Zinc models, structural

Figure 8.4 Modeled structure of an encapsulated transition metal catalyst, consisting of zinc(ii)TP) (gray), tris(meta-pyridyl)phosphine (3) (white) and M = [HRh(CO)3] (dark-gray). The different pyridylphosphine template-ligands used for assembly processes are also shown.

Two zinc enzymes with dinuclear active sites have been characterized, promoting interest in dinuclear zinc model systems. Phospholipase C from Bacillus cereus 103) contains three zinc atoms per subunit. An X-ray crystal structure determination at good resolution (1.5 A) revealed that two of these constitute a dinuclear site with a Zn—Zn distance of 3.3 A. The metal atoms are symmetrically bridged by an aspartate residue and by OH or H2O. Each zinc atom has approximate trigonal bipyramidal geometry with the ligation shown in Fig. 22. The third zinc atom is quite close to the bridged pair. 

So far our tests of the Gaussian Approximation Potentials were limited to singlespecies systems, but the framework can be extended to multispecies systems. Here we report our first attempt to model such a system, the cubic phase of gallium nitride. Gallium nitride (GaN) is a two-component semiconductor with a wurtzite or zinc-blende structure. There is a charge transfer between the two species. 

Dislocation climb model in compound semiconductors with zinc blende structure , Appl. Phys. Lett. 29, 461-463. 

J. Zhang, W. Yang, J. P. Piquemal, and P. Ren,/. Chem. Theory Comput., 8, 1314—1324 (2012). Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. 

Uncovering of the three dimentional structure of catalytic groups at the active site of an enzyme allows to theorize the catalytic mechanism, and the theory accelerates the designing of model systems. Examples of such enzymes are zinc ion containing carboxypeptidase A 1-5) and carbonic anhydrase6-11. There are many other zinc enzymes with a variety of catalytic functions. For example, alcohol dehydrogenase is also a zinc enzyme and the subject of intensive model studies. However, the topics of this review will be confined to the model studies of the former hydrolytic metallo-enzymes. 

Fig. 7. Comparison of the cluster binding fold of the water-soluble Rieske fragment from bovine heart 6ci complex (ISF, left PDB file IRIE) with the structure of ru-bredoxin (middle PDB file 7RXN) and with the zinc-ribbon motif (right PDB file ITFl). The metal binding loops are shown as ball-and-stick models of the backbone atoms.

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