Construction of an organic crystal structural model based on combined electron and powder X-ray diffraction data and the charge flipping algorithm

The structure of an organic dye 1,5-diaminoanthraquinone (DAAQ) nanowire was studied by both electron diffraction and X-ray powder diffraction. The unit cell of the crystal was determined from a series of tilted selected area electron diffraction patterns (monoclinic: a=3.78 Å, b=9.73 Å, c=15.01 Å and β=82.4°). By using precession electron diffraction, the following extinction conditions were determined, 0k0: k=2n and 00l: l=2n, which give the space group as P2₁/C (no. 14). The powder charge flipping algorithm was applied to resolve the phase problem and the structural model of the DAAQ crystal was built.     

Investigation of the local Ge concentration in Si/SiGe nanostructures by convergent-beam electron diffraction

SiGe multi quantum well structures were investigated by convergent-beam electron diffraction (CBED) measurements. Detailed layer characterizations were performed by acquiring series of bright field CBED patterns in the form of a line scan across the nanostructures in scanning transmission electron microscopy (STEM) mode. From the higher order Laue zone (HOLZ) lines the local lattice parameters were deduced. The Ge concentration corresponding to these lattice parameters was determined by means of the elasticity theory. In this work it is shown that the lattice constants can be determined locally with an accuracy of about ±0.001 to ±0.003 Å which leads to an accuracy of the corresponding Ge concentration of about 1–2%. The characteristics of the focused electron probe and its influence on the experimental data were used for an estimation of the spatial resolution of the CBED method. For comparison, experimental values regarding the spatial resolution were determined by investigating the abrupt interface between Si(1 1 1) and AlN(0 0 0 1).     

Electron microscopy of frozen biological objects: a study using cryosectioning and cryosubstitution

Freezing of bulk biological objects was investigated by X-ray cryodiffraction. Freezing at atmospheric pressure of most microscopic biological samples gives rise to large hexagonal crystals and leads to poor structural preservation of these specimens. High-pressure freezing induces the formation of different ices (hexagonal, cubic and a high-pressure form) consisting of crystals having sizes smaller than those formed at atmospheric pressure. With both freezing methods, a cryoprotectant has to be added to the biological object to avoid the formation of ice crystals. However, special cases can be encountered: some biological objects contain large amounts of natural cryoprotectant or have a low water content. In these cases, vitrification can be achieved, especially using high-pressure freezing. Cryo-sectioning can be performed on vitrified samples, and the sections studied by electron cryomicroscopy. Images and electron diffraction patterns having a resolution better than 2 and 0.2 nm, respectively, can be obtained with such sections. Because samples containing crystalline ices cannot be cryosectioned, their structure has to be studied using cryosubstitution and resin embedding. We show that bacteria, yeast, and ciliate and marine worm elytrum have cellular compartments with an organization that has not been described by classical techniques relying on chemical fixation of the tissues. A high-pressure artefact affecting the Paramecium trichocysts is described. Such artefacts are not general; for example, we show that 70% of high-pressure frozen yeast cells survive successive high-pressure freezing and thawing steps.     

Theoretical estimation for correlations of diffraction patterns from objects differently oriented in space

Coherent diffraction imaging of single biomolecules is expected to open unique opportunities for studies of non-crystalline samples. There are, however, still many technical and physical issues that need to be resolved in a more quantitative manner, especially if one aims for structural information at high resolution. Signal recorded from an object after a single shot is low. As primarily proposed in Spence and Doak (2004) and Huldt et al. (2003) [1] and [2], averaging over the diffraction patterns from many different shots is necessary, in order to achieve a signal-to-noise ratio sufficient for image reconstruction. The images of the randomly oriented molecules have to be sorted out in order to identify those corresponding to the similar spatial orientations of the objects. This procedure is called the classification of diffraction images. Here we approach the classification in the framework of pattern-to-pattern correlations, and analyse theoretically the correlations between diffraction images of differently oriented objects.     

Imaging modes for potential mapping in semiconductor devices by electron holography with improved lateral resolution

Electron holography is the highest resolving tool for dopant profiling at nanometre-scale resolution. In order to measure the object areas of interest in a hologram, both a wide field of view and a sufficient lateral resolution are required. The usual path of rays for recording holograms with an electron biprism using the standard objective lens does not meet these requirements, because the field of view amounts to some 10 nm only, however, at a resolution of 0.1 nm better than needed here. Therefore, instead of the standard objective lens, the Lorentz lens is widely used for holography of semiconductors, since it provides a field of view up to 1000 nm at a sufficient lateral resolution of about 10 nm. Since the size of semiconductor structures is steadily shrinking, there is now a need for better lateral resolution at an appropriate field of view. Therefore, additional paths of rays for recording holograms are studied with special emphasis on the parameters field of view and lateral resolution. The findings allow an optimized scheme with a field of view of 200 nm and a lateral resolution of 3.3 nm filling the gap between the existing set-ups. In addition, the Lorentz lens is no longer required for investigation of non-magnetic materials, since the new paths of rays are realized with the standard objective lens and diffraction lens. An example proves the applicability of this arrangement for future semiconductor technology.     

Structural imaging of β-Si3N4 by spherical aberration-corrected high-resolution transmission electron microscopy

Modern transmission electron microscopes (TEM) allow utilizing the spherical aberration coefficient as an additional free parameter for optimizing resolution and contrast. By tuning the spherical aberration coefficient of the objective lens, isolated nitrogen atom columns as well as the Si–N dumbbells within the six-membered ring were imaged in β-Si₃N₄ along [0 0 0 1] and [0 0 0 1¯] projections with a dumbbell spacing of 0.94 Å in white atom contrast. This has been obtained with negative or positive spherical aberration coefficient. We clarify contrast details in β-Si₃N₄ by means of extended image calculations. A simple procedure has been shown for pure phase imaging, which is restricted to linear imaging conditions.     

Interpretation of electron diffraction patterns from amorphous and fullerene-like carbon allotropes

The short range order in amorphous and fullerene-like carbon compounds has been characterized by selected area electron diffraction (SAED) patterns and compared with simulations of model nanoclusters. Broad rings in SAED pattern from fullerene-like CN_x at ∼1.2, ∼2, and ∼3.5 Å indicate short-range order similar to that in graphite, but peak shifts indicate sheet curvature in agreement with high-resolution transmission electron microscopy images. Fullerene-like CP_x exhibits rings at ∼1.6 and 2.6 Å, which can be explained if it consists of fragments with short-range order and high curvature similar to that of C₂₀.     

Microtubule structure studied by quick freezing: Cryo-electron microscopy and freeze fracture

Microtubules have been quickly frozen and examined by electron microscopy using several techniques: (1) freezing of a thin layer of solution by plunging into cryogen, followed by cryo-electron microscopy of the unstained vitrified samples; (2) freezing by the propane-jet method, followed by freeze fracturing and metal replication. The unstained frozen-hydrated microtubules show a structure in agreement with X-ray diffraction data; they differ from negatively stained particles mainly by the better preservation of cylindrical shape. Secondly, they reveal a supertwist of the profilaments that is not detected reliably by other methods. This allows a determination of the number of protofilaments and the polarity. The structural resolution of unstained microtubules is similar to that of stained ones (about 2–3 nm); it is limited by low contrast and lack of crystalline order. Propane-jet or cryo-block freezing followed by freeze fracturing reveals the structures of the inner and outer surfaces of the microtubule wall at a resolution of 4 nm or better. The outside is dominated by the longitudinal protofilaments whereas on the inside one observes tilted cross-striations. Although the freezing temperatures of the two methods are different (liquid nitrogen or helium) they yield similar results for the case of thin layers of protein solution.     

Pawley and Rietveld refinements using electron diffraction from L1₂-type intermetallic Au₃Fe₁-x nanocrystals during their in-situ order-disorder transition

During the in-situ order-disorder transition of intermetallic L1₂-type Au₃Fe_1−x nanocrystals, structural information has been retrieved from their electron diffraction patterns based on the Pawley refinement that is unrelated to the electron kinematical or dynamical scattering nature as well as the Rietveld refinement using a kinematical approximation. At room temperature, it was found that the nanocrystals contain approximately x=40% vacancies at the Fe site. Based on in-situ heating this phase displayed an irreversible order-disorder transition, with the transition temperature between 553 and 593 K. A sudden increase in lattice parameter was detected during the first heating from the ordered phase, while the second heating of the disordered phase showed only a linear relationship with temperature. From the lattice parameter measurement of the disordered phase, the coefficient of thermal expansion was estimated as 1.462×10⁻⁵ K⁻¹. The long-range order parameter S was determined by the refined site occupancies, as well as the integrated intensities of the superlattice (1 0 0) and fundamental (2 2 0) reflections using the Pawley and Rietveld refinements during the order-disorder transition. Considering the dynamical scattering effect, Blackman two-beam approximation theory was applied to corrected S, which slightly attenuated after the correction. A comparison of the electron diffraction with X-ray diffraction data was made. It was demonstrated that elemental and structural information could be retrieved through quantitative electron diffraction studies of the nanomaterials. Since the Pawley refinement algorithm does not include the electron scattering event, it is especially useful to refine the electron diffraction data regardless of the sample thickness.     

Friction force microscopy in ultrahigh vacuum: an atomic-scale study on KBr(001)

We present an atomic-scale study on friction performed by a bidirectional atomic force microscope operated in ultrahigh vacuum. Experiments on surfaces of in situ cleaved KBr crystals are presented. On a m scale the cleavage structure with monoatomic steps of 3.5 ± 0.3 Å is revealed. On the atomically flat terraces, atomic-scale resolution is achieved. The resolved square lattice shows a periodicity of 4.7 Å and corrugations of 0.3–0.7 Å and exhibits the cubic symmetry of KBr(001). The lateral (frictional) force map shows all characteristics of the stick-slip movement of the probing tip. From analysis of the friction loops, the kinetic friction force was determined as a function of load. For a load regime of -4 to 10 nN, lateral force corrugations ranging from 1 to 5 nN were found. A comparison with a novel theoretical model is discussed qualitatively.     

Fabrication and field emission properties of boron nanowire bundles

We have successfully synthesized large-scale crystalline boron nanowire bundles (BNBs) by chemical vapor deposition method. Fe₃O₄ nanoparticles were used as catalysts spreading on ceramic substrate during the reaction process. The bundles consisted of many thin boron nanowires with a mean diameter of about 25 nm and a length of several micrometers. In addition, boron nanowires are single crystals with an α-tetragonal structure and grow along [0 0 1] orientation. These nanowires have a surface electron affinity of 3.76 eV and a work function of 4.54 eV. A turn-on field of 5.1 V/μm and a threshold field of 10.5 V/μm were found in the nanowire bundles, and stable field emission was recorded at the same time.     

Validation and generalization of a method for precise size measurements of metal nanoclusters on supports

We recently described a data analysis method for precise (∼0.1 Å random error in the mean for a 200 kV instrument with a 3 Å FWHM probe size) size measurements of small clusters of heavy metal atoms on supports as imaged in a scanning transmission electron microscope, including an experimental demonstration using clusters that were primarily triosmium or decaosmium. The method is intended for low signal-to-noise ratio images of radiation-sensitive samples. We now present a detailed analysis, including a generalization to address issues of particle anisotropy and biased orientation distributions. In the future, this analysis should enable extraction of shape as well as size information, up to the noise-defined limit of information present in the image. We also present results from an extensive series of simulations designed to determine the method's range of applicability and expected performance in realistic situations. The simulations reproduce the experiments quite accurately, enabling a correction of systematic errors so that only the ∼0.1 Å random error remains. The results are very stable over a wide range of parameters. We introduce a variation on the method with improved precision and stability relative to the original version, while also showing how simple diagnostics can test whether the results are reliable in any particular instance.     

Time-resolved cryo-electron microscopy of vitrified muscular components

Biological objects may be arrested in defined stages of their activity by fast freezing and may then be structurally examined. If the time between the start of activity and freezing is controlled, structural rearrangements due to biological function can be determined. Cryo-electron microscopy shows great potential for the study of such time-dependent phenomena. This study examines the actin polymerization process using cryo-electron microscopy of vitrified specimens. Actin filaments are shown to undergo a structural change during polymerization. In the early stages of the polymerization process (t < 2 min), filaments exhibit a pronounced structural variation and frequently show a central low-density area. In the later stages of the polymerization, F-actin-ADP filaments have a more uniform appearance and rarely display a central low-density area. These findings, analysed on the basis of a previously proposed polymerization model, suggest that polymerization intermediates (F-actin-ATP and more probably F-actin-ADP-P_i) and filaments at steady state (F-actin-ADP) have different structures. To investigate the physiological relevance of these results at the cellular level, the potential of cryo-substitution in preserving the structure of muscular fibre was assessed. Optical diffraction patterns of relaxed and contracted frog cutaneous muscle are similar to the corresponding X-ray diffraction patterns. The resolution of the images extends to about 7 nm. These results show that dynamic study of muscle contraction is possible using cryo-substitution.     

Quantitative measurements of Kikuchi bands in diffraction patterns of backscattered electrons using an electrostatic analyzer

Diffraction patterns of backscattered electrons can provide important crystallographic information with high spatial resolution. Recently, the dynamical theory of electron diffraction was applied to reproduce in great detail backscattering patterns observed in the scanning electron microscope (SEM). However, a fully quantitative comparison of theory and experiment requires angle-resolved measurements of the intensity and the energy of the backscattered electrons, which is difficult to realize in an SEM. This paper determines diffraction patterns of backscattered electrons using an electrostatic analyzer, operating at energies up to 40 keV with sub-eV energy resolution. Measurements are done for different measurement geometries and incoming energies. Generally a good agreement is found between theory and experiment. This spectrometer also allows us to test the influence of the energy loss of the detected electron on the backscattered electron diffraction pattern. It is found that the amplitude of the intensity variation decreases only slowly with increasing energy loss from 0 to 60 eV.     

In-situ TEM on (de)hydrogenation of Pd at 0.5-4.5 bar hydrogen pressure and 20-400°C

We have developed a nanoreactor, sample holder and gas system for in-situ transmission electron microscopy (TEM) of hydrogen storage materials up to at least 4.5 bar. The MEMS-based nanoreactor has a microheater, two electron-transparent windows and a gas inlet and outlet. The holder contains various O-rings to have leak-tight connections with the nanoreactor. The system was tested with the (de)hydrogenation of Pd at pressures up to 4.5 bar. The Pd film consisted of islands being 15 nm thick and 50-500 nm wide. In electron diffraction mode we observed reproducibly a crystal lattice expansion and shrinkage owing to hydrogenation and dehydrogenation, respectively. In selected-area electron diffraction and bright/dark-field modes the (de)hydrogenation of individual Pd particles was followed. Some Pd islands are consistently hydrogenated faster than others. When thermally cycled, thermal hysteresis of about 10-16 °C between hydrogen absorption and desorption was observed for hydrogen pressures of 0.5-4.5 bar. Experiments at 0.8 bar and 3.2 bar showed that the (de)hydrogenation temperature is not affected by the electron beam. This result shows that this is a fast method to investigate hydrogen storage materials with information at the nanometer scale.     

Improved transfer of two-dimensional crystals from the air/water interface to specimen support grids for high-resolution analysis by electron microscopy

Electron crystallographic analysis of two-dimensional crystals grown on lipid layers at the air/water interface has been limited by loss or damage during transfer of the crystals to an electron microscope support grid. Two methods of transfer are described which are applicable on a small scale (10 microliters of protein solution) and which give greatly improved results for streptavidin crystals on biotinylated lipid layers. In the first method, a hydrophobic grid surface was produced by coating a carbon support film with a thin layer of SiO2, followed by alkylation with dimethyloctadecylchlorosilane. The transfer efficiency of protein crystals approached 50% coverage of the alkylated grid surface. The degree of order of crystals transferred to the alkylated grid surface and preserved in negative stain was significantly improved over that of crystals transferred directly to a carbon support film. In the second method, crystals at the air/water interface were transferred to a holey carbon support film. The efficiency of transfer across the holes was virtually 100% as nearly every hole was completely covered with crystals. After preservation of the crystals in 1% glucose and cooling to liquid nitrogen temperature, electron diffraction was obtained that extended to 1/2.8 A-1 resolution. This demonstrates that two-dimensional crystals grown on lipid layers at the air/water interface can be sufficiently well-ordered, even after transfer to a support grid, to yield high-resolution structural information.     

Energy resolution of an Omega-type monochromator and imaging properties of the MANDOLINE filter

We report on the energy resolution properties of an Omega-type monochromator. In a TEM/STEM setup with a MANDOLINE filter and extreme stability of the high voltage and the filter current, an energy resolution of 43 meV for 0.1 s exposure time and 87 meV for 100 s exposure time was measured at 200 kV with 40 meV monochromator slit width. The monochromized zero-loss peaks are additionally characterized by their edge steepness. Moreover a drop in the monochromized zero-loss peak by 10³ after 260 meV can be obtained even without deconvolution. For small fields of view, the energy resolution mostly does not depend on the MANDOLINE filter. With the Corrected OMEGA filter an energy resolution of 41 meV was measured for 0.03 s exposure time at 200 kV with 30 meV monochromator slit width and 77 meV for 50 s exposure time at 80 kV with 40 meV monochromator slit width. Furthermore, the MANDOLINE filter’s setup and imaging properties are presented such as isochromaticity (<5 meV) and transmissivity (T_(1 eV)=17,400 nm²), which set a new standard for imaging energy filters and allow EFTEM spectrum imaging with energy windows ≤200 meV and reasonable fields of view.     

Direct space structure solution from precession electron diffraction data: Resolving heavy and light scatterers in Pb13Mn9O25

The crystal structure of a novel compound Pb₁₃Mn₉O₂₅ has been determined through a direct space structure solution with a Monte-Carlo-based global optimization using precession electron diffraction data (a=14.177(3) Å, c=3.9320(7) Å, SG P4/m, R_F=0.239) and compositional information obtained from energy dispersive X-ray analysis and electron energy loss spectroscopy. This allowed to obtain a reliable structural model even despite the simultaneous presence of both heavy (Pb) and light (O) scattering elements and to validate the accuracy of the electron diffraction-based structure refinement. This provides an important benchmark for further studies of complex structural problems with electron diffraction techniques. Pb₁₃Mn₉O₂₅ has an anion- and cation-deficient perovskite-based structure with the A-positions filled by the Pb atoms and 9/13 of the B positions filled by the Mn atoms in an ordered manner. MnO₆ octahedra and MnO₅ tetragonal pyramids form a network by sharing common corners. Tunnels are formed in the network due to an ordered arrangement of vacancies at the B-sublattice. These tunnels provide sufficient space for localization of the lone 6s² electron pairs of the Pb²⁺ cations, suggested as the driving force for the structural difference between Pb₁₃Mn₉O₂₅ and the manganites of alkali-earth elements with similar compositions.     

Study of structures at the boundary and defects in organic thin films of perchlorocoronene by high-resolution and analytical transmission electron microscopy

Both the periodic and non-periodic structures of perchlorocoronene (C₂₄Cl₁₂) crystals were characterized by high-resolution transmission electron microscopy (HRTEM), electron diffraction (ED), electron energy-loss spectroscopy (EELS), and energy-filtered transmission electron microscopy (EFTEM). The HRTEM images at the boundary of the C₂₄Cl₁₂ crystals exhibit the flexibility of defect structures, where molecules align to compensate for the discontinuity between two different domains. Emphasized by the filtered images, it was found that the non-periodic regions are created everywhere with a small electron beam irradiation (∼10⁶ electrons nm⁻²) and then spread over the entire regions to completely destroy the periodic structures after a higher electron dose (∼2×10⁶ electrons nm⁻²). The effect of the electron beam irradiation was monitored by ED, EELS, and EFTEM, where periodic structures and content elements are well preserved up to 10⁶ electrons nm⁻², but chlorine atoms decreased with a much higher electron dose. This is explained by the breakage of the C–Cl bond to detach chlorine atoms, confirmed by energy-loss near the edge structures (ELNES) of carbon π? peaks and chlorine loss at the edge of the specimen, as well as by theoretical simulation. The detachment of chlorine is localized at the peripheral edge around a hole confirmed by core-loss EFTEM imaging.     

Friction and wear on the atomic scale

Friction force microscopy experiments have been performed under ultrahigh vacuum conditions. Within a small force regime (below 1 nN), friction without wear is observed as a function of velocity on ionic crystals and metals. The results are discussed in the framework of a refined version of the Tomlinson model, which includes thermal activation. Higher normal forces lead to abrasive wear. The debris extracted from ionic crystals can be characterized with high lateral resolution. The dependence of wear rate on velocity and normal force is investigated.