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MIT5_067F09_lec4 - Disorder A crystal is a potentially...

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Disorder A crystal is a potentially endless, three-dimensional, periodic discontinuum built up by atoms, ions or molecules. Real crystals have defects and frequently parts of molecules (or whole molecules) are found in more than one crystallographically independent orientation. Possible reasons: Z’ > 1 Twinning Disorder Soldier example from theory class… The structure is always the spatial average over the whole crystal! In most cases, only a small part of the molecule shows disorder. Anisotropic displacement ellipsoids and residual electron density are best indicators for disorder. Disordered ethyl group. Disorder 1 Figure by MIT OpenCourseWare.
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Types of Disorder Substitutional Disorder The same site in two unit cells is occupied by different types of atoms Positional Disorder One atom occupies two (or more) sites. This can be in a single unit cell (dynamic disorder = real motion) or in two (or more) different unit cells (static disorder). Mess Large voids in the lattice are filled with randomly oriented solvent molecules in the fashion of amorphously frozen liquid. No contribution to diffraction pattern, only diffuse scattering. Refinement of Disorder The refinement program needs to know the two (or more) positions for each disordered atom (that is two sets of coordinates instead of one per disordered atom) and the relative occupancies. Use free variables to refine occupancies.
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