Protonation by Water

Citrate synthase in mammals is a dimer of 49-kD subunits (Table 20.1). On each subunit, oxaloacetate and acetyl-CoA bind to the active site, which lies in a cleft between two domains and is surrounded mainly by a-helical segments (Figure 20.6). Binding of oxaloacetate induces a conformational change that facilitates the binding of acetyl-CoA and closes the active site, so that the reactive carbanion of acetyl-CoA is protected from protonation by water. 

Once formed, and depending on the nature of the nucleophile, the tetrahedral alkoxide intermediate can undergo either of two further reactions, as shown in Figure 2. Often, the tetrahedral alkoxide intermediate is simply protonated by water or acid to form an alcohol product. Alternatively, the tetrahedral intermediate can be protonated and expel the oxygen to form a new double bond between the carbonyl carbon and the nucleophile. We ll study both processes in detail in Chapter 19. 

The alkoxide ion is protonated by water to give the gem diol product and regenerate the hydroxide ion catalyst. 

Mechanism. The aqueous base deprotonates the hydrazone, and the anion produced is resonance stabilized. The carbanion picks up a proton from water, and another deprotonation by the aqueous base generates an intermediate, which is set up to eliminate a molecule of nitrogen (N2), and produce a new carbanion. This carbanion is quickly protonated by water, giving the final reduced product as alkane. 

The carbide ion ( C=C 2 ) is a Bronsted base and is readily protonated by water, resulting in the formation of the organic compound ethyne (acetylene) ... 

Alkaline earth oxides, such as CaO, are even stronger bases than the corresponding hydroxides because the oxide ion (O2-) is a stronger base than OH (Table 15.1). In fact, the O2- ion can t exist in aqueous solutions because it is immediately and completely protonated by water, yielding OH- ions ... 

A predominant isomerization of metalloles to transoidal dienes occurs when t-BuLi is used34. This isomerization involves the formation of an allylic carbanion. which is protonated by water at the position a to Si (or Ge) and is silylated at the exocyclic carbon... 

Simple olefins do not react with eaq at an appreciable rate, but compounds with an extended 7t-system such as butadiene can also accommodate an additional electron (k = 8 x 109 dm3 mol-1 s 1 Hart et al. 1964). However, as in the case of benzene, the rate is often below diffusion controlled [reaction (23) k = 7.2 x 106 dm3 mol 1 s 1 (Gordon et al. 1977) in THF, the reaction of the solvated electron with benzene is even reversible (Marasas et al. 2003)], and the resulting radical anion is rapidly protonated by water [reaction (24)]. 

A rapid protonation by water of the electron adducts of spin traps such as DMPO or 2-methyl-2-nitroso-propane yields the same species as are expected for the reaction of H" (Sargent and Gardy 1975). This prevents a distinction between eaq and 11 by using this technique. 

The properties of the purine radical anions formed by their reaction with eaq resemble those of the Cyt radical anion. Because the pKa values of the heteroatom-protonated conjugate acid of the purine radical anions are very high, the purine radical anion are rapidly protonated by water (Hissung et al. 1981a Visscher et al. 1987 von Sonntag 1991 Candeias and Steenken 1992a Candeias et al. 1992 Aravindakumar et al. 1994). For example, the dAdo radical anion... 

Of the three isomers of l-methyl-3-cyanodihydropyridines only the 1,2-isomer underwent rapid and quantitative reduction by NaBH4 in the presence of trimethoxyborane116 (Scheme 87). The role of BH3 in generating the protonating species, in contrast to the direct protonation by water suggested by other authors117,118, was clearly evident. 

Already at pH 10 and continuing down to pH 6, compounds 12 (X = H), 13 and 14 show a sharp decrease in k/s-1. Reaction is not buffer-catalyzed in this region, hence this is not due to rate-controlling protonation, by water, of a minority of enamine in equilibrium with its enammonium ion (equations 14 and 15). Nor can C-protonation by H30+ be rate-controlling since one would observe either an upward slope in the pH-rate profile (when [E] > [NH+]) or a plateau (when [NH+] > [E]). Although such characteristics in the rate profile were observed for compounds 1-3, they were not observed for the propiophenone enamines. Rather, a switch to rate-controlling nucleophilic attack on the iminium ion is indicated (equation 16) for which rate-law equation 22 is appropriate. 

Nucleophilic additions to aldeliydcs and ketones have two genera) variations, as shown in Figure 19.2. In one variation, the tetrahedral intermediate is protonated by water or acid to give an alcohol as the final product in the second variation, tlie carbonyl oxygen atom is itrotonated and then eliminated as HO or H2O to give a product witli a C=Nu bond. 

Similar to Cyt, the purine radical anions are also rapidly protonated by water [cf. reaction (15)]. The primary H adducts thus formed rmdergo a series of tautomerization reactions, eventually reaching thermodynamically more favorable H adducts [cf. reactions (16) and (17)]. ... 

Protonation by water of the ring carbon occurs only if the phenol fimction is de-protonated, apparently because only then is the electron density at the ring sufficient for protonation by the weak acid H2O. 

Loss of ethanol, followed by removal of a proton by water, gives the product ester. 

Finally the tribromo ketone adds water and CBtj is a just good enough leaving group to leave the tetrahedral intermediate with C-C bond cleavage (cf. the bromination reaction, p. 537). The anion is protonated by water as it goes. 

The intermediate is protonated by water solvent to yield the neutral aidol product and regenerate hydroxide ion. 

Pellecchia et al. have proposed the SEA-TROSY technique to identify solvent-exposed amide groups in l5N-labelled proteins. Initially, all amide magnetization is eliminated with a i5N filter, and then the magnetization of solvent-exposed amide protons is restored by exposure to water magnetization followed by detection of these amide protons by water flipback TROSY.101 Figure 5 shows a comparison of a normal TROSY spectrum and an SEA-TROSY spectrum (50-ms mixing time) of a 30-kDa complex of 15N,l3C-0 subunit and the unlabelled N-terminal domain (1-185) subunit of DNA polymerase III. 

NH3(am) -- NH, (am) + NHj Cam) = 1 x 10 at -35°C Very strong bases that are protonated by water survive in liquid ammonia. 

Reaction of eaq , produced by pulse radiolysis, with bromophenols in alkaline solutions exhibited completely different pathways . When the hydroxyl group of the hydroxyphenyl radical is dissociated, the negative charge is partly delocalized from to the site of the radical on the aromatic ring and this site then undergoes very rapid protonation by water to form a phenoxyl radical (equation 8). 

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