Identifying multiple configurations of complex molecules in dynamical processes: time resolved tunneling spectroscopy and density functional theory calculation

Probing surface properties of organic molecular layers by scanning tunneling microscopy

In view of the relevance of organic thin layers in many fields, the fundamentals, growth mechanisms, and dynamics of thin organic layers, in particular thiol-based self-assembled monolayers (SAMs) on Au(111) are systematically elaborated. From both theoretical and practical perspectives, dynamical and structural features of the SAMs are of great intrigue. Scanning tunneling microscopy (STM) is a remarkably powerful technique employed in the characterization of SAMs. Numerous research examples of investigation about the structural and dynamical properties of SAMs using STM, sometimes combined with other techniques, are listed in the review. Advanced options to enhance the time resolution of STM are discussed. Additionally, we elaborate on the extremely diverse dynamics of various SAMs, such as phase transitions and structural changes at the molecular level. In brief, the current review is expected to supply a better understanding and novel insights regarding the dynamical events happening in organic SAMs and how to characterize these processes.

Construction and physical properties of low-dimensional structures for nanoscale electronic devices

Over the past decades, construction of nanoscale electronic devices with novel functionalities based on low-dimensional structures, such as single molecules and two-dimensional (2D) materials, has been rapidly developed. To investigate their intrinsic properties for versatile functionalities of nanoscale electronic devices, it is crucial to precisely control the structures and understand the physical properties of low-dimensional structures at the single atomic level. In this review, we provide a comprehensive overview of the construction of nanoelectronic devices based on single molecules and 2D materials and the investigation of their physical properties. For single molecules, we focus on the construction of single-molecule devices, such as molecular motors and molecular switches, by precisely controlling their self-assembled structures on metal substrates and charge transport properties. For 2D materials, we emphasize their spin-related electrical transport properties for spintronic device applications and the role that interfaces among 2D semiconductors, contact electrodes, and dielectric substrates play in the electrical performance of electronic, optoelectronic, and memory devices. Finally, we discuss the future research direction in this field, where we can expect a scientific breakthrough.

Atomic-scale visualization of chiral charge density wave superlattices and their reversible switching

Chirality is essential for various phenomena in life and matter. However, chirality and its switching in electronic superlattices, such as charge density wave (CDW) superlattices, remain elusive. In this study, we characterize the chirality switching with atom-resolution imaging in a single-layer NbSe₂ CDW superlattice by the technique of scanning tunneling microscopy. The atomic arrangement of the CDW superlattice is found continuous and intact although its chirality is switched. Several intermediate states are tracked by time-resolved imaging, revealing the fast and dynamic chirality transition. Importantly, the switching is reversibly realized with an external electric field. Our findings unveil the delicate switching process of chiral CDW superlattice in a two-dimensional (2D) crystal down to the atomic scale.

Modification of the Potential Landscape of Molecular Rotors on Au(111) by the Presence of an STM Tip

Molecular rotors on solid surfaces are fundamental components of molecular machines. No matter whether the rotation is activated by heat, electric field or light, it is determined by the intrinsic rotational potential landscape. Therefore, tuning the potential landscape is of great importance for future applications of controlled molecular rotors. Here, using scanning tunneling microscopy (STM), we demonstrate that both tip-molecule distance and sample bias can modify the rotational potential of molecular rotors. We achieve the potential energy difference variations of ∼0.3 meV/pm and ∼18 meV/V between two configurations of a molecular rotor, a tetra- tert-butyl nickel phthalocyanine molecule on Au(111) substrate. Further analysis indicates that the mechanism of modifying the rotational potential is a combination of the van der Waals interaction and the interaction between the molecular dipole and an electric field. This work provides insight into the methods used to modify the effective rotational potential energy of molecular rotors.

Conformational Contrast of Surface-Mediated Molecular Switches Yields Ångstrom-Scale Spatial Resolution in Ultrahigh Vacuum Tip-Enhanced Raman Spectroscopy

Tip-enhanced Raman spectroscopy (TERS) combines the ability of scanning probe microscopy (SPM) to resolve atomic-scale surface features with the single-molecule chemical sensitivity of surface-enhanced Raman spectroscopy (SERS). Here, we report additional insights into the nature of the conformational dynamics of a free-base porphyrin at room temperature adsorbed on a metal surface. We have interrogated the conformational switch between two metastable surface-mediated isomers of meso-tetrakis(3,5-ditertiarybutylphenyl)-porphyrin (H₂TBPP) on a Cu(111) surface. At room temperature, the barrier between the porphyrin ring buckled up/down conformations of the H₂TBPP-Cu(111) system is easily overcome, and a 2.6 Å lateral resolution by simultaneous TERS and STM analysis is achieved under ultrahigh vacuum (UHV) conditions. This work demonstrates the first UHV-TERS on Cu(111) and shows TERS can unambiguously distinguish the conformational differences between neighboring molecules with Ångstrom-scale spatial resolution, thereby establishing it as a leading method for the study of metal-adsorbate interactions.

Catalytic aspects of metallophthalocyanines adsorbed on gold-electrode. Theoretical exploration of the binding nature role

We report a computational study of supramolecular complexes of metallophthalocyanines (MPcs, M = Fe, Co, Cu) on gold substrates, and the effect of the substrate on their electrocatalytic properties at the DFT and DFT-D3 levels.

Dynamics of copper-phthalocyanine molecules on Au/Ge(001)

Spatially resolved current-time scanning tunneling spectroscopy combined with current-distance spectroscopy has been used to characterize the dynamic behavior of copper-phthalocyanine (CuPc) molecules adsorbed on a Au-modified Ge(001) surface. The analyzed CuPc molecules are adsorbed in a "molecular bridge" configuration, where two benzopyrrole groups (lobes) are connected to a Au-induced nanowire, whereas the other two lobes are connected to the adjacent nanowire. Three types of lobe configurations are found: a bright lobe, a dim lobe, and a fuzzy lobe. The dim and fuzzy lobes exhibit a well-defined switching behavior between two discrete levels, while the bright lobe shows a broad oscillation band. The observed dynamic behavior is induced by electrons that are injected into the LUMO+1 orbital of the CuPc molecule. By precisely adjusting the tip-molecule distance, the switching frequency of the lobes can be tuned accurately.

Imaging the dynamics of individually adsorbed molecules

Although noise is observed in many experiments, it is rarely used as a source of information. However, valuable information can be extracted from noisy signals. The motion of particles on a surface induced, for example, by thermal activation or by the interaction with the tip of a scanning tunnelling microscope may lead to fluctuations or switching of the tunnelling current. The analysis of these processes gives insight into dynamics on a single atomic or molecular level. Unfortunately, scanning tunnelling microscopy (STM) is not a useful tool to study dynamics in detail, as it is an intrinsically slow technique. Here, we show that this problem can be solved by providing a full real-time characterization of random telegraph noise in the current signal. The hopping rate, the noise amplitude and the relative occupation of the involved states are measured as a function of the tunnelling parameters, providing spatially resolved maps. In contrast to standard STM, our technique gives access to transiently populated states revealing an electron-driven hindered rotation between the equilibrium and two metastable positions of an individually adsorbed molecule. The new approach yields a complete characterization of copper phthalocyanine molecules on Cu(111), ranging from dynamical processes on surfaces to the underlying electronic structure on the single-molecule level.

Identifying multiple configurations of complex molecules on metal surfaces

Experimental identification of molecular configurations in diffusion processes of large complex molecules has been a demanding topic in the field of molecular construction at solid surfaces. Such identification is needed in order to control the self-assembly process and the properties and configurations of the resulting structures. This paper provides an overview of state-of-the-art techniques for identification of molecular configurations in motion. First, a brief introduction to the conventional tools is presented, for example, low-energy electron diffraction and IR/Raman spectroscopy. Second, currently used techniques, scanning probe microscopy, and its application in molecular configuration identification are reviewed. In the last part, a methodology combining time-resolved tunneling spectroscopy and density functional theory calculation is reviewed in detail; this strategy has been successfully applied to two typical molecular systems, (t-Bu)₄ -ZnPc and FePc (where Pc is phthalocyanine), with molecular rotation and laterial diffusion on the Au(111) surface.

Electron-induced dynamics of heptathioether β-cyclodextrin molecules

Variable-temperature scanning tunneling microscopy (STM) and spectroscopy (STS) measurements are performed on heptathioether β-cyclodextrin (β-CD) self-assembled monolayers (SAMs) on Au. The β-CD molecules exhibit very rich dynamical behavior, which is not apparent in ensemble-averaged studies. The dynamics are reflected in the tunneling current-time traces, which are recorded with the STM feedback loop disabled. The dynamics are temperature independent, but increase with increasing tunneling current and sample bias, thus indicating that the conformational changes of the β-CD molecules are induced by electrons that tunnel inelastically. Even for sample biases as low as 10 mV, well-defined levels are observed in the tunneling current-time traces. These jumps are attributed to the excitations of the molecular vibration of the macrocyclic β-CD molecule. The results are of great importance for a proper understanding of transport measurements in SAMs.

A density functional theory study of the adsorption of uracil on the Au(100) surface

We have used plane-wave density functional theory methods to explore the adsorption modes and configurations of uracil molecules on a gold surface to gain insight into the rational design of surface functionalization. We have investigated at the molecular level, the interactions of the RNA pyrimidine base uracil molecule isolated on the single crystal (100) surface of the gold substrate to determine the structure of uracil and orientation. Our calculations have shown that the most stable adsorbate structure is the enol tautomer of uracil, which adsorbs flat onto the gold surface through one of its carbonyl atoms. This configuration, which is compatible with previous experimental findings, is thermodynamically preferred over the adsorbed keto structure by approximately 0.23 eV (22.2 kJ mol −1 ).