Publisher Summary Electron crystallography is a term that has been used to describe a quantitative crystal structure determination based on electron diffraction intensity data and/or high resolution electron microscope images. This chapter demonstrates the way experimental diffraction intensity data or images can be used in structure analyses of a wide variety of organic and biological materials to yield results that can be compared favorably with X-ray crystal structures. While electron crystallographic techniques certainly are subject to their own unique constraints for the collection of scattering data that can be interpreted directly in an ab inito structure determination, the overwhelmingly negative view of these techniques by much of the crystallographic community often is, in fact, totally unwarranted and is based largely on a number of unfortunate historical misunderstandings.

Electron crystallography of organic molecules

The ability to control the transition from a two-dimensional (2D) monolayer to the three-dimensional (3D) molecular structure in the growth of organic layers on surfaces is essential for the production of functional thin films and devices. This has, however, proved to be extremely challenging, starting from the currently limited ability to attain a molecular scale characterization of this transition. Here, through innovative application of low-dose electron diffraction and aberration-corrected transmission electron microscopy (acTEM), combined with scanning tunneling microscopy (STM), we reveal the structural changes occurring as film thickness is increased from monolayer to tens of nanometers for supramolecular assembly of two prototypical benzenecarboxylic acids – terephthalic acid (TPA) and trimesic acid (TMA) – on graphene. The intermolecular hydrogen bonding in these molecules is similar and both form well-ordered monolayers on graphene, but their structural transitions with film thickness are very different. While the structure of TPA thin films varies continuously towards the 3D lattice, TMA retains its planar monolayer structure up to a critical thickness, after which a transition to a polycrystalline film occurs. These distinctive structural evolutions can be rationalized in terms of the topological differences in the 3D crystallography of the two molecules. The templated 2D structure of TPA can smoothly map to its 3D structure through continuous molecular tilting within the unit cell, whilst the 3D structure of TMA is topologically distinct from its 2D form, so that only an abrupt transition is possible. The concept of topological protection of the 2D structure gives a new tool for the molecular design of nanostructured films.

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Monolayer-to-thin-film transition in supramolecular assemblies: the role of topological protection.

A combination of solid-state NMR (ssNMR) and electron diffraction (ED) has been used to determine the crystalline polymorphs in small-organic microcrystalline molecules. Although 13C cross-polarization magic angle spinning (CPMAS) is a widely used method for determining crystalline polymorphs, even in a mixture, it sometimes fails if the molecular conformations are similar. On the other hand, ED can, in principle, differentiate crystalline forms with different lattice parameters, even when they have very similar molecular conformations. However, its application is usually limited to inorganic molecules only. This is because the ED measurements of organic molecules are very challenging due to degradation of the sample by electron irradiation. We overcame these difficulties by the use of 1H double-quantum/single-quantum correlation experiments at very fast magic angle spinning, together with ED observations under mild electron irradiation. The experiments were demonstrated on L-histidine samples in L-histidine·HCl·H2O, orthorhombic L-histidine and monoclinic L-histidine.

Solid-state NMR meets electron diffraction: determination of crystalline polymorphs of small organic microcrystalline samples.

Freeze fracture studies of membrane lipids.

Structure of polymerizable lipid bilayers VII: lateral organization of diacetylenic phosphatidylcholines with short proximal acyl chains.

The applications of electron diffraction and diffraction contrast electron microscopy with which to study the structure and dynamics of organic thin films are discussed. The techniques of making thin film deposits on substrates and of forming free-standing thin films over holes on the substrate are described. Selected area electron diffraction and diffraction contrast imaging techniques for thin film studies are elaborated, and examples are given. Methods to reduce radiation damage and environmental protection of the thin film specimen are outlined.



The interpretation of electron diffraction and imaging data is given for three cases: (1) The effects of film tilting and molecular tilting (with respect to the film plane) are examined. (2) The detection of phase transition is illustrated. (3) The use of labels to mark film domains is shown together with the measurement of dynamic movement.

Sek-wen Hui

Papers

Electron diffraction and diffraction contrast imaging of thin organic films.