Round robin on structure analysis from 3D electron diffraction data.

The effect of the acceleration voltage on the quality of structure determination by 3D-electron diffraction

Beauveriolides, including the main beauveriolide I {systematic name: (3R,6S,9S,13S)-9-benzyl-13-[(2S)-hexan-2-yl]-6-methyl-3-(2-methylpropyl)-1-oxa-4,7,10-triazacyclotridecane-2,5,8,11-tetrone, C27H41N3O5}, are a series of cyclodepsipeptides that have shown promising results in the treatment of Alzheimer's disease and in the prevention of foam cell formation in atherosclerosis. Their crystal structure studies have been difficult due to their tiny crystal size and fibre-like morphology, until now. Recent developments in 3D electron diffraction methodology have made it possible to accurately study the crystal structures of submicron crystals by overcoming the problems of beam sensitivity and dynamical scattering. In this study, the absolute structure of beauveriolide I was determined by 3D electron diffraction. The cyclodepsipeptide crystallizes in the space group I2 with lattice parameters a = 40.2744 (4), b = 5.0976 (5), c = 27.698 (4) Å and β = 105.729 (6)°. After dynamical refinement, its absolute structure was determined by comparing the R factors and calculating the z-scores of the two possible enantiomorphs of beauveriolide I.

Structure analysis using 3D electron diffraction (3D ED, aka ADT, cRED, MicroED) data has become increasingly popular among chemists and materials scientists for its ability to solve crystal structures from single nanocrystals. Despite substantial progress in this method, it is still generally considered to provide relatively low-accuracy structure models, unsuitable for all but basic crystallographic analysis. Recent advances in data acquisition, data processing in PETS2 [1], including determination of the exact experimental geometry, and dynamical refinement in Jana2020/Dyngo [2] with modeling of the apparent crystal thickness distribution, have enabled 3D ED to answer questions about the finest details of structure, including partially occupied hydrogen positions or charge density analysis. Figure 1 shows methyl disorder in acetaminophen and charge density analysis in L-tyrosine obtained from 3D ED data. It is also possible to determine the absolute structure [3]. For this purpose, the so-called z-score has been introduced for enantiopure materials [4]. However, if certain conditions are fulfilled, the classical Flack parameter determination can be applied in electron crystallography. These advances bring electron crystallography to the same level of accuracy as X-ray diffraction, with the ability to see light atoms alongside heavy ones due to a smaller increase in scattering potential with atomic number and greater sensitivity to the absolute structure of structures consisting of only light atoms.

The absolute structure of the 3D MOF anhydrous zinc (II) tartrate with space group I222 has been determined for both [Zn(L-TAR)] and [Zn(D-TAR)] by electron diffraction using crystals of sub-micron dimensions. Dynamical refinement gives a strong difference in R factors for the correct and inverted structures. These anhydrous MOFs may be prepared phase pure from mild hydrothermal conditions. Powder X-ray diffraction indicates that isostructural or pseudo-isostructural phases can be similarly prepared for several other M2+ = Mg, Mn, Co, Ni and Cu. I222 is a relatively uncommon space group since it involves intersecting two-fold axes that place constraints on molecular crystals. However, in the case of MOFs the packing is dominated by satisfying the octahedral coordination centers. These MOFs are dense 3D networks with chiral octahedral metal centers that may be classed as Δ (for L-TAR) or Λ (for D-TAR).

Dose symmetric electron diffraction tomography (DS-EDT): Implementation of a dose-symmetric tomography scheme in 3D electron diffraction

Patent method for the extraction and determination of micro- and nano- plastics in organic and inorganic matrix samples: An application on vegetals

Results of a joint auger/esca round robin sponsored by astm committee E-42 on surface analysis. Part II. Auger results

Pair Distribution Function Obtained from Electron Diffraction: An Advanced Real-Space Structural Characterization Tool

Mechanochemical synthesis is a powerful approach to obtain new materials, limiting costs, and times. However, defected and submicrometrical-sized crystal products make critical their characterization through classical single-crystal X-ray diffraction. A valid alternative is represented by three-dimensional (3D) electron diffraction, in which a transmission electron microscope is used, like a diffractometer. This work matches a green water-based mechanochemical synthesis and 3D electron diffraction to obtain and characterize a Cu-based protocatechuate metal-organic framework (PC-MOF). Its structure has been fully refined through dynamical diffraction theory, and free water molecules could be detected in the channels of the framework. Thermal characterization, focused on the dehydration profile determination, leads to the formation of a novel high-temperature 2D coordination polymer, fully solved with 3D electron diffraction data. At last, the strong activity of the PC-MOF against cationic dyes like methylene blue has been reported.

Recent advances in 3D electron diffraction (3D ED) havesucceededin matching the capabilities of single-crystal X-ray diffraction (SCXRD),while requiring only submicron crystals for successful structuralinvestigations. One of the many diverse areas to benefit from the3D ED structural analysis is main-group chemistry, where compoundsare often poorly crystalline or single-crystal growth is challenging.A facile method for loading and transferring highly air-sensitiveand strongly oxidizing samples at low temperatures to a transmissionelectron microscope (TEM) for 3D ED analysis was successfully developedand tested on xenon(II) compounds from the XeF2–MnF4 system. The crystal structures determined on nanometer-sizedcrystallites by dynamical refinement of the 3D ED data are in completeagreement with the results obtained by SCXRD on micrometer-sized crystalsand by periodic density-functional theory (DFT) calculations, demonstratingthe applicability of this approach for structural studies of noble-gascompounds and highly reactive species in general. The compounds 3XeF2·2MnF4, XeF2·MnF4, and XeF2·2MnF4 are rare examples ofstructurally fully characterized xenon difluoride–metal tetrafluorideadducts and thus advance our knowledge of the diverse structural chemistryof these systems, which also includes the hitherto poorly characterizedfirst noble-gas compound, “XePtF6”.

3D electron diffraction (3D ED), also known as micro-crystal electron diffraction (MicroED), is a rapid, accurate, and robust method for structure determination of submicron-sized crystals. 3D ED has mainly been applied in material science until 2013, when MicroED was developed for studying macromolecular crystals. MicroED was considered as a cryo-electron microscopy method, as MicroED data collection is usually carried out in cryogenic conditions. As a result, some researchers may consider that 3D ED/MicroED data collection on crystals of small organic molecules can only be performed in cryogenic conditions. In this work, we determined the structure for sucrose and azobenzene tetracarboxylic acid (H4ABTC). The structure of H4ABTC is the first crystal structure ever reported for this molecule. We compared data quality and structure accuracy among datasets collected under cryogenic conditions and room temperature. With the improvement in data quality by data merging, it is possible to reveal hydrogen atom positions in small organic molecule structures under both temperature conditions. The experimental results showed that, if the sample is stable in the vacuum environment of a transmission electron microscope (TEM), the data quality of datasets collected under room temperature is at least as good as data collected under cryogenic conditions according to various indicators (resolution, I/σ(I), CC1/2 (%), R1, Rint, ADRA).

The enhancement of negative secondary ions yields in SIMS by the use of electropositive primary ions is well known. In previous papers, the authors of this article have reported on the simultaneous use of primary ion bombardment coupled with neutral cesium deposition to optimize the useful yields of negative secondary ions in the steady‐state regime. For electronegative elements, total ionization was achieved while the gain for the other elements attained two orders of magnitude. In this paper, we study the enhancement of negative secondary ion yields in the pre‐equilibrium regime by depositing neutral cesium onto the sample surface prior to the SIMS analysis. The main areas of application of this technique lie in the field of secondary ion imaging of sample surfaces. Of particular interest is the analysis of organic and biological samples on the Cameca NanoSIMS50 instrument. Both inorganic and organic samples will be investigated in this paper. Copyright © 2010 John Wiley & Sons, Ltd.

All crystalline materials in nature, whether inorganic, organic, or biological, macroscopic or microscopic, have their own chemical and physical properties, which strongly depend on their atomic structures. Therefore, structure determination is extremely important in chemistry, physics, materials science, etc. In the past centuries, many techniques have been developed for structure determination. The most widely used one is X-ray crystallography (single-crystal X-ray diffraction (SCXRD) and powder X-ray diffraction (PXRD)), and it remains the most important technique for structure determination of crystalline materials. Although SCXRD and PXRD are successful in many cases, a number of reasons limit their applications, such as SCXRD for nanosized crystals, intergrowth, and defects and PXRD for complex structures, multiphasic samples, impurities, peak overlaps, etc. Another most valuable technique for structure determination is electron crystallography (EC). With the electron as a probe, EC alone can also be used for structure determination, especially for crystals that are too small to be studied by SCXRD or too complex for PXRD. As electrons interact much more strongly with matter than X-rays do, both electron diffraction (ED) patterns and high-resolution transmission electron microscopy (HRTEM) images can be obtained from nanosized crystals. However, collecting a complete set of ED patterns or recording a good HRTEM image requires considerable expertise on the operation of electron microscopes and crystallography. The strong interactions between electrons and materials can also lead to dynamical effects and beam damage. These difficulties make structure determination from ED patterns and HRTEM images not straightforward. Recently, two three-dimensional (3D) electron diffraction techniques, automated electron diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed, which perform the data collection in an automated manner. Although the dynamical effects in the newly developed 3D electron diffraction techniques (ADT, RED) are reduced significantly, for some structures there are still problems with obtaining an initial model because of beam damage. The X-ray diffraction and EC methods discussed above are both powerful techniques but have their own limitations. In many complicated cases, one technique alone is not enough to solve the crystal structure, and different techniques that supply complementary structural information have to support each other for the complete structure determination. In this Account, we provide a summary of the advantages and disadvantages of X-ray diffraction (PXRD and SCXRD) and EC (HRTEM and ED) for structure determination and include a review of applications of X-ray diffraction and EC for solving complex structure problems such as peak overlap, impurities, pseudosymmetry and twinning, disordered frameworks, locating guests, aperiodic structures, etc. Some of the latest advances in structure determination are also presented briefly, namely, revealing hydrogen positions by ED, protein crystal structure solution by 3D electron diffraction, and structure determination using an X-ray free electron laser (XFEL).

Qualitative and quantitative x-ray energy dispersive spectroscopy is now used successfully to analyze many features and processes in inorganic samples. When applied to inorganic samples, however, the results are often less satisfactory due to problems of preparation of organic samples, difficulty of measuring x-rays from organic samples, damage of the sample by the electron beam, and other practical problems. In the present study we used a high voltage transmission electron microscope equipped with an energy dispersive x-ray spectrometer to examine accurate quantitative standardless analysis of thin sections of an organic sample, human dentin. Based on our experiments we found the important parameters for quantitative analysis were sample thickness and appropriate choice of model sample. Further, we show that the method of Cliff and Lorimer can be used with biological samples at 200 kV, and we show that quantitative analysis of human dentin can be carried out at 200 kV. Finally, we show that areas of human dentin can be differentiated by their morphological characteristics and x-ray analyses obtained in the transmission electron microscope.

ABSTRACTReplicate radiocarbon (14C) measurements of organic and inorganic control samples, with known Fraction Modern values in the range Fm = 0–1.5 and mass range 6 μg–2 mg carbon, are used to determine both the mass and radiocarbon content of the blank carbon introduced during sample processing and measurement in our laboratory. These data are used to model, separately for organic and inorganic samples, the blank contribution and subsequently “blank correct” measured unknowns in the mass range 25–100 μg. Data, formulas, and an assessment of the precision and accuracy of the blank correction are presented.