Bright Protrusions Research Articles

Interfacial Engineering of Mn Porphyrin/Au Electrodes for Identifying MnOx as the Active Species under Oxygen Evolution Reactions.

Understanding the influence of surface structural features at a molecular level is beneficial in guiding an electrode's mechanistic proposals for electrocatalytic reactions. The relationship between structural stability and catalytic activity significantly impacts reaction performance, even though atomistic knowledge of active sites remains a topic of discussion. In this context, this work presents scanning tunneling microscopy (STM) results for the highly ordered arrangement of manganese porphyrin molecules on a Au(111) surface; STM allows us to monitor active sites at a molecular level to focus on long-standing issues with the electrocatalytic process, especially the exact nature of the real active sites at the interfaces. After water oxidation, manganese porphyrin rapidly decomposes into active catalytic species as bright protrusions. These newly formed active species drastically lost catalytic activity, up to 82%, through only acid treatment, one of the oxide removal methods, not by deionized water and acetone treatments. STM results of the obviated active species on the Au surface by an acidic solution support the forfeited catalytic activity. In addition, it shows a 67% decrement in catalytic activity by adsorption of phosphonic acid, one of the oxide's preferred adsorption materials, compared to the pristine one. Based on these observations, we confirm that the newly formed active species, as water oxidation catalysts, mostly consist of manganese oxides. Notable findings of our work provide molecular evidence for the active sites of Au and modified Au electrodes that spur the future development of water oxidation catalysts.

Adsorption structure of macrocyclic energetic molecule DOATF on Au(111)

Furazan macrocyclic compound 3,4:7,8:11,12:15,16-tetrafurazan-1,9-dioxazo-5,13- diazocyclohexadecane (DOATF) is an ideal energetic material with high heat of formation. Here, using scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM), we investigated the adsorption structure of DOATF molecules on Au(111) surface, which shows the four furanzan rings in the STM images and a bright protrusion off the center of the molecule in the nc-AFM images. Combined with density functional theory (DFT) calculations, we confirmed that the bright feature in the nc-AFM images is an N–O coordinate bond pointing upwards in one of the two azoxy groups; while the other N–O bond pointing towards the Au(111) surface. Our work contributes for a deeper understanding of the adsorption structure of macrocyclic compounds, which would promote the designing of DOATF-metal frameworks.

Supramolecular Self-Assembly and Photo-Induced Transition of a Halogenated Azo-Benzene Molecule on Au(111) Surface

Azobenzene derivatives are a unique class of photo-switch molecules with promising potential for nanoscale optical applications. We have studied the self-assembly and photo-induced mechanical switching of azobenzene derivatives on Au(111) at the single-molecule level by using scanning tunneling microscope (STM). 4,4′-Dibromo-azobenzene (Br-AB) molecules are assembled into two types of well-ordered structures on Au(111) surfaces in the trans-isomer configuration. Br-AB molecules experienced configurational changes from trans-to-cis photo-isomerization upon the exposure to the UV light. This photo-isomerization of Br-AB molecules was observed to occur at random sites of ordered structure, evidenced by the appearance of bright protrusions with the height increment. Our results may open up new routes to engineer nanoscale photo-switch molecular devices.

Covalent and Hydrogen Bonding in Adsorption of Alanine Molecules on Si(111)7×7.

Molecular adsorption bonding configurations and specific interfacial chemistry of alanine on Si(111)7×7 have been determined by combining the results from scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). XPS spectra of the N 1s region show that alanine molecules bind to the 7×7 surface by N-Si covalent bonding, while STM imaging reveals that such N-H dissociative adsorption of alanine occurs on an adjacent Si adatom-restatom pair, with the dehydrogenated alanine moiety and dissociated H atom occupying the Si adatom and restatom sites, respectively. At a sample bias above +2 V, the dehydrogenated alanine appears as a bright round protrusion, slightly off-center from a Si adatom site and leaning toward the opposite Si adatom across the dimer wall. The off-center character can be attributed to an electrostatic attraction between the electron-rich carbonyl O of the dehydrogenated alanine and electron-deficient nearest Si adatom across the dimer wall. Our DFT calculation also shows that the monodentate O-Si bonding configuration resulting from O-H dissociative adsorption is more thermodynamically favorable than the experimentally observed N-Si bonding configuration, suggesting that the interfacial dissociative adsorption reaction is a kinetically controlled rather than a thermodynamically driven process. Alanine molecules in the second adlayer (transitional layer) are found to attach to those in the first adlayer (interfacial layer) by N···HO hydrogen bonding, as supported by the presence of the N 1s feature at 401.0 eV. An alanine molecule H-bonded to a dehydrogenated alanine in the first adlayer has also been observed in STM as a brighter and larger protrusion close to the expected location of the free OH group in the dehydrogenated first-adlayer alanine. No thick zwitterionic alanine film can be obtained at room temperature possibly due to steric constraint caused by the methyl group.

Bias-voltage dependent STM images from the 2–fold surface of the icosahedral Ag-In-Yb quasicrystal

The 2–fold surface of the icosahedral (i-)Ag–In–Yb quasicrystal has been investigated using scanning tunnelling microscopy (STM). STM data reveals a bias-voltage dependency. At high positive bias, bright protrusions are observed. At negative bias, new protrusions appear while the size of the original protrusions decreases. The STM features at both positive and negative bias polarities can be related to atomic planes intersecting the centre of Tsai-type clusters (the building blocks of the bulk structure). The bias-dependency can be explained by a change in contribution in tunnelling current from Yb and Ag/In, as expected from density of states calculations.

Chemisorption of Ethanol on Ge(100) Surface

Chemical reaction of ethanol (CH3CH2OH) with Ge(100) surface has been investigated using scanning tunneling microscopy (STM) observation and density functional theory (DFT) calculations. At low coverage, high-resolution STM images showed that ethanol dissociatively adsorbed on a single Ge dimer. The adsorption features included bright protrusions assigned to Ge–OCH2CH3 structure formed via O–H dissociation of ethanol. Real-time STM observations revealed that the molecular chain of ethanol increased gradually via successive adsorption along the dimer row direction following increased exposure to ethanol. DFT calculation results showed that the adsorption of ethanol on Ge(100) was dominated by kinetic control at room temperature. Thus, an integrated study of experimental and theoretical approaches coherently confirmed that ethanol reacts with Ge(100) via O–H dissociative adsorption and the final structure has the H–Ge–Ge–OCH2CH3 geometry on a single dimer of Ge(100).

Influence of Pb on an In/Si(111) surface on the phase transition and the surface structure

The influence of Pb atoms adsorbed on an In/Si(111) surface on the phase transition was investigated by using low-energy electron diffraction (LEED) and scanning tunneling microscopy (STM). LEED data showed that the transition temperature for the 4×1 → 8×2 structural phase transition decreased in proportion to the amount of Pb deposition. The Pb adatoms appeared as bright protrusions in an STM image taken at 90 K, suggesting that they were located high above the In atomic wires. The regions surrounding the Pb adatoms remained in the 4×1 phase while the other areas turned into the 8×2 or 4×2 phase at this temperature below the transition temperature. Near each Pb adatom, a Friedel-oscillation-like modulation with a double (×2) periodicity in the wire direction was developed. This ×2 modulation was found to be different in nature from the low-temperature 8×2 (or 4×2) phase. We suggest that a Pb-adatom-induced deep potential well is responsible for the Tc lowering and the ×2 modulation.

Anomalous hexagonal superstructure of aluminum oxide layer grown on NiAl(110) surface

A modified method for the fabrication of a highly crystallized layer of aluminum oxide on a NiAl(110) surface is reported. The fabrication method involves the multistep selective oxidation of aluminum atoms on a NiAl(110) surface resulting from successive oxygen deposition and annealing. The surface morphology and local electronic structure of the novel aluminum oxide layer were investigated by high-resolution imaging using scanning tunneling microscopy (STM) and current imaging tunneling spectroscopy. In contrast to the standard fabrication method of aluminum oxide on a NiAl(110) surface, the proposed method produces an atomically flat surface exhibiting a hexagonal superstructure. The superstructure exhibits a slightly distorted hexagonal array of close-packed bright protrusions with a periodicity of 4.5 ± 0.2 nm. Atomically resolved STM imaging of the aluminum oxide layer reveals a hexagonal arrangement of dark contrast spots with a periodicity of 0.27 ± 0.02 nm. On the basis of the atomic structure of the fabricated layer, the formation of α-Al2O3(0001) on the NiAl(110) surface is suggested.

Theoretical characterisation of point defects on a MoS2 monolayer by scanning tunnelling microscopy

Different S and Mo vacancies as well as their corresponding antisite defects in a free-standing MoS2 monolayer are analysed by means of scanning tunnelling microscopy (STM) simulations. Our theoretical methodology, based on the Keldysh nonequilibrium Green function formalism within the density functional theory (DFT) approach, is applied to simulate STM images for different voltages and tip heights. Combining the geometrical and electronic effects, all features of the different STM images can be explained, providing a valuable guide for future experiments. Our results confirm previous reports on S atom imaging, but also reveal a strong dependence on the applied bias for vacancies and antisite defects that include extra S atoms. By contrast, when additional Mo atoms cover the S vacancies, the MoS2 gap vanishes and a bias-independent bright protrusion is obtained in the STM image. Finally, we show that the inclusion of these point defects promotes the emergence of reactive dangling bonds that may act as efficient adsorption sites for external adsorbates.

Correlation between OH density and Fe electronic states of H/Fe3O4(001) film surfaces studied by scanning tunneling microscopy/spectroscopy

We report two types of adsorption structures in H/Fe3O4(001) film surfaces and the correlation between OH density and Fe electronic states, which have been studied by scanning tunneling microscopy/spectroscopy (STM/STS). Two types of bright protrusions (BPs), whose lengths along the atomic rows are different, are observed in the STM images. The shorter and longer BPs consist of Fe atoms with one and with two OH groups neighbor, respectively. In addition, STS measurements show the higher local density of states (LDOS) just below the Fermi level of Fe atoms with increasing neighboring OH groups. The variation can be attributed to the difference in the gain of electrons from H atoms, which is due to the difference in the number of neighboring OH groups. These results reveal that surface OH density is a factor for determining the LDOS just below the Fermi level of surface Fe atoms.

Pt atoms adsorbed onTiO2(110)−(1×1)studied with noncontact atomic force microscopy and first-principles simulations

We have studied the local properties of single Pt atoms adsorbed on hydroxylated ${\mathrm{TiO}}_{2}(110)$-($1\ifmmode\times\else\texttimes\fi{}1$) by combining noncontact atomic force microscopy (nc-AFM) and first-principles calculations. Room-temperature high-resolution nc-AFM images for the most frequently observed contrast modes reveal bright and elongated protrusions that can be traced back to the Pt atoms, and that are centered on the fivefold coordinated titanium rows, confined between two bridging oxygen rows. These observations are in line with the theoretical results, as the lowest energy sites for the Pt atom on the ${\mathrm{TiO}}_{2}(110)$ surface are in the neighborhood of the titanium rows, and high energy barriers have to be overcome to displace the Pt atom over the bridging oxygen rows. Single Pt atoms can be distinguished from H adsorbates (OH defects) due to their characteristic shape and binding site and, because they appear as the brightest surface features in all of the contrast modes. Force spectroscopy data over the protrusion and hole imaging modes and the corresponding tip-sample forces, simulated with O and OH terminated ${\mathrm{TiO}}_{2}$ nanoclusters, provide an explanation for this puzzling result in terms of the intrinsic strength of the interaction with the Pt adatom and the adatom and tip apex relaxations induced by the tip-sample interaction. These imaging mechanisms can be extended to other electropositive metal dopants and support the use of nc-AFM not only to characterize their adsorption structure but also to directly probe their chemical reactivity.

Electronic structure of the InP(111) $$A - \left( {\sqrt 3 \times \sqrt 3 } \right)$$ semiconductor surface

We present a first-principles theoretical study of the relative formation energies and the electronic states of the \(InP\left( {111} \right)A - \left( {\sqrt 3 \times \sqrt 3 } \right)\) surface. The energetically most favorable reconstruction has a T4-site P trimer on the surface, which exhibits a metallic band character and does not obey the electron counting rule (ECR). The stability of this structure is attributed to the balance between the ECR and the minimization of local distortion in the surface region. Our results for the simulated scanning tunneling microscopy images confirm the experimental interpretation of bright protrusions on the P trimers.

Surface structure and electronic states of epitaxialβ−FeSi2(100)/Si(001) thin films: Combined quantitative LEED,ab initioDFT, and STM study

The surface structure of epitaxial $\ensuremath{\beta}\text{\ensuremath{-}}{\mathrm{FeSi}}_{2}$(100) thin film grown on Si(001) was analyzed using the quantitative low-energy electron diffraction intensity-voltage (LEED I-V) method, ab initio density functional theory (DFT) calculations, and scanning tunneling microscopy (STM). LEED patterns measured on the $\ensuremath{\beta}\text{\ensuremath{-}}{\mathrm{FeSi}}_{2}$(100) surface reveal two domains of a $p(2\ifmmode\times\else\texttimes\fi{}2)$ reconstruction with $p2gg$ diffraction symmetry. The iron-silicide film truncation and atomic surface structure were determined by LEED I-V method: The smallest Pendry's reliability factor ${R}_{P}=0.22\ifmmode\pm\else\textpm\fi{}0.02$ was achieved for the bare $\ensuremath{\beta}\text{\ensuremath{-}}{\mathrm{FeSi}}_{2}$ film truncated by an Si layer, whereas Si and Fe ad-atom structures were excluded. Significant atomic relaxations within the topmost surface layers were revealed by the LEED I-V method and confirmed by DFT. The simulated STM patterns from the best-fit model agree well with the measured STM images on the $\ensuremath{\beta}\text{\ensuremath{-}}{\mathrm{FeSi}}_{2}(100)/\mathrm{Si}(001)\text{\ensuremath{-}}p(2\ifmmode\times\else\texttimes\fi{}2)$ surface: Four Si atoms on a surface form one bright protrusion on STM patterns. Electronic band structure analysis of the bulk and epitaxial $\ensuremath{\beta}\text{\ensuremath{-}}{\mathrm{FeSi}}_{2}$(100) was carried out. A bare truncated epitaxial film was found to be metallic. Surface electronic states were identified by a partial $k$-resolved atomic-orbital based local density-of-state analysis.

Hydrogen activation, diffusion, and clustering on CeO₂(111): a DFT+U study.

We present a comprehensive density functional theory+U study of the mechanisms underlying the dissociation of molecular hydrogen, and diffusion and clustering of the resulting atomic species on the CeO2(111) surface. Contrary to a widely held view based solely on a previous theoretical prediction, our results show conclusively that H2 dissociation is an activated process with a large energy barrier ~1.0 eV that is not significantly affected by coverage or the presence of surface oxygen vacancies. The reaction proceeds through a local energy minimum--where the molecule is located close to one of the surface oxygen atoms and the H-H bond has been substantially weaken by the interaction with the substrate--, and a transition state where one H atom is attached to a surface O atom and the other H atom sits on-top of a Ce(4+) ion. In addition, we have explored how several factors, including H coverage, the location of Ce(3+) ions as well as the U value, may affect the chemisorption energy and the relative stability of isolated OH groups versus pair and trimer structures. The trimer stability at low H coverages and the larger upward relaxation of the surface O atoms within the OH groups are consistent with the assignment of the frequent experimental observation by non-contact atomic force and scanning tunneling microscopies of bright protrusions on three neighboring surface O atoms to a triple OH group. The diffusion path of isolated H atoms on the surface goes through the adsorption on-top of an oxygen in the third atomic layer with a large energy barrier of ~1.8 eV. Overall, the large energy barriers for both, molecular dissociation and atomic diffusion, are consistent with the high activity and selectivity found recently in the partial hydrogenation of acetylene catalyzed by ceria at high H2/C2H2 ratios.

Writing with atoms: Oxygen adatoms on the MoO2/Mo(110) surface

Writing at the nanoscale using the desorption of oxygen adatoms from the oxygen-rich MoO2+x/Mo(110) surface is demonstrated by scanning tunnelling microscopy (STM). High-temperature oxidation of the Mo(110) surface results in a strained, bulk-like MoO2(010) ultra-thin film with an O-Mo-O trilayer structure. Due to the lattice mismatch between the Mo(110) and the MoO2(010), the latter consists of well-ordered molybdenum oxide nanorows separated by 2.5 nm. The MoO2(010)/Mo(110) structure is confirmed by STM data and density functional theory calculations. Further oxidation results in the oxygen-rich MoO2+x/Mo(110) surface, which exhibits perfectly aligned double rows of oxygen adatoms, imaged by STM as bright protrusions. These adatoms can be removed from the surface by scanning (or pulsing) at positive sample biases greater than 1.5 V. Tip movement along the surface can be used for controlled lithography (or writing) at the nanoscale, with a minimum feature size of just 3 nm. By moving the STM tip in a predetermined fashion, information can be written and read by applying specific biases between the surface and the tip. Open image in new window

Surface [4 + 2] Cycloaddition Reaction of Thymine on Si(111)7×7 Observed by Scanning Tunneling Microscopy

The early stage of thymine (Thy) adsorption on Si(111)7×7 surface is studied with scanning tunneling microscopy (STM) and density functional theory (DFT)-based computational method. Bright protrusions corresponding to the adsorbed thymine molecules are observed in both empty-state and filled-state STM images. These bright protrusions in the empty-state images exhibit three different degrees [lower (L), medium (M), and higher (H)] of intensities. The L and M protrusions are found on the adatom–restatom pairs in the 7 × 7 unit cell, indicating bidentate configurations for Thy adsorption. A free Thy molecule has been found to interact with the Si surface by a two-step process: Thy first undergoes keto–enol tautomerization to form the more stable dienol tautomer, which then binds to the Si adatom–restatom pair via the [4 + 2] cycloaddition reaction, leading to two different adproducts. Our DFT/B3LYP/6-31++G(d,p) calculations show three plausible cycloaddition products, with the 1,4-cyclohexadiene adproduct being more stable than 3,6- and 2,5-cyclohexadienes. Our calculations also suggest the viability of formation of a Thy molecule hydrogen-bonded with the bidentate Thy adproducts already on the surface. Statistical analysis for three different exposures of Thy on the 7 × 7 surface reveals that the L protrusion has the highest relative surface concentration (80%), with the M (16%) and H features (4%) being significantly less popular. These results lead us to attribute the L and M protrusions to the 1,4- and the 3,6-cycloaddition products, respectively, with the least popular H protrusion assigned to a Thy molecule hydrogen-bonded to the bidentate Thy, all attached to an adatom–restatom pair. The observation of [4 + 2] cycloaddition products on the Si surface confirms the formation of precursor dienol Thy tautomer. This surface-mediated two-step reaction pathway for Thy is unique for surfaces, in contrast to keto–enol tautomerization that is mainly observed in the solution phase either by acid- or base-catalyzed pathways. Our STM study coupled with our separate XPS work have demonstrated that this type of tautomerization can also be observed on Si surfaces, and this can initiate the subsequent cycloaddition reactions of Thy molecule with the surface.

Self-Directed Growth of Aligned Adenine Molecular Chains on Si(111)7×7: Direct Imaging of Hydrogen-Bond Mediated Dimers and Clusters at Room Temperature by Scanning Tunneling Microscopy

The early stage of adsorption of adenine on Si(111)7×7 is studied by scanning tunneling microscopy (STM). Bright protrusions are observed in both empty-state and filled-state STM images, indicative of molecular adsorption of adenine through dative bonding. The majority of these bright protrusions appear as dimer pairs formed by hydrogen bonding at the initial adsorption stage. The formation of dative bonds between the substrate and adenine and the feasibility of the H-bond mediated dimers are supported by ab initio DFT/B3LYP/6-31G++(d,p) calculations, and are in excellent accord with our recent X-ray photoemission data. Remarkably, these dimers are found to undergo self-organization into aligned superstructures, evidently with common link arrangements, including straight, offset, and zigzag chains, square quartets, double quartets, and other multiple dimer structures. As the exposure of adenine increases, the populations of dimers as well as the self-organized double dimer and other higher-order structures also increase. The end-to-end dimer links are found to be most prominent in the growth of adenine molecular chains, most notably aligned along the Si dimer-wall or [-1 1 0] direction of the 7×7 unit cell. The self-aligned adenine dimer molecular chains offer a natural template for catch-and-release biosensing, lithography, and molecular electronic applications.

Direct observation of hopping and merging of single Au adatoms to form dimers on Si(111)-(7 × 7)

Au single adatoms and dimers were imaged on Si(111)-(7 × 7) at different temperatures and bias voltages using a variable-temperature scanning tunneling microscope. At room temperature (RT), a single Au adatom induces sharp highlighted triangular features in the half unit cells (HUCs) of Si(111)-(7 × 7). These triangular features become fuzzy at temperatures lower than 225 K, as a result of the reduced moving speed of the single Au adatoms inside the HUCs. The formation of an Au adatom dimer was directly observed at RT when a single Au adatom in a HUC jumped into a neighboring HUC that already contained a single Au adatom. The Au adatom dimer appears either as a noisy feature in the central area of the HUC defined by three Si center adatoms or as a bright protrusion located close to a corner Si adatom site at RT. It was observed that a noisy feature also can change into a bright protrusion, inducing charge redistribution in the nearby Si adatoms in both the occupied and neighboring HUCs.

Noncontact Atomic Force Microscopy Observation of Fe3O4(001) Surface

Fe3O4 is one of the important oxide materials and its surface structure should be well understood to enable application of this material. We report the first noncontact atomic force microscopy (NC-AFM) results for Fe3O4(001) thin films. The observed films were grown homoepitaxially on magnetite thin films substrate. A low-energy electron diffraction pattern shows the well-known (√2×√2)R45° reconstructed structure. The observed minimum step height is 0.21 nm, corresponding to the distance between the same planes. We obtain two types of atomic-scale NC-AFM images. One image shows bright protrusions along the [100] and [010] directions at intervals of 0.84 nm corresponding to a unit cell of the (√2×√2)R45° reconstructed structure. The other image shows a more detailed atomic structure with 0.6 and 0.3 nm corrugations.

Surface atomic and electronic structure of Mn5Ge3on Ge(111)

The atomic and electronic structure of the Mn${}_{5}$Ge${}_{3}$(001) surface grown on Ge(111) $c$($2\ifmmode\times\else\texttimes\fi{}8$) has been studied in detail by angle-resolved photoelectron spectroscopy (ARPES), scanning tunneling microscopy (STM), and scanning tunneling spectroscopy. ARPES spectra recorded from the $\overline{\ensuremath{\Gamma}}$-$\overline{K}$-$\overline{M}$ and $\overline{\ensuremath{\Gamma}}$-$\overline{M}$-$\overline{\ensuremath{\Gamma}}$ directions of the surface Brillouin zone show six surface-related features. The STM images recorded at biases higher/lower than $\ifmmode\pm\else\textpm\fi{}$0.4 V always show a honeycomb pattern with two bright protrusions in each unit cell. At lower biases, a hexagonal, intermediate transition, and a honeycomb pattern are observed. These can be explained as arising from Mn and Ge atoms in the sublayer arranged in triangular structures and Mn atoms in the top layer arranged in a honeycomb structure, respectively. The photoemission and STM data from the germanide surface are discussed and compared to earlier published theoretical, photoelectron spectroscopy, and scanning tunneling microscopy studies.