Direct Imaging of Photoswitching Molecular Conformations Using Individual Metal Atom Markers

Atomic-Scale Imaging of Clay Mineral Nanosheets and Their Supramolecular Complexes through Electron Microscopy: A Supramolecular Chemist's Perspective

Recent advancements in electron microscopy techniques have revolutionized the ability to directly visualize and understand the intricate world of supramolecular chemistry. This paper provides a concise overview of a study delving into the atomic-scale imaging of monolayer clay mineral nanosheets and their associated supramolecular complexes. The imaging is conducted by harnessing the power of aberration-corrected scanning transmission electron microscopy (STEM). Clay mineral nanosheets, with their anionic charge and ultrathin thickness (of 1 nm), serve as a stable Coulombic host material for cationic guest molecules through electrostatic interactions, facilitating exceptional stability and control during observation. By incorporation of heavy-metal atom markers coordinated within the target molecules, high-angle annular dark field STEM enables a clear visualization of these supramolecular complexes. This approach helps to overcome the limitations of graphene-based systems and expands the possibilities of atomic-scale imaging of nonperiodic molecular assemblies formed by weak supramolecular interactions. The fusion of electron microscopy techniques with the principles of supramolecular and material chemistry offers exciting opportunities for studying the structure, behavior, and properties of complex supramolecular systems. It sheds light on the intricate molecular architectures and design principles governing these systems. This study showcases the immense potential of electron microscopy in supramolecular chemistry and invites researchers from various disciplines to explore the transformative possibilities of atomic-scale imaging in the field.

Electron beam-induced demetallation of Fe, Co, Ni, Cu, Zn, Pd, and Pt metalloporphyrins: insights in e-beam chemistry and metal cluster formations

Electron beams are versatile tools for nanoscale fabrication processes, however, the underlying e-beam chemistry remains in its infancy. Through operando transmission electron microscopy investigations, we elucidate a redox-driven cargo release of individual metal atoms triggered by electron beams. The chosen organic delivery molecule, tetraphenylporphyrin (TPP), proves highly versatile, forming complexes with nearly all metals from the periodic table and being easily processed in solution. A comprehensive cinematographic analysis of the dynamics of single metal atoms confirms the nearly instantaneous ejection of complexed metal atoms under an 80 kV electron beam, underscoring the system's broad versatility. Providing mechanistic insights, we employ density functional theory to support the proposed reductive demetallation pathway facilitated by secondary electrons, contributing novel perspectives to electron beam-mediated chemical reaction mechanisms. Lastly, our findings demonstrate that all seven metals investigated form nanoclusters once ejected from TPP, highlighting the method's potential for studying and developing sustainable single-atom and nanocluster catalysts.

Metal-Photoswitch Friendship: From Photochromic Complexes to Functional Materials

Cooperative metal-photoswitch interfaces comprise an application-driven field which is based on strategic coupling of metal cations and organic photochromic molecules to advance the behavior of both components, resulting in dynamic molecular and material properties controlled through external stimuli. In this Perspective, we highlight the ways in which metal-photoswitch interplay can be utilized as a tool to modulate a system's physicochemical properties and performance in a variety of structural motifs, including discrete molecular complexes or cages, as well as periodic structures such as metal-organic frameworks. This Perspective starts with photochromic molecular complexes as the smallest subunit in which metal-photoswitch interactions can occur, and progresses toward functional materials. In particular, we explore the role of the metal-photoswitch relationship for gaining fundamental knowledge of switchable electronic and magnetic properties, as well as in the design of stimuli-responsive sensors, optically gated memory devices, catalysts, and photodynamic therapeutic agents. The abundance of stimuli-responsive systems in the natural world only foreshadows the creative directions that will uncover the full potential of metal-photoswitch interactions in the coming years.

Mixed-Metal-Atom Markers Enable Simultaneous Imaging of Spatial Distribution in Two-Dimensional Heterogeneous Molecular Assembly by Scanning Transmission Electron Microscopy

Atomic-scale observation by aberration-corrected scanning transmission electron microscopy (STEM) is essential for characterizing supramolecular assemblies with nonperiodic structures. Identifying the relative spatial arrangement in a mixture of molecular species in an assembly is crucial for understanding chemical reaction systems occurring in the assembly. Herein, we report the first direct observation of supramolecular assemblies comprising anionic clay mineral nanosheets and two types of cationic porphyrin complexes with Pt and Pd atom markers by annular dark-field STEM, enabling the simultaneous imaging of well-mixed spatial molecular distributions. The results expand the possibility of applying electron microscopy to self-assembly structures constructed via weak supramolecular interactions on relatively thick nanosheet materials and on one- to few-atom-thick graphene analogues, which will provide important guidelines for future material design.

Real-Time, Time-Dependent Density Functional Theory Study on Photoinduced Isomerizations of Azobenzene Under a Light Field

The trans to cis photoisomerization of azobenzene and its reverse (i.e., the cis to trans) processes are studied using real-time propagation time-dependent density functional theory combined with molecular dynamics for ions. We show that the wavelength of the applied laser may significantly affect the transition process. The simulations also show that the photon-excited electrons play essential roles in the isomerization processes, in which the hot electrons couple to phonon modes that drive the transitions.

A Singular Molecule-to-Molecule Transformation on Video: The Bottom-Up Synthesis of Fullerene C60 from Truxene Derivative C60H30

Singular reaction events of small molecules and their dynamics remain a hardly understood territory in chemical sciences since spectroscopy relies on ensemble-averaged data, and microscopic scanning probe techniques show snapshots of frozen scenes. Herein, we report on continuous high-resolution transmission electron microscopic video imaging of the electron-beam-induced bottom-up synthesis of fullerene C₆₀ through cyclodehydrogenation of tailor-made truxene derivative 1 (C₆₀H₃₀), which was deposited on graphene as substrate. During the reaction, C₆₀H₃₀ transformed in a multistep process to fullerene C₆₀. Hereby, the precursor, metastable intermediates, and the product were identified by correlations with electron dose-corrected molecular simulations and single-molecule statistical analysis, which were substantiated with extensive density functional theory calculations. Our observations revealed that the initial cyclodehydrogenation pathway leads to thermodynamically favored intermediates through seemingly classical organic reaction mechanisms. However, dynamic interactions of the intermediates with the substrate render graphene as a non-innocent participant in the dehydrogenation process, which leads to a deviation from the classical reaction pathway. Our precise visual comprehension of the dynamic transformation implies that the outcome of electron-beam-initiated reactions can be controlled with careful molecular precursor design, which is important for the development and design of materials by electron beam lithography.

Metal atom-guided conformational analysis of single polynuclear coordination molecules

Microscopic observation of single molecules is a rapidly expanding field in chemistry and differs from conventional characterization techniques that require a large number of molecules. One of such form of single-molecule microscopy is high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), which is especially suitable for coordination compounds because of its atomic number-dependent contrast. However, to date, single-molecule observations using HAADF-STEM has limited to simple planar molecules. In the present study, we demonstrate a direct structural investigation of nonplanar dendronized polynuclear Ir complexes with subnanometer resolution using Ir as an atomic label. Decreasing the electron dose to the dendrimer complexes is critical for the single-molecule observation. A comparison with simulated STEM images of conformational isomers is performed to determine the most plausible conformation. Our results enlarge the potential of electron microscopic observation to realize structural analysis of coordination macromolecules, which has been impossible with conventional methods.

Self-Assembly of Bowlic Supramolecules on Graphene Imaged at the Individual Molecular Level using Heavy Atom Tagging

The self-assembly of bowlic supramolecules on graphene surface is studied with single molecular sensitivity. This is achieved by incorporating a heavy metal tag in the form of a single W atom into the tip of the molecular structure, which enables the direct imaging of molecular distribution using annular dark-field scanning transmission electron microscopy (ADF-STEM) along with graphene as an electron transparent support. The bowlic molecules have nonplanar geometry, and their orientations with respect to their graphene substrate and with each other result in various packing configurations. Statistical data on intermolecular distances is obtained from numerous measurements of the bright contrast from the single metal atom tags. The analysis shows that the bowlic molecules lie sideways on the graphene surface with favorable head-to-tail stacking, rather than sitting vertically with the bowl facing toward the graphene surface. In thicker film regions, nanoscale lamellar fringes are observed, demonstrating that large-scale aligned packing extends into 3D. Image simulations and various molecular packing schemes are discussed to help interpret the ADF-STEM images and the possible range of molecular interactions occurring. These results aid the understanding of nonplanar supramolecular assemblies on van der Waals surfaces for potential applications in molecular recognition by porous films.

Atomic-Scale Imaging of a Free-Standing Monolayer Clay Mineral Nanosheet Using Scanning Transmission Electron Microscopy

Although aberration-corrected scanning transmission electron microscope (STEM) enables the atomic-scale visualization of ultrathin 2D materials such as graphene, imaging of electron-beam sensitive 2D materials with structural complexity is an intricate problem. We here report the first atomic-scale imaging of a free-standing monolayer clay mineral nanosheet via the annular dark field (ADF) STEM. The monolayer clay nanosheet was stably observed under optimal conditions, and we confirmed that the hexagonal contrast pattern with a pore of ∼4 Å corresponds to the atomic structure of clay mineral that consisted of adjacent Si, Al, Mg, and O atoms by comparison with simulations. The findings offer the usefulness of ADF-STEM techniques for the atomic scale imaging of clay minerals and various 2D materials having electron-beam sensitivity and structural complexity than few-atom-thick graphene analogues.

Direct Imaging of Individual Molecular Binding to Clean Nanopore Edges in 2D Monolayer MoS2

We use annular dark-field scanning transmission electron microscopy (ADF-STEM) to study how solution-deposited molecules bind to the edges and surface regions around nanopores in MoS₂ monolayers. Nanopores with clean atomically flat edges and controllable mean diameter were generated by time-dependent large-area electron beam exposure during an in situ heating process, ready for subsequent molecular attachment. An organic molecule was designed to have a dithiolane end group that binds to Mo-terminated sites and a ligand structure that incorporates a single transition metal atom (Pt) marker for ADF-STEM detection. Pt atoms were used to track molecular binding around zigzag edges of MoS₂ and to predict the orientations and conformations of molecules upon binding. We found that the molecules preferred to reside on the surface of the MoS₂, pointing inward when attaching to the edge, rather than dangling out from the edge into free space, which is attributed to van der Waals interactions between the aromatic core of the molecule and the MoS₂ basal planes. These results help us understand the way solution-deposited single molecules attach to free-standing edges of 2D crystals and the influence of van der Waals forces in guiding molecular binding.

Distinctive stability of a free-standing monolayer clay mineral nanosheet via transmission electron microscopy

The distinctive stability of the monolayer clay mineral demonstrated by electron diffraction.

Photophysics Modulation in Photoswitchable Metal-Organic Frameworks

In this Review, we showcase the upsurge in the development and fundamental photophysical studies of more than 100 metal-organic frameworks (MOFs) as versatile stimuli-responsive platforms. The goal is to provide a comprehensive analysis of the field of photoresponsive MOFs while delving into the underlying photophysical properties of various classes of photochromic molecules including diarylethene, azobenzene, and spiropyran as well as naphthalenediimide and viologen derivatives integrated inside a MOF matrix as part of a framework backbone, as a ligand side group, or as a guest. In particular, the geometrical constraints, photoisomerization rates, and electronic structures of photochromic molecules integrated inside a rigid MOF scaffold are discussed. Thus, this Review reflects on the challenges and opportunities of using photoswitchable MOFs in next-generation multifunctional stimuli-responsive materials while highlighting their use in optoelectronics, erasable inks, or as the next generation of sensing devices.

Metal Atom Markers for Imaging Epitaxial Molecular Self-Assembly on Graphene by Scanning Transmission Electron Microscopy

Direct imaging of single molecules has to date been primarily achieved using scanning probe microscopy, with limited success using transmission electron microscopy due to electron beam damage and low contrast from the light elements that make up the majority of molecules. Here, we show single complex molecule interactions can be imaged using annular dark field scanning TEM (ADF-STEM) by inserting heavy metal markers of Pt atoms and detecting their positions. Using the high angle ADF-STEM Z^1.7 contrast, combined with graphene as an electron transparent support, we track the 2D monolayer self-assembly of solution-deposited individual linear porphyrin hexamer (Pt-L6) molecules and reveal preferential alignment along the graphene zigzag direction. The epitaxial interactions between graphene and Pt-L6 drive a reduction in the interporphyrin distance to allow perfect commensuration with the graphene. These results demonstrate how single metal atom markers in complex molecules can be used to study large scale packing and chain bending at the single molecule level.