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Structure determination of beam-sensitive materials by 3D electron diffraction: From pharmaceuticals to porous materials
Stockholm University, Faculty of Science, Department of Chemistry.ORCID iD: 0000-0001-8017-6740
2025 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Three-dimensional electron diffraction (3DED) has become a powerful method for structure determination of nano-/micron-sized crystalline materials. Due to their negative charge, electrons interact with both atomic nuclei and surrounding electron clouds in matter. While this strong interaction enables the study of nano-/micron-sized crystals, it also induces electron-beam damage during 3DED experiments. When electrons interact with a crystal, they can cause atomic displacement and bond breakage, which affects the structure and/or the chemistry of the specimen. This damage poses a significant challenge for 3DED studies of beam-sensitive materials.

In this thesis, eight beam-sensitive crystalline materials were investigated using 3DED, including pharmaceuticals, zeolites, and metal-organic frameworks (MOFs). To address electron-beam damage, several data acquisition strategies were developed to preserve beam-sensitive materials during 3DED experiments. These strategies include: 1) using low electron fluence, 2) cryo-cooling, and 3) the low-dose cryo-cRED (cryogenic continuous rotation electron diffraction) method, which combines the former two. These strategies reduce electron-beam damage and enhance the reliability of 3DED.

Additionally, a glovebox-assisted sample preparation workflow was developed to prepare cryo-samples under a controlled atmosphere. This approach enables 3DED studies of beam-sensitive materials that are also sensitive to air.

Using 3DED at room temperature, two new piroxicam (PXM) polymorphs were identified. To mitigate electron-beam damage, the cumulative electron fluence per dataset was reduced by adjusting data acquisition parameters related to electron flux and recording time. The structure information provided insight into the structure–property relationship between hydrogen bonding and melting point. Furthermore, the structure of anhydrous sodium valproate was determined for the first time using 3DED. To address its sensitivity to both electrons and moisture, a glovebox was used to preserve the anhydrous structure during the cryo-sample preparation. Cryogenic cooling was then employed during data collection to reduce electron-beam damage.

Moreover, the structure of ZMQ-1, the first stable meso-microporous aluminosilicate zeolite, was uncovered using 3DED. To determine the position of the organic structure-directing agents (OSDAs), the low-dose cryo-cRED method was employed to stabilize OSDA molecules against electron-beam damage. Likewise, three isostructural aluminum(III)-monocarboxylates (CAU-71-X, where X = Ac, Prop, and TGA), were studied using low-dose cryo-cRED. This combined method stabilized the highly flexible ligands, enabling both structure determination and positional disorder refinement of the CAU-71 compounds.

Place, publisher, year, edition, pages
Stockholm: Department of Chemistry, Stockholm University , 2025. , p. 64
Keywords [en]
3D electron diffraction, structure determination, beam-sensitive material, electron-beam damage, humidity-sensitive sample, glovebox-assisted sample preparation, pharmaceuticals, zeolites, metal-organic frameworks, polymorphism.
National Category
Materials Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-241607ISBN: 978-91-8107-198-6 (print)ISBN: 978-91-8107-199-3 (electronic)OAI: oai:DiVA.org:su-241607DiVA, id: diva2:1949202
Public defence
2025-05-16, Magnéli Hall, Svante Arrhenius väg 16, Stockholm, 09:00 (English)
Opponent
Supervisors
Available from: 2025-04-23 Created: 2025-04-01 Last updated: 2025-04-11Bibliographically approved
List of papers
1. Polyethylene Glycol-Assisted Melt Crystallization of Two New Piroxicam Polymorphs Revealed by 3D Electron Diffraction
Open this publication in new window or tab >>Polyethylene Glycol-Assisted Melt Crystallization of Two New Piroxicam Polymorphs Revealed by 3D Electron Diffraction
Show others...
2024 (English)In: Crystal Growth & Design, ISSN 1528-7483, E-ISSN 1528-7505, Vol. 24, no 17, p. 7298-7305Article in journal (Refereed) Published
Abstract [en]

Two new polymorphs (forms VIII and IX) of piroxicam were discovered through poly(ethylene glycol) (PEG)-assisted melt crystallization, and their structures were revealed by 3D electron diffraction (3D ED). This discovery provides insight into the potential of PEG in pharmaceutical polymorph discovery and verifies the significance of 3D ED as an essential technique for structural determination of pharmaceuticals. Furthermore, the direct contribution of intermolecular hydrogen bonding to melting points was discussed based on the structural divergency between the newly solved form VIII and the previously reported form IV. Combining PEG-assisted melt crystallization and 3D ED not only accelerated the discovery of new polymorphs but also provided unique opportunities for understanding structure-property relationships in pharmaceutical crystals.

National Category
Materials Chemistry
Identifiers
urn:nbn:se:su:diva-237784 (URN)10.1021/acs.cgd.4c00951 (DOI)2-s2.0-85202500771 (Scopus ID)
Available from: 2025-01-14 Created: 2025-01-14 Last updated: 2025-04-01Bibliographically approved
2. Unveiling the Structure of Anhydrous Sodium Valproate with 3D Electron Diffraction and a Facile Sample Preparation Workflow
Open this publication in new window or tab >>Unveiling the Structure of Anhydrous Sodium Valproate with 3D Electron Diffraction and a Facile Sample Preparation Workflow
(English)Manuscript (preprint) (Other academic)
Keywords
3D electron diffraction, sodium valproate, glovebox, plunge freeze, beam sensitivity, humidity sensitivity
National Category
Materials Chemistry
Identifiers
urn:nbn:se:su:diva-241605 (URN)
Note

Understanding the structure of an active pharmaceutical ingredient is essential for gaining insights into its physicochemical properties. Sodium valproate, one of the most effective antiepileptic drugs, was first approved for medical use in 1967. However, the structure of its anhydrous form has remained unresolved. This is because it was difficult to grow crystals of sufficient size for single-crystal X-ray diffraction (SCXRD).  Although 3D electron diffraction (3D ED) can be used for studying crystals too small for SCXRD, the crystals of anhydrous sodium valproate are extremely sensitive to both humidity and electron beams. They degrade quickly both in air and under electron beam at room temperature. In this study, we developed a glove-box assisted cryo-transfer workflow for preparation of EM grids in protected atmosphere to overcome the current challenges for studying air and beam-sensitive samples using 3D ED.  Using this technique, we successfully determined the structure of anhydrous sodium valproate, revealing a feature of Na-valproate polyhedral chains. Our results provide a robust framework for 3D ED analysis of air-sensitive crystals, greatly enhancing its utility across various scientific disciplines.

Available from: 2025-04-01 Created: 2025-04-01 Last updated: 2025-04-11Bibliographically approved
3. A stable zeolite with atomically ordered and interconnected mesopore channel
Open this publication in new window or tab >>A stable zeolite with atomically ordered and interconnected mesopore channel
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2024 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 636, no 8042, p. 368-373Article in journal (Refereed) Published
Abstract [en]

Zeolites are crystalline microporous materials constructed by corner-sharing tetrahedra (SiO4 and AlO4), with many industrial applications as ion exchangers, adsorbents and heterogeneous catalysts. However, the presence of micropores impedes the use of zeolites in areas dealing with bulky substrates. Introducing extrinsic mesopores, that is, intercrystal/intracrystal mesopores, in zeolites is a solution to overcome the diffusion barrier. Still, those extrinsic mesopores are generally disordered and non-uniform; moreover, acidity and crystallinity are always, to some extent, impaired. Thus, synthesizing thermally stable zeolites with intrinsic mesopores that are of uniform size and crystallographically connected with micropores, denoted here as intrinsic mesoporous zeolite, is highly desired but still not achieved. Here we report ZMQ-1 (Zeolitic Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, no. 1), an aluminosilicate zeolite with an intersecting intrinsic meso-microporous channel system delimited by 28 × 10 × 10-rings, in which the 28-ring has a free diameter of 22.76 Å × 11.83 Å, which reaches the mesopore domain. ZMQ-1 has high thermal and hydrothermal stability with tunable framework Si/Al molar ratios. ZMQ-1 is the first aluminosilicate zeolite with an intrinsic meso-microporous channel system. The Brønsted acidity of ZMQ-1 imparts high activity and unique selectivity in the catalytic cracking of heavy oil. The position of the organic structure-directing agent (OSDA) used for ZMQ-1 synthesis was determined from three-dimensional electron diffraction (3D ED) data, which shows the unique structure-directing role of the OSDA in the formation of the intrinsic meso-microporous zeolite. This provides an incentive for preparing other stable mesopore-containing zeolites.

National Category
Materials Chemistry
Identifiers
urn:nbn:se:su:diva-240554 (URN)10.1038/s41586-024-08206-1 (DOI)001397120900026 ()39663489 (PubMedID)2-s2.0-85211643707 (Scopus ID)
Available from: 2025-03-10 Created: 2025-03-10 Last updated: 2025-04-01Bibliographically approved
4. Isostructural 18-ring Layered Aluminum (III)−PCPs from Monocarboxylic Acids
Open this publication in new window or tab >>Isostructural 18-ring Layered Aluminum (III)−PCPs from Monocarboxylic Acids
(English)Manuscript (preprint) (Other academic)
Abstract [en]

A series of new isostructural aluminum monocarboxylates, denoted as CAU-71-X (X = -Ac, -Prop and -TGA), with the framework composition [Al9(µ3-O)2(µ-OH)12(RCOO)12] · x H2O (R = -CH3, -C2H5, -C2H4SH) were obtained by investigating a chemical system involving an aluminum salt, a series of monocarboxylic acids (acetic acid (Ac), propionic acid (Prop), and thioglycolic acid (TGA)) and sodium hydroxide in aqueous solutions. Since the CAU-71 materials were obtained as nano- to microcrystalline products, the structure determination was carried out by 3D electron diffraction (3DED). To cope with the flexibility of the functional groups of ligands, low-dose 3DED was combined with cyro-EM to stabilize the functional group. With the stabilization from both low electron fluence and cryo-protection, the structures of three isostructural aluminum monocarboxylates were determined completely with refined positional disorder of coordinating monocarboxylates. One prominent feature of this structure is the 18-ring, which consists of 18 [AlO6] octahedra held together by edge-sharing oxygen atoms and 24 monocarboxylate ligands.  This 18-ring structure forms a 2D porous layer, which is further packed into a 3D crystal by hydrogen bonding. Porosity of the CAU-71 compounds was confirmed by H2O and CO2 sorption experiments and maximum uptake capacities of 60 mg/g (~ 6 mol/mol) and 8 cm3/g [JX1] were found for CAU-71-Prop. 

Keywords
3D electron diffraction, porous coordiantion polymers, beam sensitivity, structure determination, isostructural compound
National Category
Materials Chemistry
Identifiers
urn:nbn:se:su:diva-241606 (URN)
Available from: 2025-04-01 Created: 2025-04-01 Last updated: 2025-04-11Bibliographically approved

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