Phosphorothioate Esters Research Articles

Determination of the Mechanism of Nucleophilic Reaction of Fenitrothion Using Substituted Phenoxide Nucleophiles in Aqueous Media

The mechanism of the nucleophilic displacement reaction at the phosphorus centre of organophosphates was determined. Phenoxide nucleophiles were reacted with fenitrothion (O,O-dimethyl O-(3-methyl-4-nitrophenyl) phosphorothioate) in water at 25oC and pseudo-first order rate constant measurements taken. Second-order rate constant (kNuc) was determined for the different concentrations of nucleophiles while the second-order rate constant (klg) for the investigation of 2,4-dichlorophenoxide ion with and series of aryl phosphorothioate esters was also determined. Linear free energy relationship was further determined using the Brϕnsted-type plot. The plots are linear over a range of pKaNuc of 7.15-11.10 that straddles the pKa of the leaving 3-methyl-4-nitrophenoxide ion (pKa = 7.20) with statistically acceptable linear correlations (R2 = 0.987) and (R2 = 0.980). The linearity in the traditional Brϕnsted-type plots shows the sensitivity of the nucleophilic displacement to the basicity of the nucleophiles and hence is consistent with a single transition-state mechanism whose barrier to decomposition is low hence concerted. Analysis of the values of βNuc, βLg and βeq (0.734) with the effective charge distribution in the transition state shows that it has no positive character. The Leffler index presents bond formation being slightly ahead of bond rupture.

Unusual resistance of cobalt bis dicarbollide phosphate and phosphorothioate bridged esters towards alkaline hydrolysis: The “metallacarborane effect”

The extraordinary stability of bridged O,O-[cobalt bis(dicarbollide)ion] O-(4-nitrophenyl)phosphorothioate [2]- and phosphate [3]- esters under alkali conditions was discovered. The hydrolysis of metallacarborane esters [2]- and [3]- was studied, and the kinetic and thermodynamic parameters were measured and compared with those of their organic counterparts, parathion and paraoxon. The extreme differences between the hydrolytic properties of alkyl- and metallacarborane phosphate and phosphorothioate esters are attributed to the electronic and steric effects of the metallacarborane non leaving group (“metallacarborane effect”). The known “thio effect” contributes to a lesser extent to the resistance of [2]- to the basic conditions.

Transition States and Control of Substrate Preference in the Promiscuous Phosphatase PP1.

Catalytically promiscuous enzymes are an attractive frontier for biochemistry, because enzyme promiscuities not only plausibly explain enzyme evolution through the mechanism of gene duplication but also could provide an efficient route to changing the catalytic function of proteins by mimicking this evolutionary process. PP1γ is an effectively promiscuous phosphatase for the hydrolysis of both monoanionic and dianionic phosphate ester-based substrates. In addition to its native phosphate monoester substrate, PP1γ catalyzes the hydrolysis of aryl methylphosphonates, fluorophosphate esters, phosphorothioate esters, and phosphodiesters, with second-order rate accelerations that fall within the narrow range of 1011-1013. In contrast to the different transition states in the uncatalyzed hydrolysis reactions of these substrates, PP1γ catalyzes their hydrolysis through similar transition states. PP1γ does not catalyze the hydrolysis of a sulfate ester, which is unexpected. The PP1γ active site is tolerant of variations in the geometry of bound ligands, which permit the effective catalysis even of substrates whose steric requirements may result in perturbations to the positioning of the transferring group, both in the initial enzyme-substrate complex and in the transition state. The conservative mutation of arginine 221 to lysine results in a mutant that is a more effective catalyst toward monoanionic substrates. The surprising conversion of substrate preference lends support to the notion that mutations following gene duplication can result in an altered enzyme with different catalytic capabilities and preferences and may provide a pathway for the evolution of new enzymes.

ChemInform Abstract: Development of Metal Ion Containing Catalysts for the Decomposition of Phosphorothioate Esters

AbstractReview: 75 refs.

Palladium-Catalyzed Allylic Fluorination of Cinnamyl Phosphorothioate Esters

A highly regioselective, Pd-catalyzed allylic fluorination of phosphorothioate esters is reported. This chemistry addresses several limitations of previously reported methods in which elimination and lack of reactivity were problematic. Preliminary mechanistic investigations reveal that these reactions are stereospecific and provide fluorinated products with net retention of stereochemical configuration. In analogy to other Pd-catalyzed allylic substitution reactions, this process likely proceeds through a palladium π-allyl intermediate.

Development of metal-ion containing catalysts for the decomposition of phosphorothioate esters

The widespread use of phosphorothioate esters as agricultural pesticides, chemical weapons and mechanistic probes in enzymology has sparked interest in the reactivity of these thio-substituted analogues of phosphate esters. In this brief account, we summarize the recent developments in our understanding of the mechanisms of hydrolysis (and solvolysis in methanol) of phosphorothioates containing a sulfur atom in the bridging and/or non-bridging position. A small number of highly efficient catalytic systems containing the metal ions La(III), Pd(II), Cu(II) and Zn(II) have been developed to promote the degradation of the various classes of phosphorothioate esters. The mechanisms of the base promoted solvolytic reactions in water and methanol and those of the metal catalyzed cleavage are presented, as well as a discussion of the energetics of the catalytic processes and other salient features. The aim of this review is to provide the reader with a contemporary physical organic description of phosphorothioate ester cleavage. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.

Cu(I)-Catalyzed, α-Selective, Allylic Alkylation Reactions between Phosphorothioate Esters and Organomagnesium Reagents

Regiocontrol of allylic alkylation reactions involving hard nucleophiles remains a significant challenge and continues to be an active area of research. The lack of general methods in which α-alkylation is favored underscores the need for the development of new processes for achieving this type of selectivity. We report that Cu(I) catalyzes the allylic substitution of phosphorothioate esters with excellent α-regioselectivity, regardless of the nature of the Grignard reagent that is used. To the best of our knowledge, the Cu-catalyzed allylic alkylation of phosphorothioate esters has never been described. We have also developed a simple protocol for inducing high α selectivity starting from secondary allylic halides. This is accomplished by using sodium phosphorothioates as an additive.

ChemInform Abstract: Mild Two‐Step Process for the Transition‐Metal‐Free Synthesis of Carbon—Carbon Bonds from Allylic Alcohols/Ethers and Grignard Reagents.

AbstractThe method involves the photochemically promoted allylic substitution reaction of allylic alcohols or ethers with phosphorothioic acid ester (II) followed by sp3—sp3 or sp2—sp3 bond formation of the resulting allylic phosphorothioate esters with various Grignard reagents.

Convenient Synthesis of Allylic Thioethers from Phosphorothioate Esters and Alcohols

The synthesis of allylic thioethers arising from the reaction between phosphorothioate esters and alcohols is described. The synthesis is accomplished in one step by the addition of an exogenous alkoxide to the corresponding allylic phosphorothioate ester. It is demonstrated that this process is amenable to various functional groups and a wide variety of heterocycles. In contrast to conventional methods for thioether synthesis, no malodorous sulfur compounds such as thioacetic acid or thiols are required.

Covalent binding of organophosphorothioates to albumin: a new perspective for OP-pesticide biomonitoring?

We here report on the covalent binding of various organophosphorothioate (OPT) pesticides to albumin at in vitro exposure levels that did not give rise to butyrylcholinesterase inhibition. Adduct formation occurred at the Tyr-411 residue of albumin, as was firmly corroborated by LC-tandem MS analysis of a pepsin digest of OPT-modified albumin. It cannot be excluded that other (tyrosine) residues become modified as well. A convenient method for mass spectrometric determination of the OPT tyrosine adduct has also been developed based on the pronase digestion of albumin and subsequent LC-tandem MS analysis of the digest. The resulting tyrosine phosphorothioate ester displayed favorable chromatographic and mass spectrometric properties for sensitive analysis. In vitro exposure levels of parathion and chlorpyrifos down to 1 microM could readily be assessed. The remarkable affinity of OPTs for albumin opens the way for a more complete assessment of OP pesticide exposure.

Concerted rate-limiting proton transfer to sulfur with nucleophilic attack at phosphorus — A new proposed mechanism for hydrolytic decomposition of the P=S pesticide, Diazinon, in moderately acidic sulfuric acid media

We report herein the first kinetic study of a P=S containing organophosphorus pesticide, Diazinon (1), in the moderately concentrated acid region. Product analyses (31P NMR) show that reaction occurs only at the P centre. The rate-acidity profile (kobs vs. molarity of H2SO4) appears as a curve in which the initial slight downward trace (molarity = 1 to ca. 5) is followed by sharper upward curve (molarity ca. 5 to 14). Using treatments involving the excess acidity (X) method, the A-1 and A-2 mechanistic possibilities were found to be inoperative over the full acidity range. A novel mechanism is proposed for the higher acidity (X ca. 2–6) region. This mechanism involves proton transfer to P=S from hydronium ion with concomitant proton transfer from water, which effectively delivers hydroxide to the P centre in a variant of the A-SE2 process. A putative A-2 mechanism in this region is supplanted by the proposed A-SE2 variant where the cyclic array results in proton transfer being efficiently coupled with nucleophilic attack involving water. This constitutes the first report of rate-limiting proton transfer at the P=S functionality in acid hydrolysis of this class of organophosphorus neutroxins. A 600 000-fold acceleration in the decomposition of Diazinon is associated with the change of medium from neutral aqueous solution to the most acidic medium studied (X ca. 6). Key words: phosphorothioate ester hydrolysis, acid catalysis, rate-limiting proton transfer at P=S, excess acidity analysis, new A-SE2 variant mechanism.

Thermodynamic Origin of the Increased Rate of Hydrolysis of Phosphate and Phosphorothioate Esters in DMSO/Water Mixtures

The hydrolysis rates of the dianions of phosphate and phosphorothioate esters are substantially accelerated by the addition of polar aprotic solvents such as DMSO and acetonitrile. The activation barrier DeltaG is smaller due to a lower enthalpy of activation. The enthalpy of transfer of p-nitrophenyl phosphate (pNPP) and p-nitrophenyl phosphorothioate (pNPPT), from water to 0.6 (mol) aq DMSO (60 mol % water in DMSO) were measured calorimetrically. The enthalpies of activation for the hydrolysis reactions in the two solvents permitted the calculation of the enthalpy of transfer of the transition states. This transfer is thermodynamically favorable for both the reactants and the transition states but is more favorable for the transition states. In the case of pNPP, the enthalpy of transfer of the reactant is -23.9 kcal/mol, compared to -28.3 for the transition state. The difference is greater for pNPPT, where the enthalpy of transfer of the reactant is -23.2 kcal/mol and that for the transition state is -35.3. The results show that the reduced enthalpies of activation in both hydrolysis reactions arise not from a destabilization of the reactants in the mixed solvent, but from the fact that the enthalpy of transfer of the transition states to the mixed solvent is significantly more negative than the enthalpy of transfer of the reactants.

The Thermodynamics of Phosphate versus Phosphorothioate Ester Hydrolysis.

Phosphorothioate esters are phosphate esters in which one of the nonbridging oxygen atoms has been replaced by sulfur. In the comparative hydrolysis reactions of phosphorothioate and phosphate esters, the sulfur substitution accelerates the rates of the monoesters while slowing the rates of diesters and of triesters. Previously measured enthalpies and entropies of activation for the hydrolysis reactions of the monoesters, p-nitrophenyl phosphate and p-nitrophenyl phosphorothioate, were compared to the activation parameters measured herein for the diesters, ethyl p-nitrophenyl phosphate and ethyl p-nitrophenyl phosphorothioate, and the triesters, diethyl p-nitrophenyl phosphate and diethyl p-nitrophenyl phosphorothioate. A consistent trend of a greater DeltaH++ for the phosphorothioate analogue was found in all three classes of ester. In the monoester case, a more positive DeltaS++ arising from a mechanistic difference (D(N) + A(N) for the phosphorothioate versus A(N)D(N) for the phosphate) compensates, resulting in a lower DeltaG++ for the phosphorothioate monoester. Spectroscopic investigations indicate there is no significant difference in bond order to the leaving group in phosphates, as compared to their phosphorothioate analogues, ruling this out as a contribution to the consistently higher enthalpies of activation.

The Thermodynamics of Phosphate versus Phosphorothioate Ester Hydrolysis

Phosphorothioate esters are phosphate esters in which one of the nonbridging oxygen atoms has been replaced by sulfur. In the comparative hydrolysis reactions of phosphorothioate and phosphate esters, the sulfur substitution accelerates the rates of the monoesters while slowing the rates of diesters and of triesters. Previously measured enthalpies and entropies of activation for the hydrolysis reactions of the monoesters, p-nitrophenyl phosphate and p-nitrophenyl phosphorothioate, were compared to the activation parameters measured herein for the diesters, ethyl p-nitrophenyl phosphate and ethyl p-nitrophenyl phosphorothioate, and the triesters, diethyl p-nitrophenyl phosphate and diethyl p-nitrophenyl phosphorothioate. A consistent trend of a greater DeltaH++ for the phosphorothioate analogue was found in all three classes of ester. In the monoester case, a more positive DeltaS++ arising from a mechanistic difference (D(N) + A(N) for the phosphorothioate versus A(N)D(N) for the phosphate) compensates, resulting in a lower DeltaG++ for the phosphorothioate monoester. Spectroscopic investigations indicate there is no significant difference in bond order to the leaving group in phosphates, as compared to their phosphorothioate analogues, ruling this out as a contribution to the consistently higher enthalpies of activation.

13C-31P Couplings in the Study of Conformational Properties of Some Diastereomeric Nucleoside-3′-Thiophosphate Derivatives

Synthesis and stereochemical characterization of enantiomerically pure nucleoside-3′-phosphorothioate esters and salts are reported. Vicinal carbon–phosphorus couplings reflect different predominance of the ϵ conformation in the isomeric (Rp and Sp) esters, while for the salts the ϵt conformation prevails in both stereoisomers. The influence of solvent and temperature on the conformational preferences is also described.

Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer?

The effect of electrostatic interactions on the transition-state character for enzymatic phosphoryl transfer has been a subject of much debate. In this work, we investigate the transition state for alkaline phosphatase (AP) using linear free-energy relationships (LFERs). We determined k(cat)/K(M) for a series of aryl sulfate ester monoanions to obtain the Brønsted coefficient, beta(lg), and compared the value to that obtained previously for a series of aryl phosphorothioate ester dianion substrates. Despite the difference in substrate charge, the observed Brønsted coefficients for AP-catalyzed aryl sulfate and aryl phosphorothioate hydrolysis (-0.76 +/- 0.14 and -0.77 +/- 0.10, respectively) are strikingly similar, with steric effects being responsible for the uncertainties in these values. Aryl sulfates and aryl phosphates react via similar loose transition states in solution. These observations suggest an apparent equivalency of the transition states for phosphorothioate and sulfate hydrolysis reactions at the AP active site and, thus, negligible effects of active site electrostatic interactions on charge distribution in the transition state.

Thermolytic properties of 3-(2-pyridyl)-1-propyl and 2-[N-methyl-N-(2-pyridyl)]aminoethyl phosphate/thiophosphate protecting groups in solid-phase synthesis of oligodeoxyribonucleotides.

Thermolytic groups may serve as alternatives to the conventional 2-cyanoethyl group for phosphate/thiophosphate protection in solid-phase oligonucleotide synthesis to prevent DNA alkylation by acrylonitrile generated under the basic conditions used for oligonucleotide deprotection. Additionally, thermolytic groups are attractive in the context of engineering a "heat-driven" process for the synthesis of oligonucleotides on diagnostic microarrays. In these regards, the potential application of pyridine derivatives as thermolytic phosphate/thiophosphate protecting groups has been investigated. Specifically, 2-pyridinepropanol and 2-[N-methyl-N-(2-pyridyl)]aminoethanol were incorporated into deoxyribonucleoside phosphoramidites 7a-d and 9, which were found as efficient as 2-cyanoethyl deoxyribonucleoside phosphoramidites in solid-phase oligonucleotide synthesis. Whereas the removal of 3-(2-pyridyl)-1-propyl phosphate/thiophosphate protecting groups from oligonucleotides is effected within 30 min upon heating at 55 degrees C in concentrated NH4OH or in an aqueous buffer at pH 7.0, cleavage of 2-[N-methyl-N-(2-pyridyl)]aminoethyl groups occurs spontaneously when their phosphate or phosphorothioate esters are formed during oligonucleotide synthesis. The deprotection of these groups follows a cyclodeesterification process generating the bicyclic salts 13 and 14 as side products. These salts do not alkylate or otherwise modify any DNA nucleobases and do not desulfurize a phosphorothioate diester model under conditions mimicking large-scale oligonucleotide deprotection.

Mechanisms of abiotic degradation and soil–water interactions of pesticides and other hydrophobic organic compounds. Part 3. Nucleophilic displacement at the phosphorus centre of the pesticide fenitrothion [O,O-dimethyl O-(3-methyl-4-nitrophenyl) phosphorothioate] by oxygen nucleophiles in aqueous solution: α-effect and mechanism†

Rate constants for the reaction of the title compound, 1, with a number of oxygen nucleophiles, including structurally related phenoxides and oxygen-based α-nucleophiles, have been measured in aqueous solution at 25 °C. A significant α-effect was observed, confirming participation of the nucleophile in the rate-limiting step of the reaction as well as indicating different transition states (TS) for the reaction of α-nucleophiles compared to normal ones. The Bronsted-type correlation of log kNuvs. pKa of nucleophiles shows a linear plot for the series of structurally related phenoxides in the pKa range 5.4–10.0, straddling the pKa of the leaving group (3-methyl-4-nitrophenoxide, pKa 7.20), but is curved in the highly basic region corresponding to CF3CH2O− and HO− as nucleophiles. The slope of the linear portion of the plot (βNu) is 0.49 (R2 0.988). The linearity of the plot for the series of structurally related phenoxides is consistent with a concerted mechanism for nucleophilic attack at the P center of the substrate. A value of βlg −0.39 (R2 0.973) is measured for the reaction of PhO− with substituted phenyl dimethyl phosphorothioate esters. Combining the values of βNu and βlg gives βeq = 0.88; these parameters when considered together with the effective charge distribution in the TS, demonstrate that the TS for the symmetrical reaction (in which nucleophile = leaving group = 3-methyl-4-nitrophenoxide) has no significant phosphorylium ion character. The Leffler index points to a concerted reaction in which bond formation is slightly ahead of bond rupture in the TS. Data from the present study are compared with literature data for (thio)phosphoryl group transfer. We propose that, unless special structural and/or environmental features prevail, (thio)phosphoryl transfers between phenoxides are more likely to occur via a concerted mechanism. It is shown that the TS for the concerted transfer of (EtO)2PO between two PhO− moieties shows more pentacoordinate intermediate character than the symmetrical reaction of 1 due to differences in (i) basicity of PhO−versus 3-CH3,4-NO2PhO−, and (ii) abilities of O and S in the PX (X = O, S) moiety to stabilize the incoming negative charge.

Rhenium catalyzed sulfurization of phosphorus(III) compounds with thiiranes: New reagents for phosphorothioate ester synthesis

A new method for the mild sulfurization of phosphorus(III) compounds with thiiranes catalyzed by ReOCl 3(PPh 3) 2 ( I) or ReOCl 3(SMe 2)OPPh 3) ( II) is reported. The novel catalytic sulfur transfer reactions are rapid and occur efficiently under ambient conditions in organic solvents. This methodology enabled propylene sulfide to be used as a sulfurizing agent for the synthesis of a protected nucleotide phosphorothioate ester.

New procedure for the use of high-performance liquid chromatography–electrospray ionization mass spectrometry for the analysis of nucleotides and oligonucleotides

A method is described which allows the combination of high-performance liquid chromatography (HPLC) and electrospray ionization mass spectrometry for the analysis of nucleotides and oligonucleotides without compromising the performance of either technique. The essential feature of the method uses 1,1,1,3,3,3-hexafluoro-2-isopropanol as an additive to the HPLC mobile phase. This novel additive results in both good HPLC separation and efficient negative ion mode electrospray ionization. The method is demonstrated for oligonucleotides samples such as synthetic homopolymers of thymidine (PolyT), of fragments based on the pBR322 plasmid sequence and analysis of phosphorothioate ester antisense oligonucleotides. The differentiation of phosphorylation states of natural nucleotides as well as nucleotide analogues, such as ziduvodine (AZT), is also demonstrated.