| 1. |
- Lightowler, Molly, et al.
(author)
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Phase identification and discovery of an elusive polymorph of drug-polymer inclusion complex using automated 3D electron diffraction
- 2024
-
In: Angewandte Chemie International Edition. - 1433-7851 .- 1521-3773. ; 63:16
-
Journal article (peer-reviewed)abstract
- 3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low-dose and low-bias 3D ED protocol has been implemented to identify six phases from a multiple-phase melt-crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low-dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF-PEG IC-I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF-PEG IC-II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF-PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam-sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product.
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| 2. |
- Wang, Lei, et al.
(author)
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Exploring Bronsted acids confined in the 10-ring channels of the zeolite ferrierite
- 2018
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In: CrystEngComm. - : Royal Society of Chemistry (RSC). - 1466-8033. ; 20:6, s. 699-702
-
Journal article (peer-reviewed)abstract
- Locations of Bronsted acids confined in the 10-ring channels of ferrierite have been unravelled by refining structural models of as-made and probe-molecule-adsorbed samples against powder X-ray diffraction data, respectively. By analysing both refinement results, it is suggested that Bronsted acid sites can be tailored by controlling the distribution of inorganic ions.
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| 3. |
- Yuan, Shuai, et al.
(author)
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[Ti8Zr2O12(COO)(16)] Cluster : An Ideal Inorganic Building Unit for Photoactive Metal-Organic Frameworks
- 2018
-
In: Acs Central Science. - : American Chemical Society (ACS). - 2374-7943 .- 2374-7951. ; 4:1, s. 105-111
-
Journal article (peer-reviewed)abstract
- Metal-organic frameworks (MOFs) based on Ti-oxo clusters (Ti-MOFs) represent a naturally self-assembled superlattice of TiO2 nanoparticles separated by designable organic linkers as antenna chromophores, epitomizing a promising platform for solar energy conversion. However, despite the vast, diverse, and well-developed Ti-cluster chemistry, only a scarce number of Ti-MOFs have been documented. The synthetic conditions of most Ti-based clusters are incompatible with those required for MOF crystallization, which has severely limited the development of Ti-MOFs. This challenge has been met herein by the discovery of the [Ti8Zr2O12(COO)(16)] cluster as a nearly ideal building unit for photoactive MOFs. A family of isoreticular photoactive MOFs were assembled, and their orbital alignments were fine-tuned by rational functionalization of organic linkers under computational guidance. These MOFs demonstrate high porosity, excellent chemical stability, tunable photoresponse, and good activity toward photocatalytic hydrogen evolution reactions. The discovery of the [Ti8Zr2O12(COO)(16)] cluster and the facile construction of photoactive MOFs from this cluster shall pave the way for the development of future Ti-MOF-based photocatalysts. GRAPHICS
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| 4. |
- Bengtsson, Viktor E. G., 1989-
(author)
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Crystal Structure Determination by 3D Electron Diffraction — New Software for Facilitating Data Processing
- 2022
-
Licentiate thesis (other academic/artistic)abstract
- Three-Dimensional Electron Diffraction (3DED) is a useful technique for determining crystal structures from very small crystals (hundreds of \si{\nano\meter} or less). Examples of such crystals are zeolites, metal-organic frameworks (MOFs), pharmaceuticals, and proteins. Knowledge of the structure is useful for understanding and potentially changing how the material or substance functions. This thesis includes the structure determination of the MOFs CAU-42 and CAU-45 as well as the development of the software \emph{Scipion-ED} in response to challenges during the processing of 3DED data from the two MOFs. Both MOFs displayed correlated disorder, where disorder in one part of the structure influences the configuration of disorder in nearby parts. The influence of the solvent during synthesis on the final structured is also discussed. The development and design of the software \emph{Scipion-ED} is described. It is a graphical user interface based on \emph{scipion-pyworkflow} for workflow-centric data processing. The described implementation includes the foundation for using \emph{Scipion} to process 3DED data, as well as a plugin for processing with \emph{DIALS}. Approaches are also described for extending the software to use \emph{XDS} or other programs.
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| 5. |
- Bengtsson, Viktor E. G., 1989-, et al.
(author)
-
Scipion-ED : a graphical user interface for batch processing and analysis of 3D ED/MicroED data
- 2022
-
In: Journal of applied crystallography. - : International Union of Crystallography (IUCr). - 0021-8898 .- 1600-5767. ; 55:3, s. 638-646
-
Journal article (peer-reviewed)abstract
- Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.
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| 6. |
- Bortolini, C., et al.
(author)
-
Atomic Structure of Amyloid Crystals
-
Other publication (other academic/artistic)abstract
- A deep understanding of the self-assembly and crystallization of biomolecules as highly ordered biomaterials is crucial to enable the design and the generation of complex functional systems for cutting-edge applications in nanotechnology and biomedicine. In this work, we determined the atomic structure of Aβ16-20 crystals, a fragment of amyloid-β which aberrant folding is linked to the etiology of Alzheimer’s disease, the most common cause of dementia. We detailed the hierarchical aggregation mechanism of Aβ16-20 into highly ordered crystals and revealed that the self-assembly is reversible, leading to the formation of oligomers as an intermediate. Our structural investigation combined with molecular dynamics simulations highlights how a combination of favorable non-covalent interactions drives the efficient fast self-assembly and enhanced stability. We studied the chemical and surface properties of amyloid crystals, including their mechanical properties and their capability to transmit light; the long-rang order of Aβ16-20 crystals enables them to be used as optical waveguide materials for biologically based modulation and sensing. Our results shed new light on pathogenic amyloid assembly at the atomic level and reveal the potential of amyloid crystals for applications in nanotechnology.
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| 7. |
- Broadhurst, Edward T., et al.
(author)
-
Polymorph evolution during crystal growth studied by 3D electron diffraction
- 2020
-
In: IUCrJ. - 2052-2525. ; 7, s. 5-9
-
Journal article (peer-reviewed)abstract
- 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 beta < alpha < gamma. The least stable beta polymorph forms within the first 3 min, but this begins to yield the alpha-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 similar to 100 nm. Even though the gamma-form is thermodynamically the most stable polymorph, kinetics favour the alpha-form, which dominates after prolonged standing. In the same sample, some beta and one crystallite of the gamma polymorph were also observed.
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| 8. |
- Carmona, Francisco J., et al.
(author)
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Coordination Modulation Method To Prepare New Metal-Organic Framework-Based CO-Releasing Materials
- 2018
-
In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 10:37, s. 31158-31167
-
Journal article (peer-reviewed)abstract
- Aluminum-based metal organic frameworks (MOFs), [Al(OH)(SDC)](n), (H2SDC: 4,4'-stilbenedicarboxylic acid), also known as CYCU-3, were prepared by means of the coordination modulation method to produce materials with different crystal size and morphology. In particular, we screened several reagent concentrations (20-60 mM) and modulator/ligand ratios (0-50), leading to 20 CYCU x_y materials (x: reagent concentration, y = modulator/ligand ratio) with different particle size and morphology. Noteworthy, the use of high modulator/ligand ratio gives rise to a new phase of CYCU-3 (CYCU-3' x_50 series), which was structurally analyzed. Afterward, to test the potential of these materials as CO-prodrug carriers, we selected three of them to adsorb the photo- and bioactive CO-releasing molecule (CORM) ALF794 [Mo(CNCMe2CO2H)(3)(CO)(3)] (CNCMe2CO2H = 2-isocyano-2-methyl propionic acid): (i) CYCU-3 20_0, particles in the nanometric range; (ii) CYCU-3 50_5, bar-type particles with heterogeneous size, and (iii) CYCU-3' 50_50, a new phase analogous to pristine CYCU-3. The corresponding hybrid materials were fully characterized, revealing that CYCU-3 20_0 with the smallest particle size was not stable under the drug loading conditions. Regarding the other two materials, similar ALF794 loadings were found (0.20 and 0.19 CORM/MOF molar ratios for ALF794@CYCU-3 50_5 and ALF794@CYCU-3' 50_50, respectively). In addition, these hybrid systems behave as CO-releasing materials (CORMAs), retaining the photoactive properties of the pristine CORM in both phosphate saline solution and solid state. Finally, the metal leaching studies in solution confirmed that ALF794@CYCU-3' 50_50 shows a good retention capacity toward the potentially toxic molybdenum fragments (7S% of retention after 72 h), which is the lowest value reported for a MOF-based CORMA to date.
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| 9. |
- Cho, Jung, et al.
(author)
-
EMM-25 : The Structure of Two-Dimensional 11 x 10 Medium-Pore Borosilicate Zeolite Unraveled Using 3D Electron Diffraction
- 2021
-
In: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 33:11, s. 4146-4153
-
Journal article (peer-reviewed)abstract
- The structure of the novel medium-pore borosilicate zeolite EMM-25 has been determined by continuous rotation electron diffraction (cRED). EMM-25 crystallizes in the space group Cmcm with unit cell parameters a = 11.055, b = 22.912, and c = 24.914 angstrom and a composition of IC4H8(C11H25N)(2)I (2)[Si112.5B3.5O232]. The EMM-25 framework possesses a two-dimensional channel system composed of 10-ring channels connected via 11-ring windows. Its channel system is analogous to that of the medium-pore zeolite NU-87 framework but with 11- rather than 12-ring windows, suggesting a different shape selectivity. EMM-25 was first obtained using 1,4-bis(N-methyl-N,N-dihexylammonium)butane as an organic structure directing agent (OSDA). Based on a molecular docking study of the OSDA within the pores of the determined framework structure, a new ammonium dication OSDA with an improved fit was devised. By using this new OSDA, the synthesis time was reduced 80%, from 52 to just 10 days. Furthermore, cRED data revealed a structural disorder of the EMM-25 framework present as swinging zigzag chains. The introduction of the disorder, which is a consequence of geometry relaxation, was crucial for an accurate structure refinement. Lastly, the cRED data from as-made EMM-25 showed residual potential consistent with the location of the OSDA position determined from the Rietveld refinement, concluding a complete refinement of the as-made structure based on the cRED data.
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| 10. |
- Cichocka, Magdalena Ola, et al.
(author)
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A Porphyrinic Zirconium Metal-Organic Framework for Oxygen Reduction Reaction : Tailoring the Spacing between Active-Sites through Chain-Based Inorganic Building Units
- 2020
-
In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 142:36, s. 15386-15395
-
Journal article (peer-reviewed)abstract
- The oxygen reduction reaction (ORR) is central in carbon-neutral energy devices. While platinum group materials have shown high activities for ORR, their practical uses are hampered by concerns over deactivation, slow kinetics, exorbitant cost, and scarce nature reserve. The low cost yet high tunability of metal-organic frameworks (MOFs) provide a unique platform for tailoring their characteristic properties as new electrocatalysts. Herein, we report a new concept of design and present stable Zr-chain-based MOFs as efficient electrocatalysts for ORR. The strategy is based on using Zr-chains to promote high chemical and redox stability and, more importantly, tailor the immobilization and packing of redox active-sites at a density that is ideal to improve the reaction kinetics. The obtained new electrocatalyst, PCN-226, thereby shows high ORR activity. We further demonstrate PCN-226 as a promising electrode material for practical applications in rechargeable Zn-air batteries, with a high peak power density of 133 mW cm(-2). Being one of the very few electrocatalytic MOFs for ORR, this work provides a new concept by designing chain-based structures to enrich the diversity of efficient electrocatalysts and MOFs.
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| 11. |
- Clabbers, Max T. B., et al.
(author)
-
Macromolecular crystallography using microcrystal electron diffraction
- 2021
-
In: Acta Crystallographica Section D. - 2059-7983. ; 77, s. 313-324
-
Journal article (peer-reviewed)abstract
- Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.
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| 12. |
- Clabbers, Max T. B., et al.
(author)
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MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography
- 2021
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
-
Journal article (peer-reviewed)abstract
- MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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| 13. |
- Clabbers, Max T. B., et al.
(author)
-
Visualizing drug binding interactions using microcrystal electron diffraction
- 2020
-
In: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)abstract
- Visualizing ligand binding interactions is important for structure-based drug design and fragment-based screening methods. Rapid and uniform soaking with potentially reduced lattice defects make small macromolecular crystals attractive targets for studying drug binding using microcrystal electron diffraction (MicroED). However, so far no drug binding interactions could unambiguously be resolved by electron diffraction alone. Here, we use MicroED to study the binding of a sulfonamide inhibitor to human carbonic anhydrase isoform II (HCA II). We show that MicroED data can efficiently be collected on a conventional transmission electron microscope from thin hydrated microcrystals soaked with the clinical drug acetazolamide (AZM). The data are of high enough quality to unequivocally fit and resolve the bound inhibitor. We anticipate MicroED can play an important role in facilitating in-house fragment screening for drug discovery, complementing existing methods in structural biology such as X-ray and neutron diffraction. Clabbers et al. utilize MicroED to present the structure of both apo and inhibitor-bound human carbonic anhydrase II at a high resolution to clearly identify the interaction of the inhibitor, acetazolamide. This method eases the difficulty of both crystallizing the protein and soaking the inhibitor in a smaller protein crystal.
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| 14. |
- Colyn Bwanika, Henri, et al.
(author)
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Limiting the Effects of Radiation Damage in MicroED through Dose Selection during Data Processing
-
Other publication (other academic/artistic)abstract
- Microcrystal electron diffraction (MicroED), also known as three-dimensional electron diffraction (3D ED), allows collection of diffraction data from submicron-sized crystals under low electron dose conditions, typically around 5-6 e-Å-2 in total. Despite having several advantages of MicroED over most conventional X-ray crystallographic techniques, susceptibility to radiation damage is a big problem that remains to be solved. Similar to X-ray crystallography, radiation damage to the macromolecular crystal structures in MicroED manifests in two forms, the global damage that affects the overall crystal lattice order and the site-specific damage that affects highly sensitive residues and moieties in macromolecules. In this study, we investigated data processing strategies that could be used to limit the effects of radiation damage to the crystal even when data collection is performed at high electron doses. During MicroED data collection, radiation damage increases with the number of acquired ED frames because the accumulated electron dose increases. To limit the damage, we propose to process only the first few frames of a dataset with a certain low dose cutoff. Data collected from several crystals and processed in this way can be merged to increase completeness and subsequently be used for structure refinement. According to our results, this approach improves the resolution of the data, the data statistics, the structure determination, and the quality of the final structure. The suggested approach could be especially useful in MicroED structure-based drug discovery where atomic resolution structures will provide detailed information about ligand-protein binding properties, which are essential during library screening and hit identification.
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| 15. |
- Ge, Meng, 1993-, et al.
(author)
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Direct Location of Organic Molecules in Framework Materials by Three-Dimensional Electron Diffraction
- 2022
-
In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:33, s. 15165-15174
-
Journal article (peer-reviewed)abstract
- In the study of framework materials, probing interactions between frameworks and organic molecules is one of the most important tasks, which offers us a fundamental understanding of host–guest interactions in gas sorption, separation, catalysis, and framework structure formation. Single-crystal X-ray diffraction (SCXRD) is a conventional method to locate organic species and study such interactions. However, SCXRD demands large crystals whose quality is often vulnerable to, e.g., cracking on the crystals by introducing organic molecules, and this is a major challenge to use SCXRD for structural analysis. With the development of three-dimensional electron diffraction (3D ED), single-crystal structural analysis can be performed on very tiny crystals with sizes on the nanometer scale. Here, we analyze two framework materials, SU-8 and SU-68, with organic molecules inside their inorganic crystal structures. By applying 3D ED, with fast data collection and an ultralow electron dose (0.8–2.6 e– Å–2), we demonstrate for the first time that each nonhydrogen atom from the organic molecules can be ab initio located from structure solution, and they are shown as distinct and well-separated peaks in the difference electrostatic potential maps showing high accuracy and reliability. As a result, two different spatial configurations are identified for the same guest molecule in SU-8. We find that the organic molecules interact with the framework through strong hydrogen bonding, which is the key to immobilizing them at well-defined positions. In addition, we demonstrate that host–guest systems can be studied at room temperature. Providing high accuracy and reliability, we believe that 3D ED can be used as a powerful tool to study host–guest interactions, especially for nanocrystals.
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| 16. |
- Gärtner, Erik, et al.
(author)
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Trajectory Optimization for Physics-Based Reconstruction of 3d Human Pose from Monocular Video
- 2022
-
In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. - 9781665469463 - 9781665469470
-
Conference paper (peer-reviewed)abstract
- We focus on the task of estimating a physically plausi-ble articulated human motion from monocular video. Ex-isting approaches that do not consider physics often pro-duce temporally inconsistent output with motion artifacts, while state-of-the-art physics-based approaches have either been shown to work only in controlled laboratory conditions or consider simplified body-ground contact limited to feet. This paper explores how these shortcomings can be addressed by directly incorporating a fully-featured physics engine into the pose estimation process. Given an uncon-trolled, real-world scene as input, our approach estimates the ground-plane location and the dimensions of the physi-cal body model. It then recovers the physical motion by per-forming trajectory optimization. The advantage of our for-mulation is that it readily generalizes to a variety of scenes that might have diverse ground properties and supports any form of self-contact and contact between the articu-lated body and scene geometry. We show that our approach achieves competitive results with respect to existing physics-based methods on the Human3.6M benchmark [13], while being directly applicable without re-training to more complex dynamic motions from the AIST benchmark [36] and to uncontrolled internet videos.
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| 17. |
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| 18. |
- Inge, A. Ken, et al.
(author)
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Unprecedented Topological Complexity in a Metal-Organic Framework Constructed from Simple Building Units
- 2016
-
In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 138:6, s. 1970-1976
-
Journal article (peer-reviewed)abstract
- A bismuth-based metal-organic framework (MOP), [Bi(BTC)(H2O)]center dot 2H(2)O center dot MeOH denoted CAU-17, was synthesized and found to have an exceptionally complicated structure with helical Bi-O rods cross-linked by 1,3,5-benzenetricarboxylate (BTC3-) ligands. Five crystallographically independent 1D channels including two hexagonal channels, two rectangular channels, and one triangular channel have accessible diameters of 9.6, 9.6, 3.6, 3.6, and 3.4 angstrom, respectively. The structure is further complicated by twinning. Rod-incorporated MOF structures typically have underlying nets with only one unique node and three or four unique edges. In contrast, topological analysis of CAU-17 revealed unprecedented complexity for a MOF structure with 54 unique nodes and 135 edges. The complexity originates from the rod packing and the rods themselves, which are related to aperiodic helices.
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| 19. |
- Kapaca, Elina, et al.
(author)
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Small Pore Aluminosilicate EMM-37 : Synthesis and Structure Determination Using Continuous Rotation Electron Diffraction
- 2019
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In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 58:19, s. 12854-12858
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Journal article (peer-reviewed)abstract
- A new aluminosilicate zeolite, denoted EMM-37, with a 3D small pore channel system, has been synthesized using a diquaternary ammonium molecule as the structure directing agent (SDA) and metakaolin as the aluminum source. The structures of both as-made and calcined forms of EMM-37 were solved and refined using continuous rotation electron diffraction (cRED) data. cRED is a powerful method for the collection of 3D electron diffraction data from submicron- and nanosized crystals, which allows for successful solution and refinement of complex structures in symmetry as low as P (1) over bar.
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| 20. |
- Klar, Paul B., et al.
(author)
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Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data
- 2023
-
In: Nature Chemistry. - 1755-4330 .- 1755-4349. ; 15:6, s. 848-855
-
Journal article (peer-reviewed)abstract
- Continuous-rotation 3D electron diffraction methods are increasingly popular for the structure analysis of very small organic molecular crystals and crystalline inorganic materials. Dynamical diffraction effects cause non-linear deviations from kinematical intensities that present issues in structure analysis. Here, a method for structure analysis of continuous-rotation 3D electron diffraction data is presented that takes multiple scattering effects into account. Dynamical and kinematical refinements of 12 compounds—ranging from small organic compounds to metal–organic frameworks to inorganic materials—are compared, for which the new approach yields significantly improved models in terms of accuracy and reliability with up to fourfold reduction of the noise level in difference Fourier maps. The intrinsic sensitivity of dynamical diffraction to the absolute structure is also used to assign the handedness of 58 crystals of 9 different chiral compounds, showing that 3D electron diffraction is a reliable tool for the routine determination of absolute structures.
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| 21. |
- Lenzen, Dirk, et al.
(author)
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A metal-organic framework for efficient water-based ultra-low-temperature-driven cooling
- 2019
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10
-
Journal article (peer-reviewed)abstract
- Efficient use of energy for cooling applications is a very important and challenging field in science. Ultra-low temperature actuated (T-driving< 80 degrees C) adsorption-driven chillers (ADCs) with water as the cooling agent are one environmentally benign option. The nanoscale metal-organic framework [Al(OH)(C6H2O4S)] denoted CAU-23 was discovered that possess favorable properties, including water adsorption capacity of 0.37 g(H2O)/g(sorbent) around p/p(0 )= 0.3 and cycling stability of at least 5000 cycles. Most importantly the material has a driving temperature down to 60 degrees C, which allows for the exploitation of yet mostly unused temperature sources and a more efficient use of energy. These exceptional properties are due to its unique crystal structure, which was unequivocally elucidated by single crystal electron diffraction. Monte Carlo simulations were performed to reveal the water adsorption mechanism at the atomic level. With its green synthesis, CAU-23 is an ideal material to realize ultra-low temperature driven ADC devices.
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| 22. |
- Leubner, S., et al.
(author)
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Hexahydroxytriphenylene for the synthesis of group 13 MOFs - a new inorganic building unit in a beta-cristobalite type structure
- 2020
-
In: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 49:10, s. 3088-3092
-
Journal article (peer-reviewed)abstract
- Two new, microporous MOFs of framework composition ((CH3)(2)NH2)(2)[M3O(HHTP)(HHTP center dot)], M = Al3+, Ga3+, H6HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene, are described. Electron diffraction combined with molecular simulations show that these compounds crystallize in the beta-cristobalite structure, containing a new type of trinuclear inorganic building unit for MOFs and radical anions.
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| 23. |
- Leubner, Sebastian, et al.
(author)
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Synthesis and Exfoliation of a New Layered Mesoporous Zr-MOF Comprising Hexa- and Dodecanuclear Clusters as Well as a Small Organic Linker Molecule
- 2020
-
In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 142:37, s. 15995-16000
-
Journal article (peer-reviewed)abstract
- A new layered mesoporous Zr-MOF of composition [Zr30O20(OH)26(OAc)18L18] was synthesized by employing 5-acetamidoisophthalic acid (H2L) using acetic acid as the solvent. The new MOF, denoted as CAU-45, exhibits a honeycomb structure of stacked layers which comprise both hexa- and dodecanucelar zirconium clusters. Its structure was solved from submicrometer-sized crystals by continuous rotation electron diffraction (cRED). Liquid phase exfoliation and size selection were successfully performed on the material.
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| 24. |
- Li, Shuting, et al.
(author)
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Direct structure determination of vemurafenib polymorphism from compact spherulites using 3D electron diffraction
- 2023
-
In: Communications Chemistry. - : Springer Science and Business Media LLC. - 2399-3669. ; 6
-
Journal article (peer-reviewed)abstract
- The spherulitic morphology is considered to be the most common morphology of crystalline materials and is particularly apparent in melt-crystallized products. Yet, historically, the polycrystalline nature of spherulites has hindered successful crystal structure determination. Here, we report the direct structure determination of a clinical drug, vemurafenib (VMN), in compact spherulite form using 3D electron diffraction (3D ED). VMN has four known polymorphs. We first solved the crystal structures of α-, β-, and γ-VMN from compact spherulites using 3D ED, and the resulting structures were highly consistent with those obtained by single-crystal X-ray diffraction. We then determined the crystal structure of δ-VMN—the least stable polymorph which cannot be cultivated as a single crystal—directly from the compact spherulite sample. We unexpectedly discovered a new polymorph during our studies, denoted as ε-VMN. Single crystals of ε-VMN are extremely thin and not suitable for study by X-ray diffraction. Again, we determined the structure of ε-VMN in a compact spherulite form. This successful structure elucidation of all five VMN polymorphs demonstrates the possibility of directly determining structures from melt-grown compact spherulite samples. Thereby, this discovery will improve the efficiency and broaden the scope of polymorphism research, especially within the field of melt crystallization.
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| 25. |
- Lightowler, Molly, et al.
(author)
-
Indomethacin Polymorph δ Revealed To Be Two Plastically Bendable Crystal Forms by 3D Electron Diffraction : Correcting a 47-Year-Old Misunderstanding
- 2022
-
In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 61:7
-
Journal article (peer-reviewed)abstract
- Indomethacin is a clinically classical non-steroidal anti-inflammatory drug that has been marketed since 1965. The third polymorph, Form δ, was discovered by both melt and solution crystallization in 1974. δ-indomethacin cannot be cultivated as large single crystals suitable for X-ray crystallography and, therefore, its crystal structure has not yet been determined. Here, we report the structure elucidation of δ-indomethacin by 3D electron diffraction and reveal the truth that melt-crystallized and solution-crystallized δ-indomethacin are in fact two polymorphs with different crystal structures. We propose to keep the solution-crystallized polymorph as Form δ and name the melt-crystallized polymorph as Form θ. Intriguingly, both structures display plastic flexibility based on a slippage mechanism, making indomethacin the first drug to have two plastic polymorphs. This discovery and correction of a 47-year-old misunderstanding signify that 3D electron diffraction has become a powerful tool for polymorphic structural studies.
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| 26. |
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| 27. |
- Lv, Zhong-Peng, et al.
(author)
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Visualizing noncovalent interactions and property prediction of submicron-sized charge-transfer crystals from ab-initio determined structures
- 2024
-
In: Small Methods. - 2366-9608.
-
Journal article (peer-reviewed)abstract
- The charge-transfer (CT) interactions between organic compounds are reflected in the (opto)electronic properties. Determining and visualizing crystal structures of CT complexes are essential for the design of functional materials with desirable properties. Complexes of pyranine (PYR), methyl viologen (MV), and their derivatives are the most studied water-based CT complexes. Nevertheless, very few crystal structures of CT complexes have been reported so far. In this study, the structures of two PYRs-MVs CT crystals and a map of the noncovalent interactions using 3D electron diffraction (3DED) are reported. Physical properties, e.g., band structure, conductivity, and electronic spectra of the CT complexes and their crystals are investigated and compared with a range of methods, including solid and liquid state spectroscopies and highly accurate quantum chemical calculations based on density functional theory (DFT). The combination of 3DED, spectroscopy, and DFT calculation can provide important insight into the structure-property relationship of crystalline CT materials, especially for submicrometer-sized crystals.
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| 28. |
- Ma, Chao, et al.
(author)
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Applications of X-ray and Electron Crystallography in Structural Investigations of Zeolites
- 2021
-
In: Gaodeng xuéxiào huàxué xuébào. - 0251-0790. ; 42:1, s. 188-200
-
Journal article (peer-reviewed)abstract
- Zeolites, a class of crystalline microporous materials with unique channels or cavities, have excellent performance in adsorption, separation, and catalysis. In order to correlate the structure-properly relationship, it is essential to determine the crystallographic structures of zeolite at the atomic level. In this review, a series of conventional and emerging techniques regarding X-ray crystallography and electron crystallography for characterizing the crystallographic structures of zeolites through real space and reciprocal space are introduced. Furthermore, 85 recently discovered novel zeolites are systemically summarized based on the structure determination approaches and their chemical compositions. Nine zeolites with different framework type codes(FTCs) are further highlighted due to their unique synthetic methodologies or structural features.
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| 29. |
- Roslova, Maria, et al.
(author)
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InsteaDMatic : towards cross-platform automated continuous rotation electron diffraction
- 2020
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In: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 53, s. 1217-1224
-
Journal article (peer-reviewed)abstract
- A DigitalMicrograph script, InsteaDMatic, has been developed to facilitate rapid automated 3D electron diffraction/microcrystal electron diffraction data acquisition by continuous rotation of a crystal with a constant speed, denoted as continuous rotation electron diffraction. The script coordinates microscope functions, such as stage rotation, and camera functions relevant for data collection, and stores the experiment metadata. The script is compatible with any microscope that can be controlled by DigitalMicrograph and has been tested on both JEOL and Thermo Fisher Scientific microscopes. A proof of concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit-cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.
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| 30. |
- Shin, Jiho, et al.
(author)
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Targeted Synthesis of Two Super-Complex Zeolites with Embedded Isoreticular Structures
- 2016
-
In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 55:16, s. 4928-4932
-
Journal article (peer-reviewed)abstract
- A novel structural coding approach combining structure solution, prediction, and the targeted synthesis of new zeolites with expanding complexity and embedded isoreticular structures was recently proposed. Using this approach, the structures of two new zeolites in the RHO family, PST-20 and PST-25, were predicted and synthesized. Herein, by extending this approach, the next two higher generation members of this family, PST-26 and PST-28, have been predicted and synthesized. These two zeolites have much larger unit cell volumes (422 655 Å3 and 614 912 Å3, respectively) than those of the lower generations. Their crystallization was confirmed by a combination of both powder X-ray and electron diffraction techniques. Aluminate and water concentrations in the synthetic mixture were found to be the two most critical factors influencing the structural expansion of embedded isoreticular zeolites under the synthetic conditions studied herein.
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| 31. |
- Svensson Grape, Erik, et al.
(author)
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Breathing Metal-Organic Framework Based on Flexible Inorganic Building Units
- 2020
-
In: Crystal Growth & Design. - : American Chemical Society (ACS). - 1528-7483 .- 1528-7505. ; 20:1, s. 320-329
-
Journal article (peer-reviewed)abstract
- Five novel bismuth carboxylate coordination polymers were synthesized from biphenyl-3,4′,5-tricarboxylic acid (H3BPT) and [1,1′:4′,1′′]terphenyl-3,3′′,5,5′′-tetracarboxylic acid (H4TPTC). One of the phases, [Bi(BPT)]·2MeOH (denoted SU-100, as synthesized), is the first example, to the best of our knowledge, of a reversibly flexible bismuth-based metal–organic framework. The material exhibits continuous changes to its unit cell parameters and pore shape depending on the solvent it is immersed in and the dryness of the sample. Typically, in breathing carboxylate-based MOFs, flexibility occurs through tilting of the organic linkers without significantly altering the coordination environment around the cation. In contrast to this, the continuous breathing mechanism in SU-100 involves significant changes to bond angles within the Bi2O12 inorganic building unit (IBU). The flexibility of the IBU of SU-100 reflects the nondiscrete coordination geometry of the bismuth cation. A disproportionate increase in the solvent accessible void volume was observed when compared to the expansion of the unit cell volume of SU-100. Additionally, activated SU-100 (SU-100-HT) exhibits a large increase in unit cell volume, yet has the smallest void volume of all the studied samples.
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| 32. |
- Wang, Bin, et al.
(author)
-
A Porous Cobalt Tetraphosphonate Metal-Organic Framework : Accurate Structure and Guest Molecule Location Determined by Continuous-Rotation Electron Diffraction
- 2018
-
In: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 24:66, s. 17429-17433
-
Journal article (peer-reviewed)abstract
- Single-crystal electron diffraction has shown to be powerful for structure determination of nano- and submicron-sized crystals that are too small to be studied by single-crystal X-ray diffraction. However, it has been very challenging to obtain high quality electron diffraction data from beam sensitive crystals such as metal-organic frameworks (MOFs). It is even more difficult to locate guest species in the pores of MOF crystals. Here, we present synthesis of a novel porous cobalt MOF with 1D channels, [Co-2(Ni-H4TPPP)]center dot 2DABCO center dot 6H(2)O, (denoted Co-CAU-36; DABCO=1,4-diazabicyclo[2.2.2]octane), and its structure determination using continuous rotation electron diffraction (cRED) data. By combining a fast hybrid electron detector with low sample temperature (96 K), high resolution (0.83-1.00 angstrom) cRED data could be obtained from eight Co-CAU-36 crystals. Independent structure determinations were conducted using each of the eight cRED datasets. We show that all atoms in the MOF framework could be located. More importantly, we demonstrate for the first time that organic molecules in the pores, which were previously difficult to find, could be located using the cRED data. A comparison of eight independent structure determinations using different datasets shows that structural models differ only on average by 0.03(2) angstrom for the framework atoms and 0.10(6) and 0.16(12) angstrom for DABCO and water molecules, respectively.
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| 33. |
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| 34. |
- Wang, Yunchen, et al.
(author)
-
On the quality of the continuous rotation electron diffraction data for accurate atomic structure determination of inorganic compounds
- 2018
-
In: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 51, s. 1094-1101
-
Journal article (peer-reviewed)abstract
- The continuous rotation electron diffraction (cRED) method has the capability of providing fast three-dimensional electron diffraction data collection on existing and future transmission electron microscopes; unknown structures could be potentially solved and refined using cRED data collected from nano-and submicrometre-sized crystals. However, structure refinements of cRED data using SHELXL often lead to relatively high R1 values when compared with those refined against single-crystal X-ray diffraction data. It is therefore necessary to analyse the quality of the structural models refined against cRED data. In this work, multiple cRED data sets collected from different crystals of an oxofluoride (FeSeO3F) and a zeolite (ZSM-5) with known structures are used to assess the data consistency and quality and, more importantly, the accuracy of the structural models refined against these data sets. An evaluation of the precision and consistency of the cRED data by examination of the statistics obtained from the data processing software DIALS is presented. It is shown that, despite the high R1 values caused by dynamical scattering and other factors, the refined atomic positions obtained from the cRED data collected for different crystals are consistent with those of the reference models refined against single-crystal X-ray diffraction data. The results serve as a reference for the quality of the cRED data and the achievable accuracy of the structural parameters.
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| 35. |
- Xia, Changjiu, et al.
(author)
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Heterogeneous oxidation of cyclohexanone catalyzed by TS-1 : Combined experimental and DFT studies
- 2015
-
In: Cuihuà xuébào. - 0253-9837 .- 1872-2067. ; 36:6, s. 845-854
-
Journal article (peer-reviewed)abstract
- The reaction mechanism of the oxidation of cyclohexanone catalyzed by titanium silicate zeolite Received 26 February 21515 TS-1 using aqueous H2O2 as the oxidant was investigated by combining density function theory (DFT) calculations with experimental studies. DFT calculations showed that H2O2 was adsorbed and activated at the tetrahedral Ti sites. By taking into account the adsorption energy, molecular size, steric hindrance and structural information, a reaction mechanism of Baeyer-Villiger oxidation catalyzed by TS-1 that involves the activation of H2O2 was proposed. Experimental studies showed that the major products of cyclohexanone oxidation by H2O2 catalyzed by a hollow TS-1 zeolite were epsilon-carprolactone, 6-hydroxyhexanoic acid, and adipic acid. These products were analyzed by GC-MS and were in good agreement with the proposed mechanism. Our studies showed that the reaction mechanism on TS-1 zeolite was different from that on Sn-beta zeolite.
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| 36. |
- Xiao, Kefeng, et al.
(author)
-
Nanofluidic voidless electrode for electrochemical capacitance enhancement in gel electrolyte
- 2021
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
-
Journal article (peer-reviewed)abstract
- Porous electrodes with extraordinary capacitances in liquid electrolytes are oftentimes incompetent when gel electrolyte is applied because of the escalating ion diffusion limitations brought by the difficulties of infilling the pores of electrode with gels. As a result, porous electrodes usually exhibit lower capacitance in gel electrolytes than that in liquid electrolytes. Benefiting from the swift ion transport in intrinsic hydrated nanochannels, the electrochemical capacitance of the nanofluidic voidless electrode (5.56% porosity) is nearly equal in gel and liquid electrolytes with a difference of -1.8%. In gel electrolyte, the areal capacitance reaches 8.94 F cm(-2) with a gravimetric capacitance of 178.8 F g(-1) and a volumetric capacitance of 321.8 F cm(-3). The findings are valuable to solid-state electrochemical energy storage technologies that require high-efficiency charge transport.
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| 37. |
- Xu, Hongyi, et al.
(author)
-
A Rare Lysozyme Crystal Form Solved Using Highly Redundant Multiple Electron Diffraction Datasets from Micron-Sized Crystals
- 2018
-
In: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 26:4, s. 667-675
-
Journal article (peer-reviewed)abstract
- Recent developments of novel electron diffraction techniques have shown to be powerful for determination of atomic resolution structures from micronand nano-sized crystals, too small to be studied by single-crystal X-ray diffraction. In this work, the structure of a rare lysozyme polymorph is solved and refined using continuous rotation MicroED data and standard X-ray crystallographic software. Data collection was performed on a standard 200 kV transmission electron microscope (TEM) using a highly sensitive detector with a short readout time. The data collection is fast (similar to 3 min per crystal), allowing multiple datasets to be rapidly collected from a large number of crystals. We show that merging data from 33 crystals significantly improves not only the data completeness, overall I/sigma and the data redundancy, but also the quality of the final atomic model. This is extremely useful for electron beam-sensitive crystals of low symmetry or with a preferred orientation on the TEM grid.
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| 38. |
- Xu, Hongyi, et al.
(author)
-
Electron Beam-Induced Transformation in High-Density Amorphous Ices
- 2020
-
In: Journal of Physical Chemistry B. - : AMER CHEMICAL SOC. - 1520-6106 .- 1520-5207. ; 124:41, s. 9283-9288
-
Journal article (peer-reviewed)abstract
- Amorphous ice is commonly used as a noncrystalline matrix for protecting sensitive biological samples in cryogenic electron microscopy (cryo-EM). The amorphization process of water is complex, and at least two amorphous states of different densities are known to exist, high- and low-density amorphous ices (HDA and LDA). These forms are considered to be the counterparts of two distinct liquid states, namely, high- and low-density liquid water. Herein, we investigate the HDA to LDA transition using electron diffraction and cryo-EM. The observed phase transition is induced by the impact of electrons, and we discuss two different mechanisms, namely, local heating and beam-induced motion of water molecules. The temperature increase is estimated by comparison with X-ray scattering experiments on identically prepared samples. Our results suggest that HDA, under the conditions used in our cryo-EM measurements, is locally heated above its glass-transition temperature.
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| 39. |
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| 40. |
- Xu, Hongyi, et al.
(author)
-
Solving a new R2lox protein structure by microcrystal electron diffraction
- 2019
-
In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:8
-
Journal article (peer-reviewed)abstract
- Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure-an R2lox enzyme-solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-angstrom resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.
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| 41. |
- Yan, Nana, et al.
(author)
-
Probing locations of organic structure-directing agents (OSDAs) and host-guest interactions in CHA-type SAPO-34/44
- 2018
-
In: Microporous and Mesoporous Materials. - : Elsevier BV. - 1387-1811 .- 1873-3093. ; 264, s. 55-59
-
Journal article (peer-reviewed)abstract
- In this work, we have synthesized four SAPO-34/44 (framework type code: CHA) samples by utilizing different organic structure-directing agent (OSDA) such as cyclohexylamine (CA), n-butylamine (BA), diisopropylamine (DIPA), and dipropylamine (DPA). An approach combining Rietveld refinement and simulated annealing has been successfully applied to determine the location of the individual OSDA and the host (inorganic framework)-guest (OSDA) interaction. The final Rietveld refinements show that 1) one cha cage can be occupied by either two OSDAs (CA and BA) in the up-and-down arrangement or one OSDA (DIPA and DPA) in the longitudinal configuration and 2) the classical hydrogen bond between CA/BA and the inorganic framework in SAPO-44-CA and SAPO-34-BA could be identified. The host-guest interactions among these four samples are also investigated by FT-IR, which are consistent with Rietveld refinement results. The approach employed here could be applicable for the host-guest investigation in other crystalline porous materials.
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| 42. |
- Yang, Taimin, et al.
(author)
-
A Comparison of Structure Determination of Small Organic Molecules by 3D Electron Diffraction at Cryogenic and Room Temperature
- 2021
-
In: Symmetry. - : MDPI AG. - 2073-8994. ; 13:11
-
Journal article (peer-reviewed)abstract
- 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).
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| 43. |
- Yang, Taimin, 1991-, et al.
(author)
-
Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking method
- 2022
-
In: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 55:6, s. 1583-1591
-
Journal article (peer-reviewed)abstract
- Three-dimensional electron diffraction (3D ED) has become an effective technique to determine the structures of submicrometre- (nanometre-)sized crystals. In this work, energy-filtered 3D ED was implemented using a post-column energy filter in both STEM mode and TEM mode [(S)TEM denoting (scanning) transmission electron microscope]. The setups for performing energy-filtered 3D ED on a Gatan imaging filter are described. The technique and protocol improve the accessibility of energy-filtered 3D ED post-column energy filters, which are available in many TEM laboratories. In addition, a crystal tracking method in STEM mode using high-angle annular dark-field imaging is proposed. This method enables the user to monitor the crystal position while collecting 3D ED data at the same time, allowing a larger tilt range without foregoing any diffraction frames or imposing extra electron dose. In order to compare the differences between energy-filtered and unfiltered 3D ED data sets, three well known crystallized inorganic samples have been studied in detail. For these samples, the final R1 values improved by 10–30% for the energy-filtered data sets compared with the unfiltered data sets, and the structures became more chemically reasonable. Possible reasons for improvement are also discussed.
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| 44. |
- Yang, Taimin, 1991-, et al.
(author)
-
Single-crystal structure determination of nanosized metal–organic frameworks by three-dimensional electron diffraction
- 2022
-
In: Nature Protocols. - : Springer Science and Business Media LLC. - 1754-2189 .- 1750-2799. ; 17:10, s. 2389-2413
-
Journal article (peer-reviewed)abstract
- Metal–organic frameworks (MOFs) have attracted considerable interest due to their well-defined pore architecture and structural tunability on molecular dimensions. While single-crystal X-ray diffraction (SCXRD) has been widely used to elucidate the structures of MOFs at the atomic scale, the formation of large and well-ordered crystals is still a crucial bottleneck for structure determination. To alleviate this challenge, three-dimensional electron diffraction (3D ED) has been developed for structure determination of nano- (submicron-)sized crystals. Such 3D ED data are collected from each single crystal using transmission electron microscopy. In this protocol, we introduce the entire workflow for structural analysis of MOFs by 3D ED, from sample preparation, data acquisition and data processing to structure determination. We describe methods for crystal screening and handling of crystal agglomerates, which are crucial steps in sample preparation for single-crystal 3D ED data collection. We further present how to set up a transmission electron microscope for 3D ED data acquisition and, more importantly, offer suggestions for the optimization of data acquisition conditions. For data processing, including unit cell and space group determination, and intensity integration, we provide guidelines on how to use electron and X-ray crystallography software to process 3D ED data. Finally, we present structure determination from 3D ED data and discuss the important features associated with 3D ED data that need to be considered. We believe that this protocol provides critical details for implementing and utilizing 3D ED as a structure determination platform for nano- (submicron-)sized MOFs as well as other crystalline materials.
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| 45. |
- Yao, Qiaofeng, et al.
(author)
-
Supercrystal engineering of atomically precise gold nanoparticles promoted by surface dynamics
- 2023
-
In: Nature Chemistry. - : Springer Science and Business Media LLC. - 1755-4330 .- 1755-4349. ; 15:2, s. 230-239
-
Journal article (peer-reviewed)abstract
- The controllable packing of functional nanoparticles (NPs) into crystalline lattices is of interest in the development of NP-based materials. Here we demonstrate that the size, morphology and symmetry of such supercrystals can be tailored by adjusting the surface dynamics of their constituent NPs. In the presence of excess tetraethylammonium cations, atomically precise [Au25(SR)18]− NPs (where SR is a thiolate ligand) can be crystallized into micrometre-sized hexagonal rod-like supercrystals, rather than as face-centred-cubic superlattices otherwise. Experimental characterization supported by theoretical modelling shows that the rod-like crystals consist of polymeric chains in which Au25 NPs are held together by a linear SR–[Au(I)–SR]4 interparticle linker. This linker is formed by conjugation of two dynamically detached SR–[Au(I)–SR]2 protecting motifs from adjacent Au25 particles, and is stabilized by a combination of CH⋯π and ion-pairing interactions between tetraethylammonium cations and SR ligands. The symmetry, morphology and size of the resulting supercrystals can be systematically tuned by changing the concentration and type of the tetraalkylammonium cations.
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| 46. |
- Yun, Yifeng, et al.
(author)
-
Phase identification and structure determination from multiphasic crystalline powder samples by rotation electron diffraction
- 2014
-
In: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 47, s. 2048-2054
-
Journal article (peer-reviewed)abstract
- Phase identification and structure characterization are important in synthetic and materials science. It is difficult to characterize the individual phases from multiphase crystalline powder samples, especially if some of the phases are unknown. This problem can be solved by combining rotation electron diffraction (RED) and powder X-ray diffraction (PXRD). Four phases were identified on the same transmission electron microscopy grid from a multiphase sample in the Ni-Se-O-Cl system, and their structures were solved from the RED data. Phase 1 (NiSeO3) was found in the Inorganic Crystal Structure Database using the information from RED. Phase 2 (Ni3Se4O10Cl2) is an unknown compound, but it is isostructural to Co3Se4O10Cl2, which was recently solved by single-crystal X-ray diffraction. Phase 3 (Ni5Se6O16Cl4H2) and Phase 4 (Ni5Se4O12Cl2) are new compounds. The fact that there are at least four different compounds in the as-synthesized material explains why the phase identification and structure determination could not be done by PXRD alone. The RED method makes phase identification from such multiphase powder samples much easier than would be the case using powder X-ray diffraction. The RED method also makes structure determination of submicrometre-sized crystals from multiphase samples possible.
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| 47. |
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| 48. |
- Zhao, Jingjing, 1988-, et al.
(author)
-
A simple pressure-assisted method for MicroED specimen preparation
-
Other publication (other academic/artistic)abstract
- Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal contents. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.
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| 49. |
- Zhao, Jingjing, et al.
(author)
-
A simple pressure-assisted method for MicroED specimen preparation
- 2021
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
-
Journal article (peer-reviewed)abstract
- Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate carbon hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal concentrations. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.
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| 50. |
- Zhao, Jingjing, 1988-
(author)
-
Push the limitations of crystal structure determination by 3D electron diffraction : From inorganic porous materials to biomolecules
- 2021
-
Doctoral thesis (other academic/artistic)abstract
- Structure elucidation is fundamental to understanding the chemical and physical properties of a material. Three-dimensional electron diffraction (3D ED) has shown great power for structure determination of nanometer- or submicrometer-sized crystals that are either too small or too complex for X-ray diffraction. 3D ED can be applied to a wide range of crystalline materials from inorganic materials, small organic molecules, to macromolecules. In this thesis, continuous rotation electron diffraction (cRED), also known as micro-crystal electron diffraction (MicroED) in macromolecular crystallography, has been applied for the determination of interesting novel crystal structures. New methods and protocols have been developed to push the current limitations of crystal structure determination by 3D ED.The structure of silicate zeolite PST-24 is highly disordered. A combination of cRED with high-resolution transmission electron microscopy (HRTEM) revealed its unique channel system with varying dimensionality from 2D to 3D. The aluminum metal-organic framework CAU-23 nanocrystals form aggregates and are very beam sensitive. Its structure, as determined by cRED, is built by twisted helical Al-O chains connected by TDC2- linkers, forming a chiral structure with square channels. The unique structure of CAU-23 provides high stability and high water adsorption capacity, making it an ideal material for ultra-low temperature adsorption driven chillers.A simple pressure-assisted specimen preparation method, denoted Preassis, has been developed to overcome the challenges in the application of MicroED on biological samples with high viscosity and low crystal concentration. It has been successfully applied for the specimen preparation of several bio-molecular crystals including a novel R2lox metalloenzyme, which was crucial for its structure determination. Furthermore, an investigation of the influence of radiation damage on lysozyme crystals was performed to improve the data quality and final structural model. Finally, the crystal structure of acetylated amyloid-β fragment Ac-Aβ16-20, related to Alzheimer’s disease, has been studied. The crystal has an active optical wave-guiding property with an excitation wavenumber of 488 nm due to its unique packing of Ac-KLVFF β–sheets.
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