 1 1). TPyP adsorbs in a flat geometry at a distance of 5.6 Å from the surface. The dihedral angle of the pyridyl rings is found to be 70°. The molecular structure remains largely unaffected by the adsorption. The structure of the molecular adlayer should thus be determined mainly by lateral intermolecular interactions. These conclusions are confirmed by scanning tunnelling microscopy observations. Upon metalation spin-polarized states with strong Fe d-character appear in Fe-TPyP near the centre of the gap between the highest occupied and the lowest unoccupied states of a TPyP molecule. We find also that the gap is widened in the presence of Fe. This implies a shift of 0.3 eV of unoccupied states as identified by scanning tunnelling spectroscopy simulations and confirmed by experimental data.     

Interpretation of scanning tunneling microscopy and atomic force microscopy images of 1T-TiS2

The surface of 1T-TiS₂ was examined by scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The STM and AFM images of this compound were interpreted on the basis of the partial electron density ρ(r,E_F) and total electron density ρ(r) of a slab which consists of six (001) 1T-TiS₂ layers. Electronic structure calculations were performed using the ab-initio Hartree–Fock program crystal. It was found that the bright spots in experimental STM images correspond to sulfur atoms at both positive and negative bias voltages. The AFM image showed a periodicity which can be explained by the atomic corrugation at the surface. Structural defects on the surface were also investigated, and their interpretation constitutes experimental proof that only sulfur atoms were detected by scanning probe microscopies.     

Insight into STM image contrast of n-tetradecane and n-hexadecane molecules on highly oriented pyrolytic graphite

Two-dimensional ordered patterns of n-tetradecane (n-C₁₄H₃₀) and n-hexadecane (n-C₁₆H₃₄) molecules at liquid/graphite interface have been directly imaged using scanning tunneling microscope (STM) under ambient conditions. STM images reveal that the two different kinds of molecules self-organize into ordered lamellar structures in which alkane chains of the molecules extend along one of three equivalent lattice axes of highly oriented pyrolytic graphite (HOPG) basal plane. For n-C₁₄H₃₀ molecules, the molecular axes are observed to tilt by 60° with respect to inter-lamellar trough lines and the carbon backbones of the alkane chains are perpendicular to the HOPG basal plane in an all-trans conformation. However, for n-C₁₆H₃₄ molecules, the molecular axes are perpendicular to lamellar borders (90°) and the planes of the all-trans carbon skeletons are parallel to the graphite basal plane. The results clearly indicate that outmost hydrogen atoms of the alkane chains dominate atom-scaled features of the STM images. That is, in the case of long-chain alkane molecules, topographic effects dominantly determine STM image contrast of the methylene regions of the alkane chains that are adsorbed on HOPG.     

AFM analysis of MgB2 films and nanostructures

For the fabrication of superconducting devices based on nanostructured thin films, the quality of the starting surface is often of crucial importance. For example, the transport properties of superconducting nanobridges are strongly affected by the geometry and the edge definition of the nanostructures. In this work, we report about AFM characterization of magnesium diboride films and nanobridges fabricated in view of application in superconducting electronics. MgB₂ films, obtained by co-deposition method followed by annealing in situ on silicon nitride substrate, have been nanostructured by electron beam lithography and ion milling. The analysis of the AFM images by the height-height correlation function shows that the films have a self-affine smooth textured surface with a RMS roughness of 20 nm. Furthermore, the nanobridges are continuous, with a well-defined geometry and a rounded profile, and the nanostructuration process does not significantly affect the film morphology.     

STM/STS characterization of platinum silicide nanostructures grown on a Pt(1 1 1) surface

Formation of the platinum silicides nanostructures and their electronic properties have been studied using scanning tunneling microscopy and scanning tunneling spectroscopy. The investigated structures have been grown by solid state epitaxy upon deposition of the Si atoms (coverage about 0.2 ML) and sequential annealing at temperature range 600-1170 K. The formation of the Pt₂Si and PtSi islands was investigated until the Si atoms embedded into the Pt substrate at the 1170 K. The images of the silicides structures and Pt substrates with atomic resolution have been recorded. The evolution of the spectroscopic curves both for substrates and nanostructures, corresponding to the structural and sizes changes, have been shown.     

Molecular resolution of an organic monolayer by dynamic AFM

We report molecularly resolved dynamic AFM-measurements of a monolayer of perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA) epitaxially grown on Ag(110). Preparation and experiments were performed under UHV conditions. The frequency-modulation AFM technique was applied. Received: 26 February 1998 / Revised: 13 May 1998 / Accepted: 8 June 1998     

Growth process of atomically flat anodic films on titanium under potentiostatical electrochemical treatment in H2SO4 solution

The as-deposited titanium film on silicon wafer was electrochemically treated in potential sweep and potential step modes in 0.1 M H₂SO₄ solution at 30 °C. Under the anodization conditions of potential sweep and properly modulated cyclic voltammetry (CV), nanoscale grains, step-terrace structure and atomic images were clearly observed on the surface of anodic oxide film on titanium. Under potential step conditions, if the anodization time was short (1 s), no grains could be found on the anodic oxide film surface, even though the potential was high up to 9000 mV. Moreover, whatever potential sweep or potential step mode was performed, sufficient time (low sweep rate means a prolonged anodization time) was needed for the formation of nanoscale grains, atomically flat surface and step-terrace structure on the anodized titanium film.     

A combined in situ AFM and SEM study of the interaction between celestite (0 0 1) surfaces and carbonate-bearing aqueous solutions

In this paper, we present in situ atomic force microscopy (AFM) observations of the interaction between celestite (SrSO₄) (0 0 1) surfaces and Na₂CO₃ aqueous solutions. The observations indicate that the interaction is characterized by a rapid alteration (carbonatation) and dissolution of the original surface, shortly followed by the formation of a new phase. EDX analyses indicate that the new phase is strontianite (SrCO₃). Its crystallization involves the formation and spreading of islands of about 2.75 nm in height, which chiefly occurs on the step edges of the dissolving celestite substrate. The thickness of the islands remains almost constant during their spreading, which occurs mainly parallel to the celestite [0 1 0] direction. As a result of the progressive coalescence of the islands, a fairly homogeneous epitaxial layer forms on the celestite (0 0 1) face. At the initial stages, the formation of islands on the celestite (0 0 1) faces enhances dissolution, indicating the existence of a coupling between dissolution and crystallization reactions. Our measurements on series of AFM images provided quantitative information about coupled dissolution-growth rates on a nanoscale. The effect of the coupled reactions on the celestite (0 0 1) surface on a microscopic scale was also studied by scanning electron microscopy (SEM).     

Scanning probe microscopy study of exfoliated oxidized graphene sheets

Exfoliated oxidized graphene (OG) sheets, suspended in an aqueous solution, were deposited on freshly cleaved HOPG and studied by ambient AFM and UHV STM. The AFM images revealed oxidized graphene sheets with a lateral dimension of 5–10 μm. The oxidized graphene sheets exhibited different thicknesses and were found to conformally coat the HOPG substrate. Wrinkles and folds induced by the deposition process were clearly observed. Phase imaging and lateral force microscopy showed distinct contrast between the oxidized graphene and the underlying HOPG substrate. The UHV STM studies of oxidized graphene revealed atomic scale periodicity showing a (0.273 ± 0.008) nm × (0.406 ± 0.013) nm unit cell over distances spanning few nanometers. This periodicity is identified with oxygen atoms bound to the oxidized graphene sheet. I(V) data were taken from oxidized graphene sheets and compared to similar data obtained from bulk HOPG. The dI/dV data from oxidized graphene reveals a reduction in the local density of states for bias voltages in the range of ±0.1 V.     

Self-organization of surfactant molecules on solid surface: an STM study of sodium alkyl sulfonates

Adsorption and self-organization of sodium alkyl sulfonates (STS and SHS) on HOPG have been studied by using in situ scanning tunneling microscopy (STM). Both SHS and STS molecules adsorb on HOPG surface and form long-range well-ordered monolayers. The molecular rows and the axes of alkyl chain of the molecules cross each other at angles of 60° and 90° in the STS and SHS layers, respectively. Molecular details such as sulfonate functional group (head) and alkyl chain are clearly imaged. The neighboring molecules in different rows form a “head to head” configuration. Structural models for the molecular arrangement of the two adlayers are proposed.