Published papers

The adsorption and dissociation of water on a Ru(0001) surface containing a small amount (≤3%) of carbon impurities was studied by scanning tunneling microscopy (STM). Various surface species are formed depending on the temperature. These include molecular H2O, H2O−C complexes, H, O, OH, and CH. Clusters of either pure H2O or mixed H2O−OH species are also formed. Each of these species produces a characteristic contrast in the STM images and can be identified by experiment and by ab initio total energy calculations coupled with STM image simulations. Manipulation of individual species via excitation of vibrational modes with the tunneling electrons was used as supporting evidence.

Scanning tunneling microscopy and scanning tunneling spectroscopy combined with first-principles calculations have been applied to investigate the (111) surface of a naturally grown Fe3⁢O4 single crystal. The commonly observed surface is determined as a layer of Fe cations at tetrahedral sites, known as the Fetet1 termination. A surface terminated with Fe cations at octahedral sites, another proposed termination in previous studies, is found only when the surface was prepared under oxygen-poor conditions. Scanning tunneling spectra at room temperature and at 77 K indicate that the (111) surface undergoes a metal-insulator transition.

A two-dimensional fluorinated fullerene (C60F36) superstructure has been successfully formed on Au(111) and was investigated using scanning tunneling microscopy (STM) and density functional theory calculations. Although there exist three isomers (C3, C1, and T) in our molecular source, STM images of the molecules in the well-ordered region all appear identical, with 3-fold symmetry. This observation together with the differences in the calculated lowest unoccupied molecular orbital (LUMO) distribution among the three isomers suggests that a well-ordered monolayer consists of only the C3 isomer. Because of the strong electron-accepting ability of C60F36, the adsorption orientation can be explained by localized distribution of its LUMO, where partial electron transfer from Au(111) occurs. Intermolecular C–F···π electrostatic interactions are the other important factor in the formation of the superstructure, which determines the lateral orientation of C60F36 molecules on Au(111). On the basis of scanning tunneling spectra obtained inside the superstructure, we found that the LUMO is located at 1.0 eV above the Fermi level (EF), while the highest occupied molecular orbital (HOMO) is at 4.6 eV below the EF. This large energy gap with the very deep HOMO as well as uniform electronic structure in the molecular layer implies a potential for application of C60F36 to an electron transport layer in organic electronic devices.

A scanning tunneling microscopy study of a photochromic diarylethene adsorbed on Au and Cu reveals the reversal of thermodynamic stability between its two isomers compared to the gas phase, in solution, and its single crystal, which could result from the molecule–substrate interaction such as charge transfer and hybridization.

The structure and growth of water films on surfaces is reviewed, starting from single molecules to two-dimensional wetting layers, and liquid interfaces. This progression follows the increase in temperature and vapor pressure from a few degrees Kelvin in ultra-high vacuum, where Scanning Tunneling and Atomic Force Microscopies (STM and AFM) provide crystallographic information at the molecular level, to ambient conditions where surface sensitive spectroscopic techniques provide electronic structure information. We show how single molecules bind to metal and non-metal surfaces, their diffusion and aggregation. We examine how water molecules can be manipulated by the STM tip via excitation of vibrational and electronic modes, which trigger molecular diffusion and dissociation. We review also the adsorption and structure of water on non-metal substrates including mica, alkali halides, and others under ambient humid conditions. We finally discuss recent progress in the exploration of the molecular level structure of solid-liquid interfaces, which impact our fundamental understanding of corrosion and electrochemical processes.

meso-Dibenzoporphycene molecules adsorbed on the Ag(111) surface and on 2-monolayer-thick NaCl films were studied using submolecular resolution atomic force microscopy (AFM), scanning tunneling microscopy (STM), and first-principles calculations to clarify their stability and tautomerization behavior. We have found that the bonding of the molecules with the surface is determined by the interplay of different contributions, including the interaction of the π-aromatic orbitals of the benzene rings and the metal-coordination bond of the lone-pair electrons of the imine nitrogen atoms with the metal atoms (Ag, Na) on each substrate. The strength of the latter ultimately governs the molecular adsorption configuration and determines the nature and energy barriers for tautomerization. On Ag(111), the interaction of the imine nitrogen atoms with the Ag atoms deforms the macrocycle of porphycene, leading to a distinct AFM contrast that allows a clear identification of the molecule in its cis tautomeric form. In contrast, on NaCl films, the weaker interaction with the Na atoms leads to a flatter geometry and very similar adsorption configurations for the cis- and trans-forms, which cannot be distinguished in AFM experiments. Although weak, the dominant role of this local N-Na interaction, compared to the essentially nondirectional dispersive interactions, results in a new type of tautomerization process. In this case, the transfer of hydrogen atoms within the porphycene cavity is accompanied by a significant displacement of the whole molecule to a new site to reach a new minimum energy adsorption configuration. Our theoretical calculations indicate that this lateral translation, rather than the intramolecular H transfer, dominates the activation energy on NaCl. This novel tautomerization behavior, which we have identified on a rather inert ionic surface, might also be present on other weakly interacting substrates.

Visualization of periodically aligned pores in organic frameworks is a key to the understanding of their structural control. Comparing to monolayer-thick self-assembled molecular networks, real-space nanoscale characterization of thicker films, especially obtaining information on the stacking manner of molecules is challenging. Here, we report an atomic force microscopy study of hydrogen-bonded thin films fabricated at the air/liquid interface. The presence of one-dimensional channels is evidenced by resolving honeycomb structures over the films with the thickness variation of more than several nanometers. We also demonstrate that the film thickness can be controlled by the ratio of mixed solvent rather than the surface pressure during the fabrication at the air/liquid interface.

Molecular dynamics simulation using the reactive force field was performed to investigate the stability and formation mechanisms of organic porous thin films made of 1,3,5-tris(4-carboxyphenyl) benzene (BTB) molecules fabricated at the air/water interface. A single-layer honeycomb structure is found to be unstable, whereas thicker films are stable, which is consistent with experimental findings. The slight corrugation of the existing film produces local charge variation that attracts isolated molecules via the Coulomb interaction. When the isolated molecule approaches the film, a hydrogen bond is formed, and then the molecule adjusts the adsorption configuration by itself to maximize both horizontal and vertical intermolecular interactions. The key to the initial hydrogen bond formation is suggested to be the density of the molecules provided in the system as well as the spontaneous alignment of the BTB molecules to the solution/water interface. Our study showed that the BTB film is stable, and the molecules are self-assembled without external forces in the quasi-two-dimensional system. These results suggest that the dominant factor for the film formation at the air/water interface is interactions among BTB molecules and confinement to the two-dimensional space.

Understanding the structure of catalyst surfaces with adsorbed molecules is key to improving catalyst design. Scanning tunneling microscopy (STM) allows the observation of adsorption states and sites and provides insights into diffusion and desorption processes; however, the presence of multiple types of molecules on the surface presents challenges such as the identification of species and verification of reaction progress, particularly at room temperature or higher. In this study, we develop a protocol for the height classification analysis of STM images using the Watershed algorithm. This method is applied to a system involving the co-adsorption of H the Fe 3 O 4 2 O and CO on (111) surface, which represents the beginning of the water-gas shift reaction. Water molecules and dissociated OH species were identified in STM images of the Fe 3 O 4 (111) surface following the adsorption of water. Furthermore, gradual changes in the types of surface species were observed upon exposure of the surface to CO, indicating reaction progression. Our observations suggest that CO may react with molecular water rather than with dissociated OH on Fe sites. Despite its simplicity, the height classification analysis effectively identifies changes in the adsorbates on the catalyst surface. This method can be extended to other catalyst surfaces with adsorbed gasses.

Carbon black (CB) has wide range of industrial applications, including in the manufacturing of automobile tires, rubber products, inks, and plastics. To improve the properties of the target products and establish recycling systems, it must be fully characterized. However, characterization of CB is challenging owing to its structural complexity and the limitation of conventionally used experimental techniques, especially for surface structures at the nanoscale. In this study, we characterized the surface structures of two commercial CB via atomic force and scanning tunneling microscopy. Analysis of well-dispersed aggregates on atomically flat solid surfaces revealed primary particles of diverse sizes. The particle surfaces lacked edges, grooves, and steps that should be observed between stacked graphene sheets, which contradicts the widely accepted crystallite model. Observed images suggest that the graphene sheets exhibit a size distribution, inferring that multiple non-uniformly sized small graphene sheets are stacked turbostratically, with each sheet displaying a localized curvature rather than the ideal planar form. Varying size of sheets and curvature indicate the presence of a decent number of edges terminated with hydrogen and oxygen-containing functional groups. This interpretation was corroborated by conventional spectroscopic techniques: Raman spectroscopy, X-ray photoelectron spectroscopy, temperature-programmed desorption, and infrared absorption spectroscopy.

We observed a modification of transition pathways in polarized resonance Raman spectroscopy during tip-enhanced Raman spectroscopy (TERS) analysis of metallic carbon nanotubes (CNTs). At a spatial resolution reaching up to the sub-nanometer regime, the signal intensity of the typical D-band is observed to be even higher than the intensity of the G-band all over the probed CNTs in TERS imaging. The measured D-band is attributed to the non-vertical transitions of electrons in k-space that are facilitated by highly confined near-field light at the tip–sample junction of our scanning tunneling microscope based TERS system. The D-band signal was observed even when the CNTs were excited by light polarized perpendicular to the tube axis that corresponds to electronic excitations between different cutting line numbers of a CNT. By combining the electron pathways brought about by both the near-field light and its polarization, we found a unique optical transition of electrons of CNTs in near-field Raman spectroscopy.

Understanding how carbon dioxide (CO2) behaves and interacts with surfaces is paramount for the development of sensors and materials to attempt CO2 mitigation and catalysis. Here, we combine simultaneous atomic force microscopy (AFM) and scanning tunneling microscopy (STM) using CO-functionalized probes with density functional theory (DFT)-based simulations to gain fundamental insight into the behavior of physisorbed CO2 molecules on a gold(111) surface that also contains one-dimensional metal–organic chains formed by 1,4-phenylene diisocyanide (PDI) bridged by gold (Au) adatoms. We resolve the structure of self-assembled CO2 islands, both confined between the PDI–Au chains as well as free-standing on the surface and reveal a chiral arrangement of CO2 molecules in a windmill-like structure that encloses a standing-up CO2 molecule and other foreign species existing at the surface. We identify these species by the comparison of height-dependent AFM and STM imaging with DFT-calculated images and clarify the origin of the kagome tiling exhibited by this surface system. Our results show the complementarity of AFM and STM using functionalized probes and their potential, when combined with DFT, to explore greenhouse gas molecules at surface-supported model systems.

Understanding the reversible transformation between two isomeric states of organic molecules under external stimulation is essential for advancing single-molecule device development. Photochromic diarylethene (DAE) derivatives are promising candidates for single molecular switching elements. This study investigates the single-molecule reactions of the closed-form isomer of a DAE derivative on Cu(111) using scanning tunneling microscopy (STM). A novel ring-opening pathway, distinct from the well-known photochromic isomerization, was discovered. Electron injection into the lowest unoccupied molecular orbitals induces the sequential anchoring of molecules to the substrate through the dehydrogenation of a methyl group at the 2-position of the thiophene ring. This mechanism was revealed by density functional theory calculations and STM simulations. The adsorption configurations for singly and doubly dehydrogenated DAEs were identified. Based on these findings, a new reaction mechanism extending beyond reversible isomeric reactions is proposed for DAE on Cu(111). The present work establishes a novel framework for future studies on single-molecule switching phenomena on metal substrates.

High spatial resolution tip-enhanced Raman spectroscopy (TERS) measurements were carried out under ambient conditions on graphene nanobubbles with various associated structural features. The resulting signals were analyzed with consideration of the characteristic features inherent to high resolution TERS. Compared to flat graphene regions, nanobubbles and their associated nanoconvex pinning sites demonstrated enhanced TERS signals, attributed to the efficient coupling between the strong tip-enhanced electric field and out-of-plane deformations in graphene. Strong coupling with highly confined near-field light activates the D bands even in the absence of defects, with intensity depending on the degree of deformations. While the D band is observed across the nanobubbles, some local regions exhibit a weaker D band intensity compared to the surrounding areas. Given the finite number of hexagonal lattices within the area of highly confined near-field, this reduction in intensity is likely to result from defects that cause missing hexagonal lattices. These findings highlight the capability of near-field induced Raman signals in probing high resolution features of nanomaterials even under ambient conditions, providing deeper insights into their characteristics in situ.

Precise control over coordination structures and orientation is crucial for integrating metal–organic framework (MOF) thin films into functional devices. In this study, we combined atomic force microscopy with nano-Fourier transform infrared spectroscopy to definitively characterize local coordination bonding in a representative MOF thin film, NAFS-1, fabricated at the air/liquid interface. Our nanoscale analysis revealed structural inhomogeneities often obscured in macroscopic measurements. Additionally, we identified several characteristic regions in NAFS-1, including areas with uncoordinated carboxyl groups and with large, elevated features exhibiting effective coordination. Furthermore, omitting the water-rinsing step, usually conducted after transferring a film to the substrate to eliminate surface contaminants, increased structural inhomogeneity while promoting coordination bonding on average. These results highlight the importance of local characterization in understanding film crystallinity and uniformity and provide critical insights into the MOF thin-film formation mechanism at the air/liquid interface.