Structure determination by X-ray diffraction

The situation is different for other examples—for example, the peptide hormone glucagon and a small peptide, metallothionein, which binds seven cadmium or zinc atoms. Here large discrepancies were found between the structures determined by x-ray diffraction and NMR methods. The differences in the case of glucagon can be attributed to genuine conformational variability under different experimental conditions, whereas the disagreement in the metallothionein case was later shown to be due to an incorrectly determined x-ray structure. A re-examination of the x-ray data of metallothionein gave a structure very similar to that determined by NMR. 

The HIV-l protease is a remarkable viral imitation of mammalian aspartic proteases It is a dimer of identical subunits that mimics the two-lobed monomeric structure of pepsin and other aspartic proteases. The HIV-l protease subunits are 99-residue polypeptides that are homologous with the individual domains of the monomeric proteases. Structures determined by X-ray diffraction studies reveal that the active site of HIV-l protease is formed at the interface of the homodimer and consists of two aspartate residues, designated Asp and Asp one contributed by each subunit (Figure 16.29). In the homodimer, the active site is covered by two identical flaps, one from each subunit, in contrast to the monomeric aspartic proteases, which possess only a single active-site flap. 

Our understanding of the importance of steric factors was initiated by structure determinations by X-ray diffraction techniques of two trans-diols of benz[a]anthracene (89), XVI and XVII, shown in Figure 12. The crystal structures showed diequatorial... 

Dicyanofuroxan (3,4-dicyano-l,2,5-oxadiazole 2-oxide), the precursor to the NCCNO (see structure 11) species, has been studied in the solid and gas phases to obtain both structural and electronic information. The solid-state structure determined by X-ray diffraction gives an orthorhombic space group PnaZ, with a= 10.2578(14), b = 10.8818(12), and c= 10.2259(15) A. There are two independent molecules with similar geometries in the asymmetric unit. The gas-phase molecule was characterized by Hel photoelectron, Hel and HLtti(3i7 photoionization, and IR spectroscopy. The... 

A large variety of organotin carboxylates have been prepared, and their structures determined by X-ray diffraction. Part of the impetus for this work has been the search for anticancer drugs, and the aim of relating activity to structure. The early work on structure has been thoroughly reviewed,346 as well as recent developments,347 including the structural work on the organotin derivatives of amino acids and peptides.348... 

Here, perspective views of the structures determined by X-ray diffraction and Newmann projections are presented, together with the names given... 

In order to understand the interactions between these bis-intercalating drugs and IMA more fully, we have crystallized several complexes of them and undertaken the structure determination by x-ray diffraction technique. One of the crystal forms diffracts to 1.6 A resolution with a space group of F222. The crystal structure was determined by the multiple isomorphous replacement method using three different heavy atom derivatives. The structure was refined to an R-factor of 19% and there were moderate number of solvent molecules clearly visible. The crystal... 

An examination of the stereochemistry of the H+ ion is complicated by a number of factors. Because it has no electron core, hydrogen is difficult to locate using X-rays which are scattered by electrons. In earlier structure determinations its presence was often ignored because it made no contribution to the X-ray diffraction pattern and could not therefore be located. Even when H is included in the model, its position can rarely be accurately determined and in any case the centre of its electron density is usually displaced from the nucleus towards the donor anion by around 20 pm. Accurate positions of the H+ nuclei can be found using neutron diffraction which has provided sufficient information to reveal the essential characteristics of hydrogen bond geometries, but in many of the structures determined by X-ray diffraction the positions of the H cations have had to be inferred from the positions of their neighbouring anions. 

Literature references in Figure 2 correspond to structural determinations by X-ray diffraction. 

The complexes typically have square pyramidal (11) or bipyramidal structure (12) with vanadyl oxygen apical, the vanadium atom lying 0.035-0.055 A above the plane defined by the equatorial ligands.354 There have been reports of five-coordinate trigonal bipyramidal complexes (13) with structures determined by X-ray diffraction techniques. 

Most forms of the furan ring are common, however in the Cambridge file of structures determined by X-ray diffraction there are (at the time of writing) 28 978 entries of which 1829 are furan derivatives of one kind or another. Radicals involving furan nuclei have attracted some attention but are not discussed here except to mention two leading references <80AHCt27)31, 82AHC(30)167>. 

Note the relationship of the dimethylbenzimida-zole to the ring system of riboflavin (Box 15-B). Several molecules of ammonia could be released from amide linkages by hydrolysis, but all attempts to remove the cobalt reversibly from the ring system were unsuccessful. The structure was determined in 1956 by Dorothy C. Hodgkin and coworkers using X-ray diffraction.13 At that time, it was the largest organic structure determined by X-ray diffraction. The complete laboratory synthesis was accomplished in 1972.c... 

The tetrasilacyclobipentylidene Me2 i( 2CH2Me2Sid =dSiMe2CH2CH2 i-Me2, was readily reduced by lithium or sodium in THF to give dark red solutions containing the corresponding dianion, which was isolated in alkali metal salts with coordinated THF. The structures, determined by X-ray diffraction, showed that the cations were three coordinate (to Cl, C2, and Ol Fig. 38). The sodium compound 62 has Na-C 248.7(4) and 250.1(4) pm, at the short end of the range for this kind of contact. The central C-C bond is stretched from 136.9(2) in the free alkene to 157.9(15) pm in the... 

In the knowledge-based approach presented here, the strategy is to derive potentials from known protein structures determined by X-ray diffraction. These structures are investigated with regard to the distributions of their atoms and atom-atom interactions. It is expected that these distributions contain information about typical native-like proteins. The next step is to relate these distributions to an energy-like quantity [1,5-12]. 

The possibility of formation of dimeric structures should be taken into account in the syntheses of metal-halide complexes of other ligands. In this respect, the transformation (3.72) is interesting and representative, in which not only monomeric mononuclear 637, but also dinuclear 638 complexes were isolated and their structures determined by x-ray diffraction [89] ... 

Whereas two methyl N-substituents are inefficient in transmitting the chiral information encoded at the rear side of the heterocyclic ligand (Entry 1 in Table 1), the stereoselectivity is improved by the introduction of N-benzyl substituents (Entry 2). The steric repulsion between the ferf-butyl and benzyl groups leads to a C2 symmetric arrangement of the latter with respect to the carbene donor function as is apparent in the molecular structure determined by X-ray diffraction for the silver(I) complex 20 [51]. In this way the chirality in the heterocycle is transmitted towards the reaction center. Introduction of methoxy groups in the meta-position of the phenyl rings of the benzyl substituents slightly increases the selectivity of the catalyst (Entry 3). 

In the N3 bridged compounds, there is a stronger electron-electron interaction through the N/ bridging molecule between two adjacent Ni spins, than between the NO2 bridged compounds. A cluster model constructed on the basis of the accurate structure determined by X-ray diffraction is used in the DV-Xa calculation for NINAZ, NDMAZ, and NDMAP. These are typical Haldane gap materials, which include the N3-bridging ligand. 

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