Fundamentals of Phosphate Transfer

Abstract

Historically, the chemistry of phosphate transfer-a class of reactions fundamental to the chemistry of Life-has been discussed almost exclusively in terms of the nucleophile and the leaving group. Reactivity always depends significantly on both factors; but recent results for reactions of phosphate triesters have shown that it can also depend strongly on the nature of the nonleaving or "spectator" groups. The extreme stabilities of fully ionised mono- and dialkyl phosphate esters can be seen as extensions of the same effect, with one or two triester OR groups replaced by O(-). Our chosen lead reaction is hydrolysis-phosphate transfer to water: because water is the medium in which biological chemistry takes place; because the half-life of a system in water is an accepted basic index of stability; and because the typical mechanisms of hydrolysis, with solvent H2O providing specific molecules to act as nucleophiles and as general acids or bases, are models for reactions involving better nucleophiles and stronger general species catalysts. Not least those available in enzyme active sites. Alkyl monoester dianions compete with alkyl diester monoanions for the slowest estimated rates of spontaneous hydrolysis. High stability at physiological pH is a vital factor in the biological roles of organic phosphates, but a significant limitation for experimental investigations. Almost all kinetic measurements of phosphate transfer reactions involving mono- and diesters have been followed by UV-visible spectroscopy using activated systems, conveniently compounds with good leaving groups. (A "good leaving group" OR* is electron-withdrawing, and can be displaced to generate an anion R*O(-) in water near pH 7.) Reactivities at normal temperatures of P-O-alkyl derivatives-better models for typical biological substrates-have typically had to be estimated: by extended extrapolation from linear free energy relationships, or from rate measurements at high temperatures. Calculation is free from these limitations, able to handle very slow reactions as readily as very fast ones, and capable of predicting rate constants with levels of accuracy acceptable to the experimentalist. We present an updated overview of phosphate transfer, with particular reference to the mechanisms of the reactions of alkyl derivatives and triesters. The intention is to present a holistic (not comprehensive!) overview of the reactivity of typical phosphate esters, in terms familiar to the working chemist, at a level sufficient to support informed predictions of reactivity for structures of interest.

Analysis of the RNA Binding Specificity Landscape of C5 Protein Reveals Structure and Sequence Preferences that Direct RNase P Specificity

“…Linear free energy relationships between rate and equilibrium constants for the same reaction can provide information on how changes in molecular structure affect the reaction mechanism. Linear free energy relationships are used extensively in mechanistic studies of physical organic chemistry (Kirby and Nome, 2015; Lassila et al, 2011) and protein folding (Fersht et al, 1992; Matouschek and Fersht, 1993; Sosnick, 2008). There limits to interpreting free energy relationships arising from differences in ground state, multiple reaction channels, and changes in mechanism (Farcasiu, 1975; Jencks, 1985).…”

Cleaving paraoxon with hydroxylamine: Ammonium oxide isomer favors a Frontside attack mechanism

“…Kirby and Nome recently summarized our understanding of the reactions of phosphate esters, including triesters, pointing out the possibility of formation, under certain conditions, of intermediate phosphoranes during A N + D N degradation reactions; as also reported elsewhere in studies that only considered the characteristics of the leaving group, OR * . Kirby and Nome go further, reporting that in addition to the OR * group (Figure ), the equatorial OR substituent groups also contribute to the stability of the intermediate . In addition, they pointed out that the half‐lives of the intermediates are reduced in the case of electron‐withdrawing groups in the apical position, which is the preferential position for the strongest electron‐withdrawing group.…”

“…Although simplified mechanisms may be of interest from the didactic perspective, the reactions of phosphate esters are far more complex than those of the equivalent carbonate esters. Phosphate monoesters, diesters, and triesters have different hydrolysis reaction susceptibilities, which takes their study to a higher level of complexity . Nature itself makes distinctions among the different forms, with phosphate triesters being foreign to living organisms, including humans, where their metabolism is very slow, compared with that of monoesters and diesters.…”

“…This behavior of the triesters in terms of their substituents makes their reactivity complex, and consequently they have been the focus of a very large number of studies. A full understanding of their reactivity could, for example, enable the synthesis of better bioselective pesticides.…”

Physical Organic Chemistry: A Personal Reflection

“…So a logical choice for a postdoctoral stay was the Jencks group at Brandeis. W. P. (Bill) Jencks was a Doctor of Medicine who had diversified into POC via a postdoc with Woodward, and had recently published a beautifully systematic mechanistic study of carboxylic acyl transfer in water, which provided the model for our study of phosphate transfer to nucleophiles, and the inspiration for further work on phosphate transfer over the next 50 years 1b. Jencks′ Catalysis in Chemistry and Biochemistry 2 was the influential text that summed up this systematic approach to mechanistic investigation for the contemporary generation.…”