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 TDC^2- 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-Aβ_16-20, 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.

3D electron diffraction (3D ED) has evolved as a powerful method for ab initio structure determination from sub micrometer-sized crystals. It can be used to elucidate the arrangement of atoms in crystalline materials and to provide insights into the laws of nature that govern the properties of matter. This thesis explores the advantages, challenges, and applications of 3D ED in structure determination of zeolites. It demonstrates that 3D ED can be used to reveal not only the framework structures but also structure details, which facilitates the study of zeolite chemistry.

Zeolites are porous silicate materials used in a wide range of applications as shape-selective ion-exchangers, catalysts, and adsorbents. They feature regularly arranged pores of molecular dimensions that can discriminate between molecules with sub-Ångström precision. However, zeolites often crystallize as polycrystalline powders, and their structures are complex and difficult to determine.

In this thesis, eight zeolites have been investigated by 3D ED. The structures of three novel materials, PST-24, EMM-59, and EMM-25 are determined. The silicate PST-24 exhibits columnal disorder that yields varying intracrystalline channel dimensionality, which is unprecedented in zeolites. The borosilicate EMM-59 consists of intersecting 3D 12 × 10 × 10-ring channels and is one of the most complex zeolites. The boron sites in the framework can be located by both 3D ED and integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM). Structure refinement reveals structural changes upon calcination associated to the change of boron coordination. EMM-25 is also a borosilicate with 2D 11 × 10-ring channels. 3D ED reveals that the EMM-25 structure contains zigzag chains that are disordered with two configurations. Further investigations show that similar disorders also exist in other zeolites containing zigzag chains, i.e., EU-1, ITQ-27, and nonasil. We show that disordered atomic sites that are beyond the data resolution can also be identified and refined using 3D ED data.

Furthermore, factors that impact the location of organic guest species in zeolites using 3D ED are investigated. Because of the disorder and flexibility of the organic species in EMM-25 and EMM-59, only their average locations can be found using 3D ED. Therefore, we selected a STW-type zeolite HPM-1 with chiral channels for further study. HPM-1 was synthesized using 2-ethyl-1,3,4-trimethylimidazolium cations, and the guest species are intact and ordered in the channels of HPM-1, as previously determined by single crystal X-ray diffraction. We demonstrate that is possible to locate guest species using continuous rotation 3D ED data. Their atomic positions are refined against 3D ED data through both kinematical and dynamical refinements. Finally, the effect of electron fluence on the location of the organic guest species in the zeolite is investigated.