The electronic origin of contrast reversal in bias-dependent STM images of nanolines

Self-organized Bi lines that are only 1.5 nm wide can be grown without kinks or breaks on Si(0 0 1) surfaces to lengths of up to 500 nm. Constant-current topographical images of the lines, obtained with the scanning tunneling microscope, have a striking bias dependence. Although the lines appear darker than the Si terraces at biases below ≈∣1.2∣ V, the contrast reverses at biases above ≈∣1.5∣ V. Between these two ranges the lines and terraces are of comparable brightness. It has been suggested that this bias dependence may be due to the presence of a semiconductor-like energy gap within the line. Using ab initio calculations it is demonstrated that the energy gap is too small to explain the experimentally observed bias dependence. Consequently, at this time, there is no compelling explanation for this phenomenon. An alternative explanation is proposed that arises naturally from calculations of the tunneling current, using the Tersoff–Hamann approximation, and an examination of the electronic structure of the line.

MgO/Ag(001) interface structure and STM images from first principles

The interface of MgO/Ag(001) has been studied with density functional theory applied to slabs. We have found that regular MgO films show a small adhesion to the silver substrate, the binding can be increased in off-stoichiometric regimes, either by the presence of O vacancies at the oxide film or by a small excess of O atoms at the interface between the ceramic to the metal. By means of theoretical methods, the scanning tunneling microscopy signatures of these films is also analyzed in some detail. For defect free deposits containing 1 or 2 ML and at low voltages, tunnelling takes place from the surface Ag substrate, and at large positive voltages Mg atoms are imaged. If defects, oxygen vacancies, are present on the surface of the oxide they introduce much easier channels for tunnelling resulting in big protrusions and controlling the shape of the image, the extra O stored at the interface can also be detected for very thin films.

Using Surface Spectroscopy to Help Interpret STM Images of Chemisorbed Molecules: Application to the Study of the Hydrogenation of Ketones and a-Ketoesters on Pt

Depuis que la haute énantiopureté est nécessaire dans l’industrie pharmaceutique, les études visant à découvrir les mécanismes pour l’hydrogénation énantiosélective de cétones ou céto-esters sur les surfaces, et à rechercher de nouveaux et plus performants catalyseurs asymétriques, sont d’une grande importance. La microscopie à effet tunnel (STM), la spectroscopie infrarouge de réflexion-absorption, la spectroscopie de désorption à température programmée et la spectrométrie de photoélectrons induits par rayons X sont des méthodes performantes facilitant la compréhension des mécanismes de réaction. En plus de nous permettre de comprendre les mécanismes réactionnels, les études peuvent fournir des informations sur la dynamique des réactions en catalyse hétérogène ainsi que sur le développement de la théorie de la fonctionnelle de la densité (DFT) afin de calculer des interactions faibles dans les processus de surface. D’autres parts, les calculs DFT fournissent une aide essentielle à l’interprétation des données de STM et spectroscopie de surface. Dans cette thèse, certains cétones et céto-esters sur la surface de platine sont étudiées par les techniques sophistiquées mentionnées ci-dessus. Mes études démontrent que la combinaison de l’utilisation de la spectroscopie de routine, des nanotechnologies et de nombreux calculs élaborés, est une méthode efficace pour étudier les réactions à la surface car ces techniques explorent les différents aspects de la surface ainsi que s’entraident mutuellement lors de certaines interprétations.

Adlayer Structures of DL-Homocysteine and L-Homocysteine Thiolactone on Au(111) Surface: an in situ STM Study

The adsorption Of DL-homocysteine (Hcy) and L-homocysteine thiolactone (HTL) on Au(1 1 1) electrode was investigated in 0.1 M HClO4 by cyclic voltammetry and in situ scanning tunneling microscopy (STM). Hcy and HTL molecules formed highly ordered adlayers on Au(1 1 1) surface. High-resolution STM images revealed the orientation and packing arrangement in the ordered adlayers. Hcy molecules formed (2root3 x 3root3)R30degrees adlayer structure and H-bonds between carboxyl groups were assumed to be responsible for the origin of tail-to-tail or head-to-head molecular arrangement, while HTL molecules formed (4 x 6) adlayer structure, and two different orientations and appearances in the ordered adlayer were found. Structural models were proposed for the two adlayers.

STM OF FOLDED AND UNFOLDED HEMOGLOBIN MOLECULES ELECTROCHEMICALLY DEPOSITED ON HIGHLY ORIENTED PYROLYTIC-GRAPHITE

The structural characterization of folded and unfolded haemoglobin has been performed by scanning tunnelling microscopy (STM) for the first time. STM images show an oval-shaped pattern for the folded structure of this protein, and moreover two dimers consisting of one haemoglobin molecule can be clearly discerned. The dimensions of a folded molecule were determined as 6.4 x 5.4 x 0.7 nm(3), which are in good agreement with the known size obtained from X-ray analysis. We have found that unfolding of haemoglobin molecules on the surface of highly oriented pyrolytic graphite (HOPG) can be achieved by electrochemical deposition. The STM analysis indicates clearly that the tertiary structure of the protein was lost by electrochemical deposition, and most of the haemoglobin molecules were almost fully extended and exhibited a twisted rope-like or a rod-like aggregated structure. Our investigation demonstrates the capability of the electrochemical method in denaturing this redox protein and in preparing stable biological samples for use in STM imaging.

SrTiO3(001)(2x1) reconstructions: First-principles calculations of surface energy and atomic structure compared with scanning tunneling microscopy images

(1x1) and (2x1) reconstructions of the (001) SrTiO3 surface were studied using the first-principles full-potential linear muffin-tin orbital method. Surface energies were calculated as a function of TiO2 chemical potential, oxygen partial pressure and temperature. The (1x1) unreconstructed surfaces were found to be energetically stable for many of the conditions considered. Under conditions of very low oxygen partial pressure the (2x1) Ti2O3 reconstruction [Martin R. Castell, Surf. Sci. 505, 1 (2002)] is stable. The question as to why STM images of the (1x1) surfaces have not been obtained was addressed by calculating charge densities for each surface. These suggest that the (2x1) reconstructions would be easier to image than the (1x1) surfaces. The possibility that the presence of oxygen vacancies would destabilise the (1x1) surfaces was also investigated. If the (1x1) surfaces are unstable then there exists the further possibility that the (2x1) DL-TiO2 reconstruction [Natasha Erdman Nature (London) 419, 55 (2002)] is stable in a TiO2-rich environment and for p(O2)>10(-18) atm.

Identification of adsorbed molecules via STM tip manipulation: CO, H₂O, and O₂ on TiO₂ anatase (101)

While Scanning Tunneling Microscopy (STM) has evolved as an ideal tool to study surface chemistry at the atomic scale, the identification of adsorbed species is often not straightforward. This paper describes a way to reliably identify H2O, CO and O2 on the TiO2 anatase (101) surface with STM. These molecules are of a key importance in the surface chemistry of this and many other (photo-) catalytic materials. They exhibit a wide variety of contrasts in STM images, depending on the tip condition. With clean, metallic tips the molecules appear very similar, i.e., as bright, dimer-like features located in the proximity of surface Ti5c atoms. However, each species exhibits a specific response to the electric field applied by the STM tip. It is shown that this tip–adsorbate interaction can be used to reliably ascertain the identity of such species. The tip–adsorbate interactions, together with comparison of experimental and calculated STM images, are used to analyse and revisit the assignments of molecular adsorbed species reported in recent studies.

Substrate effects in the supramolecular assembly of 1,3,5-benzene tricarboxylic acid on graphite and graphene

The behavior of small molecules on a surface depends critically on both molecule–substrate and intermolecular interactions. We present here a detailed comparative investigation of 1,3,5-benzene tricarboxylic acid (trimesic acid, TMA) on two different surfaces: highly oriented pyrolytic graphite (HOPG) and single-layer graphene (SLG) grown on a polycrystalline Cu foil. On the basis of high-resolution scanning tunnelling microscopy (STM) images, we show that the epitaxy matrix for the hexagonal TMA chicken wire phase is identical on these two surfaces, and, using density functional theory (DFT) with a non-local van der Waals correlation contribution, we identify the most energetically favorable adsorption geometries. Simulated STM images based on these calculations suggest that the TMA lattice can stably adsorb on sites other than those identified to maximize binding interactions with the substrate. This is consistent with our net energy calculations that suggest that intermolecular interactions (TMA–TMA dimer bonding) are dominant over TMA–substrate interactions in stabilizing the system. STM images demonstrate the robustness of the TMA films on SLG, where the molecular network extends across the variable topography of the SLG substrates and remains intact after rinsing and drying the films. These results help to elucidate molecular behavior on SLG and suggest significant similarities between adsorption on HOPG and SLG.

Supramolecular ordering in oligothiophene−fullerene monolayers

Scanning tunneling microscopy (STM) of monolayers comprising oligothiophene and fullerene molecular semiconductors reveals details of their molecular-scale phase separation and ordering with potential implications for the design of organic electronic devices, in particular future bulk heterojunction solar cells. Prochiral terthienobenzenetricarboxylic acid (TTBTA) self-assembles at the solution/graphite interface into either a porous chicken wire network linked by dimeric hydrogen bonding associations of COOH groups (R22(8)) or a close-packed network linked in a novel hexameric hydrogen bonding motif (R66(24)). Analysis of high-resolution STM images shows that the chicken wire phase is racemically mixed, whereas the close-packed phase is enantiomerically pure. The cavities of the chicken wire structure can efficiently host C60 molecules, which form ordered domains with either one, two, or three fullerenes per cavity. The observed monodisperse filling and long-range co-alignment of fullerenes is described in terms of a combination of an electrostatic effect and the commensurability between the graphite and molecular network, which leads to differentiation of otherwise identical adsorption sites in the pores.

The equilibrium geometry and electronic structure of Bi nanolines on clean and hydrogenated Si(001) surfaces

The equilibrium geometry, electronic structure and energetic stability of Bi nanolines on clean and hydrogenated Si(001) surfaces have been examined by means of ab initio total energy calculations and scanning tunnelling microscopy. For the Bi nanolines on a clean Si surface the two most plausible structural models, the Miki or M model (Miki et al 1999 Phys. Rev. B 59 14868) and the Haiku or H model (Owen et al 2002 Phys. Rev. Lett. 88 226104), have been examined in detail. The results of the total energy calculations support the stability of the H model over the M model, in agreement with previous theoretical results. For Bi nanolines on the hydrogenated Si(001) surface, we find that an atomic configuration derived from the H model is also more stable than an atomic configuration derived from the M model. However, the energetically less stable (M) model exhibits better agreement with experimental measurements for equilibrium geometry. The electronic structures of the H and M models are very similar. Both models exhibit a semiconducting character, with the highest occupied Bi-derived bands lying at ~0.5 eV below the valence band maximum. Simulated and experimental STM images confirm that at a low negative bias the Bi lines exhibit an 'antiwire' property for both structural models.

The geometry of Bi nanolines on Si(0 0 1)

A study of the Bi nanoline geometry on Si(0 0 1) has been performed using a combination of ab initio theoretical technique and scanning tunnelling microscopy (STM). Our calculations demonstrate decisively that the recently proposed Haiku geometry is a lower energy configuration than any of the previously proposed line geometries. Furthermore, we have made comparisons between STM constant-current topographs of the lines and Tersoff–Haman STM simulations. Although the Haiku and the Miki geometries both reproduce the main features of the constant-current topographs, the simulated STM images of the Miki geometry have a dark stripe between the dimer rows that does not correspond well with experiment.

Two-dimensional self-assembly of a symmetry-reduced tricarboxylic acid

Investigations of the self-assembly of simple molecules at the solution/solid interface can provide useful insight into the general principles governing supramolecular chemistry in two dimensions. Here, we report on the assembly of 3,4′,5-biphenyl tricarboxylic acid (H3BHTC), a small hydrogen bonding unit related to the much-studied 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), which we investigate using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. STM images show that H3BHTC assembles by itself into an offset zigzag chain structure that maximizes the surface molecular density in favor of maximizing the number density of strong cyclic hydrogen bonds between the carboxylic groups. The offset geometry creates “sticky” pores that promote solvent coadsorption. Adding coronene to the molecular solution produces a transformation to a high-symmetry host–guest lattice stabilized by a dimeric/trimeric hydrogen bonding motif similar to the TMA flower structure. Finally, we show that the H3BHTC lattice firmly immobilizes the guest coronene molecules, allowing for high-resolution imaging of the coronene structure.