High-resolution Scanning Tunneling Microscopy Images Research Articles

New insights into the structure of the Ag(111)-p(4 × 4)-O phase: high-resolution STM and DFT study.

The atomic structure of the Ag(111)-p(4 × 4)-O phase was reexamined with scanning tunneling microscopy (STM) and density functional theory. We discovered two different phases with the same (4 × 4) periodicity and demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images. Using bias dependencies of the STM images, we have shown that the p(4 × 4) phase is highly nonuniform, with local oxygen coverage varying from 1/8 ML up to 1/2 ML.

Remote regulation on the hydration sites of adenine molecules via derivatization

Hydration, as a ubiquitous and vital phenomenon in nature, has attracted great attention in the field of surface science concerning the fundamental interactions between water and organic molecules. However, the role of functional group derivatization is still elusive in terms of its potential impact on hydration. By the combination of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, the hydration of 9mA molecules was realized on Au(111) in real space, forming 9mA–H2O–9mA structures. In comparison with the hydration of adenine molecules, methyl derivatization is experimentally found to remotely regulate the hydration sites from the imidazole ring to the pyrimidine ring and is further theoretically revealed to allow intramolecular electron redistribution and, therefore, steer the priority of the hydration sites. These results provide sub-molecular understandings of the relationship between derivatization and hydration, which would shed light on the regulation of hydration processes in chemically and biologically related systems.

Epitaxial growth of Si thin films with hexagonal close-packed structures on metal substrates.

We have studied the epitaxial growth of Si thin films on the Cd(0001) surface using low-temperature scanning tunneling microscopy. When deposited at low temperatures (100K), Si atoms form dendritic islands with triangular shapes, indicating the existence of anisotropic edge diffusion in the process of Si film growth. After annealing to elevated temperatures, the triangular dendritic Si islands become hexagonal compact islands. Moreover, the 2D Si islands located on two different substrate terraces exhibit different heights due to the influence of quantum-well states in Cd(0001) films. Based on high-resolution scanning tunneling microscopy images, it is observed that the first, second, and third Si layers show the pseudomorphic 1 × 1 structure. In particular, the first and second layer islands reveal the opposite triangles, indicating the hexagonal close-packed stacking of Si atoms. These results provide important information for the growth of pristine Si films on metal substrates and the understanding of Si-metal interaction.

Visualizing Chiral Interactions in Carbohydrates Adsorbed on Au(111) by High-Resolution STM Imaging.

Carbohydrates are the most abundant organic material on Earth and the structural "material of choice" in many living systems. Nevertheless, design and engineering of synthetic carbohydrate materials presently lag behind that for protein and nucleic acids. Bottom-up engineering of carbohydrate materials demands an atomic-level understanding of their molecular structures and interactions in condensed phases. Here, high-resolution scanning tunneling microscopy (STM) is used to visualize at submolecular resolution the three-dimensional structure of cellulose oligomers assembled on Au(1111) and the interactions that drive their assembly. The STM imaging, supported by ab initio calculations, reveals the orientation of all glycosidic bonds and pyranose rings in the oligomers, as well as details of intermolecular interactions between the oligomers. By comparing the assembly of D- and L-oligomers, these interactions are shown to be enantioselective, capable of driving spontaneous enantioseparation of cellulose chains from its unnatural enantiomer and promoting the formation of engineered carbohydrate assemblies in the condensed phases.

Self-Assembly of Glutamic Acid and Serine on Au(111)

Amino acids provide novel and superior performance for two-dimensional materials and bio-based devices. The interaction and adsorption of amino acid molecules on substrates have thus attracted extensive research for exploring the driving forces involved in the formation of nanostructures. Nevertheless, the interactions within amino acid molecules on inert surfaces have not been fully understood. Herein, from the interplay of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, we show the self-assembled structures of Glu and Ser molecules on Au(111), which are dominated by intermolecular hydrogen bonds, and further investigate their most stable structural models at the atomic scale. This study would be of fundamental importance in understanding the formation processes of biologically relevant nanostructures and provide possibilities for chemical modification.

Formation and Thermal Stability of Ordered Self-Assembled Monolayers by the Adsorption of Amide-Containing Alkanethiols on Au(111).

We examined the surface structure, binding conditions, electrochemical behavior, and thermal stability of self-assembled monolayers (SAMs) on Au(111) formed by N-(2-mercaptoethyl)heptanamide (MEHA) containing an amide group in an inner alkyl chain using scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and cyclic voltammetry (CV) to understand the effects of an internal amide group as a function of deposition time. The STM study clearly showed that the structural transitions of MEHA SAMs on Au(111) occurred from the liquid phase to the formation of a closely packed and well-ordered β-phase via a loosely packed α-phase as an intermediate phase, depending on the deposition time. XPS measurements showed that the relative peak intensities of chemisorbed sulfur against Au 4f for MEHA SAMs formed after deposition for 1 min, 10 min, and 1 h were calculated to be 0.0022, 0.0068, and 0.0070, respectively. Based on the STM and XPS results, it is expected that the formation of a well-ordered β-phase is due to an increased adsorption of chemisorbed sulfur and the structural rearrangement of molecular backbones to maximize lateral interactions resulting from a longer deposition period of 1 h. CV measurements showed a significant difference in the electrochemical behavior of MEHA and decanethiol (DT) SAMs as a result of the presence of an internal amide group in the MEHA SAMs. Herein, we report the first high-resolution STM image of well-ordered MEHA SAMs on Au(111) with a (3 × 2√3) superlattice (β-phase). We also found that amide-containing MEHA SAMs were thermally much more stable than DT SAMs due to the formation of internal hydrogen networks in MEHA SAMs. Our molecular-scale STM results provide new insight into the growth process, surface structure, and thermal stability of amide-containing alkanethiols on Au(111).

Study of stereochemical crystallization of racemic mixtures of [5] and [7]thiaheterohelicene molecules on Ag(111) surface by scanning tunneling microscopy and Raman scattering spectroscopy

The crystallization of a racemic mixture of [5] and [7]thiaheterohelicene molecules into two-dimensional highly ordered molecular domains on a Ag(111) surface was investigated by scanning tunneling microscopy (STM) at 80 K. We observed that the crystallization of both thiaheterohelicene molecules on a Ag(111) surface was strongly affected by stereospecific interactions resulting from different numbers of aromatic rings incorporated into the helical skeletons of molecules. [5]Thiaheterohelicene molecules crystallized predominant into a few racemate polymorphic molecular domains, allowing us to obtain high-resolution STM images with the unambiguous identification of the absolute handedness of enantiomeric species. In contrast, the stereochemical chiral interactions among [7]thiaheterohelicene molecules led to the formation of one type of racemate molecular domain consisting of self-assembled zigzagged twin rows. X-ray photoelectron spectroscopy investigation strongly suggests weak interaction between thiaheterohelicene molecules and Ag(111) surface and lack of formation the S-Ag chemical bond. Surface-enhanced Raman spectroscopy combined with theoretical calculation based on a density functional theory was applied to the chemical verification of molecules adsorbed on a plasmonic silver surface for future tip-enhanced Raman spectroscopy.

Thermal oxidation process on Si(113)-(3 × 2) investigated using high-temperature scanning tunneling microscopy.

Thermal oxidation of Si(113) in a monolayer regime was investigated using high-temperature scanning tunneling microscopy (STM). Dynamic processes during thermal oxidation were examined in three oxidation modes – oxidation, etching, and transition modes – in the third of which both oxidation and etching occur. A precise temperature–pressure growth mode diagram was obtained via careful measurements for Si(113), and the results were compared with those for Si(111) in the present work and Si(001) in the literature. Initial oxidation processes were identified based on high-resolution STM images.

Morphology and electronic properties of incipient soot by scanning tunneling microscopy and spectroscopy

Soot nucleation is one of the most complex and debated steps of the soot formation process in combustion. In this work, we used scanning tunneling microscopy (STM) and spectroscopy (STS) to probe morphological and electronic properties of incipient soot particles formed right behind the flame front of a lightly sooting laminar premixed flame of ethylene and air. Particles were thermophoretically sampled on an atomically flat gold film on a mica substrate. High-resolution STM images of incipient soot particles were obtained for the first time showing the morphology of sub-5 nm incipient soot particles. High-resolution single-particle spectroscopic properties were measured confirming the semiconductor behavior of incipient soot particles with an electronic band gap ranging from 1.5 to 2 eV, consistent with earlier optical and spectroscopic observations.

Compressed sensing for scanning tunnel microscopy imaging of defects and disorder

Compressed sensing (CS) is a valuable technique for reconstructing measurements in numerous domains. CS has not yet gained widespread adoption in scanning tunneling microscopy (STM), despite potentially offering the advantages of lower acquisition time and enhanced tolerance to noise. Here we applied a simple CS framework, using a weighted iterative thresholding algorithm for CS reconstruction, to representative high-resolution STM images of superconducting surfaces and adsorbed molecules. We calculated reconstruction diagrams for a range of scanning patterns, sampling densities, and noise intensities, evaluating reconstruction quality for the whole image and chosen defects. Overall we find that typical STM images can be satisfactorily reconstructed down to 30\% sampling - already a strong improvement. We furthermore outline limitations of this method, such as sampling pattern artifacts, which become particularly pronounced for images with intrinsic long-range disorder, and propose ways to mitigate some of them. Finally we investigate compressibility of STM images as a measure of intrinsic noise in the image and a precursor to CS reconstruction, enabling a priori estimation of the effectiveness of CS reconstruction with minimal computational cost.

Self-assemblies of TTF derivatives with fluorinated phenyls and pyridine group

The self-assembly characteristics of tetrathiafulvalene (TTF) derivatives molecules 1–3 at the 1-phenyloctane/HOPG (HOPG = highly oriented pyrolytic graphite) interface had been carefully studied by scanning tunneling microscopy (STM) method. The number of F atoms on the phenyl group had significantly affected the self-assembly structures. High-resolution STM images make clear the different assembly structures between the molecules 1–3, which attribute to the different F atom numbers and pyridine group in the molecule. Density functional theory (DFT) calculations have been performed to reveal the formation mechanism.

On-Surface Fabrication of Bimetallic Metal-Organic Frameworks through the Synergy and Competition among Noncovalent Interactions.

Two-dimensional metal-organic frameworks (2D-MOFs) are attracting more attention due to their unique properties. Various 2D-MOF structures have been fabricated on surfaces in which either only one kind of metal was incorporated or only one kind of noncovalent interaction was involved in a bimetallic network. However, 2D-MOFs involving different kinds of noncovalent interactions and multiple metal components are more complex and less predictable. Here, we choose the uracil (U) molecule together with alkali metals [sodium (Na) and cesium (Cs)] and a transition metal [iron (Fe)] as model systems and successfully construct two kinds of bimetallic 2D-MOFs through the synergy and competition among noncovalent interactions, which is revealed by the high-resolution scanning tunneling microscopy imaging and density functional theory calculations. Such a systematic study may help to improve our fundamental understanding of the interaction mechanism of noncovalent bonds and, moreover, lead to further investigations of the unprecedented functions of surface-supported 2D-MOF structures.

Single Molecular Adsorption of Terbium(III) Bis-phthalocyaninato (TbPc2) Governed by Two Surface Reconstructions of Perovskite Type SrVO3 Epitaxial Ultrathin Film

Using low temperature scanning tunneling microscopy (STM), we observed a single molecule magnet, Tb3+ double decker molecule TbPc2 (Pc = phthalocyaninato), adsorbed on a perovskite type transition metal oxide SrVO3 ultrathin film. TbPc2 molecules adsorbed intact and flat on two surface reconstructions of SrVO3, -R45° and -R26.6°, with different configurations. High resolution STM images revealed that the adsorption configurations were governed by the adatom structure of each surface reconstruction according to the proposed adsorption configurations.

Directional observations of guanine and cytosine pairing structures on HOPG

Abstract The molecular self-assembly of deoxyribonucleic acid (DNA) plays an important role in understanding how nucleic acids form and can be exploited to construct nanostructures. In this study, scanning tunneling microscopy (STM) was used to observe nanostructures that form from co-adsorption of the guanine (G) and cytosine (C) complementary DNA bases on a highly oriented pyrolytic graphite surface. The high-resolution STM images show that the well-ordered co-adsorption structures are attributed to the rows formed from Watson–Crick G–C pairs, which are distinct from the structures observed for individual G–C components. The observed co-adsorption structure was modeled by density functional theory calculations, which provide information on the intermolecular interactions underlying its formation.

Construction of poly-naphthalocyanine linked by [4]-radialene-like structures on silver surfaces

Cyclic-conjugated linkages between planar-macrocydic molecules contribute to the robustness of the two-dimensional (2D) polymerization and extension of π-interactions. The fabrication of such linkages in 2D polymers remains challenging. Combining scanning tunneling microscope (STM) measurements and density functional theory (DFT) calculations, we demonstrate a linear polymerization of metal-free naphthalocyanine (NPc) molecules with [4]-radialene-like linkages on silver surfaces. Experimentally, by depositing NPc molecules on the Ag(110) surface and subsequent annealing up to 750 K, one-dimensional polymers are constructed along the [ $$1\overline 1 0$$ ] direction. High-resolution STM images show a stem-leaf-like feature. STM simulations based on a linear polymer of NPc molecules linked by four-membered carbon rings, [4]-radialene-like structure, agree well with the experimental observations. DFT calculations reveal that the polymerization process includes detaching two-terminal H atoms of NPc molecules along [ $$1\overline 1 0$$ ] direction, then bonding with a neighboring dehydrogenated NPc molecule by forming a four-membered ring. The dehydrogenation process can be promoted by on-surface impurities such as additional H atoms. Similar polymerizations have been achieved on Ag(111) surfaces in an amorphous way. Moreover, the energy gap of the NPc molecule decreases after linear polymerization, suggesting a red-shift for its optical absorption/scattering spectrum. Our study offers a new route to polymerize conjugated molecules with extended planar π-interactions.

Structural, Electronic, and Vibrational Properties of a Two-Dimensional Graphdiyne-like Carbon Nanonetwork Synthesized on Au(111): Implications for the Engineering of sp-sp2 Carbon Nanostructures.

Graphdiyne, atomically thin two-dimensional (2D) carbon nanostructure based on sp-sp2 hybridization is an appealing system potentially showing outstanding mechanical and optoelectronic properties. Surface-catalyzed coupling of halogenated sp-carbon-based molecular precursors represents a promising bottom-up strategy to fabricate extended 2D carbon systems with engineered structure on metallic substrates. Here, we investigate the atomic-scale structure and electronic and vibrational properties of an extended graphdiyne-like sp-sp2 carbon nanonetwork grown on Au(111) by means of the on-surface synthesis. The formation of such a 2D nanonetwork at its different stages as a function of the annealing temperature after the deposition is monitored by scanning tunneling microscopy (STM), Raman spectroscopy, and combined with density functional theory (DFT) calculations. High-resolution STM imaging and the high sensitivity of Raman spectroscopy to the bond nature provide a unique strategy to unravel the atomic-scale properties of sp-sp2 carbon nanostructures. We show that hybridization between the 2D carbon nanonetwork and the underlying substrate states strongly affects its electronic and vibrational properties, modifying substantially the density of states and the Raman spectrum compared to the free standing system. This opens the way to the modulation of the electronic properties with significant prospects in future applications as active nanomaterials for catalysis, photoconversion, and carbon-based nanoelectronics.

C60 self-orientation on hexagonal boron nitride induced by intermolecular coupling

A deep grasp of the properties of the interface between organic molecules and hexagonal boron nitride (h-BN) is essential for the full implementation of these two building blocks in the next generation of electronic devices. Here, using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS), we report on the geometric and electronic features of C60 evaporated on a single layer of h-BN grown on a Rh(110) surface under ultra-high vacuum. Two different molecular assemblies of C60 on the h-BN/Rh(110) surface were observed. The first STM study at room temperature (RT) and at low temperatures (40 K) looked at the molecular orientation of C60 on a two-dimensional layered material. Intramolecular-resolution images demonstrate the existence of a phase transition of C60 over the h-BN/Rh(110) surface similar to that found on bulk solid C60. At RT molecules exhibit random orientations, while at 40 K such rotational disorder vanishes and they adopt a common orientation over the h-BN/Rh(110) surface. The decrease in thermal energy allows recognition between C60 molecules, and they become equally oriented in the configuration at which the van der Waals intermolecular interactions are optimized. Bias-dependent submolecular features obtained by means of high-resolution STM images are interpreted as the highest occupied and lowest unoccupied molecular orbitals. STS data showed that fullerenes are electronically decoupled from the substrate, with a negligible charge transfer effect if any. Finally, the very early stages of multilayer growth were also investigated.

Influence of functional groups on the self-assembly of liquid crystals

Functional groups in the molecule play an important role in the molecular organization process. To reveal the influence of functional groups on the self-assembly at interface, herein, the self-assembly structures of three liquid crystal molecules, which only differ in the functional groups, are explicitly characterized by using scanning tunneling microscopy (STM). The high-resolution STM images demonstrate the difference between the supramolecular assembly structures of three liquid crystal molecules, which attribute to the hydrogen bonding interaction and π-π stacking interaction between different functional groups. The density functional theory (DFT) results also confirm the influence of these functional groups on the self-assemblies. The effort on the self-assembly of liquid crystal molecules at interface could enhance the understanding of the supramolecular assembly mechanism and benefit the further application of liquid crystals.

Solvent-Dependent Self-Assemblies and Pyridine Modulation of a Porphyrin Molecule at Liquid/Solid Interfaces.

On the highly oriented pyrolytic graphite (HOPG) surface, a new porphyrin molecule MT-4 containing a porphine core with six alkyl chains and two carboxyl groups has been explored using scanning tunneling microscopy (STM) technology. Solvent and pyridine regulation have been proved to be two effective ways to control and tune the supramolecular structure of MT-4 at interfaces. Different high-resolution STM (HR-STM) images with highly ordered and closely packed arrangements were gained at the corresponding liquid-solid interface, including phenyl octane (PO), 1-heptanoic acid (HA), and 1-hexanol. Except for the solvent effect, introducing pyridine derivatives such as 4,4'-vinylenedipyridine (DPE) and 4,4'-((1E,1'E)-(2,5-bis(octyloxy)-1,4-phenylene) bis(ethene-2,1-diyl)) dipyridine (PEBP-C8) is also effective to modulate the self-assembly of MT-4. With careful analysis of the STM pictures and the density functional theory (DFT) computational exploration, we figured out the molecular model, interaction energies, and self-assembly mechanism of each system at the interface. This work provides a simple and effective approach for quickly building diverse nanoarchitectures by utilizing different noncovalent interactions. Meanwhile, it would give a perspective to regulate and control self-assembly arrays for devising novel molecular-based materials through more optimal strategies.

Atomistic Positioning of Defects in Helium Ion Treated Single-Layer MoS2.

Structuring materials with atomic precision is the ultimate goal of nanotechnology and is becoming increasingly relevant as an enabling technology for quantum electronics/spintronics and quantum photonics. Here, we create atomic defects in monolayer MoS2 by helium ion (He-ion) beam lithography with a spatial fidelity approaching the single-atom limit in all three dimensions. Using low-temperature scanning tunneling microscopy (STM), we confirm the formation of individual point defects in MoS2 upon He-ion bombardment and show that defects are generated within 9 nm of the incident helium ions. Atom-specific sputtering yields are determined by analyzing the type and occurrence of defects observed in high-resolution STM images and compared with Monte Carlo simulations. Both theory and experiment indicate that the He-ion bombardment predominantly generates sulfur vacancies.