The depiction of crystal structures

Lists of atomic positions are not very helpful when a variety of structures have to be compared. This chapter describes attempts to explain and systematise the vast amount of structural data now available. The original aim of ways of comparing similar structures was to provide a set of empirical guidelines for use in the determination of a new crystal structure. With sophisticated computer methods now available, this approach is rarely employed, but one empirical rule, the bond-valence method, (see Section 7.8 below), is widely used in structural studies. 

Most data is available for inorganic solids, as these have been studied longest and in greatest detail. The commonest ways of describing these structures is either as built up by packing together spheres, or else in terms of polyhedra linked by corners and edges. The description of structures 

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The X-ray crystal structure of platinated duplex DNA dodecamer d(CCTCTG G TCTCC) d(GGAGACCAGAGG), where G G represents the binding sites (G-N7) of m-[Pt(NH3)2]2+, is depicted in Figure 12 [67]. The coordination of Pt(II) to adjacent guanine bases distorts the... 

Some exchange reactions of complexes 112 and 115 have been studied. From the X-ray crystal structure analyses, it appears that trimethylgallium is rather loosely bound to the (r 2-aryne)- and (r 2-cydohexyne) metallocene building blocks in the dimetalla-bicyclic complexes 112 and 115, respectively (Scheme 7.34). Therefore, it was tempting to investigate whether it was possible to reverse the reactions depicted in Schemes 7.32 and 7.33 using these specific examples to carry out thermally induced exchange reactions. 

Fryzuk demonstrated the high reactivity of the amide function present in the P-amide-P pincer Ir complex 60 towards dihydrogen [28]. In fact, heterolyhc dihydrogen activation by the Ir(III)-amide bond present in the pincer complex 60 led to the stable Ir(III)-alkyl-amino-hydrido complex 61, as outUned in Equation 6.16. The X-ray crystal structure of the amine product is depicted in Figure 6.14. 

The X-ray crystal structure of the inorganic phosphate (an inhibitor) complex of alkaline phosphatase from E. coli (9) showed that the active center consists of a Zn2Mg(or Zn) assembly, where the two zinc(II) atoms are 3.94 A apart and bridged by the bidentate phosphate (which suggests a phosphomonoester substrate potentially interacting with two zinc(II), as depicted in Fig. 2), and the Mg (or the third Zn) is linked to one atom of the zinc pair by an aspartate residue at a distance... 

There has been considerable speculation concerning the role of carbide in the iron base catalyst. The carbide was originally depicted as an intermediate in the reaction (7), but more recent work indicates the contrary (3). It now appears more probable that the lattice between carbide crystals or between groupings of carbide and relatively fewer oxide or even free iron crystals offers the form of pore structure required for both high activity and selectivity. 

Figure 1. (a) X-ray crystal structure of horse-heart ferricytochrome c.8 All protein atoms are shown in the C.-P.-K. form, while the heme group is shown in the stick form. All Arg and Lys residues are colored blue, while Glu and Asp are colored in red, to contrast the destribution of the most ionizable side chains, (b) The X-ray crystal structure of horse heart ferricytochrome c in complex with horse cytochrome c peroxidase (cep).9 The peroxidase is shown as a molecular surface model, with blue regions depicting positive and red representing negative electrostatic potential. Note the cluster of negative potential on ccp that surrounds the contact interface. 

Established cases of metal binding to the exocyclic amino groups of guanine bases are rare. Amino group mercuration has been reported for 1-methylguanosine (169e), and the X-ray crystal structure of a dianionic 9-methylguanine complex with Pt(II) at N7, and Hg(II) at both N1 and N2 has been determined (237). The compound has been depicted in Fig. 19. The pK values have not been determined. 

The homoleptic lanthanide(III) benzamidinates 20-23 can be regarded as analogues of the well known tris(cyclopentadienyl)lanthanide complexes (C5H5)3Ln [7, 8]. One of the most characteristic reactions of the homoleptic cyclopentadienyls is the formation of 1 1 adducts with Lewis bases such as ethers, nitriles, esters etc. [7, 8], Recently it was discovered that the homoleptic lanthanide benzamidinates [PhC(NSiMe3)2]3Ln (20) form similar adducts with THF and nitrile ligands such as acetonitrile or benzonitrile [59]. The molecular and crystal structures of two benzonitrile adducts (26g, h) have been determined by X-ray diffraction. Figure 8 depicts the molecular structure of the europium... 

For several of the siliconium salts crystal structure analyses were obtained, confirming the pentacoordination and the ionic nature of the compounds (well separated cations and anions). The crystal structures for 90a(OTf), 90c(OTf), 91a(OTf), 91a(AlCl4), and 93a(OTf) are depicted in Figs. 47-51, respectively. Further structural support is found in the 29Si NMR chemical shifts (Table XXVI). A remarkable observation in Table XXVI is the nearly equal 29Si chemical shifts of siliconium salts sharing the same silicon complex, but with different anions [e.g. 91a(OTf), 91a(Br), and 91a(AlCl4)] the equal shifts are the evidence that the siliconium cations are essentially independent of... 

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