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Готові списки джерел за темами / 3D Electron diffraction / Статті в журналах

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Статті в журналах з теми "3D Electron diffraction"

Автор: Grafiati

Опубліковано: 11 січня 2025

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1

Gemmi, Mauro, and Arianna E. Lanza. "3D electron diffraction techniques." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 75, no. 4 (August 1, 2019): 495–504. http://dx.doi.org/10.1107/s2052520619007510.

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3D electron diffraction is an emerging technique for the structural analysis of nanocrystals. The challenges that 3D electron diffraction has to face for providing reliable data for structure solution and the different ways of overcoming these challenges are described. The route from zone axis patterns towards 3D electron diffraction techniques such as precession-assisted electron diffraction tomography, rotation electron diffraction and continuous rotation is also discussed. Finally, the advantages of the new hybrid detectors with high sensitivity and fast readout are demonstrated with a proof of concept experiment of continuous rotation electron diffraction on a natrolite nanocrystal.

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2

Cho, Jungyoun, and Xiaodong Zou. "Revealing structural details with 3D electron diffraction/microcrystal electron diffraction." Acta Crystallographica Section A Foundations and Advances 78, a1 (July 29, 2022): a217. http://dx.doi.org/10.1107/s2053273322097820.

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3

Beanland, R. "3D electron diffraction goes multipolar." IUCrJ 11, no. 3 (April 26, 2024): 277–78. http://dx.doi.org/10.1107/s2052252524003774.

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4

Schröder, Rasmus R., and Christoph Burmester. "Improvements in electron diffraction of frozen hydrated crystals by energy filtering and large-area single-electron detection." Proceedings, annual meeting, Electron Microscopy Society of America 51 (August 1, 1993): 666–67. http://dx.doi.org/10.1017/s0424820100149167.

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Diffraction patterns of 3D protein crystals embedded in vitrious ice are critical to record. Inelastically scattered electrons almost completely superimpose the diffraction pattern of crystals if the thickness of the crystal is higher than the mean free path of electrons in the specimen. Figure 1 shows such an example of an unfiltered electron diffraction pattern from a frozen hydrated 3D catalase crystal. However, for thin 2D crystals electron diffraction has been the state of the art method to determine the Fourier amplitudes for reconstructions to atomic level, and in one case the possibility of obtaining Fourier phases from diffraction patterns has been studied. One of the main problems could be the background in the diffraction pattern due to inelastic scattering and the recording characteristics for electrons of conventional negative material.It was pointed out before, that the use of an energy filtered TEM (EFTEM) and of the Image Plate as a large area electron detector gives considerable improvement for detection of diffraction patterns.

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5

Schmidt, Ella Mara, Yasar Krysiak, Paul Benjamin Klar, Lukas Palatinus, Reinhard B. Neder та Andrew L. Goodwin. "3D-ΔPDF from electron diffraction data". Acta Crystallographica Section A Foundations and Advances 77, a2 (14 серпня 2021): C80. http://dx.doi.org/10.1107/s0108767321095994.

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6

Gemmi, Mauro, Enrico Mugnaioli, Tatiana E. Gorelik, Ute Kolb, Lukas Palatinus, Philippe Boullay, Sven Hovmöller, and Jan Pieter Abrahams. "3D Electron Diffraction: The Nanocrystallography Revolution." ACS Central Science 5, no. 8 (July 19, 2019): 1315–29. http://dx.doi.org/10.1021/acscentsci.9b00394.

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7

Mei, Kaili, Kejia Zhang, Jungu Xu, and Zhengyang Zhou. "The Application of 3D-ED to Distinguish the Superstructure of Sr1.2Ca0.8Nb2O7 Ignored in SC-XRD." Crystals 13, no. 6 (June 8, 2023): 924. http://dx.doi.org/10.3390/cryst13060924.

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Анотація:

Compared to X-rays, electrons have stronger interactions with matter. In electron diffraction, the low-order structure factors are sensitive to subtle changes in the arrangement of valence electrons around atoms when the scattering vector is smaller than the critical scattering vector. Therefore, electron diffraction is more advantageous for studying the distribution of atoms in the structure with atomic numbers smaller than that of sulfur. In this work, the crystal structure of Sr1.2Ca0.8Nb2O7 (SCNO-0.8) was analyzed using single-crystal X-ray diffraction (SC-XRD) and three-dimensional electron diffraction (3D-ED) techniques, respectively. Interestingly, the superstructure could only be identified by the 3D-ED technique, while no signal corresponding to the superstructure was detected from the SC-XRD data. The superstructure in SCNO-0.8 was disclosed to be caused by different tilting of NbO6 octahedra and the displacements of Sr/Ca atoms in the different atomic layers perpendicular to the a-axis. Therefore, the application of 3D-ED provides an effective method for studying superstructures caused by ordered arrangements of light atoms.

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8

NISHIYAMA, Yusuke. "3D Electron Diffraction and Solid-State NMR." Nihon Kessho Gakkaishi 64, no. 3 (August 31, 2022): 201–2. http://dx.doi.org/10.5940/jcrsj.64.201.

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9

Meents, A., V. Hennicke, M. Hachmann, A. Rodrigues, W. Brehm, P. Reinke, J. Meyer, et al. "3D structure determination with MeV electron diffraction." Acta Crystallographica Section A Foundations and Advances 79, a2 (August 22, 2023): C309. http://dx.doi.org/10.1107/s2053273323093063.

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10

Palatinus, Lukáš, Cinthia Corrêa, Gwladys Mouillard, Philippe Boullay, and Damien Jacob. "Accurate structure refinement from 3D electron diffraction data." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C374. http://dx.doi.org/10.1107/s2053273314096259.

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Structure determination from electron diffraction data has seen an enormous progress over the past few years. At present, complex structures with hundreds of atoms in the unit cell can be solved from electron diffraction using the concept of electron diffraction tomography (EDT), possibly combined with precession electron diffraction (PED) [1]. Unfortunately, the initial model is typically optimized using the kinematical approximation to calculate model diffracted intensities. This approximation is quite inaccurate for electron diffraction and leads to high figures of merit and inaccurate results with unrealistically low standard uncertainties. The obvious remedy to the problem is the use of dynamical diffraction theory to calculate the model intensities in structure refinement. This technique has been known and used before, but it has not become very popular, because good fits could be obtained only for sufficiently perfect and sufficiently thin crystals. It has been shown recently on several zone-axis patterns [2] that the quality of the refinement can be improved by using precession electron diffraction. In the present contribution we demonstrate that the same approach can be successfully used to refine crystal structures against non-oriented patterns acquired by EDT combined with PED (PEDT in short). Because the PEDT technique provides three-dimensional diffraction information, it can be used for a complete structure refinement. Several test examples demonstrate that the dynamical structure refinement yields better figures of merit and more accurate results than the refinement using kinematical approximation.

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11

Vlahakis, Niko, James Holton, Nicholas K. Sauter, Peter Ercius, Aaron S. Brewster, and Jose A. Rodriguez. "3D Nanocrystallography and the Imperfect Molecular Lattice." Annual Review of Physical Chemistry 75, no. 1 (June 28, 2024): 483–508. http://dx.doi.org/10.1146/annurev-physchem-083122-105226.

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Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.

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12

Hovmöller, Sven, Devinder SINGH, Wei Wan, Yifeng Yun, Benjamin Grushko, and Xiaodong Zou. "Quasicrystal approximants solved by Rotation Electron Diffraction (RED)." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1195. http://dx.doi.org/10.1107/s2053273314088044.

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We have developed single crystal electron diffraction for powder-sized samples, i.e. < 0.1μm in all dimensions. Complete 3D electron diffraction is collected by Rotation Electron Diffraction (RED) in about one hour. Data processing takes another hour. The crystal structures are solved by standard crystallographic techniques. X-ray crystallography requires crystals several micrometers big. For nanometer sized crystals, electron diffraction and electron microscopy (EM) are the only possibilities. Modern transmission EMs are equipped with the two things that are necessary for turning them into automatic single crystal diffractometers; they have CCD cameras and all lenses and the sample stage are computer-controlled. Two methods have been developed for collecting complete (except for a missing cone) 3D electron diffraction data; the Rotation Electron Diffraction (RED) [1] and Automated Electron Diffraction Tomography (ADT) by Kolb et al. [2]. Because of the very strong interaction between electrons and matter, an electron diffraction pattern with visible spots is obtained in one second from a submicron sized crystal in the EM. By collecting 1000-2000 electron diffraction patterns, a complete 3D data set is obtained. The geometry in RED is analogous to the rotation method in X-ray crystallography; the sample is rotated continuously along one rotation axis. The data processing results in a list of typically over 1000 reflections with h,k,l and Intensity. The unit cell is typically obtained correctly to within 1%. Space group determination is done as in X-ray crystallography from systematically absent reflections, but special care must be taken because occasionally multiple electron diffraction can give rise to very strong forbidden reflections. At +/-60° tilt with 0.1° steps, a complete data collection will be some 1200 frames. With one second exposures this takes about one hour. There is no need to align the crystal orientation. The reciprocal lattice can be rotated and displayed at any direction of view. Sections such as hk0, hk1, hk2, h0l and so on can easily be cut out and displayed. We have solved over 50 crystal structures by RED in one year. These include the most complex zeolites ever solved and quasicrystal approximants, such as the pseudo-decagonal approximants PD2 [3] and PD1 in AlCoNi. Observed and calculated sections of reciprocal space (cut at 1.0Å) are shown in Fig. 1. Notice the 10-fold symmetry of strong reflections.

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13

Xu, Hongyi, and Xiaodong Zou. "Structure determination of biomolecules by 3D electron diffraction." Acta Crystallographica Section A Foundations and Advances 77, a2 (August 14, 2021): C236. http://dx.doi.org/10.1107/s0108767321094460.

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14

Kodjikian, Stéphanie, Holger Klein, Christophe Lepoittevin, Céline Darie, Pierre Bordet, Christophe Payen, and Catherine Deudon. "Identifying almost identical phases by 3D electron diffraction." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C373. http://dx.doi.org/10.1107/s2053273314096260.

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Magnetically frustrated materials have been the subject of many studies over the last decades. In search for a 3-dimensional quantum spin liquid, where quantum-mechanical fluctuations prevent magnetic order, different phases of stoichiometry Ba3NiSb2O9 have recently [1] been synthesized some of them at high pressure. Two of these phases are hexagonal. The hexagonal phases (space groups P63/mmc and P63mc, respectively) have different structures but cell parameters that differ by less than 1%. Similar phases have been obtained with Cu [2] or Co [3]. These phases are well distinguished by powder X-ray diffraction when they appear in sufficient quantity in a newly synthesized powder. When these phases are present only in minor quantities, which is a common situation when synthesizing new materials, only transmission electron microscopy can give structural information on a very local scale. However, the accuracy of unit cell parameter determination by electron diffraction (usually 1% or worse) and the identical extinction conditions for the 2 space groups don't permit to distinguish between the two phases. Convergent beam electron diffraction could show the difference between the centrosymmetric and non-centrosymmetric space groups provided a suitably oriented particle can be found. In this work we propose a different method of distinguishing structures in such complicated cases by actually solving the structure. Sufficient in-zone axis precession electron diffraction and/or electron diffraction tomography data can be obtained from any crystal regardless of its orientation. In the subsequent structure solution we have tested both space groups. The quality (or absence thereof) of the structure solutions obtained clearly makes it possible to distinguish between the two hexagonal structures.

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15

Palatinus, Lukas, and Petr Brázda. "Data processing of 3D precession electron diffraction data." Acta Crystallographica Section A Foundations and Advances 75, a2 (August 18, 2019): e406-e406. http://dx.doi.org/10.1107/s2053273319091502.

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16

Midgley, Paul. "Precession Electron Diffraction." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C12. http://dx.doi.org/10.1107/s2053273314099872.

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The strong Coulombic interaction between a high energy electron and a thin crystal film gives rise to electron diffraction patterns encoded with information that is remarkably sensitive to the crystal potential. That exquisite sensitivity can be advantageous, for example in the determination of local symmetry and bonding, but can also be problematic in that in general the dynamical scattering inherent in electron diffraction prohibits the use of conventional crystallographic methods to recover structure factor phase information and solve unknown structures. One way to reduce this problem is to use precession electron diffraction (PED), introduced 20 years ago [1] as the electron analogue of Buerger's X-ray technique, in which the electron beam is first rocked in a hollow cone above the sample and then de-rocked below, the net effect of which is equivalent to precessing the sample about a stationary electron beam. PED is now used almost routinely as a starting point to solve crystal structures that cannot be solved for a variety of reasons using x-ray or neutron methods. In this keynote lecture we explore why the PED technique has been successful for structure determination, focussing on the PED geometry, the variation of intensities with precession angle and specimen thickness, and how this `mimics' kinematic behaviour, and the use of unconventional structure solution and refinement approaches [2]. New acquisition geometries will be discussed that rely on tilt series of PED patterns to yield a more complete 3D data set. The lecture will focus on how PED has been used also as a method for nanoscale orientation mapping [3], providing more information than conventional electron diffraction and a robust method with which to determine local crystallographic orientation. By scanning the beam, accurate orientation images can be derived from series of PED patterns and, by combining with tomographic methods, sub-volume orientation information is also available.

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17

Lanza, Arianna, Eleonora Margheritis, Enrico Mugnaioli, Valentina Cappello, Gianpiero Garau, and Mauro Gemmi. "Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme." IUCrJ 6, no. 2 (January 15, 2019): 178–88. http://dx.doi.org/10.1107/s2052252518017657.

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Recent advances in 3D electron diffraction have allowed the structure determination of several model proteins from submicrometric crystals, the unit-cell parameters and structures of which could be immediately validated by known models previously obtained by X-ray crystallography. Here, the first new protein structure determined by 3D electron diffraction data is presented: a previously unobserved polymorph of hen egg-white lysozyme. This form, with unit-cell parameters a = 31.9, b = 54.4, c = 71.8 Å, β = 98.8°, grows as needle-shaped submicrometric crystals simply by vapor diffusion starting from previously reported crystallization conditions. Remarkably, the data were collected using a low-dose stepwise experimental setup consisting of a precession-assisted nanobeam of ∼150 nm, which has never previously been applied for solving protein structures. The crystal structure was additionally validated using X-ray synchrotron-radiation sources by both powder diffraction and single-crystal micro-diffraction. 3D electron diffraction can be used for the structural characterization of submicrometric macromolecular crystals and is able to identify novel protein polymorphs that are hardly visible in conventional X-ray diffraction experiments. Additionally, the analysis, which was performed on both nanocrystals and microcrystals from the same crystallization drop, suggests that an integrated view from 3D electron diffraction and X-ray microfocus diffraction can be applied to obtain insights into the molecular dynamics during protein crystal growth.

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18

Dimmeler, E., K. C. Holmes, and R. R. Schröder. "Determination of Tilt Parameters in Electron Diffraction Patterns of 3D-Microcrystals." Microscopy and Microanalysis 3, S2 (August 1997): 1049–50. http://dx.doi.org/10.1017/s1431927600012137.

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Electron crystallography of thin three-dimensional (3D) protein crystals requires very exact determination of tilt angles and spot profiles to obtain correct merging of diffraction spot amplitudes. The reciprocal lattice of 3D microcrystals consists of ellipsoidal spot profiles which are very extended in the direction normal to the crystal face (z*). To extrapolate from the intensity measured in a section to the total spot intensity, two features need to be known very exactly: 1. the orientation of reciprocal lattice relative to the Ewald sphere, 2. the 3D-shape of the spot cloud.Fig. 1 shows a tilt series of one frozen hydrated catalase crystal, in the order of recording. The third diffraction pattern gives the highest resolution because it is untilted and therefore the electrons have the shortest path length. In the current experimental data taken at 120 keV electron energy inelastic scattering within the crystal leads to a dramatic loss of elastic information in highly tilted patterns.

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19

Hovmöller, S., P. Oleynikov, J. Sun, D. Zhang, and X. Zou. "Quantitative 3D electron diffraction data by precession and electron rotation methods." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (August 23, 2008): C76. http://dx.doi.org/10.1107/s0108767308097560.

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20

Polovinkin, Vitaly, Krishna Khakurel, Michal Babiak, Borislav Angelov, Bohdan Schneider, Jan Dohnalek, Jakob Andreasson, and Janos Hajdu. "Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures." Journal of Applied Crystallography 53, no. 6 (October 13, 2020): 1416–24. http://dx.doi.org/10.1107/s1600576720013096.

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Electron crystallography of sub-micrometre-sized 3D protein crystals has emerged recently as a valuable field of structural biology. In meso crystallization methods, utilizing lipidic mesophases, particularly lipidic cubic phases (LCPs), can produce high-quality 3D crystals of membrane proteins (MPs). A major step towards realizing 3D electron crystallography of MP crystals, grown in meso, is to demonstrate electron diffraction from such crystals. The first task is to remove the viscous and sticky lipidic matrix that surrounds the crystals without damaging the crystals. Additionally, the crystals have to be thin enough to let electrons traverse them without significant multiple scattering. In the present work, the concept that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can be used to remove excess host lipidic mesophase matrix is experimentally verified, and then the crystals are thinned to a thickness suitable for electron diffraction. In this study, bacteriorhodopsin (BR) crystals grown in a lipidic cubic mesophase of monoolein were used as a model system. LCP from a part of a hexagon-shaped plate-like BR crystal (∼10 µm in thickness and ∼70 µm in the longest dimension), which was flash-frozen in liquid nitrogen, was milled away with a gallium FIB under cryogenic conditions, and a part of the crystal itself was thinned into a ∼210 nm-thick lamella with the ion beam. The frozen sample was then transferred into an electron cryo-microscope, and a nanovolume of ∼1400 × 1400 × 210 nm of the BR lamella was exposed to 200 kV electrons at a fluence of ∼0.06 e Å−2. The resulting electron diffraction peaks were detected beyond 2.7 Å resolution (with an average peak height to background ratio of >2) by a CMOS-based Ceta 16M camera. The results demonstrate that cryo-FIB milling produces high-quality lamellae from crystals grown in lipidic mesophases and pave the way for 3D electron crystallography on crystals grown or embedded in highly viscous media.

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21

Gorelik, Tatiana E., Berkin Nergis, Tobias Schöner, Janis Köster, and Ute Kaiser. "3D electron diffraction of mono- and few-layer MoS2." Micron 146 (July 2021): 103071. http://dx.doi.org/10.1016/j.micron.2021.103071.

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22

Cho, Jungyoun, Xiaodong Zou, and Tom Willhammar. "Unravelling unforeseen disorders in silicates with 3D electron diffraction." Acta Crystallographica Section A Foundations and Advances 77, a2 (August 14, 2021): C1283. http://dx.doi.org/10.1107/s0108767321084324.

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23

Broadhurst, Edward Thomas. "Polymorphism within molecular systems revelaed by 3D electron diffraction." Acta Crystallographica Section A Foundations and Advances 77, a2 (August 14, 2021): C1282. http://dx.doi.org/10.1107/s0108767321084336.

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24

Klar, Paul Benjamin, Petr Brázda, Yasar Krysiak, Mariana Klementová, and Lukas Palatinus. "Absolute configuration directly determined from 3D electron diffraction data." Acta Crystallographica Section A Foundations and Advances 77, a2 (August 14, 2021): C210. http://dx.doi.org/10.1107/s0108767321094721.

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25

Gemmi, Mauro, Enrico Mugnaioli, Roman Kaiukov, Stefano Toso, Luca De Trizio, and Liberato Manna. "3D electron diffraction on nanoparticles with a complex structure." Acta Crystallographica Section A Foundations and Advances 77, a2 (August 14, 2021): C78. http://dx.doi.org/10.1107/s010876732109601x.

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26

Hovmöller, Sven, Daliang Zhang, Daniel Grüner, Xiaodong Zou, and Peter Oleynikov. "Collecting 3D electron diffraction data for crystal structure determination." Acta Crystallographica Section A Foundations of Crystallography 65, a1 (August 16, 2009): s228. http://dx.doi.org/10.1107/s0108767309095312.

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27

Zou, X., D. Zhang, P. Oleynikov, J. Sun, and S. Hovmöller. "3D Structure Determination from HRTEM and Electron Diffraction Tomography." Microscopy and Microanalysis 15, S2 (July 2009): 56–57. http://dx.doi.org/10.1017/s1431927609099413.

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28

Nannenga, Brent. "Biomolecular structure determination by electron diffraction of 3D microcrystals." Acta Crystallographica Section A Foundations and Advances 74, a2 (August 22, 2018): e5-e5. http://dx.doi.org/10.1107/s2053273318095189.

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29

Agbemeh, V. E., D. Sonaglioni, I. Andrusenko, E. Husanu, and M. Gemmi. "Structural study of organic cocrystals using 3D electron diffraction." Acta Crystallographica Section A Foundations and Advances 78, a2 (August 23, 2022): a635. http://dx.doi.org/10.1107/s2053273322091380.

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30

Bourda, L., S. Ito, C. Göb, P. Van Der Voort, and K. Van Hecke. "Electron diffraction analysis of a 3D covalent organic framework." Acta Crystallographica Section A Foundations and Advances 79, a2 (August 22, 2023): C1097. http://dx.doi.org/10.1107/s2053273323085248.

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31

Cordero Oyonarte, Erica, L. Rebecchi, V. Pralong, I. Kriegel, and P. Boullay. "3D electron diffraction for accurate structure analysis of nanoparticles." Acta Crystallographica Section A Foundations and Advances 80, a1 (August 26, 2024): e304-e304. https://doi.org/10.1107/s2053273324096955.

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32

Hata, Satoshi, Hiromitsu Furukawa, Takashi Gondo, Daisuke Hirakami, Noritaka Horii, Ken-Ichi Ikeda, Katsumi Kawamoto, et al. "Electron tomography imaging methods with diffraction contrast for materials research." Microscopy 69, no. 3 (March 2, 2020): 141–55. http://dx.doi.org/10.1093/jmicro/dfaa002.

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Анотація:

ABSTRACT Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) enable the visualization of three-dimensional (3D) microstructures ranging from atomic to micrometer scales using 3D reconstruction techniques based on computed tomography algorithms. This 3D microscopy method is called electron tomography (ET) and has been utilized in the fields of materials science and engineering for more than two decades. Although atomic resolution is one of the current topics in ET research, the development and deployment of intermediate-resolution (non-atomic-resolution) ET imaging methods have garnered considerable attention from researchers. This research trend is probably not irrelevant due to the fact that the spatial resolution and functionality of 3D imaging methods of scanning electron microscopy (SEM) and X-ray microscopy have come to overlap with those of ET. In other words, there may be multiple ways to carry out 3D visualization using different microscopy methods for nanometer-scale objects in materials. From the above standpoint, this review paper aims to (i) describe the current status and issues of intermediate-resolution ET with regard to enhancing the effectiveness of TEM/STEM imaging and (ii) discuss promising applications of state-of-the-art intermediate-resolution ET for materials research with a particular focus on diffraction contrast ET for crystalline microstructures (superlattice domains and dislocations) including a demonstration of in situ dislocation tomography.

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33

Jiang, Linhua, Dilyana Georgieva, Igor Nederlof, Zunfeng Liu, and Jan Pieter Abrahams. "Image Processing and Lattice Determination for Three-Dimensional Nanocrystals." Microscopy and Microanalysis 17, no. 6 (November 18, 2011): 879–85. http://dx.doi.org/10.1017/s1431927611012244.

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AbstractThree-dimensional nanocrystals can be studied by electron diffraction using transmission cryo-electron microscopy. For molecular structure determination of proteins, such nanosized crystalline samples are out of reach for traditional single-crystal X-ray crystallography. For the study of materials that are not sensitive to the electron beam, software has been developed for determining the crystal lattice and orientation parameters. These methods require radiation-hard materials that survive careful orienting of the crystals and measuring diffraction of one and the same crystal from different, but known directions. However, as such methods can only deal with well-oriented crystalline samples, a problem exists for three-dimensional (3D) crystals of proteins and other radiation sensitive materials that do not survive careful rotational alignment in the electron microscope. Here, we discuss our newly released software AMP that can deal with nonoriented diffraction patterns, and we discuss the progress of our new preprocessing program that uses autocorrelation patterns of diffraction images for lattice determination and indexing of 3D nanocrystals.

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34

Yang, Taimin, Hongyi Xu, and Xiaodong Zou. "Improving data quality for 3D electron diffraction (3D-ED) by Gatan Image Filter." Acta Crystallographica Section A Foundations and Advances 77, a2 (August 14, 2021): C160—C161. http://dx.doi.org/10.1107/s0108767321095210.

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35

Zou, Xiaodong. "Single Crystal 3D Rotation Electron Diffraction from Nano-sized Crystals." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C366. http://dx.doi.org/10.1107/s2053273314096338.

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Electron crystallography is an important technique for structure analysis of nano-sized materials. Crystals too small or too complicated to be studied by X-ray diffraction can be investigated by electron crystallography. However, conventional TEM methods requires high TEM skills and strong crystallographic knowledge, which many synthetic materials scientists and chemists do not have. We recently developed the software-based Rotation Electron Diffraction (RED) method for automated collection and processing of 3D electron diffraction data. Complete single crystal 3D electron diffraction data can be collected from nano- and micron-sized crystals in less than one hour by combining electron beam tilt and goniometer tilt, which are controlled by the RED – data collection software.3 The unit cell, possible space groups and electron diffraction intensities can be obtained from the RED data using the RED data processing software. The figure below illustrates the data collection and data processing of a zeolite silicalite-1 by RED. 1427 ED frames were collected in less than 1 hour from a crystal of 800 x 400 x 200 nm in size. A 3D reciprocal lattice of silicalite-1 was reconstructed from the ED frames, from which the unit cell parameters and space group were determined (P21/n, a=20.02Å, b=20.25Å, c=13.35Å, alfa=90.130, beta=90.740, gamma=90.030. It was possible to cut the 3D reciprocal lattice perpendicular to any directions and study the reflection conditions. The reflection intensities could be extracted. The structure of the calcined silicalite-1 could be solved from the RED data by routine direct methods using SHELX-97. All 78 unique Si and O atoms could be located and refined to an accuracy better than 0.08 Å. The RED method has been applied for structure solution of a wide range of crystals and shown to be very powerful and efficient. Now a structure determination can be achieved within a few hours, from the data collection to structure solution. We will present several examples including unknown inorganic compounds, metal-organic frameworks and organic structures solved from the RED data. Different parameters that affect the RED data quality and thus the structure determination will be discussed. The methods are general and can be applied to any crystalline materials.

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36

Su, Jie, Yue-Biao Zhang, Yifeng Yun, Hiroyasu Furukawa, Felipe Gándara, Adam Duong, Xiaodong Zou, and Omar Yaghi. "The First Covalent Organic Framework solved by Rotation Electron Diffraction." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C191. http://dx.doi.org/10.1107/s2053273314098088.

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Covalent organic frameworks (COFs) represent an exciting new type of porous organic materials, which are constructed with organic building units via strong covalent bonds.[1] The structure determination of COFs is challenging, due to the difficulty in growing sufficiently large crystals suitable for single crystal X-ray diffraction, and low resolution and peak broadening for powder X-ray diffraction. Crystal structures of COFs are typically determined by modelling building with the aid of geometry principles in reticular chemistry and powder X-ray diffraction data. Here, we report the single-crystal structure of a new COF (COF-320) determined by 3D rotation electron diffraction (RED),[2] a technique applied in this context for the first time. The RED method can collect an almost complete three-dimensional electron diffraction dataset, and is a useful technique for structure determination of micron- and nanosized single crystals. To minimize electron beam damage, the RED dataset was collected at 89 K. 3D reciprocal lattice of COF-320 was reconstructed from the ED frames using the RED – data processing software[2]. As the resolution of the RED data only reached 1.6 Å, the simulated annealing parallel tempering algorithm in the FOX software package [3] was used to find a starting molecular arrangement from the 3D RED data. Finally, the crystal structure of COF-320 was solved in the space group of I-42d and refined using the SHELXL software package. The single-crystal structure of COF-320 exhibits a 3D extended framework by linking the tetrahedral organic building blocks and biphenyl linkers through imine-bonds forming a highly porous 9-fold interwoven diamond net.

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37

Nakano, Miki, Osamu Miyashita, Slavica Jonic, Changyong Song, Daewoong Nam, Yasumasa Joti, and Florence Tama. "Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL." Journal of Synchrotron Radiation 24, no. 4 (June 14, 2017): 727–37. http://dx.doi.org/10.1107/s1600577517007767.

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The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on theXmippsoftware package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

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38

Leung, Helen W., Roy C. B. Copley, Duncan N. Johnstone, and Paul A. Midgley. "Combining 3D electron diffraction with scanning electron diffraction to investigate nanocrystals within a long-acting injectable pharmaceutical formulation." Acta Crystallographica Section A Foundations and Advances 80, a1 (August 26, 2024): e305-e305. https://doi.org/10.1107/s2053273324096943.

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39

Miao, John. "Beyond Crystallography: Coherent Diffraction Imaging and Atomic Resolution Electron Tomography." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C5. http://dx.doi.org/10.1107/s205327331409994x.

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The discovery and interpretation of X-ray diffraction from crystals by von Laue, Henry and Lawrence Bragg about a century ago marked the beginning of a new era for visualizing the three-dimensional (3D) atomic structures in crystals. In 1999, the methodology of X-ray crystallography was extended to allow the structure determination of non-crystalline specimens, which is known as coherent diffraction imaging (CDI) or lensless imaging. In CDI, the diffraction pattern of a non-crystalline sample or a nanocrystal is first measured and then directly phased to obtain an image. The well-known phase problem is solved by combining the oversampling method with iterative algorithms. In the first part of the talk, I will present the principle of CDI and illustrate some applications using synchrotron radiation and X-ray free electron lasers (XFELs). In the second part of the talk, I will present a general tomographic method for determining the 3D local structure of materials at atomic resolution. By combining scanning transmission electron microscopy (STEM) with a novel data acquisition and image reconstruction method known as equally sloped tomography (EST), we achieve electron tomography at 2.4 Å resolution and observe nearly all the atoms in a multiply-twinned Pt nanoparticle. We find the existence of atomic steps at 3D twin boundaries of the Pt nanoparticle and, for the first time, image the 3D core structure of edge and screw dislocations in materials at atomic resolution. We expect this atomic resolution electron tomography method to find application in solid state physics, materials sciences, nanoscience, chemistry and biology.

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40

Gammer, Christoph, Clemens Mangler, Hans-Peter Karnthaler, and Christian Rentenberger. "Three-Dimensional Analysis by Electron Diffraction Methods of Nanocrystalline Materials." Microscopy and Microanalysis 17, no. 6 (November 4, 2011): 866–71. http://dx.doi.org/10.1017/s1431927611011962.

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AbstractTo analyze nanocrystalline structures quantitatively in 3D, a novel method is presented based on electron diffraction. It allows determination of the average size and morphology of the coherently scattering domains (CSD) in a straightforward way without the need to prepare multiple sections. The method is applicable to all kinds of bulk nanocrystalline materials. As an example, the average size of the CSD in nanocrystalline FeAl made by severe plastic deformation is determined in 3D. Assuming ellipsoidal CSD, it is deduced that the CSD have a width of 19 ± 2 nm, a length of 18 ± 1 nm, and a height of 10 ± 1 nm.

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41

Gorelik, Tatiana E., Stefan Habermehl, Aleksandr A. Shubin, Tim Gruene, Kaname Yoshida, Peter Oleynikov, Ute Kaiser, and Martin U. Schmidt. "Crystal structure of copper perchlorophthalocyanine analysed by 3D electron diffraction." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 77, no. 4 (July 29, 2021): 662–75. http://dx.doi.org/10.1107/s2052520621006806.

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Copper perchlorophthalocyanine (CuPcCl16, CuC32N8Cl16, Pigment Green 7) is one of the commercially most important green pigments. The compound is a nanocrystalline fully insoluble powder. Its crystal structure was first addressed by electron diffraction in 1972 [Uyeda et al. (1972). J. Appl. Phys. 43, 5181–5189]. Despite the commercial importance of the compound, the crystal structure remained undetermined until now. Using a special vacuum sublimation technique, micron-sized crystals could be obtained. Three-dimensional electron diffraction (3D ED) data were collected in two ways: (i) in static geometry using a combined stage-tilt/beam-tilt collection scheme and (ii) in continuous rotation mode. Both types of data allowed the crystal structure to be solved by direct methods. The structure was refined kinematically with anisotropic displacement parameters for all atoms. Due to the pronounced crystal mosaicity, a dynamic refinement was not feasible. The unit-cell parameters were verified by Rietveld refinement from powder X-ray diffraction data. The crystal structure was validated by many-body dispersion density functional theory (DFT) calculations. CuPcCl16 crystallizes in the space group C2/m (Z = 2), with the molecules arranged in layers. The structure agrees with that proposed in 1972.

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42

Harrison, Patrick, Xuyang Zhou, Saurabh Mohan Das, Nicola Viganò, Pierre Lhuissier, Michael Herbig, Wolfgang Ludwig, and Edgar Rauch. "Reconstructing grains in 3D through 4D Scanning Precession Electron Diffraction." Microscopy and Microanalysis 27, S1 (July 30, 2021): 2494–95. http://dx.doi.org/10.1017/s1431927621008898.

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43

Zou, Xiaodong, Peter Oleynikov, Daliang Zhang, Tom Willhammar, and Sven Hovmöller. "Complete 3D electron diffraction data collection - new methods and applications." Acta Crystallographica Section A Foundations of Crystallography 66, a1 (August 29, 2010): s67. http://dx.doi.org/10.1107/s0108767310098570.

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44

Broadhurst, Edward T., Hongyi Xu, Max T. B. Clabbers, Molly Lightowler, Fabio Nudelman, Xiaodong Zou, and Simon Parsons. "Polymorph evolution during crystal growth studied by 3D electron diffraction." IUCrJ 7, no. 1 (January 1, 2020): 5–9. http://dx.doi.org/10.1107/s2052252519016105.

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3D electron diffraction (3DED) has been used to follow polymorph evolution in the crystallization of glycine from aqueous solution. The three polymorphs of glycine which exist under ambient conditions follow the stability order β < α < γ. The least stable β polymorph forms within the first 3 min, but this begins to yield the α-form after only 1 min more. Both structures could be determined from continuous rotation electron diffraction data collected in less than 20 s on crystals of thickness ∼100 nm. Even though the γ-form is thermodynamically the most stable polymorph, kinetics favour the α-form, which dominates after prolonged standing. In the same sample, some β and one crystallite of the γ polymorph were also observed.

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45

Klementová, Mariana, Lukas Palatinus, and Paul Klar. "3D Electron Diffraction for Structure Analysis of Challenging Inorganic Materials." Microscopy and Microanalysis 26, S2 (July 30, 2020): 750–51. http://dx.doi.org/10.1017/s143192762001572x.

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46

Roslova, Maria, Stef Smeets, Bin Wang, Thomas Thersleff, Hongyi Hu, and Xiaodong Zou. "Automated electron diffraction: 3D structure determination with sub-ångström resolution." Acta Crystallographica Section A Foundations and Advances 75, a2 (August 18, 2019): e407-e407. http://dx.doi.org/10.1107/s2053273319091496.

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47

Andrusenko, Iryna, Victoria Hamilton, Enrico Mugnaioli, Arianna Lanza, Charlie Hall, Jason Potticary, Simon R. Hall, and Mauro Gemmi. "The Crystal Structure of Orthocetamol Solved by 3D Electron Diffraction." Angewandte Chemie International Edition 58, no. 32 (August 5, 2019): 10919–22. http://dx.doi.org/10.1002/anie.201904564.

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48

Andrusenko, Iryna, Victoria Hamilton, Enrico Mugnaioli, Arianna Lanza, Charlie Hall, Jason Potticary, Simon R. Hall, and Mauro Gemmi. "The Crystal Structure of Orthocetamol Solved by 3D Electron Diffraction." Angewandte Chemie 131, no. 32 (July 11, 2019): 11035–38. http://dx.doi.org/10.1002/ange.201904564.

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49

Gurung, K., P. Brázda, and L. Palatinus. "Crystal structure study of xenon compounds using 3D electron diffraction." Acta Crystallographica Section A Foundations and Advances 78, a2 (August 23, 2022): a620. http://dx.doi.org/10.1107/s2053273322091513.

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50

Nunes, Pedro, Matus Krajnak, Adriana L. Klyszejko, and Alistair C. Siebert. "3D Electron Diffraction of Small Molecules on the MerlinEM Detector." Microscopy and Microanalysis 29, Supplement_1 (July 22, 2023): 1014. http://dx.doi.org/10.1093/micmic/ozad067.511.

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