High-resolution Scanning Tunneling Microscopy Images Research Articles

On-Surface Synthesis of Adenine Oligomers via Ullmann Reaction.

Despite the fact that DNA bases have been well-studied on surface, the on-surface synthesis of one-dimensional DNA analogs through in situ reactions is still an interesting topic to be investigated. Herein, from the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we have delicately designed a halogenated derivative of adenine as precursor to realize the combination of DNA bases and Ullmann reaction, and then successfully synthesized adenine oligomers on Au(111) via Ullmann coupling. This model system provides a possible bottom-up strategy of fabricating adenine oligomers on surface, which may further give access to man-made DNA strands with multiple bases.

Comment on “Different STM images of the superstructure on a clean Si(133)-6 × 2 surface” (JETP Letters 105, 477 (2017))

In the recent paper by Teys [JETP Letters 105 (8), 477-483 (2017)], an atomic model for the Si(331) reconstructed surface (hereby referred to as T-model) was proposed on the basis of high-resolution scanning tunneling microscopy (STM) images. While detailing the virtues against previous and abandoned models, the author avoids any reference to the rather distinct 8P-model advocated few weeks earlier by Zhachuk and Teys [R. Zhachuk, S. Teys, Phys. Rev. B 95, 041412 (2017)], casting doubts to his own work. Formulated that way, findings from Ref. [JETP Letters 105 (8), 477-483 (2017)] leave readers of JETP Letters with a partial and confusing view of the problem, and above all, leaves the observations open to ambiguous interpretation. The 8P-model is also based on STM measurements, and unlike the T-model, passed through the scrutiny of first-principles calculations. The present comment reconciles Ref. [JETP Letters 105 (8), 477-483 (2017)] with the literature by supplementing the discussion with a missing and critical account on the stability and electronic structure of the T- versus 8P-models of Si(331).

Synthesis of borophene nanoribbons on Ag(110) surface

We present the successful synthesis of single-atom-thick borophene nanoribbons (BNRs) by self-assembly of boron on Ag(110) surface. The scanning tunneling microscopy (STM) studies reveal high quality BNRs: all the ribbons are along the [-110] direction of Ag(110), and can run across the steps on the surface. The width of ribbons is distributed in a narrow range around 10.3 nm. High resolution STM images revealed four ordered surface structures in BNRs. Combined with DFT calculations, we found that all the four structures of boron nanoribbons consist of the boron chains with different width, separated by hexagonal hole arrays. The successful synthesis of BNRs enriches the low dimensional allotrope of boron and may promote further applications of borophene

STM study of the Ga thin films grown on Si(111) surface

Structural evolution of Ga thin films grown on the Si(111)-3×3-Ga template have been investigated with a low-temperature scanning tunneling microscopy (STM). The first Ga layer exhibits a stripe structure along the base vectors of Si(111) lattices. Individual Ga dimers have been directly visualized from the high-resolution STM images of the first Ga layer. The second Ga layer reveals a pseudo 1×1 structure with respect to the Si(111). A new 5×5 phase has been found in the second Ga layer when annealing the sample to 120℃. Further annealing to 150℃ leads to the formation of 6.3×6.3 phase, which is more stable than the 5×5 phase. The existences of a variety of superstructures of Ga films demonstrates the delicate balance between the interactions of Si(111)-Ga and Ga-Ga. These results shed important light on the epitaxial growth mechanism of Ga films on semiconductor surfaces.

Self-Assembled Structures of Benzoic Acid on Au(111) Surface

Electrochemical scanning tunneling microscopy combined with cyclic voltammetry were employed to explore the self-assembly of benzoic acid (BA) on a Au(111) substrate surface in a 0.1-M HClO4 solution. At the negatively charged surface, BA molecules form two highly ordered physisorbed adlayers with their phenyl rings parallel to the substrate surface. High-resolution scanning tunneling microscopy images reveal the packing arrangement and internal molecular structures. The striped pattern and zigzag structure of the BA adlayers are composed of parallel rows of dimers, in which two BA molecules are bound through a pair of O–H···O hydrogen bonds. Increasing the electrode potential further to positive charge densities of Au(111) leads to the desorption of the physisorbed hydrogen-bonded networks and the formation of a chemisorbed adlayer. BA molecules change their orientation from planar to upright fashion, which is accompanied by the deprotonation of the carboxyl group. Furthermore, potential-induced formation and dissolution of BA adlayers were also investigated. Structural transitions between the various types of ordered adlayers occur according to a nucleation and growth mechanism.

Real-space evidence of the formation of the GCGC tetrad and its competition with the G-quartet on the Au(111) surface.

From the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we show the first real-space evidence of the formation of GCGC tetrad on an Au(111) surface, and further investigate its competition with the well-known G-quartet with the aid of NaCl under ultrahigh vacuum (UHV) conditions.

Single-layer ZnS supported on Au(111): A combined XPS, LEED, STM and DFT study

Single-layer of ZnS, consisting of one atomic layer of ZnS(111) plane, has been grown on Au(111) and characterized using X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED) and scanning tunneling microscopy (STM). While the LEED measurement indicates a coincidence structure of ZnS-(3×3)/Au(111)-(4×4), high resolution STM images reveal hexagonal unit cells of 6.7×6.7Å2 and 11.6×11.6Å2, corresponding to √3 and 3 times the unit cell of the ideal zincblende ZnS-(1×1), respectively, depending on the tunneling conditions. Calculations based on density functional theory (DFT) indicate a significantly reconstructed non-planar structure of ZnS single-layer on Au(111) with 2/3 of the S anions being located nearly in the plane of the Zn cations and the rest 1/3 of the S anions protruding above the Zn plane. The calculated STM image shows similar characteristics to those of the experimental STM image. Additionally, the DFT calculations reveal the different bonding nature of the S anions in ZnS single-layer supported on Au(111).

Si Nanoribbons on Ag(110) Studied by Grazing-Incidence X-Ray Diffraction, Scanning Tunneling Microscopy, and Density-Functional Theory: Evidence of a Pentamer Chain Structure.

We report a combined grazing incidence x-ray diffraction (GIXD), scanning tunneling microscopy (STM), and density-functional theory (DFT) study which clearly elucidates the atomic structure of the Si nanoribbons grown on the missing-row reconstructed Ag(110) surface. Our study allows us to discriminate between the theoretical models published in the literature, including the most stable atomic configurations and those based on a missing-row reconstructed Ag(110) surface. GIXD measurements unambiguously validate the pentamer model grown on the reconstructed surface, obtained from DFT. This pentamer atomistic model accurately matches the high-resolution STM images of the Si nanoribbons adsorbed on Ag(110). Our study closes the long-debated atomic structure of the Si nanoribbons grown on Ag(110) and definitively excludes a honeycomb structure similar to that of freestanding silicene.

Investigation of the Effect of Thermal Annealing on Poly(3-hexylthiophene) Nanofibers by Scanning Probe Microscopy: From Single-Chain Conformation and Assembly Behavior to the Interfacial Interactions with Graphene Oxide.

Poly(3-hexylthiophene) (P3HT) has been widely used in devices owing to its excellent properties and structural features. However, devices based on pure P3HT have not exhibited high performance. Strategies, such as thermal annealing and surface doping, have been used to improve the electrical properties of P3HT. In this work, different from previous studies, the effect of thermal annealing on P3HT nanofibers are examined, ranging from the single polymer chain conformation to chain packing, and the interfacial interactions with graphene oxide (GO) at nanoscale dimensions, by using scanning tunneling microscopy (STM), atomic force microscopy (AFM) and Kelvin probe force microscopy (KPFM). High-resolution STM images directly show the conformational changes of single polymer chains after thermal annealing. The morphology of P3HT nanofibers and the surface potential changes of the P3HT nanofibers and GO is further investigated by AFM and KPFM at the nanoscale, which demonstrate that the surface potentials of P3HT decrease, whereas that of GO increases after thermal annealing. All of the results demonstrate the stronger interfacial interactions between P3HT and GO occur after thermal treatments due to the changes in P3HT chain conformation and packing order.

Adlayer structures of anthracenthiol on Au(111) after removal of covering multilayers with probe scan

Self-assembled monolayers (SAMs) of anthracene-2-thiol (AnT) on Au(111) have been investigated using scanning tunneling microscopy (STM). A preparation of AnT-SAMs from ethanolic solutions results in a deposition of multilayer films. As a result, the general features that have been frequently observed for different systems of thiol-modified gold surfaces are hidden in AnT-SAMs. The thin overlayers on top of the chemisorbed anthracenethiolate monolayer are removed by the STM-tip after a repetitive scanning over the same part of the SAM at nondestructive imaging conditions. After ∼2h of consecutive and continuous STM scanning, smooth AnT-SAM surfaces were formed. The polished surfaces contain vacancy depressions rather than the elevated gold islands which are typically formed after the adsorption of purely aromatic thiols such as AnT on Au(111). The STM data showed the coexistence of two distinct stable commensurate phases, namely, α and β. High-resolution STM images revealed a (3×8) structure for the α phase and a (7×4) R11° structure for the β phase whose unit cells contain, respectively, four and two molecules. The β phase was found to be 50% less densely packed than the α phase. The lower molecular density of the β phase should be correlated with a significantly larger tilt angle of the AnT molecular backbone with respect to the surface normal.

Real-Space Evidence of Rare Guanine Tautomer Induced by Water.

Water is vital for life as a solvent. Specifically, it has been well established that DNA molecules are hydrated in vivo, and water has been found to be responsible for the presence of some noncanonical DNA base tautomers. Theoretical investigations have shown that the existence of water could significantly influence the relative stability of different DNA base tautomers, reduce the energy barrier of tautomeric conversions, and thus promote the formation of some rare base tautomers. In this work, we report the real-space experimental evidence of rare base tautomers. From the high-resolution scanning tunneling microscopy imaging, we surprisingly find the formation of the rare guanine tautomer, i.e., G/(3H,7H) form, on the Au(111) surface by delicately introducing water into the system. The key to the formation of this rare tautomer is proposed to be the "water bridge" that largely reduces the energy barriers of intramolecular proton-transfer processes as revealed by extensive density functional theory calculations. The real-space experimental evidence and the proposed mechanism make a step forward toward the fundamental understanding of water-assisted base tautomerization processes.

Lepidocrocite-like TiO2 and TiO2(110)–(1 × 2) supported on W(100)

Ultrathin films of TiO2 were grown on a W(100)–O(2 × 1) substrate and characterised with a combination of scanning tunneling microscopy (STM) and low energy electron diffraction. In addition to islands of rutile TiO2(110) with (1 × 1) termination that were reported previously, we also observed rutile TiO2(110) islands with a (1 × 2) film termination. A lepidocrocite-like TiO2 nanosheet was also observed on the W(100) surface. High resolution STM images show that the nanosheet grows in the principal orthogonal directions of the W(100) substrate and forms a commensurate (1 × 7) coincident cell.

Dehydrogenative Homocoupling of Alkyl Chains on Cu(110).

Through the interplay of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, the stepwise dehydrogenative homocoupling of alkyl chains on Cu(110) is demonstrated, proceeding from the intact chain, via the dehydrogenative intermediates, to the formation of the divers final coupling products.

Atomic-Scale Insight into Tautomeric Recognition, Separation, and Interconversion of Guanine Molecular Networks on Au(111)

Although tautomerization may directly affect the chemical or biological properties of molecules, real-space investigation on the tautomeric behaviors of organic molecules in a larger area of molecular networks has been scarcely reported. In this paper, we choose guanine (G) molecule as a model system. From the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we have successfully achieved the tautomeric recognition, separation, and interconversion of G molecular networks (formed by two tautomeric forms G/9H and G/7H) with the aid of NaCl on the Au(111) surface in ultrahigh vacuum (UHV) conditions. Our results may serve as a prototypical system to provide important insights into tautomerization related issues, which should be intriguing to biochemistry, pharmaceutics, and other related fields.

Deprotonated Water Dimers: The Building Blocks of Segmented Water Chains on Rutile RuO2(110)

Despite the importance of RuO2 in photocatalytic water splitting and catalysis in general, the interactions of water with even its most stable (110) surface are not well understood. In this study we employ a combination of high-resolution scanning tunneling microscopy imaging with density functional theory based ab initio molecular dynamics, and we follow the formation and binding of linear water clusters on coordinatively unsaturated ruthenium rows. We find that clusters of all sizes (dimers, trimers, tetramers, extended chains) are stabilized by donating one proton per every two water molecules to the surface bridge bonded oxygen sites, in contrast with water monomers that do not show a significant propensity for dissociation. The clusters with odd number of water molecules are less stable than the clusters with even number and are generally not observed under thermal equilibrium. For all clusters with even numbers, the dissociated dimers represent the fundamental building blocks with strong intradimer hydrogen bonds and only very weak interdimer interactions resulting in segmented water chains.

Role of Specific Intermolecular Interactions for the Arrangement of Ni(II)-5, 10, 15, 20-Tetraphenyltetrabenzoporphyrin on Cu(111)

We have studied the coverage-dependent adsorption behavior of Ni(II)-5,10,15,20-tetraphenyltetrabenzoporphyrin on Cu(111) by scanning tunneling microscopy (STM) at room temperature. At medium coverages, the molecules self-assemble into two-dimensional islands, due to mutual stabilization through intermolecular interactions. Altogether, three different supramolecular arrangements coexist at low-to-medium coverages. On the basis of high-resolution STM images and density functional theory calculations, models for the three arrangements and the corresponding intramolecular conformations of the individual molecules are proposed. The observed polymorphism is attributed to a complex interplay of specific T-type and π–π stacking interactions between the phenyl groups. For Ni(II)-meso-tetrakis (4-tert-butylphenyl) benzoporphyrin, in which the aromatic periphery is modified by the attachment of tert-butyl groups, only one supramolecular arrangement on Cu(111) is found. This difference highlights the fact that the c...

Tunneling electron induced molecular electroluminescence from individual porphyrin J-aggregates

We investigate molecular electroluminescence from individual tubular porphyrin J-aggregates on Au(111) by tunneling electron excitations in an ultrahigh-vacuum scanning tunneling microscope (STM). High-resolution STM images suggest a spiral tubular structure for the porphyrin J-aggregate with highly ordered “brickwork”-like arrangements. Such aggregated nanotube is found to behave like a self-decoupled molecular architecture and shows red-shifted electroluminescence characteristics of J-aggregates originated from the delocalized excitons. The positions of the emission peaks are found to shift slightly depending on the excitation sites, which, together with the changes in the observed spectral profiles with vibronic progressions, suggest a limited exciton coherence number within several molecules. The J-aggregate electroluminescence is also found unipolar, occurring only at negative sample voltages, which is presumably related to the junction asymmetry in the context of molecular excitations via the carrier injection mechanism.

Temperature-triggered chemical switching growth of in-plane and vertically stacked graphene-boron nitride heterostructures.

In-plane and vertically stacked heterostructures of graphene and hexagonal boron nitride (h-BN-G and G/h-BN, respectively) are both recent focuses of graphene research. However, targeted synthesis of either heterostructure remains a challenge. Here, via chemical vapour deposition and using benzoic acid precursor, we have achieved the selective growth of h-BN-G and G/h-BN through a temperature-triggered switching reaction. The perfect in-plane h-BN-G is characterized by scanning tunnelling microscopy (STM), showing atomically patched graphene and h-BN with typical zigzag edges. In contrast, the vertical alignment of G/h-BN is confirmed by unique lattice-mismatch-induced moiré patterns in high-resolution STM images, and two sets of aligned selected area electron diffraction spots, both suggesting a van der Waals epitaxial mechanism. The present work demonstrates the chemical designability of growth process for controlled synthesis of graphene and h-BN heterostructures. With practical scalability, high uniformity and quality, our approach will promote the development of graphene-based electronics and optoelectronics.

Self-Assembled Patterns and Young’s Modulus of Single-Layer Naphthalocyanine Molecules on Ag(111)

Structural and mechanical properties of self-assembled metal-free naphthalocyanine (H2Nc) films on a Ag(111) surface are studied. Six self-assembled domains are observed by scanning tunneling microscopy (STM). Combining the high-resolution STM images and density functional theory (DFT) based calculations, we found that molecules adsorbed flatly on the substrate by forming six different interlocked square-like unit cells with different lattice parameters. DFT calculations indicated comparable adsorption energies for all the configurations. Six domains with different lattice parameters present different strain states, giving us a possibility to evaluate the Young’s modulus of the metal-free naphthalocyanine films on the Ag(111) surface. We found that the Young’s modulus of H2Nc is comparable to those of typical conjugated organic-molecule-based crystals (e.g., naphthalene), providing useful information for future applications when the elastic properties should be concerned.

Deposition of copper multilayers on Au(111) in sulfuric acid solution: An electrochemical scanning tunneling microscopy study

The co-adsorption of submono-, mono- and multi-layers of Cu with sulfate anions on a Au(111) electrode surface was investigated in electrochemical environment (0.1 mM CuSO4 + 0.1 M H2SO4) by cyclic voltammetry (CV) and in-situ scanning tunneling microscopy (STM). Correlated with the STM investigations the CV measurements indicate co-adsorption/-desorption processes of Cu of submono-, mono- and multi-layer coverages with sulfuric acid species on Au(111). The formation of a quasi-hexagonal Moiré superstructure on terraces of copper multilayers was observed in situ by STM. In detail the observed Moiré-structure is similar but not identical to the one observed on the (111) surface of bulk copper. High resolution STM images show the formation of a 3×7-like sulfate structure on all multilayer copper terraces.