Penta-coordinated

Whether the formation of alkene 3 proceeds directly from alkoxide 4 or via a penta-coordinated silicon-species 6, is not rigorously known. In certain cases—e.g. for /3-hydroxydisilanes (R = SiMes) that were investigated by Hrudlik et al —the experimental findings suggest that formation of the carbon-carbon bond is synchronous to formation of the silicon-oxygen bond ... 

First, we must say a word about the naming of A. For many years these species were called carbonium ions , though it was suggested as long ago as 1902 that this was inappropriate because -onium usually refers to a covalency higher than that of the neutral atom. Nevertheless, the name carbonium ion was well established and created few problems until some years ago, when George Olah and his co-workers found evidence for another type of intermediate in which there is a positive charge at a carbon atom, but in which the formal covalency of the carbon atom is 5 rather than 3. The simplest example is the methanonium ion CHj (see p. 770). Olah proposed that the name carbonium ion be henceforth reserved for penta-coordinated positive... 

Zn -PDF, 37 pM versus E. coli Fe -PDF), it was successfully used to provide co-crystals bound in the active site of both Co - and Zn -E. coli PDF [58], These structures reveal that the H-phosphonate binds to the metal in a monodentate fashion, adopting a tetrahedral coordination state similar to that of the native resting state of the enzyme. This is in contrast to later co-crystal structures obtained with more potent hydroxamic acid or reverse hydroxamate inhibitors, which bind to the metal in a bidentate fashion vide infra). Presumably these bidentate inhibitors mimic the true transition state of the enzyme, in which the metal centre slips to a penta-coordinate geometry in order to activate the Wformyl carbonyl of the substrate [56, 67]. 

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. 

Tetra- and penta-coordinate carbon-substituted heavy ketones stabilized by the coordination of nitrogen atoms... 

Table 5 Tetra- and penta-coordinate double-bond compounds between heavier group 14 and 16 elements bearing nitrogen substituents...

The Co system is more reactive as well as much more selective than the Ni and Rh catalyst systems (Table XVII). The best systems allow almost 100% conversion with almost 100% yield of c -l,4-hexadiene. The best of the Ni and Rh systems known so far are still far from such amazing selectivity. The tremendous difference between the Ni system and the Co or Fe system must be linked to the difference in the nature of the coordination structures of the complexes, i.e., hexacoordinated (octahedral complexes) in the case of Co and Fe and tetra- or penta-coordinated (square planar or square pyramidal) complexes in the case of Ni. The larger number of coordination sites allows the Co and Fe complex to utilize chelating phosphines which are more effective than monodentate phosphines for controlling the selectivity discussed here. These same ligands are poison for the Ni (and Rh) catalyst system, as shown earlier. 

Complex C (Scheme 21) seems to shows stable penta-coordination for apparently very different reasons. The compound is cationic, but the counterion is a non-coordinating tetraarylborate. Interestingly, neither the dichloromethane solvent nor the diethylether present in the reaction mixture seem to coordinate to the open site in solution. The compound was crystallized from a tetrahydrofuran/pentane mixture as the tetrahy-drofuran (THF) solvate, but in the crystal structure, the THF is remote from the open site at platinum. The open site is shielded somewhat by the methyl groups of the protonated TpMe2 ligand, but it does not appear completely inaccessible. A reasonable explanation for the... 

Figure 11, Density of states of a water sample, referring to two-, three-, tetra- and penta-coordinated 3D clusters and to the total of the sample, as resulting from MD simulation, T=305 K. Dotted lines indicate vibrational frequencies for a single water molecule in gas phase.

Several zinc enzymes that catalyse the hydrolysis of phosphoesters have catalytic sites, which contain three metal ions in close proximity (3-7 A from each other). These include (Figure 12.11) alkaline phosphatase, phospholipase C and nuclease PI. In phospholipase C and nuclease PI, which hydrolyse phosphatidylcholine and single-stranded RNA (or DNA), respectively, all three metal ions are Zn2+. However, the third Zn2+ ion is not directly associated with the dizinc unit. In phospholipase C, the Zn-Zn distance in the dizinc centre is 3.3 A, whereas the third Zn is 4.7 and 6.0 A from the other two Zn2+ ions. All three Zn2+ ions are penta-coordinate. Alkaline phosphatase, which is a non-specific phos-phomonoesterase, shows structural similarity to phospholipase C and PI nuclease however,... 

In an article published independently at the same time, Stuehr and Ikeda-Saito89 used the purified bNOS and iNOS to reach the same conclusions. While the paper was under review, the authors mention that White and Marietta had reported earlier that the iron was a heme and was used as an oxidant. Using the same type of study, they found that the iron prophyrin and its CO derivative had the expected properties and proposed that the iron is penta-coordinated, with a cysteine thiolate as the fifth coordinate. A third publication confirmed the results when McMillan and coworkers90 used bNOS grown in human kidney cells. These workers obtained similar data for the light absorption of the enzyme and its CO spectrum. They also speculate on very similar sequences in the three types of purified enzyme that might be the porphyrin binding site. 

Finally, we examine azurin, a blue protein (FW = 14 000) devoted to bacterial electron transport, the copper centre of which has a penta-coordinate trigonal bipyramidal geometry, at variance with all the other cupredoxins, Figure 39.73... 

Fig. 5. Square pyramidal geometry of penta-coordinate metalloporphyrins (see Ref. (73))...

The structural features of the linear R-Cu-R arrangement are identical to those observed for other [R2CU] anionic units discussed previously (cf. Fig. 1.31). The [Li2CN(THF)2(PMDTA)2] cationic unit consists of a central cyanide moiety, to which two lithium atoms are bound in end-on fashion. Coordination saturation at each lithium atom is achieved by coordination of the three nitrogen atoms of the PMDTA molecule and one THF molecule, rendering each lithium atom penta-coordinate. Recent H, Li HOESY experiments showed that this ionic structure found in the solid state is probably retained in polar solvents such as THF [140]. 

Mechanism for protonation of alkenes was previously discussed in Section 13.5.1. In general, protonation of alkenes is an exothermic process. Protonation of alkanes was discussed in Section 13.5.2. There wiU be further discussion on this step in Section 13.8.4 within the context of alkane cracking mechanisms. The formation of a penta-coordinated carbonium ion from alkane protonation is typically an endothermic process, the reverse being true for deprotonation. 

As we showed previously in this chapter, silicon easily expands its valence shell to become a penta-coordinated species. Therefore, it is expected that an intramolecular transfer of organosilicon group from X to Y may occur via a radical mechanism, provided that the R substituents on the silicon atom are not good leaving groups (Reaction 6.20). 

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