Proton transfer sites

Large numbers of reactions of interest to chemists only take place in strongly acidic or strongly basic media. Many, if not most, of these reactions involve proton transfer processes, and for a complete description of the reaction the acidities or basicities of the proton transfer sites have to be determined or estimated. These quantities are also of interest in their own right, for the information available from the numbers via linear free energy relationships (LFERs), and for other reasons. 

A PCET reaction is described by four separate transfer sites derived from a donor and an acceptor for both an electron and a proton [5]. This four state description of PCET gives rise to two important considerations. A geometric aspect to PCET arises when considering the different possible spatial configurations of the four transfer sites. A HAT reaction comprises just one possible arrangement - where the electron and proton transfer sites are coincidental - however this need not be the case for PCET in general. In addition, the two-dimensional reaction space spanned by the four PCET states shown in Fig. 17.1 encompasses infinite mechanistic possibilities (i.e., pathways) for the coordinated transfer of an electron and a proton. These two issues of geometry and mechanism must be taken into account... 

For aspartate aminotransferase, Lys-258 forms a Schiff base with PLP. Formation of the enzyme-substrate Schiff base rotates the coenzyme and places the a-hydrogen to be removed in the immediate vicinity of Lys-258, which is then responsible for proton transfer. Site-directed mutagenesis studies are also consis-... 

This indeed is not an easy task to examine because it may well be that it is only at certain sites in a membrane that there is sufficient electronic conductivity for the electrode to function. It may well be that our model of a biological electrode (say a membrane) is a model of an insulating layer in which are insulated a number of wires, and this would mean that the proteins which are part of biomembranes, and which stick through them, may be the source of the transport between the two sides of the membrane and an origin of an electron and proton transfer site at the protein-solution interface (Figure 19). 

Still another type of adsorption system is that in which either a proton transfer occurs between the adsorbent site and the adsorbate or a Lewis acid-base type of reaction occurs. An important group of solids having acid sites is that of the various silica-aluminas, widely used as cracking catalysts. The sites center on surface aluminum ions but could be either proton donor (Brpnsted acid) or Lewis acid in type. The type of site can be distinguished by infrared spectroscopy, since an adsorbed base, such as ammonia or pyridine, should be either in the ammonium or pyridinium ion form or in coordinated form. The type of data obtainable is illustrated in Fig. XVIII-20, which shows a portion of the infrared spectrum of pyridine adsorbed on a Mo(IV)-Al203 catalyst. In the presence of some surface water both Lewis and Brpnsted types of adsorbed pyridine are seen, as marked in the figure. Thus the features at 1450 and 1620 cm are attributed to pyridine bound to Lewis acid sites, while those at 1540... 

To make this more specific let us consider the proton transfer from conjugate base A (site A) to base B (site B),... 

Even without a cage effect, the entropy effect will be somewhat more favorable for ortho reaction when hydrogen bonding to an azine-nitrogen atom generates the necessary nucleophile. The possibility of proton transfers between the solvent molecules (MeOH) near the reaction site and the more distant MeO is expected to produce a favorable increase (relative to other solvents) in the entropy of activation, which can reinforce the effect of a favorable point of... 

Exercise 5.3. Construct an EVB potential surface for a proton transfer from Cys-25 to an active site of water molecules in papain. 

FIGURE 5.9. The relationship between Ag and AG for proton transfer reactions in the active site of trypsin. 

To realize the reason for this result from a simple intuitive point of view it is important to recognize that the ionized form of Aspc is more stable in the protein-active site than in water, due to its stabilization by three hydrogen bonds (Fig. 7.7). This point is clear from the fact that the observed pKa of the acid is around 3 in chymotrypsin, while it is around 4 in solution. As the stability of the negative charge on Aspc increases, the propensity for a proton transfer from Hisc to Aspc decreases. 

Transition state theory, 46,208 Transmission factor, 42,44-46,45 Triosephosphate isomerase, 210 Trypsin, 170. See also Trypsin enzyme family active site of, 181 activity of, steric effects on, 210 potential surfaces for, 180 Ser 195-His 57 proton transfer in, 146, 147 specificity of, 171 transition state of, 226 Trypsin enzyme family, catalysis of amide hydrolysis, 170-171. See also Chymotrypsin Elastase Thrombin Trypsin Plasmin Tryptophan, structure of, 110... 

The mechanism for the lipase-catalyzed reaction of an acid derivative with a nucleophile (alcohol, amine, or thiol) is known as a serine hydrolase mechanism (Scheme 7.2). The active site of the enzyme is constituted by a catalytic triad (serine, aspartic, and histidine residues). The serine residue accepts the acyl group of the ester, leading to an acyl-enzyme activated intermediate. This acyl-enzyme intermediate reacts with the nucleophile, an amine or ammonia in this case, to yield the final amide product and leading to the free biocatalyst, which can enter again into the catalytic cycle. A histidine residue, activated by an aspartate side chain, is responsible for the proton transference necessary for the catalysis. Another important factor is that the oxyanion hole, formed by different residues, is able to stabilize the negatively charged oxygen present in both the transition state and the tetrahedral intermediate. 

In order to account for the inability of many enzymes to bind the protonated form of the basic inhibitors or permanently cationic ones better than uncharged analogs (for example, yS-o-galactosidase from E. coli, and P-v>-glucosidase from almonds), it was proposed that the enzyme could proton-ate the inhibitor at the active site by a cationic acid (for example, protonated histidine). If proton transfer cannot occur, the attractive forces due to the carboxylate would be canceled by the repulsion from the cationic acid. Experimental evidence for this proposal is, however, still lacking. In fi-D-gn-lactosidase from E. coli, a tyrosine is presumed to be responsible for the protonation of substrates. ... 

We used DFT to optimize the geometries of various Hammett bases on cluster models of zeolite Brpnsted sites. For p-fluoronitrobenzene and p-nitrotoluene, two indicators with strengths of ca. -12 for their conjugate acids, we saw no protonation in the energy minimized structures. Similar calculations using the much more strongly basic aniline andogs of these molecules demonstrated proton transfer from the zeolite cluster to the base. We carried out F and experimental NMR studies of these same Hammett indicators adsorbed into zeolites HY and HZSM-5. 

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