High-resolution Scanning Tunneling Microscopy Images Research Articles

Two-Dimensional Carbon Incorporation into Si(001): C Amount and Structure ofSi(001)−c(4×4)

The C amount and the structure of the Si(001)-c(4 x 4) surface is studied using scanning tunneling microscopy (STM) and ab initio calculations. The c(4 x 4) phase is found to contain 1/8 monolayer C (1 C atom in each primitive unit cell). From the C amount and the symmetry of high-resolution STM images, it is inferred that the C atoms substitute the fourth-layer site below the dimer row. We construct a structure model relying on ab initio energetics and STM simulations. Each C atom induces an on-site dimer vacancy and two adjacent rotated dimers on the same dimer row. The c(4 x 4) phase constitutes the subsurface Si(0.875)C(0.125) delta layer with two-dimensionally ordered C atoms.

Self-Assembly of Small Polycyclic Aromatic Hydrocarbons on Graphite: A Combined Scanning Tunneling Microscopy and Theoretical Approach

Self-assembled monolayers of chrysene and indene on graphite have been observed and characterized individually with scanning tunneling microscopy (STM) at 80 K under low-temperature, ultrahigh vacuum conditions. These molecules are small, polycyclic aromatic hydrocarbons (PAHs) containing no alkyl chains or functional groups that are known to promote two-dimensional self-assembly. Energy minimization and molecular dynamics simulations performed for small groups of the molecules physisorbed on graphite provide insight into the monolayer structure and forces that drive the self-assembly. The adsorption energy for a single chrysene molecule on a model graphite substrate is calculated to be 32 kcal/mol, while that for indene is 17 kcal/mol. Two distinct monolayer structures have been observed for chrysene, corresponding to high- and low-density assemblies. High-resolution STM images taken of chrysene with different bias polarities reveal distinct nodal structure that is characteristic of the molecular electronic state(s) mediating the tunneling process. Density functional theory calculations are utilized in the assignment of the observed electronic states and possible tunneling mechanism. These results are discussed within the context of PAH and soot particle formation, because both chrysene and indene are known reaction products from the combustion of small hydrocarbons. They are also of fundamental interest in the fields of nanotechnology and molecular electronics.

High-Resolution Scanning Tunneling Microscopy Images of Molecular Overlayers Prepared by a New Molecular Beam Deposition Apparatus with Spray-Jet Technique

We developed a new molecular beam deposition apparatus using a spray-jet technique for high-quality thin film preparation of nonsublimable molecules. The apparatus was used to deposit chloro[tri-tert-butyl-subphthalocyaninato]boron(III) (TBSubPc) molecules on an Au(111) surface for analysis by low-temperature scanning tunneling microscopy (STM). Highly resolved images, in which tert-butyl groups in a TBSubPc molecule were clearly identifiable, were obtained. The image quality and the resolution of these images compared favorably well to STM images taken on reference samples which were sublimed onto Au (111) from a heated crucible.

Mesoscopic self-organization of a self-assembled supramolecular rectangle on highly oriented pyrolytic graphite and Au(111) surfaces

A self-assembled supramolecular metallacyclic rectangle was investigated with scanning tunneling microscopy on highly oriented pyrolytic graphite and Au(111) surfaces. The rectangles spontaneously adsorb on both surfaces and self-organize into well ordered adlayers. On highly oriented pyrolytic graphite, the long edge of the rectangle stands on the surface, forming a 2D molecular network. In contrast, the face of the rectangle lays flat on the Au(111) surface, forming linear chains. The structures and intramolecular features obtained through high-resolution scanning tunneling microscopy imaging are discussed.

Rearrangement of up-and-down terrace in Si(1 1 0) “16 × 2” induced by Sn adsorption

We have studied Sn/Si(1 1 0) surface structures with scanning tunneling microscopy (STM). The unique dense-step structure in a clean Si(1 1 0) “16 × 2” phase is successfully modified as a function of Sn coverage up to 0.4 monolayer (ML). The width of about 2.5 nm of the up-and-down terrace (“16 × 2”) is broadened stepwise by Sn adsorption passing through the “28 × 2” phase (0.2 ML), the mixture of “14 × 2” and “7 × 2” (0.3 ML) and the “7 × 2” (0.4 ML) phases. In particular, the “28 × 2” phase is formed by the ordered up-and-down terrace structures of about 4 nm width. High-resolution STM images clearly reveal that in the series of structural changes, the Si pentagons, which are the elemental structures of the “16 × 2” phase [T. An, M. Yoshimura, I. Ono, K. Ueda, Phys. Rev. B 61 (2000) 3006], rearrange in accordance with Sn trimers. The relaxation process of the surface stress plays a key role in determining the surface morphology.

Atomic topography and self-assembly of one-dimensional potassium chains on theInAs(110)surface

One-dimensional (1D) potassium chains, obtained on the $\mathrm{InAs}(110)$ surface, are studied by scanning tunneling microscopy (STM). The $(2\ifmmode\times\else\texttimes\fi{}n)$ symmetry in the low energy electron diffraction pattern, becoming a $c(2\ifmmode\times\else\texttimes\fi{}6)$ structure at the completion of the first layer, is explained by the various spacing $D$ between alkali chains in the [001] direction. The distribution of $D$ as a function of the chain density suggests the presence of a repulsive interaction among the chains, which drives the self-assembling of the 1D structures. The origin of the interaction is discussed in comparison with the model proposed for the $\mathrm{Cs}∕\mathrm{InAs}(110)$ interface, showing the general validity of the model for this class of chain structures. The atomic structure of an isolated chain is investigated by high-resolution STM images, revealing the asymmetry in the charge density induced by $\mathrm{K}$ adatoms and a modification of the As-related charge density of the topmost substrate layer.

Atomic structure of anAl–Co–Nidecagonal quasicrystalline surface

We have analyzed the structure and composition of the first layer of an ${\text{Al}}_{72}{\text{Co}}_{16}{\text{Ni}}_{12}$ tenfold surface by means of scanning tunneling microscopy (STM), ion scattering spectroscopy (ISS), and Auger electron spectroscopy (AES). High-resolution STM images reveal local structures that have decagonal symmetry in addition to the usual pentagonal symmetry of the surface. This quasicrystal surface resembles a random tiling instead of an ideal quasiperiodic tiling. After annealing at $1100\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, the total surface atomic density found by ISS is $(9\ifmmode\pm\else\textpm\fi{}1)\ifmmode\times\else\texttimes\fi{}{10}^{14}\phantom{\rule{0.3em}{0ex}}{\text{cm}}^{\ensuremath{-}2}$. The surface densities of Al and TM (transition metal, i.e., Co and Ni) are determined as $(8\ifmmode\pm\else\textpm\fi{}1)\ifmmode\times\else\texttimes\fi{}{10}^{14}\phantom{\rule{0.3em}{0ex}}{\text{cm}}^{\ensuremath{-}2}$ and $(1.0\ifmmode\pm\else\textpm\fi{}0.2)\ifmmode\times\else\texttimes\fi{}{10}^{14}\phantom{\rule{0.3em}{0ex}}{\text{cm}}^{\ensuremath{-}2}$, respectively from ISS, indicating a similar density of Al and much lower density of the TM atoms in the surface layer than in a truncated bulk. The Al surface atomic density agrees well with the number of corrugation maxima in the STM images. A model of the arrangement of the Al atoms in the top layer is presented. Scanning tunneling spectroscopy (STS) is performed to study the local electronic structure. The STS spectrum at the corrugation maxima is similar to that at the corrugation minima. A few $\ensuremath{\approx}0.12\phantom{\rule{0.3em}{0ex}}\text{nm}$ high protrusions in the STM images are attributed to local oxide clusters due to their STS spectra different from the corrugation maxima and through in situ STM observations during exposure to ${\mathrm{O}}_{2}$ gas at $2\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}6}\phantom{\rule{0.3em}{0ex}}\text{Pa}$ at RT.

Direct STM Investigation of Cinchona Alkaloid Adsorption on Cu(111)

Scanning tunneling microscopy (STM) combined with cyclic voltammetry has been employed to investigate the adsorption of cinchonine on Cu(111). Similar to cinchonidine, cinchonine forms a long-range ordered adlayer with (4 x 4) symmetry on the substrate. The structural details on molecular adsorption were obtained by high-resolution STM images. On the basis of the previous results and obtained STM images, the quinoline ring is proposed to lie parallel to Cu(111) and serve as an anchoring group. The chiral quinuclidine moiety extends out of the surface to facilitate the interaction with the prochiral reactants.

Adlayers of C60−C60 and C60−C70 Fullerene Dimers Formed on Au(111) in Benzene Solutions Studied by STM and LEED

Scanning tunneling microscopy (STM) and low-energy electron diffraction were used to reveal the structures of ordered adlayers of [2+2]-type C60-C60 fullerene dimer (C120) and C60-C70 cross-dimer (C130) formed on Au(111) by immersingit in abenzene solution containing C120 or C130 molecules. High-resolution STM images clearly showed the packing arrangements and the electronic structures of C120 and C130 on the Au(111) surface in ultrahigh vacuum. The (2 square root3 x 4square root3)R30 degrees, (2square root3 x 5square root3)R30 degrees, and (7 x 7) structures were found for the C120 adlayer on the Au(111) surface, whereas C130 molecules were closely packed on the surface. Each C60 or C70 monomer cage was discerned in the STM image of a C130 molecule.

Adlayer Structures of Calixarenes on Au(111) Surface Studied with STM

In-situ scanning tunneling microscopy (STM) and cyclic voltammetry have been employed to investigate conformation-related adlayer structures of four calixarenes, three calix[4]arenes with specific conformations and one calix[6]arene. All the molecules form ordered adlayers on the Au(111) surface in 0.1 M HClO4 under the potential control. For calix[4]arenes, different adlayers are organized on the basis of their specific conformations, indicating that conformations might be used to obtain desired structures. A well-defined adlayer is observed for calix[6]arene. The results demonstrate that the conformation of calixarenes can be immobilized on the Au(111) surface through adsorption, although various conformations of the molecule are reported in solution. The reason is ascribed to the intermolecular and molecule−substrate interactions. On the basis of high-resolution STM images, structural models are tentatively proposed for the ordered adlayers of calixarenes.

High-resolution scanning tunneling microscopy imaging of Escherichia coli lysine transfer ribonucleic acid

We have obtained high-resolution scanning tunneling microscopy (STM) images of Escherichia coli lysine transfer ribonucleic acid (tRNA) adsorbed onto Cu(111) substrates using a pulse injection method. One of the two arms of the L-shaped structure of the observed tRNA is longer than the other. Because hydrogen bonds that maintain the unique three-dimensional structure of tRNAs exist in the hinge region and in one arm of L-shaped structures that include the anticodon stem, we concluded that the longer arm in the L-shaped structure includes the anticodon stem, and the shorter arm includes the acceptor stem. This work supports the view that STM is a powerful tool for obtaining high-resolution images of biomolecules that are too difficult to crystallize.

3×2reconstruction of the Sm/Si(111) interface

The initial formation of the samarium/silicon interface is studied by combining scanning tunneling microscopy (STM), low-energy electron diffraction, and ab initio pseudopotential calculations. A $\mathrm{Si}(111)3\ifmmode\times\else\texttimes\fi{}2$-Sm reconstruction is formed at a Sm coverage of 1/6 monolayer. High-resolution STM images reveal a strong bias-voltage dependence for the $3\ifmmode\times\else\texttimes\fi{}2$ reconstruction. In the empty-state STM images, the rows with a $\ifmmode\times\else\texttimes\fi{}2$ periodicity are shown at high bias voltages, and attributed to Sm atoms. At low bias voltage, an additional double row feature with a $\ifmmode\times\else\texttimes\fi{}1$ periodicity appears and dominates the empty-state image as the bias voltage decreases. The paired protrusions with the $\ifmmode\times\else\texttimes\fi{}1$ periodicity in the double rows in the empty-state image are attributed to Si atoms. In the filled-state STM images, double rows of protrusions forming zigzag chains with a $3\ifmmode\times\else\texttimes\fi{}1$ structure are observed and assigned to Si atoms. We propose a honeycomb chain-channel model for the $3\ifmmode\times\else\texttimes\fi{}2$ phase, common to alkali metals and alkaline-earth metals on Si(111). Simulated STM images based on this model are in excellent agreement with experiment.

STM Study of Multiple Bonding Configurations and Mechanism of 1,3-Cyclohexadiene Attachment on Si(100)-2 × 1

Scanning tunneling microscopy (STM) was used to investigate the reaction of 1,3-cyclohexadiene with Si dimers on the bare Si(100) surface. Detailed, high-resolution STM images show a distribution of surface products. In addition to the intradimer [2 + 2] and [4 + 2] reaction products previously reported, two different [2 + 2] conformers are identified. Empty state STM images also show interdimer [4 + 2] reactions involving neighboring dimers in the same row and in adjacent rows. The former are shown to be the dominant surface product despite the presence of unpaired dangling bonds on two adjacent dimers. These results are interpreted in terms of a reaction mechanism in which the reduced ring strain favors the kinetic interdimer [4 + 2] product over the thermodynamically stable [4 + 2] intradimer product.

Specific ethene surface activation on silver oxide covered Ag[111] from the interplay of STM experiment and theory.

High-resolution scanning tunneling microscopy (STM) images at 5 K, simultaneously resolving the molecular adsorbate and the honeycomb structure of the well-defined Ag[111]-p(4 x 4)+Ag(1.83)O substrate, assign the adsorption site for ethene on the silver oxide surface. Ethene molecules are exclusively adsorbed above a particular subset of Ag(delta)(+) sites in the hexagonal rings of the oxide. Extensive density functional theory (DFT) slab calculations confirm that this is the most stable site, with an adsorption energy of 0.4 eV (39 kJ mol(-1)). Adsorption is accompanied by a large deformation of the hexagonal oxide ring and a significant increase in the C-C bond length. STM image simulations provide qualitative agreement with the experimental images, and the molecular orientation is discussed with the help of simple molecular orbital arguments.

Adsorption of Enantiomeric and Racemic Tyrosine on Cu(111): A Scanning Tunneling Microscopy Study

The adsorption of enantiomers and a racemic mixture of tyrosine (tyr) on Cu(111) has been investigated by cyclic voltammetry and electrochemical scanning tunneling microscopy. D-tyr and L-tyr molecules adsorb on Cu(111) and show a (4 x 4) structure. The mirror symmetry between two adlayers is demonstrated by high-resolution scanning tunneling microscope images. The spontaneous separation of racemate into homochiral domains is observed. The result presented here is hoped to supply direct evidence for the chiral adlayer ordering at the solid/liquid interface.

The surface of Sr 2Ru 0.9Mo 0.1O 4: a LEED and STM study

In the unconventional superconductor Sr 2RuO 4, substitution of a small amount of Mo for Ru destroys the superconducting state. We have used low energy electron diffraction (LEED) and scanning tunneling microscopy (STM) to study the cleaved (1 0 0) surface of the Mo-doped strontium ruthenate: Sr 2Ru 0.9Mo 0.1O 4. Excellent LEED patterns indicate a well-ordered surface similar to Sr 2RuO 4. The analysis of LEED- I( V) spectra revealed that the (Ru/Mo)O 6 octahedra at the surface are rotated alternating clockwise and counterclockwise by 8.8° ± 2.5° about the direction of the surface normal, which is identical to these on the surface of Sr 2RuO 4. But the high-resolution STM images of Sr 2Ru 0.9Mo 0.1O 4 show a surface fundamentally different from that of Sr 2RuO 4. The STM images are surprisingly inhomogeneous without clear atomic resolution. This indicates a local spatial roughness in the electronic structure induced by the Mo doping.

Ｓｉ（００１）ｃ（４×４）‐Ｓｎの走査トンネル顕微鏡―同軸型直衝突イオン散乱分光法による解析

The c (4×4) super-lattice structure of Sn/Si (001) system has been studied using scanning tunneling microscopy (STM) and coaxial impact collision ion scattering spectroscopy (CAICISS). After heating at 1200°C, the clean Si (001) 2×1 surface is confirmed by using low-energy electron diffraction (LEED) and STM. After Sn deposition of 0.5 monolayer (ML), successively annealed it at 600°C, a c (4×4) super-lattice structure is formed. We obtain three kinds of protrusions in high-resolution STM images of Si (001) c (4×4) -Sn structure. One of them is very similar to that of recently reported c (4×4) -Si reconstruction. Others are new protrusions in c (4×4) -Sn, so it seems that these are ascribed to Sn dimer. We analyzed CAICISS spectra scattered from Sn atoms, compared with simulated results. As a result, Sn dimer is found to be buckled. Thus, we proposed the mixed ad-dimer model for c (4×4) -Sn structure.

Structure of Linear Double-Stranded Deoxyribonucleic Acid Adsorbed on Cu(111) Surfaces: a Low-Temperature Scanning Tunneling Microscopy Study

We have obtained high-resolution scanning tunneling microscopy (STM) images of poly(dA-dT)·poly(dA-dT) and poly(dG-dC)·poly(dG-dC) adsorbed on Cu(111) substrates. STM revealed that the two deoxyribonucleic acid molecules have different adsorbed structures and topographic heights. We concluded that the observed structural differences originate from the inherent differences in the stability of the adenine–thymine (A–T) and guanine–cytosine (G–C) base pairs.

Manipulation and characterization of xenon-metalloporphyrin complexation with a scanning tunneling microscope.

The formation of a series of Xe-CuEtioI [Cu(II) etioporphyrin I] complexes on Cu(001) surface was identified by scanning tunneling microscopy (STM) at cryogenic condition. The binding sites of xenon to CuEtioI molecule were directly revealed by high-resolution STM images in combination with controlled manipulation. The interaction between xenon atoms and CuEtioI in the on-top configuration is suggestive of a charge-induced dipole interaction. The structural parameters obtained with the STM complement results from spectroscopic studies of van der Waals complexes.

Dimers at Ge/Si(001) surfaces: Ge coverage dependent quenching, reactivation of flip-flop motion, and interaction with dimer vacancy lines

We studied Ge coverage $({\ensuremath{\theta}}_{\mathrm{Ge}})$ dependent quenching, reactivation of the flip-flop motion, and interaction with dimer vacancy lines (DVLs) of dimers on Ge/Si(001) surfaces using a scanning tunneling microscope (STM) combined with a molecular beam epitaxy apparatus. Deposition of $\ensuremath{\sim}0.3\mathrm{ML}$ (monolayer) Ge quenched the flip-flop motion, making all dimers asymmetric. Further deposition introduced DVLs at ${\ensuremath{\theta}}_{\mathrm{Ge}}>~\ensuremath{\sim}0.5\mathrm{ML},$ and symmetric dimer domains appeared again locally at $\ensuremath{\theta}>~1.5\mathrm{ML}.$ High-resolution STM images indicated that asymmetric dimer rows always invert their phase in alternation with buckled dimer's up-end at the DVLs. Low-temperature STM images indicated that the symmetric dimer domains were due to flip-flopping of asymmetric dimers activated by large ${\ensuremath{\theta}}_{\mathrm{Ge}}$ at room temperature. The symmetric dimer domains extended along the dimer rows over the DVLs due to the phase correlation.