Crystal structure also

Three common uses of RBS analysis exist quantitative depth profiling, areal concentration measurements (atoms/cm ), and crystal quality and impurity lattice site analysis. Its primary application is quantitative depth profiling of semiconductor thin films and multilayered structures. It is also used to measure contaminants and to study crystal structures, also primarily in semiconductor materials. Other applications include depth profilii of polymers, high-T superconductors, optical coatings, and catalyst particles. ... 

In all cases, broad diffuse reflections are observed in the high interface distance range of X-ray powder diffraction patterns. The presence of such diffuse reflection is related to a high-order distortion in the crystal structure. The intensity of the diffuse reflections drops, the closer the valencies of the cations contained in the compound are. Such compounds characterizing by similar type of crystal structure also have approximately the same type of IR absorption spectra [261]. Compounds with rock-salt-type structures with disordered ion distributions display a practically continuous absorption in the range of 900-400 cm 1 (see Fig. 44, curves 1 - 4). However, the transition into a tetragonal phase or cubic modification, characterized by the entry of the ions into certain positions in the compound, generates discrete bands in the IR absorption spectra (see Fig. 44, curves 5 - 8). 

Metals are crystalline in structure and the individual crystals contain positive metal ions. The outer valency electrons appear to be so loosely held that they are largely interspersed amongst the positive ions forming an electron cloud which holds the positive ions together. The mobility of this electron cloud accounts for the electrical conductivity. The crystal structure also explains the hardness and mechanical strength of metals whereas the elasticity is explained by the ability of the atoms and ions to slide easily over each other. Metals can be blended with other metals to produce alloys with specific properties and applications. Examples include ... 

Me2C6H3NC, Bu NC) have been prepared by treatment of the silver sulfinate with [AuCIL]. The crystal structure also consists of pairs of the homoleptic derivatives [Au(PPh3)2]+[Au(S20-p-Tol)2] (571) bonded through aurophilic interactions.276... 

The crystal structure of the cobalt-substituted enzyme was obtained with bicarbonate bound to the metal (Iverson et al. 2000). The structure shows Asn 202 and Gln75 hydrogen bonded to the metal-bound bicarbonate, suggestzing potential roles for these residues in either transition-state stabilization or orientation and polarization of CO2 for attack from the zinc-hydroxyl (Fig. 11.5). The crystal structure also shows three discrete conformations for Glu 84, suggesting a role for this residue in the transfer of protons out of the active site indeed, kinetic analyses of Glu 84 variants combined with chemical rescue experiments establish this residue as critical for proton transfer (Tripp and Ferry 2000). The location of Glu 62 adjacent to Glu 84 suggests a potential role in proton transfer as well. Although kinetic analyses of site-specific variants establish an essential role for Glu 62 in the CO2 hydration steps (Eqs. 11.3 and 11.4), the results were inconclusive regarding an additional role in proton transfer (Eqs. 11.5 and 11.6). 

Additional interactions and rearrangements in the transition state with other rescuing bases may take place because it is known from crystal structures that substrate atoms are not in line for nucleophilic attack in the hammerhead ribozyme (at least not in the published crystal structures). Also, a metal ion located -20 A away from the catalytic site was shown to be crucial for catalysis. This same metal ion appeared likely to take on an additional ligand in the transition state, suggesting that conformational changes had to take place before catalysis. ... 

Crystal structure contains other aminoglycosides, which do not bind to the A-site. Crystal structure also contains the off state of the A-site. 

Crystallography studies showed that imatinib binds to an inactive form of Abl [36,37]. In this bound conformation the activation loop of the Abl kinase domain is distinct from that of both the inactive and active forms of the SFKs, explaining why imatinib does not inhibit these kinases. The crystal structure also revealed that the Thr 315 residue was involved in a key hydrogen bonding interaction with the C-2 amino group of imatinib. 

Figure 4.7 shows top-down views of the fee (001), (111), and (110) surfaces. These views highlight the different symmetry of each surface. The (001) surface has fourfold symmetry, the (111) surface has threefold symmetry, and the (110) has twofold symmetry. These three fee surfaces are all atomically flat in the sense that on each surface every atom on the surface has the same coordination and the same coordinate relative to the surface normal. Collectively, they are referred to as the low-index surfaces of fee materials. Other crystal structures also have low-index surfaces, but they can have different Miller indices than for the fee structure. For bcc materials, for example, the surface with the highest density of surface atoms is the (110) surface. 

Catenane 7 exists in a well defined conformation in which two identical macro-cycles are interlocked and held together by six hydrogen-bonds. The crystal structure also revealed the chirality of the ground state conformation. 

The crystal structures also provided an explanation for the different substrate specificities of trypsin, chymotrypsin,... 

The structures of the biologically active forms of B12 were solved relatively recently (1961) (78) and were shown to contain a cobalt atom surrounded by a corrin ring as shown in Fig. 16 (80). The crystal structure also showed a cobalt-carbon a bond which was quite surprising since the few compounds with cobalt-carbon a- bonds known at that time were quite unstable (79). The corrin ring is similar to the porphyrin ring, but its greater saturation imports less rigidity than the porphyrin. Corrinoids with the axial 5,6-dimethylbenzimidazole substituent are called cobalamins. Vitamin B12 with Co(III) and CN in the top axial position is... 

Implicit in the foregoing discussion is that increased temperature, which increases thermal motions of atoms in a crystal structure, also contributes to... 

Fig. 7. (A) Structural model of rhodopsin showing the location of cysteine substitution mutants in the C-terminal tail (325, 326, 328, 331, 332, 335-340). Mutants at 331 and 332 are not represented because these sites were not modeled in the crystal structure. Also shown are sites in C3 (dark spheres at 242, 245, 246, 249) and 65 in Cl discussed in the text. Dotted lines indicate sequences not modeled in the crystal structure. (B) Top row EPR spectra of 326R1 and 338R1, representing sites in the proximal and distal portions of the C-terminal tail, respectively center and bottom rows the two components of a and (3, respectively, resolved by spectral subtraction. In 338R1, the immobilized component is minor and is nearly invisible in the experimental spectrum.

Interestingly, these crystal structures also make it possible to understand more subtle differences among the inhibitory effects of different macrolides. As a peptide elongates, the portion of the macrolide it first encounters will be the sugar branch that extends from C5 of the lactone ring (Fig. 4.6) towards the peptidyl... 

The carbinolamine bond observed in these crystal structures has not been detected biochemically. Nevertheless, its formation may explain the results of a number of previous biochemical experiments. Modification or removal of the aldehyde group from a macrolide results in 100-fold increases in minimum inhibitory concentrations (MIC) [22-28]. Furthermore, mutation of Hm A2103 (Ec 2062) to guanine (which has an 06 instead of N6) confers resistance specifically to macrolides that have an aldehyde group at C6, but not to others [29]. It seems likely that the carbinolamine bonds observed in these crystal structures also form in vivo, and are physiologically relevant to the inhibitory effects of macrolides. 

The main conclusion drawn from the MD simulations is that the proteins are highly flexible. The parts of the proteins that have high B-factors in the crystal structure also show great flexibility in the dynamics. The same regions are flexible in both runs, but the internal correlations of movements differ. This is reflected in the CPCA score plot the snapshots of each of the two CYP2C9 runs and the X-ray structures showed up in a different quadrant and did not overlap at any time point of the simulation. Thus, the molecular dynamics simulations cover a different CPCA space from the crystal structures with and without substrate bound, independent of the different starting structures. 

A more recent search of the CSD for alkali metal/caibonyl crystal structures also confirmed these results. The average Li—O bond length and the Li—O—C bond angle were found to be 1.99 0.07 A... 

X-ray single crystal structures also enable understanding of the recognition behavior of ATPH at fhe molecular level. [22] The ATPH complexes of 33-37 are shown in Figs 6.6 and 6.7. Particularly notable structural features of these ATPH-carbo-nyl complexes are the Al-O-C angles and Al-O distances (Tab. 6.2), which confirm fhat fhe size and shape of fhe cavity change flexibly, depending on the substrate. 

---