Characterization of the boron profile and coordination in altered glass layers by EEL spectroscopy.

Electron energy-loss spectroscopy was used to characterize the boron profile and its coordination (BIII and BIV), along the complex alteration layer of glass samples altered for 511 days at 50 °C in solution containing FeCl2, MgCl2 and/or CaCl2. To reach this goal, the impact of both TEM operating conditions and sample preparation on the determination of the boron coordination was first studied using mineralogical and pristine glasses reference samples. Then, the boron concentration profiles were characterized in the glass alteration layer. These profiles were found to be S-shaped with a thickness around forty nanometers. The proportion of BIII was found to decrease with the boron total concentration (from the pristine glass to the gel layer), which suggests a higher bonding strength for BIV bonds than that of BIII bonds under the alteration conditions. These findings are of tremendous interest to advance further in the understanding of glass alteration mechanisms.

Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor Conformations.

"Biased" G protein-coupled receptor (GPCR) agonists preferentially activate pathways mediated by G proteins or ß-arrestins. Here, we use double electron-electron resonance spectroscopy to probe the changes that ligands induce in the conformational distribution of the angiotensin II type I receptor. Monitoring distances between 10 pairs of nitroxide labels distributed across the intracellular regions enabled mapping of four underlying sets of conformations. Ligands from different functional classes have distinct, characteristic effects on the conformational heterogeneity of the receptor. Compared to angiotensin II, the endogenous agonist, agonists with enhanced Gq coupling more strongly stabilize an "open" conformation with an accessible transducer-binding site. ß-arrestin-biased agonists deficient in Gq coupling do not stabilize this open conformation but instead favor two more occluded conformations. These data suggest a structural mechanism for biased ligand action at the angiotensin receptor that can be exploited to rationally design GPCR-targeting drugs with greater specificity of action.

Application of Electron Microscopes in Nanotoxicity Assessment.

In this chapter, we highlight the applications of electron microscopes (EMs) in nanotoxicity assessment. EMs can provide detailed information about the size and morphology of nanomaterials (NMs), their localization in cells and tissues, the nano-bio interactions, as well as the ultrastructural changes induced by NMs exposure. Here, we share with the readers how we prepare the tissue sample, and the different types of EMs used among the nanotoxicologists. It is possible to deploy conventional EMs along or in combination with other analytical techniques, such as electron energy loss spectroscopy (EELS), energy dispersive X-ray spectroscopy (EDS or EDX), and TEM-assisted scanning transmission X-ray microscopy (STXM), toward further elemental and chemical characterization. Appropriate images are inserted to illustrate throughout this chapter.

Application of EELS and EFTEM to the life sciences enabled by the contributions of Ondrej Krivanek.

The pioneering contributions of Ondrej Krivanek to the development of electron energy loss spectrometers, energy filters, and detectors for transmission and scanning transmission electron microscopes have provided researchers with indispensible tools across a wide range of disciplines in the physical sciences, ranging from condensed matter physics, to chemistry, mineralogy, materials science, and nanotechnology. In addition, the same instrumentation has extended its reach into the life sciences, and it is this aspect of Ondrej Krivanek's influential contributions that will be surveyed here, together with some personal recollections. Traditionally, electron microscopy has given a purely morphological view of the biological structures that compose cells and tissues. However, the availability of high-performance electron energy loss spectrometers and energy filters offers complementary information about the elemental and chemical composition at the subcellular scale. Such information has proven to be valuable for applications in cell and structural biology, microbiology, histology, pathology, and more generally in the biomedical sciences.

Damage-free vibrational spectroscopy of biological materials in the electron microscope.

Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an 'aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be 'safely' investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C-H, N-H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope.

Monte Carlo Simulations of Electron Energy-Loss Spectra with the Addition of Fine Structure from Density Functional Theory Calculations.

A new approach is presented to introduce the fine structure of core-loss excitations into the electron energy-loss spectra of ionization edges by Monte Carlo simulations based on an optical oscillator model. The optical oscillator strength is refined using the calculated electron energy-loss near-edge structure by density functional theory calculations. This approach can predict the effects of multiple scattering and thickness on the fine structure of ionization edges. In addition, effects of the fitting range for background removal and the integration range under the ionization edge on signal-to-noise ratio are investigated.

High Resolution STEM-EELS Study of Silver Nanoparticles Exposed to Light and Humic Substances.

Nanoparticles (NPs) are defined as particles with at least one dimension between 1 and 100 nm or with properties that differ from their bulk material, which possess unique properties. The extensive use of NPs means that discharge to the environment is likely increasing, but fate, behavior, and effects under environmentally relevant conditions are insufficiently studied. This paper focuses on the transformations of silver nanoparticles (AgNPs) under simulated but realistic environmental conditions. High resolution aberration-corrected scanning transmission electron microscopy (HAADF STEM) coupled with electron energy loss spectroscopy (EELS) and UV-vis were used within a multimethod approach to study morphology, surface chemistry transformations, and corona formation. Although loss, most likely by dissolution, was observed, there was no direct evidence of oxidation from the STEM-EELS. However, in the presence of fulvic acid (FA), a 1.3 nm oxygen-containing corona was observed around the AgNPs in water; modeled data based on the HAADF signal at near atomic resolution suggest this was an FA corona was formed and was not silver oxide, which was coherent (i.e., fully coated in FA), where observed. The corona further colloidally stabilized the NPs for periods of weeks to months, dependent on the solution conditions.

High-energy resolution electron energy-loss spectroscopy study of interband transitions characteristic to single-walled carbon nanotubes.

An electron energy-loss spectroscopic (EELS) study using a monochromator transmission electron microscope was conducted for investigating the dielectric response of isolated single-walled carbon nanotubes (SWCNTs) owing to interband transitions characteristic to chiral structures. Individual chiral structures of the SWCNTs were determined by electron diffraction patterns. EELS spectra obtained from isolated SWCNTs showed sharp peaks below π plasmon energy of 5 eV, which were attributed to the characteristic interband transitions of SWCNTs. In addition, unexpected shoulder structures were observed at the higher energy side of each sharp peak. Simulations of EELS spectra by using the continuum dielectric theory showed that an origin of the shoulder structures was because of the surface dipole mode along the circumference direction of the SWCNT. It was noticed that the electron excitation energies obtained by EELS were slightly higher than those of optical studies, which might be because of the inelastic scattering process with the momentum transfers. To interpret the discrepancy between the EELS and optical experiments, it is necessary to conduct more accurate simulation including the first principle calculation for the band structure of SWCNTs.

Biological applications of energy-filtered TEM.

The techniques of electron energy-loss spectroscopy (EELS) and energy-filtered TEM (EFTEM) are routinely applied in the physical sciences to map the distribution of elements at the nanoscale. EELS can also provide details of the bonding/valence of elements through variations in the fine structure of elemental peaks in the spectrum. While applications of these techniques in biology are less prevalent, their ability to detect both the light elements (e.g., C, N, O, P, S) that form the building blocks of biological systems and heavier elements (e.g., metals) makes them potentially important techniques for investigating local chemical variations in tissues and cells. Successful application of EELS and EFTEM in biology requires both an understanding of the techniques themselves and expertise in specimen preparation. Care must be taken to avoid the diffusion of elements during the preparation process to avoid artifacts in the resulting element maps. The power of the techniques is demonstrated here using tissue from a marine mollusc (chiton).

Numerical simulation of Electron Energy Loss Spectroscopy using a Generalized Multipole Technique.

We numerically simulate low-loss Electron Energy Loss Spectroscopy (EELS) of isolated spheroidal nanoparticles, using an electromagnetic model based on a Generalized Multipole Technique (GMT). The GMT is fast and accurate, and, in principle, flexible regarding nanoparticle shape and the incident electron beam. The implemented method is validated against reference analytical and numerical methods for plane-wave scattering by spherical and spheroidal nanoparticles. Also, simulated electron energy loss (EEL) spectra of spherical and spheroidal nanoparticles are compared to available analytical and numerical solutions. An EEL spectrum is predicted numerically for a prolate spheroidal aluminum nanoparticle. The presented method is the basis for a powerful tool for the computation, analysis and interpretation of EEL spectra of general geometric configurations.

Valence electron energy-loss spectroscopy study of ZrSiO4 and ZrO2.

ZrSiO4 (zircon) and m-ZrO2 (zirconia) are fundamental and industrially important materials. This work reports the detailed valence electron energy-loss spectroscopy (VEELS) studies of these compounds. The dielectric response functions, as well as single-electron interband transition spectra, are derived from VEELS data for both ZrSiO4 and m-ZrO2, in the range 5-50 eV using the Kramers-Kronig analysis method. Our interpretation of the interband transitions is given with the aid of ab initio calculations of density of states. The bandgap energies for both materials are also measured using VEELS. The surface and bulk plasmons are identified: the surface plasmon peaks locate at around 12 eV, and two bulk plasmon peaks are ∼15-16 eV and ∼25-27 eV, respectively. Although similarities in the VEELS exist between ZrSiO4 and m-ZrO2, two major differences are also noticed and explained in terms of composition and structure differences.

Method for local temperature measurement in a nanoreactor for in situ high-resolution electron microscopy.

In situ high-resolution transmission electron microscopy (TEM) of solids under reactive gas conditions can be facilitated by microelectromechanical system devices called nanoreactors. These nanoreactors are windowed cells containing nanoliter volumes of gas at ambient pressures and elevated temperatures. However, due to the high spatial confinement of the reaction environment, traditional methods for measuring process parameters, such as the local temperature, are difficult to apply. To address this issue, we devise an electron energy loss spectroscopy (EELS) method that probes the local temperature of the reaction volume under inspection by the electron beam. The local gas density, as measured using quantitative EELS, is combined with the inherent relation between gas density and temperature, as described by the ideal gas law, to obtain the local temperature. Using this method we determined the temperature gradient in a nanoreactor in situ, while the average, global temperature was monitored by a traditional measurement of the electrical resistivity of the heater. The local gas temperatures had a maximum of 56 °C deviation from the global heater values under the applied conditions. The local temperatures, obtained with the proposed method, are in good agreement with predictions from an analytical model.

HREM analysis of graphite-encapsulated metallic nanoparticles for possible medical applications.

High resolution electron microscopy has been applied to study the structure of metallic nanoparticles. These have sparked considerable interest as contrast agents in the field of biological imaging, including in magnetic resonance imaging (MRI) and computed tomography (CT). Here, we describe a method of synthesizing sub-10nm superparamagnetic metal and alloy nanoparticles by reduction of metallic salts. Annealing at 900°C in a methane/hydrogen environment forms a thin graphitic-carbon shell which is expected to improve stability, biocompatibility, and functionalization. Subsequent high resolution electron microscopy verifies graphitization and allows for crystallographic analysis. Most particles consist of single crystals in the phase predicted for the bulk material at the annealing temperature. Electron energy loss spectroscopy, energy dispersive X-ray spectroscopy and lattice constant measurements show large variation in composition for alloy nanoparticles from a single synthesis. The magnetization relaxation time (T2) measurements demonstrate that Fe and AuFe nanoparticles compete with commercially available iron oxide MRI contrast agents. X-ray attenuation measurements of an AuFe alloy nanoparticle solution gave a relative radiodensity of 280 Hounsfield Units, demonstrating promise as a dual-purpose contrast agent in CT and MRI. Long term stability in an atmospheric environment was also tested, with no signs of corrosion or oxidation after several years of storage.

Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope.

A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems.

Microscopy Hacks: development of various techniques to assist quantitative nanoanalysis and advanced electron microscopy.

For development of advanced materials, characterization using a scanning transmission electron microscope (STEM) including analysis via X-ray energy-dispersive spectrometry and electron energy-loss spectrometry is essential. Recent advances in aberration-corrected instruments have offered large-scale data acquisition at a high resolution for limited acquisition times both in imaging and in analysis. Further advanced procedures are required to analyze such large-scale datasets more efficiently including quantification. In addition, more simplified tuning procedures are crucial to the best possible resolution in the latest aberration-corrected instruments. In this review article, several approaches to perform advanced electron microscopy, which the author has been developing with his colleague, are described as 'Microscopy Hacks'. These are (i) quantification and elemental/chemical-imaging procedures, (ii) advanced statistical approaches to handle large-scale datasets and (iii) instrument characterization and tuning procedures including the latest development of an ad hoc autotuning procedure for aberration-corrected STEM imaging.

Development of an environmental high-voltage electron microscope for reaction science.

Environmental transmission electron microscopy and ultra-high resolution electron microscopic observation using aberration correctors have recently emerged as topics of great interest. The former method is an extension of the so-called in situ electron microscopy that has been performed since the 1970s. Current research in this area has been focusing on dynamic observation with atomic resolution under gaseous atmospheres and in liquids. Since 2007, Nagoya University has been developing a new 1-MV high voltage (scanning) transmission electron microscope that can be used to observe nanomaterials under conditions that include the presence of gases, liquids and illuminating lights, and it can be also used to perform mechanical operations to nanometre-sized areas as well as electron tomography and elemental analysis by electron energy loss spectroscopy. The new instrument has been used to image and analyse various types of samples including biological ones.

Quantifying the low-energy limit and spectral resolution in valence electron energy loss spectroscopy.

While the development of monochromators for scanning transmission electron microscopes (STEM) has improved our ability to resolve spectral features in the 0-5 eV energy range of the electron energy loss spectrum, the overall benefits relative to unfiltered microscopes have been difficult to quantify. Simple curve fitting and reciprocal space models that extrapolate the expected behavior of the zero-loss peak are not enough to fully exploit the optimal spectral limit and can hinder the ease of interpreting the resulting spectra due to processing-induced artifacts. To address this issue, here we present a quantitative comparison of two processing methods for performing ZLP removal and for defining the low-energy spectral limit applied to three microscopes with different intrinsic emission and energy resolutions. Applying the processing techniques to spectroscopic data obtained from each instrument leads in each case to a marked improvement in the spectroscopic limit, regardless of the technique implemented or the microscope setup. The example application chosen to benchmark these processing techniques is the energy limit obtained from a silicon wedge sample as a function of thickness. Based on these results, we conclude on the possibility to resolve statistically significant spectral features to within a hundred meV of the native instrumental energy spread, opening up the future prospect of tracking phonon peaks as new and improved hardware becomes available.

Elemental mapping by electron energy loss spectroscopy in biology.

Over the past decades there have been significant advances in transmission electron microscopy for biological applications, including in energy filtering and spectrum imaging, which are techniques based on the principles of electron energy loss spectroscopy. These imaging modalities allow quantitative mapping of specific chemical elements with high sensitivity and spatial resolution. This chapter describes the experimental and computational procedures for elemental mapping in two dimensions as well as a more recent extension to three dimensions, which can reveal quantitative distributions of elements in cells on a macromolecular scale.

Atomic imaging and spectroscopy of low-dimensional materials with interrupted periodicities.

Identification of individual atoms and examination of their electronic properties in materials are the ultimate goal of all microscopy-based analytical techniques. Here, we demonstrate successful single-atom imaging and spectroscopy in low-dimensional materials using (scanning) transmission electron microscopy together with electron energy-loss spectroscopy (EELS). Edges and point defects in single-layered materials such as graphene, hexagonal boron nitride and WS(2) nanoribbons are investigated by annular dark-field imaging and EELS fine-structure analysis. Individual dopant atoms are unambiguously identified in nano-peapods. It is noteworthy that irradiation damage and specimen contamination even at the single-atom level are crucial issues in these experiments.

Nanoscale mapping of plasmon resonances of functional multibranched gold nanoparticles.

The optical response of multibranched gold nanoparticles is studied by means of electron energy-loss spectroscopy (EELS) in aberration corrected STEM mode. In every case the plasmon response is constant and variations in the maxima positions were found to be dependent on the branches aspect ratio. The good spatial resolution combined with the high energy resolution (0.18 eV) of the monochromated electron beam allows mapping the different plasmonic modes along the entire nanoparticles ranging from 0.7 eV up to 2.25 eV.