Crystal structure diffraction

The statement was made in an earlier session that the thermal parameters determined by crystal structure diffraction analysis should be considered virtually meaningless, in contrast to positional parameters for which estimated standard errors should be multiplied by a factor of five. LEVY commented as follows ... 

The active surface of a zeolite is internal and intrinsic to the crystal structure. Diffraction techniques can therefore yield direct data on those structural features that control catalytic or sorptive performance. However, zeolite characteristics hamper the effective application of diffraction methods. Zeolite constituents have, generally, low atomic numbers and the normalized scattering power of a zeolite unit cell is relatively small. Zeolites have open firework structures supporting accessible void volumes which can be as much as 50% of the total crystal volume [1-3]. The void spaces are either empty (and hence contributing no scattered intensity to the measured diffraction pattern) or filled with species that are have positional or dynamic disorder and hence contribute to the diffraction peaks almost exclusively at low scattering angles. 

The structure of the metallocene cation energy minimised with the Car-Parrinello method agrees well with the experimentally obtained crystal structures of related complexes. Typical features of the structure as obtained from X-ray diffraction on crystals of very similar neutral complexes (e.g., the dichlorides), such as small differences in distances between C atoms within a cyclopentadienyl (Cp) ring, as well as differences in distances between the C atoms of the Cp ring and the Zr atom, were revealed from the simulations. 

The two major databases containing information obtained from X-ray structure analysis of small molecules are the Cambridge Structural Database (CSD) [25] and the Inorganic Crystal Structure Database (ICSD) [26] both are available as in-house versions. CSD provides access to organic and organometallic structures (mainly X-ray structures, with some structures from neutron diffraction), data which are mostly unpublished. The ICSD contains inorganic structures. 

All of these crystal structures have been analyzed using X-ray or neutron diffraction... 

Gavezzotti A and G Filippini 1996. Computer Prediction of Organic Crystal Structures Using Partial X-ray Diffraction Data, journal of the American Chemical Society 118 7153-7157. 

Crystal Structure. Diamonds prepared by the direct conversion of well-crystallized graphite, at pressures of about 13 GPa (130 kbar), show certain unusual reflections in the x-ray diffraction patterns (25). They could be explained by assuming a hexagonal diamond stmcture (related to wurtzite) with a = 0.252 and c = 0.412 nm, space group P63 /mmc — Dgj with four atoms per unit cell. The calculated density would be 3.51 g/cm, the same as for ordinary cubic diamond, and the distances between nearest neighbor carbon atoms would be the same in both hexagonal and cubic diamond, 0.154 nm. 

Despite considerable efforts very few membrane proteins have yielded crystals that diffract x-rays to high resolution. In fact, only about a dozen such proteins are currently known, among which are porins (which are outer membrane proteins from bacteria), the enzymes cytochrome c oxidase and prostaglandin synthase, and the light-harvesting complexes and photosynthetic reaction centers involved in photosynthesis. In contrast, many other membrane proteins have yielded small crystals that diffract poorly, or not at all, using conventional x-ray sources. However, using the most advanced synchrotron sources (see Chapter 18) it is now possible to determine x-ray structures from protein crystals as small as 20 pm wide which will permit more membrane protein structures to be elucidated. 

The major STEM analysis modes are the imaging, diffraction, and microanalysis modes described above. Indeed, this instrument may be considered a miniature analytical chemistry laboratory inside an electron microscope. Specimens of unknown crystal structure and composition usually require a combination of two or more analysis modes for complete identification. 

Metallurgists, also, were slow to feel at ease with the new techniques, and did not begin to exploit X-ray diffraction in any significant way until 1923. Michael Polanyi (1891-1976), in an account of his early days in research (Polanyi 1962) describes how he and Herman Mark determined the crystal structure of white tin from a single crystal in 1923 just after they had done this, they received a visit from a Dutch colleague who had independently determined the same structure. The visitor vehemently maintained that Polanyi s structure was wrong in Polanyi s words, only after hours of discussion did it become apparent that his structure was actually the same as ours, but looked different because he represented it with axes turned by 45° relative to ours . 

The formation of acyl halide-Lewis acid complexes have been observed by several methods. For example, both 1 1 and 1 2 complexes of acetyl chloride, with AICI3 can be observed by NMR spectroscopy. The existence of acylium ions has been demonstrated by X-ray diffraction studies on crystalline salts. For example, crystal structure determinations have been reported for /i-methylphenylacylium and acetylium ions as SbFg salts. There is also a good deal of evidence from NMR measurements which demonstrates that acylium ions can exist in nonnucleophilic solvents. " The positive charge on acylium ions is delocalized onto the oxygen atom. This delocalization is demonstrated in particular by the short O—C bond lengths in acylium ions, which imply a major contribution from the structure having a triple bond ... 

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