Crystallographic study Crystals

The reaction of a mixture of 1,5,9-cyclododecatriene (CDT), nickel acetylacetonate [3264-82-2], and diethylethoxyalurninum in ether gives red, air-sensitive, needle crystals of (CDT)Ni [12126-69-1] (66). Crystallographic studies indicate that the nickel atom is located in the center of the 12-membered ring of (CDT)Ni (104). The latter reacts readily with 1,5-cyclooctadiene (COD) to yield bis(COD) nickel [1295-35-8] which has yellow crystals and is fairly air stable, mp 142°C (dec) (20). Bis(COD)nickel also can be prepared by the reaction of 1,5-COD, triethylaluminum, and nickel acetylacetonate. 

Chemical conversion of compounds to intermediates of known absolute configuration is a method routinely used to determine absolute configuration (86). This is necessary because x-ray analysis is not always possible suitable crystals are required and deterrnination of the absolute configuration of many crystalline molecules caimot be done because of poor resolution. Such poor resolution is usually a function of either molecular instability or the complex nature of the molecule. For example, the relative configuration of the macroHde immunosuppressant FK-506 (105) (Fig. 8), which contains 14 stereocenters, was determined by x-ray crystallographic studies. However, the absolute configuration could only be elucidated by chemical degradation and isolation of L-pipecoUc acid (110) (80). 

According to an X-ray crystallographic study, 2-(A-phenylamino)thia-zole forms in the crystal dimers of the imino tautomers, which are linked together by the intramolecular NH—N bonds [77AX(B)106]. 

Crystallographic study of 2,5-DSP and poly-2,5-DSP demonstrated that the polymerization proceeded with retention of the space group (Pbca) of the starting 2,5-DSP crystal (Sasada et al., 1971 Nakanishi et al., 1972a). The result was the first evidence of an organic reaction which proceeded in the crystal lattice. 

The interest in the structures of simple R2Si(OH)2 compounds lies in the fact that one of them, Bu 2Si(OH)2, forms a discotic liquid crystalline phase (308,309). Despite many attempts, it has not proved possible to obtain crystals of Bu 2Si(OH)2 suitable for a crystallographic study, the material obtained from various solvents usually being of a fine fibrous nature. The discotic phase of Bu 2Si(OH)2 has been proposed (309) to be due to the formation of dimeric disks of molecules which remain on breaking the interdimer hydrogen bonds in a structure of type 65 at the transition between crystal and mesophase. As has been described, structure type 65 is found for several diols similar to Bu 2Si(OH)2, and it is thus quite likely that Bu 2Si(OH)2 does indeed have the proposed structure. 

Before our work [39], only one catalytic mechanism for zinc dependent HDACs has been proposed in the literature, which was originated from the crystallographic study of HDLP [47], a histone-deacetylase-like protein that is widely used as a model for class-I HDACs. In the enzyme active site, the catalytic metal zinc is penta-coordinated by two asp residues, one histidine residues as well as the inhibitor [47], Based on their crystal structures, Finnin et al. [47] postulated a catalytic mechanism for HDACs in which the first reaction step is analogous to the hydroxide mechanism for zinc proteases zinc-bound water is a nucleophile and Zn2+ is five-fold coordinated during the reaction process. However, recent experimental studies by Kapustin et al. suggested that the transition state of HDACs may not be analogous to zinc-proteases [48], which cast some doubts on this mechanism. 

A better idea of the real size of an ion in a molecule can now be obtained from a study of electron density distributions, which it has recently become possible to obtain from accurate X-ray crystallographic studies of crystals. Figure 2.2 shows a contour map of the electron density distribution obtained in an X-ray crystallographic study of crystalline sodium chloride. The position of minimum electron density between two adjacent ions seems to be... 

For parameters taken from crystal structures, no systematic predictions can be made of how the intermolecular interactions in the crystal may affect distances and angles. These potential solid state effects preclude comparisons within a level of several hundredths of an A for bond lengths and several degrees for angles. Operational effects are particularly large for C-H bonds, which are characteristically smaller in crystallographic studies compared to those found by the other methods. 

A growing number of protein crystal structures has provided solid evidence that in many phosphoesterase enzymes, two and sometimes even three, di- or trivalent metal ions are involved in substrate transformation. Consequently, the high catalytic efficiency is, in part, the result of a perfectly coordinated catalytic cooperation of the metal ions. Dinu-clear phosphoiyl transfer enzymes have been discussed thoroughly in recent reviews [1-3]. Therefore, this chapter (Section 2) only gives a brief description of enzymes for which two-metal promotion of phos-phoester hydrolysis was proposed on the basis of detailed mechanistic or crystallographic studies (Table 1). 

H. Kuhl, J. Kruip, A. Seidler, A. Krieger-Liszkay, M. Bunker, D. Bald, J.A. Scheidig, M. Rogner (2000) Towards structural determination of the water-splitting enzyme. Purification, crystallization, and preliminary crystallographic studies of photosystem II from a thermophilic cyanobacterium. J. Biol. Chem., 275 20652-20659... 

In the course of the synthetic efforts to isolate 59, a co-crystal containing the starting aminotriazole compound 60 could be obtained depending on the mode of purification (chromatography or crystallization) <2004AXC733>. Crystallographic study of these products showed that the molecules 59 are linked into simple chains, whereas in 60 the components are linked by combination of two-center N-H- N and N-H- O hydrogen bonds. 

Much of the impetus for the study of hydrogen bonded network structures of 24 and bipy or other linear N-donor ligands has come from the desire to perform time-resolved crystallographic studies of photoactive guest species embedded within the network as a guest [58,62,63]. Embedding a photoactive species within a network structure effectively dilutes it in the solid state. The advantages of this include improved uniformity of illumination of the crystal, less photons are... 

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