Theoretical Studies of the Hydroxide-Catalyzed P−O Cleavage Reactions of Neutral Phosphate Triesters and Diesters in Aqueous Solution:  Examination of the Changes Induced by H/Me Substitution

Iché-Tarrat, Nathalie; Barthelat, Jean‐Claude; Rinaldi, Daniel; Vigroux, Alain

doi:10.1021/jp0550558

Cited by 50 publications

(50 citation statements)

References 63 publications

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“…4) involved in transferring a proton from water to the diester anion, the predicted rate for the reaction through this mechanism is Ϸ3 ϫ 10 Ϫ19 s Ϫ1 . These comparisons and the associated errors do not allow a clear distinction to be made between the two mechanisms using our data, although recent calculations (13) give very good agreement with the triester-like mechanism. Comparing the rate of reaction of the methyl triester and corresponding diester with hydroxide, we note that the effect of neutralizing the phosphoryl group is to accelerate this reaction by Ϸ10 9 fold.…”

Section: Discussioncontrasting

confidence: 78%

The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA

Schroeder

Lad

Wyman

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

240

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Phosphodiester linkages, including those that join the nucleotides of DNA, are highly resistant to spontaneous hydrolysis. The rate of water attack at the phosphorus atom of phosphodiesters is known only as an upper limit, based on the hydrolysis of the dimethyl phosphate anion. That reaction was found to proceed at least 99% by C-O cleavage, at a rate suggesting an upper limit of 10 ؊15 s ؊1 for P-O cleavage of phosphodiester anions at 25°C. To evaluate the rate enhancement produced by P-O cleaving phosphodiesterases such as staphylococcal nuclease, we decided to establish the actual value of the rate constant for P-O cleavage of a simple phosphodiester anion. In dineopentyl phosphate, C-O cleavage is sterically precluded so that hydrolysis occurs only by P-O cleavage. Measurements at elevated temperatures indicate that the dineopentyl phosphate anion undergoes hydrolysis in water with a t 1/2 of 30,000,000 years at 25°C, furnishing an indication of the resistance of the internucleotide linkages of DNA to water attack at phosphorus. These results imply that staphylococcal nuclease (k cat ‫؍‬ 95 s ؊1 ) enhances the rate of phosphodiester hydrolysis by a factor of Ϸ10 17 . In alkaline solution, thymidylyl-3 -5 -thymidine (TpT) has been reported to decompose 10 5 -fold more rapidly than does dineopentyl phosphate. We find however that TpT and thymidine decompose at similar rates and with similar activation parameters, to a similar set of products, at pH 7 and in 1 M KOH. We infer that the decomposition of TpT is initiated by the breakdown of thymidine, not by phosphodiester hydrolysis.DNA hydrolysis ͉ DNA stability ͉ nuclease ͉ rate enhancement ͉ phosphate ester P hosphoric acid diesters are, in general, exceedingly unreactive in water (1-3), so that the phosphodiester linkages that join the nucleotides of DNA are highly resistant to spontaneous hydrolysis. By extrapolation of earlier model experiments at elevated temperatures, the uncatalyzed hydrolysis of dimethyl phosphate in neutral solution was found to proceed with an estimated rate constant of Ϸ2 ϫ 10 Ϫ13 s Ϫ1 at 25°C, corresponding to a half-time of 140,000 years. That reaction was found to proceed at least 99% by C-O cleavage, suggesting an upper limit of Ϸ1 ϫ 10 Ϫ15 s Ϫ1 at 25°C on the rate constant for spontaneous P-O cleavage of a phosphodiester anion, the reaction that is catalyzed by many phosphodiesterases (4).More recently, a rate constant of 6 ϫ 10 Ϫ7 s Ϫ1 has been reported for the decomposition of thymidylyl-3Ј-5Ј-thymidine (TpT) at 80°C in 1 M KOH (5). Extrapolation of the results obtained earlier for dimethyl phosphate hydrolysis in neutral solution (4), to 80°C, would indicate a rate Ϸ10 5 -fold slower. That discrepancy might indicate a major role for catalysis by hydroxide, but the hydrolysis of another dialkyl phosphodiester, bis-3-(4-carboxyphenyl)neopentyl phosphate (Np* 2 P), in which ␥-branching of the leaving alcohol prevents C-O cleavage (Fig. 1), also proceeds Ϸ10 5 -fold more slowly in 1 M KOH (6).In an effort to resolve that discre...

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Section: Discussioncontrasting

confidence: 78%

The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA

Schroeder

Lad

Wyman

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

240

View full text Add to dashboard Cite

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“…The maxima obtained from the enthalpy profiles, which may slightly differ from the maxima arising from DE or DG profiles, were used to locate the relevant transition-state structures in solution. [22] All calculations (including geometry optimizations) were performed in a dielectric continuum by using the multipolar expansion (MPE) [30][31][32][33] model developed at Nancy, with which we did not encounter the convergence problems recently described in geometry optimizations with the polarizable continuum model (PCM). [34,35] Probably, the higher efficiency of the MPE method over the PCM method in geometry optimization calculations comes from the fact that the basic equations of the former model are well adapted to analytically compute the energy derivatives.…”

Section: Methodsmentioning

confidence: 99%

“…[33] Moreover, the MPE method leads to results basically identical to PCM, as shown by Curutchet et al, [36] provided that the same cavity characteristics are assumed, although the MPE model demands significantly less computational time. [33] Preliminary calculations [22] indicated that the MPE solvation code is especially efficient and accurate to model S N 2(P) reactions in solution by providing activation energies (DH°) within good chemical accuracy (< 1 kcal mol À1 ). [22] Therefore, all calculations throughout this work were done by using this model.…”

Section: Methodsmentioning

confidence: 99%

“…[22] The primary objective of these preliminary calculations was to validate a proper modeling approach to determine realistic free-energy pathways in solution for S N 2(P) reactions involving OH À attack on protonated phosphate esters. Here, we have applied this methodology to evaluate the SAC proposal for the hydrolysis of three representative phosphate monoester dianions: 2,4-dinitrophenyl phosphate (pK lg = 4.07), phenyl phosphate (pK lg = 9.95), and methyl phosphate (pK lg = 15.5).…”

Section: Introductionmentioning

confidence: 99%

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Theoretical Evaluation of the Substrate‐Assisted Catalysis Mechanism for the Hydrolysis of Phosphate Monoester Dianions

Iché-Tarrat

Ruiz‐López

Barthelat

et al. 2007

Chemistry A European J

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Quantum chemistry methods coupled with a continuum solvation model have been applied to evaluate the substrate-assisted catalysis (SAC) mechanism recently proposed for the hydrolysis of phosphate monoester dianions. The SAC mechanism, in which a proton from the nucleophile is transferred to a nonbridging phosphoryl oxygen atom of the substrate prior to attack, has been proposed in opposition to the widely accepted mechanism of direct nucleophilic reaction. We have assessed the SAC proposal for the hydrolysis of three representative phosphate monoester dianions (2,4-dinitrophenyl phosphate, phenyl phosphate, and methyl phosphate) by considering the reactivity of the hydroxide ion toward the phosphorus center of the corresponding singly protonated monoesters. The reliability of the calculations was verified by comparing the calculated and the observed values of the activation free energies for the analogous S(N)2(P) reactions of F- with the monoanion of the monoester 2,4-dinitrophenyl phosphate and its diester analogue, methyl 2,4-dinitrophenyl phosphate. It was found that the orientation of the phosphate hydrogen atom has important implications with regard to the nature of the transition state. Hard nucleophiles such as OH- and F- can attack the phosphorus atom of a singly protonated phosphate monoester only if the phosphate hydrogen atom is oriented toward the leaving-group oxygen atom. As a result of this proton orientation, the SAC mechanism in solution is characterized by a small Brønsted coefficient value (beta(lg)=-0.25). This mechanism is unlikely to apply to aryl phosphates, but becomes a likely possibility for alkyl phosphate esters. If oxyanionic nucleophiles of pK(a)<11 are involved, as in alkaline phosphatase, then the S(N)2(P) reaction may proceed with the phosphate hydrogen atom oriented toward the nucleophile. In this situation, a large negative value of beta(lg) (-0.95) is predicted for the substrate-assisted catalysis mechanism.

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“…As a result, phosphate esters have been the subject of extensive experimental 3,6-13 and theoretical [14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32] studies (though the precise mechanisms of both the solution and enzyme catalyzed reactions remain controversial, see e.g. [6][7][8]12,14,15,25,26,29,[33][34][35] ). In contrast, while there has been some significant work on the hydrolysis of sulfate esters (see e.g.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Comparison ofp-Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer

Kamerlin

2011

J. Org. Chem.

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Both phosphoryl and sulfuryl transfer are ubiquitous in biology, being involved in a wide range of processes, ranging from cell division to apoptosis. Additionally, it is becoming increasingly clear that enzymes that can catalyze phosphoryl transfer can often cross-catalyze sulfuryl-transfer (and vice versa).However, while there have been extensive experimental and theoretical studies performed on phosphoryl transfer, the body of available research on sulfuryl transfer is comparatively much smaller.The present work presents a direct theoretical comparison of p-nitrophenyl phosphate and sulfate monoester hydrolysis, both of which are considered prototype systems for probing phosphoryl and sulfuryl transfer respectively. Specifically, free energy surfaces have been generated using density functional theory, by initial geometry optimization in PCM using the 6-31+G* basis set and the B3LYP density functional, followed by single point calculations using the larger 6-311+G** basis set and the COSMO continuum model. The resulting surfaces have been then used to identify the relevant transition states, either by further unconstrained geometry optimization, or from the surface itself where possible.Additionally, configurational entropies were evaluated using a combination of the quasiharmonic approximation and the restraint release approach and added to the calculated activation barriers as a correction. Finally, the overall activation entropy was estimated by approximating the solvent contribution to the total activation entropy using the Langevin dipoles solvation model. We have reproduced both the experimentally observed activation barriers and the observed trend in the activation entropies with reasonable accuracy, as well providing a comparison of calculated and observed 15 N and 18 O kinetic isotope effects. We demonstrate that, counterintuitively, the hydrolysis of the p-nitrophenyl sulfate proceeds through a more expa show that the solvation effects upon moving from the ground state to the transition state are quite different for both reactions, suggesting that the enzymes that catalyze these reactions would need active 4 sites with quite different electrostatic preorganization for the efficient catalysis of either reaction (despite which many enzymes can catalyze both phosphoryl and sulfuryl transfer). We believe that such a comparative study is an important foundation for understanding the molecular basis for phosphatesulfate cross promiscuity within members of the alkaline phosphatase superfamily.

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Theoretical Studies of the Hydroxide-Catalyzed P−O Cleavage Reactions of Neutral Phosphate Triesters and Diesters in Aqueous Solution: Examination of the Changes Induced by H/Me Substitution

Cited by 50 publications

References 63 publications

The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA

The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA

Theoretical Evaluation of the Substrate‐Assisted Catalysis Mechanism for the Hydrolysis of Phosphate Monoester Dianions

Theoretical Comparison ofp-Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer

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