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.

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.

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-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.

Electron energy-loss safe-dose limits for manganese valence measurements in environmentally relevant manganese oxides.

Manganese (Mn) oxides are among the strongest mineral oxidants in the environment and impose significant influence on mobility and bioavailability of redox-active substances, such as arsenic, chromium, and pharmaceutical products, through oxidation processes. Oxidizing potentials of Mn oxides are determined by Mn valence states (2+, 3+, 4+). In this study, the effects of beam damage during electron energy-loss spectroscopy (EELS) in the transmission electron microscope have been investigated to determine the "safe dose" of electrons. Time series analyses determined the safe dose fluence (electrons/nm(2)) for todorokite (10(6) e/nm(2)), acid birnessite (10(5)), triclinic birnessite (10(4)), randomly stacked birnessite (10(3)), and δ-MnO(2) (<10(3)) at 200 kV. The results show that meaningful estimates of the mean Mn valence can be acquired by EELS if proper care is taken.

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.

Structural and spatial associations between Fe, O, and C in the network structure of the Leptothrix ochracea sheath surface.

The structural and spatial associations of Fe with O and C in the outer coat fibers of the Leptothrix ochracea sheath were shown to be substantially similar to the stalk fibers of Gallionella ferruginea, i.e., a central C core, probably of bacterial origin, and aquatic Fe interacting with O at the surface of the core.

From electron energy-loss spectroscopy to multi-dimensional and multi-signal electron microscopy.

This review intends to illustrate how electron energy-loss spectroscopy (EELS) techniques in the electron microscope column have evolved over the past 60 years. Beginning as a physicist tool to measure basic excitations in solid thin foils, EELS techniques have gradually become essential for analytical purposes, nowadays pushed to the identification of individual atoms and their bonding states. The intimate combination of highly performing techniques with quite efficient computational tools for data processing and ab initio modeling has opened the way to a broad range of novel imaging modes with potential impact on many different fields. The combination of Angström-level spatial resolution with an energy resolution down to a few tenths of an electron volt in the core-loss spectral domain has paved the way to atomic-resolved elemental and bonding maps across interfaces and nanostructures. In the low-energy range, improved energy resolution has been quite efficient in recording surface plasmon maps and from them electromagnetic maps across the visible electron microscopy (EM) domain, thus bringing a new view to nanophotonics studies. Recently, spectrum imaging of the emitted photons under the primary electron beam and the spectacular introduction of time-resolved techniques down to the femtosecond time domain, have become innovative keys for the development and use of a brand new multi-dimensional and multi-signal electron microscopy.

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.

Visualizing plasmon coupling in closely spaced chains of Ag nanoparticles by electron energy-loss spectroscopy.

Anisotropic plasmon coupling in closely spaced chains of Ag nanoparticles is visualized using electron energy-loss spectroscopy in a scanning transmission electron microscope. For dimers as the simplest chain, mapping the plasmon excitations with nanometer spatial resolution and an energy resolution of 0.27 eV intuitively identifies two coupling plasmons. The in-phase mode redshifts from the ultraviolet region as the interparticle spacing is reduced, reaching the visible range at 2.7 eV. Calculations based on the discrete-dipole approximation confirm its optical activeness, where the longitudinal direction is constructed as the path for light transportation. Two coupling paths are then observed in an inflexed four-particle chain.

Iron sources used by the nonpathogenic lactic acid bacterium Lactobacillus sakei as revealed by electron energy loss spectroscopy and secondary-ion mass spectrometry.

Lactobacillus sakei is a lactic acid bacterium naturally found on meat. Although it is generally acknowledged that lactic acid bacteria are rare species in the microbial world which do not have iron requirements, the genome sequence of L. sakei 23K has revealed quite complete genetic equipment dedicated to transport and use of this metal. Here, we aimed to investigate which iron sources could be used by this species as well as their role in the bacterium's physiology. Therefore, we developed a microscopy approach based on electron energy loss spectroscopy (EELS) analysis and nano-scale secondary-ion mass spectrometry (SIMS) in order to analyze the iron content of L. sakei cells. This revealed that L. sakei can use iron sources found in its natural ecosystem, myoglobin, hemoglobin, hematin, and transferrin, to ensure long-term survival during stationary phase. This study reveals that analytical image methods (EELS and SIMS) are powerful complementary tools for investigation of metal utilization by bacteria.

A-band methyl halide dissociation via electronic curve crossing as studied by electron energy loss spectroscopy.

Excitation of the A-band low-lying electronic states in the methyl halides, CH(3)I, CH(3)Br, CH(3)Cl, and CH(3)F, has been investigated for the (n-->sigma*) transitions, using electron energy loss spectroscopy (EELS) in the range of 3.5-7.5 eV. For the methyl halides, CH(3)I, CH(3)Br, and CH(3)Cl, three components of the Q complex ((3)Q(1), (3)Q(0), and (1)Q(1)) were directly observed, with the exception of methyl fluoride, in the optically forbidden EELS experimental conditions of this investigation. The effect of electronic-state curve crossing emerged in the transition probabilities for the (3)Q(0) and (1)Q(1) states, with spin-orbit splitting observed and quantified against results from recent ab initio studies.

Determination of complex dielectric functions at HfO(2)/Si interface by using STEM-VEELS.

The complex dielectric functions and refractive index of atomic layer deposited HfO(2) were determined by the line scan method of the valence electron energy loss spectrum (VEELS) in a scanning transmission electron microscope (STEM). The complex dielectric functions and dielectric constant of monoclinic HfO(2) were calculated by the density functional theory (DFT) method. The resulting two dielectric functions were relatively well matched. On the other hand, the refractive index of HfO(2) was measured as 2.18 by VEELS analysis and 2.1 by DFT calculation. The electronic structure of HfO(2) was revealed by the comparison of the inter-band transition strength, obtained by STEM-VEELS, with the density of states (DOS) calculated by DFT calculation.

Chemical shift of electron energy-loss near-edge structure on the nitrogen K-edge and titanium L3-edge at TiN/Ti interface.

We investigated the chemical shift of the electron energy-loss near-edge structure (ELNES) for the nitrogen K-edge and titanium L3-edge measured from the interface region between a titanium nitride layer and a titanium layer. Both the titanium nitride and titanium layers were prepared by a sputtering method. Elemental analysis for nitride and titanium in the vicinity of the interface region was performed using a standard technique in electron energy-loss spectroscopy. It was demonstrated that both the ELNES of nitrogen K-edge and titanium L3-edge presented the chemical shift, more or less, depending on the composition of TiNx. The experimental findings were interpreted using a first-principles band structure calculation. The chemical shifts of nitrogen K-edge and titanium L3-edge can be used as fingerprinting for readily distinguishing the composition of TiNx.

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.

Sub-cellular localization of manganese in the basal ganglia of normal and manganese-treated rats An electron spectroscopy imaging and electron energy-loss spectroscopy study.

We have studied at the ultrastructural level the presence of manganese (Mn) in rat basal ganglia, which are target regions of the brain for Mn toxicity. The rats underwent a moderate level of Mn exposure induced per os for 13 weeks. Mn was detected by means of electron spectroscopy imaging (ESI) and electron energy-loss spectroscopy (EELS) analyses on perfusion fixed samples embedded in resin. While no significant contamination by exogenous Mn occurred during the processing procedures, less than 50% of endogenous Mn was lost during fixation and dehydration of the brain samples. The residual Mn ions in the samples appeared as discrete particles, localized in selected sub-cellular organelles in a cell, suggesting that no significant translocation had occurred in the surrounding area. In control rats, the Mn sub-cellular localization and relative content were the same in neurons and astrocytes of rat striatum and globus pallidus: the Mn level was highest in the heterochromatin and in the nucleolus, intermediate in the cytoplasm, and lowest in the mitochondria (p<0.001). After chronic Mn treatment, while no ultrastructural damage was detected in the neurons and glial cells, the largest rate of Mn increase was noted in the mitochondria of astrocytes (+700%), an intermediate rate in the mitochondria of neurons (+200%), and the lowest rate in the nuclei (+100%) of neurons and astrocytes; the Mn level in the cytoplasm appeared unchanged. EELS analysis detected the specific spectra of Mn L(2,3) (peak at DeltaE = 665 eV) in such organelles, confirming the findings of ESI. Although a consistent loss of Mn occurred during the processing of tissue samples, ESI and EELS can be useful methods for localization of endogenous Mn in embedded tissues. The high rate of Mn sequestration in the mitochondria of astrocytes in vivo may partly explain the outstanding capacity of astrocytes to accumulate Mn, and their early dysfunction in Mn neurotoxicity. The high level of Mn in the heterochromatin and nucleoli of neurons and astrocytes in basal conditions and its further increase after Mn overload should provide insight into new avenues of investigating the role of Mn in the normal brain and a baseline for future Mn toxicity studies.

Volcano structure in atomic resolution core-loss images.

A feature commonly present in simulations of atomic resolution electron energy loss spectroscopy images in the scanning transmission electron microscope is the volcano or donut structure. In the past this has been understood in terms of a geometrical perspective using a dipole approximation. It is shown that the dipole approximation for core-loss spectroscopy begins to break down as the probe forming aperture semi-angle increases, necessitating the inclusion of higher order terms for a quantitative understanding of volcano formation. Using such simulations we further investigate the mechanisms behind the formation of such structures in the single atom case and extend this to the case of crystals. The cubic SrTiO3 crystal is used as a test case to show the effects of nonlocality, probe channelling and absorption in producing the volcano structure in crystal images.

Comparison of the electronic structure of a thermoelectric skutterudite before and after adding rattlers: an electron energy loss study.

Skutterudites, with rattler atoms introduced in voids in the crystal unit cell, are promising thermoelectric materials. We modify the binary skutterudite with atomic content Co(8)P(24) in the cubic crystal unit cell by adding La as rattlers in all available voids and replacing Co by Fe to maintain charge balance, resulting in La(2)Fe(8)P(24). The intention is to leave the electronic structure unaltered while decreasing the thermal conductivity due to the presence of the rattlers. We compare the electronic structure of these two compounds by studying the L-edges of P and of the transition elements Co and Fe using electron energy loss spectroscopy (EELS). Our studies of the transition metal white lines show that the 3d electron count is similar for Co and Fe in these compounds. As elemental Fe has one electron less than Co, this supports the notion that each La atom donates three electrons. The L-edges of P in these two skutterudites are quite similar, signalling only minor differences in electronic structure. This is in reasonable agreement with density functional theory (DFT) calculations, and with our multiple scattering FEFF calculations of the near edge structure. However, our experimental plasmon energies and dielectric functions deviate considerably from predictions based on DFT calculations.

Dose-limited spectroscopic imaging of soft materials by low-loss EELS in the scanning transmission electron microscope.

Spectroscopic imaging in the scanning transmission electron microscope (STEM) using spatially resolved electron energy-loss spectroscopy (EELS) provides one of the few ways to quantitatively measure the real-space nanoscale morphology of soft materials such as polymers and biological tissue. This paper describes the basic principles of this technique and outlines some of the important attributes that define the achievable spatial resolution. Many soft materials can be differentiated from each other as well as from solvents based on their EELS fingerprints. Applying a multiple least squares (MLS) fitting algorithm using such spectral fingerprints to analyze spatially resolved spectrum datasets enables the quantitative mapping of the different components in a specimen. However, in contrast to TEM studies of many inorganic materials where the spatial resolution is limited principally by the spherical aberration of the objective lens, the spatial resolution associated with the imaging of radiation-sensitive soft materials is limited by the total electron dose to which they can be exposed before suffering irrevocable chemical or structural damage. The Rose criterion provides a simple guide to enhance the so-called dose-limited spatial resolution relevant to soft-materials imaging. By using the low-loss portion of an EELS spectrum where the inelastic scattering cross-sections are highest together with improvements in data-collection efficiency and post-acquisition data processing, the dose-limited resolution in spectrum images of solvated polymers has moved into the sub 10nm regime. This resolution is sufficient to solve important applications-oriented problems associated with hetero interfaces, nanoscale mixing, and nanophase separation.

Image simulation for electron energy loss spectroscopy.

Aberration correction of the probe forming optics of the scanning transmission electron microscope has allowed the probe-forming aperture to be increased in size, resulting in probes of the order of 1 A in diameter. The next generation of correctors promise even smaller probes. Improved spectrometer optics also offers the possibility of larger electron energy loss spectrometry detectors. The localization of images based on core-loss electron energy loss spectroscopy is examined as function of both probe-forming aperture and detector size. The effective ionization is nonlocal in nature, and two common local approximations are compared to full nonlocal calculations. The affect of the channelling of the electron probe within the sample is also discussed.