Fluorine in Shark Teeth: Its Direct Atomic‐Resolution Imaging and Strengthening Function

Atomic‐resolution imaging of beam‐sensitive biominerals is extremely challenging, owing to their fairly complex structures and the damage caused by electron irradiation. Herein, we overcome these difficulties by performing aberration‐corrected electron microscopy with low‐dose imaging techniques, and report the successful direct atomic‐resolution imaging of every individual atomic column in the complex fluorapatite structure of shark tooth enameloid, which can be of paramount importance for teeth in general. We demonstrate that every individual atomic column in shark tooth enameloid can be spatially resolved, and has a complex fluorapatite structure. Furthermore, ab initio calculations show that fluorine atoms can be covalently bound to the surrounding calcium atoms, which improves understanding of their caries‐reducing effects in shark teeth.     

In situ scanning probe microscopy and new perspectives in analytical chemistry

The resolution of scanning tunnelling microscopy (STM) and other scanning probe microscopies is unprecedented but the techniques are fraught with limitations as analytical tools. These limitations and their relationship to the physical mechanisms of image contrast are first discussed. Some new options based on in situ STM, which hold prospects for molecular- and mesoscopic-scale analytical chemistry, are then reviewed. They are illustrated by metallic electro-crystallisation and -dissolution, and in situ STM spectroscopy of large redox molecules. The biophysically oriented analytical options of in situ atomic force microscopy, and analytical chemical perspectives for the new microcantilever sensor techniques are also discussed.     

Structural and Chemical Analysis of Materials with High Spatial Resolution

 An understanding of the correlation between microstructures and properties of materials require the characterization of the material on many different length scales. Often the properties depend primarily on the atomistics of defects, such as dislocations and interfaces. The different techniques of transmission electron microscopy allow the characterization of the structure and of the chemical composition of materials with high spatial resolution to the atomic level: high resolution transmission electron microscopy allows the determination of the position of the columns of atoms (ions) with high accuracy. The accuracy which can be achieved in these measurements depends not only on the instrumentation but also on the quality of the transmitted specimen and on the scattering power of the atoms (ions) present in the analyzed column. The chemical composition can be revealed from investigations by analytical microscopy which includes energy dispersive X-ray spectroscopy, mainly quantitatively applied for heavy elements, and electron energy-loss spectroscopy. Furthermore, the energy-loss near-edge structure of EELS data results in information on the local band structure of unoccupied states of the excited atoms and, therefore, on bonding. A quantitative evaluation of convergent beam electron diffraction results in information on the electron charge density distribution of the bulk (defect-free) material. The different techniques are described and applied to different problems in materials science. It will be shown that nearly atomic resolution can be achieved in high resolution electron microscopy and in analytical electron microscopy. Recent developments in electron microscopy instrumentation will result in atomic resolution in the foreseeable future.     

Resolving the Unpaired‐Electron Orbital Distribution in a Stable Organic Radical by Kondo Resonance Mapping

The adsorption geometry and the electronic structure of a Blatter radical derivative on a gold surface were investigated by a combination of high‐resolution noncontact atomic force microscopy and scanning tunneling microscopy. While the hybridization with the substrate hinders direct access to the molecular states, we show that the unpaired‐electron orbital can be probed with Ångström resolution by mapping the spatial distribution of the Kondo resonance. The Blatter derivative features a peculiar delocalization of the unpaired‐electron orbital over some but not all moieties of the molecule, such that the Kondo signature can be related to the spatial fingerprint of the orbital. We observe a direct correspondence between these two quantities, including a pronounced nodal plane structure. Finally, we demonstrate that the spatial signature of the Kondo resonance also persists upon noncovalent dimerization of molecules.     

Electron Cryo‐microscopy as a Tool for Structure‐Based Drug Development

For decades, X‐ray crystallography and NMR have been the most important techniques for studying the atomic structure of macromolecules. However, as a result of size, instability, low yield, and other factors, many macromolecules are difficult to crystallize or unsuitable for NMR studies. Electron cryo‐microscopy (cryo‐EM) does not depend on crystals and has therefore been the method of choice for many macromolecular complexes that cannot be crystallized, but atomic resolution has mostly been beyond its reach. A new generation of detectors that are capable of sensing directly the incident electrons has recently revolutionized the field, with structures of macromolecules now routinely being solved to near‐atomic resolution. In this review, we summarize some of the most recent examples of high‐resolution cryo‐EM structures. We put particular emphasis on proteins with pharmacological relevance that have traditionally been inaccessible to crystallography. Furthermore, we discuss examples where interactions with small molecules have been fully characterized at atomic resolution. Finally, we stress the current limits of cryo‐EM, and methodological issues related to its usage as a tool for drug development.     

On‐Surface Bottom‐Up Synthesis of Azine Derivatives Displaying Strong Acceptor Behavior

On‐surface synthesis is an emerging approach to obtain, in a single step, precisely defined chemical species that cannot be obtained by other synthetic routes. The control of the electronic structure of organic/metal interfaces is crucial for defining the performance of many optoelectronic devices. A facile on‐surface chemistry route has now been used to synthesize the strong electron‐acceptor organic molecule quinoneazine directly on a Cu(110) surface, via thermally activated covalent coupling of para‐aminophenol precursors. The mechanism is described using a combination of in situ surface characterization techniques and theoretical methods. Owing to a strong surface‐molecule interaction, the quinoneazine molecule accommodates 1.2 electrons at its carbonyl ends, inducing an intramolecular charge redistribution and leading to partial conjugation of the rings, conferring azo‐character at the nitrogen sites.     

Chemical Imaging of Monolayers on Metal Surfaces: Applications in Corrosion,Catalysis, and Self‐Assembled Monolayers

In situ techniques are indispensable to understanding many topics in surface chemistry. As a consequence, several spectroscopic methods have been developed to provide molecular‐level information that only spectroscopy can supply. However, as important as this information is, it is just as critical to realize that nearly all surfaces under investigation have spatial heterogeneities of the order of nanometers to millimeters; thus, spatial analysis is very important to the overall interpretation. This Minireview focuses on a few of the recent developments in spectroscopic techniques that can provide spatial, spectroscopic, and in situ information. These techniques include photo‐electron microscopy, infrared and Raman imaging, and nonlinear optical imaging vibrational spectroscopy as applied to topics in corrosion, catalysis and self‐assembled monolayers.     

Integrated Transmission Electron and Single‐Molecule Fluorescence Microscopy Correlates Reactivity with Ultrastructure in a Single Catalyst Particle

Establishing structure–activity relationships in complex, hierarchically structured nanomaterials, such as fluid catalytic cracking (FCC) catalysts, requires characterization with complementary, correlated analysis techniques. An integrated setup has been developed to perform transmission electron microscopy (TEM) and single‐molecule fluorescence (SMF) microscopy on such nanostructured samples. Correlated structure–reactivity information was obtained for 100 nm thin, microtomed sections of a single FCC catalyst particle using this novel SMF‐TEM high‐resolution combination. High reactivity in a thiophene oligomerization probe reaction correlated well with TEM‐derived zeolite locations, while matrix components, such as clay and amorphous binder material, were found not to display activity. Differences in fluorescence intensity were also observed within and between distinct zeolite aggregate domains, indicating that not all zeolite domains are equally active.     

Highly Intact and Pure Oxo‐Functionalized Graphene: Synthesis and Electron‐Beam‐Induced Reduction

Controlling the chemistry of graphene is necessary to enable applications in materials and life sciences. Research beyond graphene oxide is targeted to avoid the highly defective character of the carbon framework. Herein, we show how to optimize the synthesis of oxo‐functionalized graphene (oxo‐G) to prepare high‐quality monolayer flakes that even allow for direct transmission electron microscopy investigation at atomic resolution (HRTEM). The role of undesired residuals is addressed and sources are eliminated. HRTEM provides clear evidence for the exceptional integrity of the carbon framework of such oxo‐G sheets. The patchy distribution of oxo‐functionality on the nm‐scale, observed on our highly clean oxo‐G sheets, corroborates theoretical predictions. Moreover, defined electron‐beam irradiation facilitates gentle de‐functionalization of oxo‐G sheets, a new route towards clean graphene, which is a breakthrough for localized graphene chemistry.     

Make them Blink: Probes for Super‐Resolution Microscopy

In recent years, a number of approaches have emerged that enable far‐field fluorescence imaging beyond the diffraction limit of light, namely super‐resolution microscopy. These techniques are beginning to profoundly alter our abilities to look at biological structures and dynamics and are bound to spread into conventional biological laboratories. Nowadays these approaches can be divided into two categories, one based on targeted switching and readout, and the other based on stochastic switching and readout of the fluorescence information. The main prerequisite for a successful implementation of both categories is the ability to prepare the fluorescent emitters in two distinct states, a bright and a dark state. Herein, we provide an overview of recent developments in super‐resolution microscopy techniques and outline the special requirements for the fluorescent probes used. In combination with the advances in understanding the photophysics and photochemistry of single fluorophores, we demonstrate how essentially any single‐molecule compatible fluorophore can be used for super‐resolution microscopy. We present examples for super‐resolution microscopy with standard organic fluorophores, discuss factors that influence resolution and present approaches for calibration samples for super‐resolution microscopes including AFM‐based single‐molecule assembly and DNA origami.     

In Situ Formation of Au–Pd Bimetallic Active Sites Promoting the Physically Mixed Monometallic Catalysts in the Liquid‐Phase Oxidation of Alcohols

The catalytic oxidation of alcohols with molecular oxygen on supported nanometallic catalysts represents one of the green methods in a crucial process for the synthesis of fine chemicals. We have designed an experiment using physically mixed Au/AC and Pd/AC (AC=activated carbon) as the catalyst in the liquid‐phase oxidation of benzyl alcohol by aerobic oxygen. The evolution of the physically mixed catalyst structures at different stages in the catalytic reaction was investigated by aberration‐corrected high‐resolution transmission electron microscopy and spatially resolved element mapping techniques at the nanometre scale, and they were also compared with the structure of the bimetallic alloy. For the first time we show the formation of surface Au–Pd bimetallic sites by reprecipitation of Pd onto Au nanoparticles. Negligible Au leaching was observed. The in situ structural evolution can be directly correlated to the great enhancement of the catalyst activity. Moreover, we distinguish the different behaviours of Au and Pd, thus suggesting an oxygen differentiating mechanism for Au and Pd sites. The findings are of great importance to both the understanding of the structure–activity correlation and the design of highly active catalysts in green chemistry.     

Microscopic features of methacrylate polymers with zwitterionic pendant groups determined by various techniques

The objective of this work was to determine microscopic structural features of three methacrylate polymers with different numbers of diethylene glycol residues and zwitterionic pendant groups. X‐ray diffraction, electron microscopy, and scanning probe microscopy techniques were employed. X‐ray data led to the adoption of a model made up of molecular aggregates forming lamellar domains, establishing in this way ordered characteristics of these kinds of polymers. Scanning electron microscopy images provided evidence of the occurrence of a lamellar structure forming the morphology of the polymers. This was corroborated by atomic force microscopy experiments. Transmission electron microscopy revealed that the lamellar aggregates conformed into clusters immersed in a polymeric matrix. From phase‐contrast images, information on the homogeneity of the composition at a molecular surface level was obtained. Then, the techniques provided evidence of the lamellar domain characteristics of the studied sulfobetaines. The crystallinity was a function of the number of ethoxy groups because as this number increased, the crystallinity became lower © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1152–1160, 2005     

New Tools for Investigating Electromagnetic Hot Spots in Single‐Molecule Surface‐Enhanced Raman Scattering

Surface‐enhanced Raman scattering (SERS) is quickly growing as an analytical technique, because it offers both molecular specificity and excellent sensitivity. For select substrates, SERS can even be observed from single molecules, which is the ultimate limit of detection. This review describes recent developments in the field of single‐molecule SERS (SM‐SERS) with a focus on new tools for characterizing SM‐SERS‐active substrates and how they interact with single molecules on their surface. In particular, techniques that combine optical spectroscopy and microscopy with electron microscopy are described, including correlated optical and transmission electron microscopy, correlated super‐resolution imaging and scanning electron microscopy, and correlated optical microscopy and electron energy loss spectroscopy.     

In Situ Visualization of Block Copolymer Self‐Assembly in Organic Media by Super‐Resolution Fluorescence Microscopy

Analytical methods that enable visualization of nanomaterials derived from solution self‐assembly processes in organic solvents are highly desirable. Herein, we demonstrate the use of stimulated emission depletion microscopy (STED) and single molecule localization microscopy (SMLM) to map living crystallization‐driven block copolymer (BCP) self‐assembly in organic media at the sub‐diffraction scale. Four different dyes were successfully used for single‐colour super‐resolution imaging of the BCP nanostructures allowing micelle length distributions to be determined in situ. Dual‐colour SMLM imaging was used to measure and compare the rate of addition of red fluorescent BCP to the termini of green fluorescent seed micelles to generate block comicelles. Although well‐established for aqueous systems, the results highlight the potential of super‐resolution microscopy techniques for the interrogation of self‐assembly processes in organic media.     

Atomic Force Microscopy for Molecular Structure Elucidation

Using scanning probe microscopy techniques, at low temperatures and in ultrahigh vacuum, individual molecules adsorbed on surfaces can be probed with ultrahigh resolution to determine their structure and details of their conformation, configuration, charge states, aromaticity, and the contributions of resonance structures. Functionalizing the tip of an atomic force microscope with a CO molecule enabled atomic‐resolution imaging of single molecules, and measurement of their adsorption geometry and bond‐order relations. In addition, by using scanning tunneling microscopy and Kelvin probe force microscopy, the density of the molecular frontier orbitals and the electric charge distribution within molecules can be mapped. Combining these techniques yields a high‐resolution tool for the identification and characterization of individual molecules. The single‐molecule sensitivity and the possibility of atom manipulation to induce chemical reactions with the tip of the microscope open up unique applications in chemistry, and differentiate scanning probe microscopy from conventional methods for molecular structure elucidation. Besides being an aid for challenging cases in natural product identification, atomic force microscopy has been shown to be a powerful tool for the investigation of on‐surface reactions and the characterization of radicals and molecular mixtures. Herein we review the progress that high‐resolution scanning probe microscopy with functionalized tips has made for molecular structure identification and characterization, and discuss the challenges it will face in the years to come.     

Progress in the direct structural characterization of fibrous amphiphilic supramolecular assemblies in solution by transmission electron microscopic techniques

The self-assembly of amphiphilic molecules into fibrous structures has been the subject of numerous studies over past decades due to various current and promising technical applications. Although very different in their head group chemistry many natural as well as synthetic amphiphilic compounds derived from carbohydrates, carbocyanine dyes, or amino acids tend to form fibrous structures by molecular self-assembly in water predominantly twisted ribbons or tubes. Often a transition between these assembly structures is observed, which is a phenomenon already theoretically approached by Wolfgang Helfrich and still focus point in current research. With the development of suitable sample preparation and electron optical imaging techniques, cryogenic transmission electron microscopy (cryo-TEM) in combination with three-dimensional (3D) reconstruction techniques has become a particular popular direct characterization technique for supramolecular assemblies in general. Here we review the recent progress in deriving precise structural information from cryo-TEM data of particularly fibrous structures preferably in three dimensions.     

Trapping of Oxygen Vacancies at Crystallographic Shear Planes in Acceptor‐Doped Pb‐Based Ferroelectrics

The defect chemistry of the ferroelectric material PbTiO₃ after doping with Fe^III acceptor ions is reported. Using advanced transmission electron microscopy and powder X‐ray and neutron diffraction, we demonstrate that even at concentrations as low as circa 1.7 % (material composition approximately ABO_2.95), the oxygen vacancies are trapped into extended planar defects, specifically crystallographic shear planes. We investigate the evolution of these defects upon doping and unravel their detailed atomic structure using the formalism of superspace crystallography, thus unveiling their role in nonstoichiometry in the Pb‐based perovskites.     

Synthesis of Honeycomb‐Structured Beryllium Oxide via Graphene Liquid Cells

Using high‐resolution transmission electron microscopy and electron energy‐loss spectroscopy, we show that beryllium oxide crystallizes in the planar hexagonal structure in a graphene liquid cell by a wet‐chemistry approach. These liquid cells can feature van‐der‐Waals pressures up to 1 GPa, producing a miniaturized high‐pressure container for the crystallization in solution. The thickness of as‐received crystals is beyond the thermodynamic ultra‐thin limit above which the wurtzite phase is energetically more favorable according to the theoretical prediction. The crystallization of the planar phase is ascribed to the near‐free‐standing condition afforded by the graphene surface. Our calculations show that the energy barrier of the phase transition is responsible for the observed thickness beyond the previously predicted limit. These findings open a new door for exploring aqueous‐solution approaches of more metal‐oxide semiconductors with exotic phase structures and properties in graphene‐encapsulated confined cells.     

Evolution of Surface Morphology with Introduction of Stacking Faults in Zeolites

This paper sets out to try to determine some of the nanoscopic details of template action in zeolites. The problem has been addressed by monitoring the effects of competitive templating using, in particular, atomic force microscopy and high‐resolution scanning electron microscopy. Using these techniques, it is possible to determine the subtle crystal growth changes that occur as a result of altering the concentration of these competitive templating agents. This work concerns the two important intergrowth systems MFI–MEL and FAU–EMT. It was found that some organic templating agents provide much greater structure‐directing specificity. So much so in the case of the MFI–MEL system that a 2 mol % doping with the highly specific tetrapropylammonium cation drastically changes the fundamental growth processes. Furthermore, the effect of template crowding is shown to reduce specificity. This work shows how extensive frustrated intergrowth structures can still be accommodated within a nominal zeolite single crystal.     

原子分辨显微分析技术研究进展

非接触原子力显微技术(NC-AFM)近年来发展迅速. NC-AFM对单个分子的成像和谱学实现了原子分辨和单个化学键分辨. NC-AFM自身功能的拓展及其与不同探针技术的联用将为材料、物理、化学和生命科学有关的研究提供崭新的思路. 本文首先介绍NC-AFM和qPlus 传感器的基本原理, 然后讨论原子尺度的相互作用力和短程力的精确测量, 总结近年来NC-AFM在原子尺度的化学结构成像、化学识别、电子结构性质分析以及原子操纵技术中的研究进展, 并讨论了开尔文探针力显微技术(KPFM)在局域接触势差(LCPD)测量方面的应用. 最后展望了NC-AFM面临的挑战和发展机遇.