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.

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.

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.