Contacting a single molecular wire by STM manipulation

The Lander molecule (C₉₀H₉₈) consists of a long polyaromatic molecular wire and four lateral di-tert-butyl-phenyl spacer groups, designed to maintain the molecular wire parallel above the substrate. It represents a model system for investigating the electronic contacts of a molecular wire to a nanoscale metallic electrode. In this article, some recent manipulation experiments of single Lander molecules by low temperature scanning tunneling microscopy (LT-STM) are presented. The selective adsorption of the molecule, the molecule-induced reconstruction of copper substrates, and their application to the investigation of contacts between molecules and nanostructures or between molecules are discussed. Manipulation experiments are reported, where the molecular wire part of a Lander molecule is contacted to a monoatomic step and to a two-atom-wide metallic nanostructure. The contact is characterized by the apparent height of the contact point in STM images and, in case of the Cu(111) substrate, by the perturbation observed in the electronic standing wave patterns. PACS 68.37.Ef; 72.80.Le; 68.65.La; 85.65.+h     

STM tip-enhanced photoluminescence from porphyrin film

Tunneling electrons-induced molecular fluorescence in organic film is enhanced by the surface plasmons. The plasmon enhancement can be expected not only by the plasmons of the substrate but also by the noble metal tip of scanning tunneling microscope (STM). In this report we investigate the tip effect in photoluminescence of meso-tetrakis(3,5-di-tertiarybutyl-phenyl)porphyrin (H₂TBPP) film on indium tin oxide (ITO) combined with a STM. The experimental result shows the PL of molecules is enhanced by an Ag tip. This enhancement factor is evaluated larger than 2000.     

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.     

Internal structure of C60 fullerence molecules as revealed by low-temperature STM

We have performed Scanning Tunneling Microscopy (STM) in ultra-high vacuum at low temperatures (5 and 50K) of unordered and ordered C₆₀ layers adsorbed on a Au(110) surface. STM topographs of the frozen C₆₀ molecules reveal four symmetric patterns within single molecules, which may be associated with different orientations of the fullerenes on a highly corrugated gold substrate.     

STM characterisation of organic molecules on H-terminated Si(111)

We present the first high resolution STM images of organic molecules on the technological important hydrogen terminated silicon surface. Ordered layers of PTCDA and PTCDI were prepared on this surface by organic molecular beam epitaxy. The submolecular contrast of these molecules on Si(111)/H obtained in the high resolution images agrees with the corresponding images on HOPG and MoS₂ substrates.     

STM spectroscopy of an organic superconductor

Electron tunneling spectroscopy of the organic superconductor κ-(BEDT-TTF)₂Cu(NCS)₂using low temperature scanning tunneling microscope (STM) is reported. The tunneling differential conductance in the superconducting phase was obtained in theb–cplane of a single crystal, by varying the tip position on the sample surface. The differential conductance is reduced near zero bias voltage and enhanced at the gap edge, associated with the superconducting gap structure below[formula] K. The gap width differs slightly from sample to sample, while the overall functional shape of the conductance is sample-independent. The tunneling conductance is reduced to almost zero near zero bias voltage, while it is finite inside the gap edge. The curve obtained cannot be fit to the BCS density of states withs-wave pairing symmetry, even if the life-time broadening of one-electron levels is taken into account. Finite conductance inside the gap edge suggests anisotropy of the gap. However, the conductance curve obtained is not explained by a simpled-wave symmetry for Δ(k). The reduced conductance near zero bias voltage suggests a finite gap. An anisotropic model with a finite gap, in which Δ(k) varies depending on the direction ink-space, is examined. The tunneling conductance in the low-energy region is almost fit by the model with Δ_min = 2 meV and Δ_max = 6 meV. The finite conductance is explained by introducing a small effect of life time broadening. We conclude that the gap is anisotropic and is finite (at least Δ_min = 2 meV) on the entire Fermi surface.     

Direct STM observation of electronic structure modification of naphthacenequinone molecules due to photoisomerization

Light-induced conformational transformations of the naphthacenequinone (NQ) molecules are observed by scanning tunneling microscopy (STM). NQ molecules packed in a Langmuir-Blodgett (LB) film are shown to form stable ordered structures on a surface of highly oriented pyrolytic graphite (HOPG). The local density of electronic states is found to exhibit the distinct peak which is characteristic of two-dimensional conductivity. An additional subband of empty electronic states is found for NQ molecules in form A but not in form B. The constant-height STM images of individual molecules in form A demonstrate an additional structure that is indicative of a conformational transition of the NQ molecules. This transition involves the transfer of the phenoxy group from one oxygen to another. Pis’ma Zh. éksp. Teor. Fiz. 68, No. 6, 486–490 (25 September 1998)     

An STM investigation of the interaction and ordering of pentacene molecules on the Ag/Si(1 1 1)-(√3×√3)R30° surface

Scanning tunneling microscopy has been used to study the ordering of pentacene (C₂₂H₁₄) molecules on the Ag/Si(1 1 1)-(√3×√3)R30° surface at room temperature. Two solid phases, S1 and S2, are observed at coverages of ∼0.35 monolayer (ML) and ∼1.0 ML respectively. It is shown that the solid phase S1 has a high-order commensurate lattice, Ag/Si(1 1 1)-(25 × 25)-pentacene, containing 75 molecules. The structure of this phase is determined from STM measurements at very low coverages where it is possible to image both the pentacene molecules and the structure of the Ag/Si(1 1 1) substrate. Two adsorption sites are identified, a three-fold hollow site at the centre of a Ag-trimer (CA-site) and a six-fold hollow site at the centre of the hexagonal arrangement of silver atoms (CB-site). A higher pentacene coverage of ∼1 ML lead to a molecular reorganization and forms a new commensurate structure Ag/Si(1 1 1)-(2 × 3)-pentacene, containing two molecules per unit cell. Because low energy electron diffraction patterns were not obtainable for this system, the structure of this second phase is determined by using the bias voltage as a tunable parameter to “focus” on either the molecular film or on the substrate. In this phase adsorption takes place exclusively on the Ag-trimer (CA) site and the CB-site is lost because of strong lateral molecule-molecule interactions. The role of competition between intermolecular and molecule-substrate interactions and the nature of the adsorption sites in determining the structure of the pentacene layers is discussed.     

STM/STS study of electronic states in highly underdoped Bi2212

Local density of states (LDOS) and the lattice structure of highly underdoped Bi₂Sr₂CaCu₂O_8+δ with T_c = 22 K and 30 K were investigated by a low temperature scanning tunneling microscope. The modulation structure of the Bi–O surface was strongly depressed in the highly underdoped samples. The depression was observed only in the samples subject to the strong reduction annealing process, suggesting that the strong reduction in excess oxygen could destroy the modulation structure. At a time, patch-like inhomogeneity in the gap map sometimes disappeared, indicating that the existence of excess oxygen has an important role in the patch formation. Analysis on the LDOS with various doping levels showed that there was no crossover energy, which separates a pseudogap and a superconducting gap and is proportional to T_c.     

Characterization of 1T-TiSe2 surface by means of STM and XPD experiments and model calculations

Scanning tunneling microscopy (STM) and X-ray photoelectron diffraction (XPD) are applied to study the surface of layered dichalcogenide 1T-TiSe₂. XPD pattern simulation for the 1T-TiSe₂ surface is performed in the approach of electron multiple scattering within the EDAC code: considered are models of structural defects in the 1T-TiSe₂ lattice, relaxation contraction (expansion) of surface layers and van der Waals gap, and deviation of the 1T-TiSe₂ surface geometry from the basal plane (001). The atomic structure of 1T-TiSe₂ surface layers is reconstructed from the XPD pattern on Se(LMM) and Ti2p core level using the photoelectron holography scattering pattern extraction algorithm with maximum entropy method (SPEA-MEM). The results of the 3D reconstruction are in agreement with the XPD pattern simulation data. In both cases, the TiSe₂ surface corresponds to 1T polytype; an increase is observed in the parameter a₀ and in the van der Waals gap between two surface slabs. It is assumed that similar structural distortions of the 1T-TiSe₂ lattice lead to the formation of an energy gap between the valence band and the conduction band of titanium diselenide, which was observed earlier by photoemission spectroscopy and follows from the theoretical calculations.     

STM investigation of the adsorption and temperature dependent reactions of ethylene on Pt(111)

The adsorption and reactions of ethylene adsorbed in UHV on Pt(111) have been studied as a function of temperature by STM. The STM images taken at 160K show an ordered structure of adsorbed ethylene. Annealing to 300 K produces ethylidyne (C-CH₃) irreversibly, as has been demonstrated by a wide variety of surface science techniques. The ethylidyne on Pt(111) is not visible to the STM at room temperature. Cooling the sample allows direct observation of the ethylidyne ordered structure by STM. Annealing above 430 K results in further dehydrogenation, eventually leaving only carbon on the surface. The decomposition products appear as small clusters which are localized and uniformly distributed over the surface. Further annealing to temperatures >800 K results in the growth of graphite islands on the Pt(111) surface. The annealed graphite islands exhibit several supersturctures with lattice parameters of up to 22 Å, which are thought to result from the higher order commensurability with the Pt(111) substrate at different relative rotations.     

Theory of vortex lattice effects on STM spectra in d-wave superconductors

The theory of scanning tunneling spectroscopy of low-energy quasiparticle (QP) states in vortex lattices of d-wave superconductors is developed taking account of the effects caused by an extremely large extension of QP wavefunctions in the nodal directions and the band structure in the QP spectrum. The oscillatory structures in STM spectra, which correspond to van Hove singularities, are analyzed. Theoretical calculations carried out for finite temperatures and scattering rates are compared with recent experimental data for high-T _c cuprates.     

Self-assembled monolayer of o-aminothiophenol on Fe(1 1 0) surface: a combined study by electrochemistry, in situ STM, and molecular simulations

Electrochemical measurements, in situ scanning tunneling microscopy (STM) observation, and molecular mechanics (MM) simulations were performed to study the physiochemical properties such as the corrosion-inhibition effect and the optimal packing structure of o-aminothiophenol (OATP) self-assembled monolayer (SAM) formed on Fe(1 1 0) surface in 0.1 M NaClO₄ solution. The formation of OATP SAMs drastically depressed the Faradaic processes at the Fe(1 1 0) surface and reduced the electrical double-layer capacitance at the electrode/electrolyte interface, revealing the anticorrosion property and the blocking behavior of OATP adlayers. Two-dimensional ordered molecular arrays of OATP on Fe(1 1 0) surface with a p(2 × 2) commensurate structure were observed by STM measurements. MM calculations showed that the p(2 × 2) packing pattern is indeed the preferable structure for OATP molecules adsorbed on Fe(1 1 0), in accordance with STM experiments. The OATP SAM on Fe(1 1 0) is ≈0.50 nm in thickness and with a dielectric constant of ∼7.0.     

Real-time STM observation of molecular dynamics on a metal surface

Dynamic processes of molecular assembly on a metal surface were examined using scanning tunneling microscopy (STM). Molecules of a porphyrin derivative were deposited on a Cu(1 1 1) surface and were found to be highly mobile at room temperature. The real-time STM observation enabled visualization of molecular activity such as surface diffusion, domain formation and phase transition. The high mobility of the molecules caused build-up and break-down of molecular domains. Metastability of the molecular assembly caused various domain formations with different molecular alignments, including square and hexagonal motifs. A phase transition from a hexagonal to a square domain structure was successfully observed by sequential STM imaging.     

STM studies of PTCDA supramolecular self-assembling on anisotropic surfaces of reconstructed InSb

Self-assembly of 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) molecules on a c(8 × 2) reconstructed InSb(0 0 1) surface as well as on an asymmetrical (1 × 3) InSb(0 0 1) is investigated by means of high resolution scanning tunneling microscopy. The formation of well-ordered one-dimensional molecular lines is observed at low coverage on a former face, whereas on the latter molecules are found as isolated entities. At room temperature spontaneous hopping between energetically similar sites is observed within the lines. At a monolayer coverage flat molecular surface is obtained for both reconstructions, on the c(8 × 2) the layer is composed of neighboring one-dimensional lines, on the (1 × 3) molecular structure does not reveal any long range order. Application of the special experimental procedure provides direct comparison of molecule behavior on both reconstructions of the same sample.     

The surface structure of icosahedral Al68Pd23Mn9 measured by STM and LEED

For the first time the surface structure of an icosahedral quasicrystal has been successfully investigated in Ultra-High Vacuum (UHV) by Scanning Tunneling Microscopy (STM) and Low-Energy Electron Diffraction (LEED). After cleaning an i-Al₆₈Pd₂₃Mn₉ sample in UHV by cycles of ion-sputtering and annealing at temperatures close to the melting point atomically flat terraces are observed by STM. Successive step heights show quasiperiodic order according to the Fibonacci chain. The normals of these terraces are parallel to a five-fold axis as revealed by highly resolved STM images. On the terraces five-fold stars and pentagonal holes are observed. Their orientation is the same on all terraces investigated. Additionally to this long-range orientational order, a high degree of quasiperiodic order is found for the pentagonal holes. This indicates that the quasiperiodic order of this highly ordered and thermodynamically stable quasicrystal extends even up to the surface. Both the step heights and the distances between the pentagonal holes well agree with the values derived from a structural model of this material. Five-fold symmetric LEED patterns can be analysed by means of the Fourier transform of a Fibonacci pentagrid as suggested by the STM data. The analysis yields the same line separations within the pentagrid as deduced from the STM experiments.     

Morphology and orientational disorder of C70 single crystals

C₇₀ single crystals, free from solvent contamination, were grown via vapor phase transport technique. The (0001) face of the C₇₀ crystal was imaged with Atomic Force Microscopy (AFM) under ambient atmosphere. Low-resolution images of a freshly prepared crystal revealed well-ordered faceted regions with multiple terraces extending over a region of several hundred square nanometers. The terraced structure in the images indicates that the crystals formed as a layer growth. In the high-resolution images, C₇₀ molecules were resolved in a hexagonal close packed (hcp) structure with an average center-to-center distance of 10.5±0.5 Å. After one month's exposure to the ambient atmosphere, the molecules rearranged into a mixed structure consisting of hcp and face centered cubic (fcc) regions.     

Simulations of iodine adsorbed Ge(0 0 1) surface and its STM images

A layer of iodine at Ge(0 0 1) surface develops an ordered structure of iodine atoms bound to Ge dimers. Here are discussed atomic structures of Ge(0 0 1) surface covered by 0.25 monolayer of iodine. The p(2×4), p(2×2), c(2×4) and p(1×4) surface structures are found in calculations. The structure with two iodine atoms of the dissociated I₂ molecule adsorbed at both ends of the same germanium dimer is found to be energetically favourable over iodine adsorption at neighbouring dimers. Simulated STM images of the obtained surface structures are presented and compared with experimental data.     

The equivalent potential of water molecules for electronic structure of alanine

Using ab initio calculations based on density functional theory, an equivalent potential of water molecules for the electronic structure of Ala in solution has been obtained. The calculation process consists of three steps: first, the geometric structure of Ala + nH₂O system is determined by searching for the lowest energy of the system using free cluster calculation method. Second, based on the geometric structure obtained, the electronic structure of Ala with the potential of water molecules is calculated using a self-consistent cluster-embedding method. Finally, after replacing water molecules with dipoles, the electronic structure of Ala with the potential of dipoles is calculated. The dipoles are adjusted so the electronic structure of Ala with the potential of dipoles is close to that of water molecules. The calculated results show that the main effect of water molecules is to raise the state for methyl CH₃ by about 0.14 Ry, raising all other eigenvalues by about 0.059 Ry, and widening the energy gap by about 25%. In contrast, the replacement of water molecules by dipoles is comparatively efficient, showing that the effect of water molecules on the electronic structure of Ala can be simulated by a dipole potential, which would be a shortcut calculation.     

Intramolecular structures of C60 and C84 molecules on Si(1 1 1)-7 × 7 surfaces by scanning tunneling microscopy

The intramolecular features of carbon 60 and carbon 84 molecules on Si(1 1 1)-7 × 7 surfaces were studied under a UHV-scanning tunneling microscope. Carbon molecules preferentially appear in faulted halves, rather than in unfaulted halves and corner holes; they are embedded in silicon substrates. The orientation and details of the structure of carbon molecules are determined by applying various sample biases to the silicon substrate. As compared with other fullerenes, a bright pentagonal ring with nebulous clusters which represents the cage structure is clearly observed on top of carbon 60 molecules. The bright stripes associated with partitioned curves which depict eight features of asymmetrical C₈₄ molecules are also investigated on Si(1 1 1)-7 × 7 surfaces. The orientations and possible configurations of C₆₀ and C₈₄ are considered in this work. The energy differences for various features of C₆₀ and C₈₄ molecules are estimated and discussed. The corresponding models with respect to each intramolecular feature are proposed and compared with recent theoretical calculation.