Saturated proton , active site

Effect of the Relative Position of Saturated Proton(s) at the Active Site... 

Abstract The ab initio pseudopotential plane wave DPT simulation of the structure and properties of zeolite active sites and elementary catalytic reactions are discussed through the example of the protonation of water and the first step in the protolytic cracking mechanism of saturated hydrocarbons. 

The percolation model suggests that it may not be necessary to have a rigid geometry and definite pathway for conduction, as implied by the proton-wire model of membrane transport (Nagle and Mille, 1981). For proton pumps the fluctuating random percolation networks would serve for diffusion of the ion across the water-poor protein surface, to where the active site would apply a vectorial kick. In this view the special nonrandom structure of the active site would be limited in size to a dimension commensurate with that found for active sites of proteins such as enzymes. Control is possible conduction could be switched on or off by the addition or subtraction of a few elements, shifting the fractional occupancy up or down across the percolation threshold. Statistical assemblies of conducting elements need only partially fill a surface or volume to obtain conduction. For a surface the percolation threshold is at half-saturation of the sites. For a three-dimensional pore only one-sixth of the sites need be filled. 

The ER domain is -310 residues in length, and catalyses the ultimate reduction of the biosynthetic intermediate. The current view regarding the reaction mechanism is that it proceeds by Michael addition. The pro-4/ hydride of NADPH attacks the p-carbon forming an enolate intermediate within the binding pocket. The subsequent step is then dependent upon the residues available in the active site [89]. A recent crystal structure of spinosyn ER2 (SpnER2) revealed that a tyrosine in the active site could provide a proton to produce the fully saturated intermediate [90]. However, in cases where the tyrosine is not present, a conserved lysine residue could fulfil the same role (Fig. 1.26). 

X is NR R2. The substituent is converted to a Z substituent via the low-lying a orbital, and the ring is deactivated toward further electrophilic attack. The ortho and para channels lead to products. The interaction diagram for an X -substituted pentadienyl cation, substituted in the 1-, 2-, and 3-positions, as models of the transition states for the ortho, meta, and para channels, are too complex to draw simple conclusions. The HOMO and LUMO of the three pentadienyl cations with an amino substituent are shown in Figure 11.3. Notice that the LUMO of each is suitable to activate the C—H bond at the saturated site toward abstraction by the base. Curiously, the meta cation has the lowest LUMO and should most readily eliminate the proton. The stabilities of the transition states should be in the order of the Hiickel n energies. These are 6a — 8.7621/ , 6a — 8.499 / , and 6a — 8.718 / , respectively. Thus the ortho and para channels are favored over the meta channel, and the ortho route is slightly preferred over the para route. Experimentally, para substitution products are often the major ones in spite of there being two ortho pathways. The predominance of para products is usually attributed to steric effects. 

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