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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)

Efficient intramolecular general acid catalysis of nucleophilic attack on a phosphodiester.

The hydrolysis of methyl 8-dimethylamino-1-naphthyl phosphate 4 and its reactions with a representative range of nucleophiles are catalyzed by the dimethylammonium group at acidic pH with rate accelerations of the order of 106. The reaction persists up to pH 7 because the strong intramolecular hydrogen bond, which is the key to efficient general acid catalysis, is present also in the reactant. The sensitivity to the basicity of the nucleophile (Brønsted beta(nuc) = 0.29) lies between values measured previously for mono- and triesters. The comparisons suggest that general acid catalyzed reactions of phosphate mono- or diesters with strongly basic oxyanion nucleophiles (like those derived from a serine oxygen or a bound water molecule in an enzyme active site) will be fastest when their negative charges are neutralized by protonation. Reactions with NH2OH and its N-methylated derivatives show an apparent alpha-effect, but NH2OMe reacts no faster than a primary amine of similar basicity. It is suggested that the reaction involving NH2OH as an oxygen nucleophile proceeds through the pre-equilibrium formation of the tautomer H3N+-O- as the active nucleophile: ab initio calculations support this idea.[1]


  1. Efficient intramolecular general acid catalysis of nucleophilic attack on a phosphodiester. Kirby, A.J., Lima, M.F., da Silva, D., Roussev, C.D., Nome, F. J. Am. Chem. Soc. (2006) [Pubmed]
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