如何处理无序(晶体解析).pptVIP

Some Strategies for the Refinement of Disordered Crystal Structures Ng Seik Weng Department of Chemistry University of Malaya Kuala Lumpur Malaysia The assumption of perfect periodicity is a basic assumption of crytallography. However, real crystals are not perfect. The vibration of some atoms 2 - 3 times those of other atoms of the same molecular fragment. Peaks in the difference map that are too close to existing atoms to form plausible bonds. Atoms that are too close to symmetry elements in the space group to produce chemically-reasonable bonding. Anyway, the data are mothballed because the structures cannot be published. SHELXL-97 The mathematics is unstable and some restraints must be used to hold the mathematics together. There will be more variables to be refined. The data must be reasonably good, e.g., I 2? is large and Rint small. Which SHELX commands to use depend on the disorder. And it is very messy to treat disorder. The energy barrier to rotation of CO2CH2CH3 radical is of the order of kT – there is nothing you can do about the data. Disorder in a –CH2CH2CH2CH3 chain Fitting phenyl rings Rings must be separated by more than 0.5 ?. Pyridyl rings can also be fitted as hexagons. ‘AFIX 66’ for phenyl rings Can be used for non-centric space groups because there are fewer reflections, or if there is a spread of C—C distances. A phenylene ring disordered along the C1–C4 axis As the anion lies on a center-of-inversion, ‘AFIX 66’ cannot be used. DFIX pairs of distances, and FLAT some atoms. Disorder in a cyclopentyl ring DFIX the C—C to 1.50 ? and the C…C…C distance to 2.45 ? so that the angle is 109.5°. Perchlorate ions are usually disordered: any molecular fragment that is spherical will be disordered. Look for water near the ion. Disorder over a center-of-inversion Use a ‘PART –1’ command to suppress symmetry. Refine the ring with ‘AFIX 66’. Some atoms to have full and other half occupancy. Disorder of 15-crown-5: an odd number of atoms