Carbanion-like Transition State Research Articles

Role of a Guanidinium Cation–Phosphodianion Pair in Stabilizing the Vinyl Carbanion Intermediate of Orotidine 5′-Phosphate Decarboxylase-Catalyzed Reactions

The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate (OMP) decarboxylase (OMPDC) from Saccharomyces cerevisiae catalyzed reactions of OMP and 5-fluoroorotidine 5'-monophosphate (FOMP), respectively, a 7.2 kcal/mol stabilization of the vinyl carbanion-like transition state for enzyme-catalyzed exchange of the C-6 proton of 5-fluorouridine 5'-monophosphate (FUMP), but no stabilization of the transition states for enzyme-catalyzed decarboxylation of truncated substrates 1-(β-d-erythrofuranosyl)orotic acid and 1-(β-d-erythrofuranosyl) 5-fluorouracil. These observations show that the transition state stabilization results from formation of a protein cation-phosphodianion pair, and that there is no detectable stabilization from an interaction between the side chain and the pyrimidine ring of substrate. The 5.6 kcal/mol side chain interaction with the transition state for the decarboxylation reaction is 50% of the total 11.2 kcal/mol transition state stabilization by interactions with the phosphodianion of OMP, whereas the 7.2 kcal/mol side chain interaction with the transition state for the deuterium exchange reaction is a larger 78% of the total 9.2 kcal/mol transition state stabilization by interactions with the phosphodianion of FUMP. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex, whereas the effect on the enzyme-catalyzed decarboxylation of OMP is expressed predominantly as a change in the Michaelis constant Km. These results are rationalized by a mechanism in which the binding of OMP, compared with that for FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation.

Catalysis by Orotidine 5′-Monophosphate Decarboxylase: Effect of 5-Fluoro and 4′-Substituents on the Decarboxylation of Two-Part Substrates

The syntheses of two novel truncated analogs of the natural substrate orotidine 5'-monophosphate (OMP) for orotidine 5'-monophosphate decarboxylase (OMPDC) with enhanced reactivity toward decarboxylation are reported: 1-(β-d-erythrofuranosyl)-5-fluoroorotic acid (FEO) and 5'-deoxy-5-fluoroorotidine (5'-dFO). A comparison of the second-order rate constants for the OMPDC-catalyzed decarboxylations of FEO (10 M⁻¹ s⁻¹) and 1-(β-d-erythrofuranosyl)orotic acid (EO, 0.026 M⁻¹ s⁻¹) shows that the vinyl carbanion-like transition state is stabilized by 3.5 kcal/mol by interactions with the 5-F substituent of FEO. The OMPDC-catalyzed decarboxylations of FEO and EO are both activated by exogenous phosphite dianion (HPO₃²⁻), but the 5-F substituent results in only a 0.8 kcal stabilization of the transition state for the phosphite-activated reaction of FEO. This provides strong evidence that the phosphite-activated OMPDC-catalyzed reaction of FEO is not limited by the chemical step of decarboxylation of the enzyme-bound substrate. Evidence is presented that there is a change in the rate-limiting step from the chemical step of decarboxylation for the phosphite-activated reaction of EO, to closure of the phosphate gripper loop and an enzyme conformational change at the ternary E•FEO•HPO₃²⁻ complex for the reaction of FEO. The 4'-CH₃ and 4'-CH₂OH groups of 5'-dFO and orotidine, respectively, result in identical destabilizations of the transition state for the unactivated decarboxylation of 2.9 kcal/mol. By contrast, the 4'-CH₃ group of 5'-dFO and the 4'-CH₂OH group of orotidine result in very different 4.7 and 8.3 kcal/mol destabilizations of the transition state for the phosphite-activated decarboxylation. Here, the destabilizing effect of the 4'-CH₃ substituent at 5'-dFO is masked by the rate-limiting conformational change that depresses the third-order rate constant for the phosphite-activated reaction of the parent substrate FEO.

OMP Decarboxylase: Phosphodianion Binding Energy Is Used To Stabilize a Vinyl Carbanion Intermediate

Orotidine 5'-monophosphate decarboxylase (OMPDC) catalyzes the exchange for deuterium from solvent D(2)O of the C-6 proton of 1-(β-d-erythrofuranosyl)-5-fluorouracil (FEU), a phosphodianion truncated product analog. The deuterium exchange reaction of FEU is accelerated 1.8 × 10(4)-fold by 1 M phosphite dianion (HPO(3)(2-)). This corresponds to a 5.8 kcal/mol stabilization of the vinyl carbanion-like transition state, which is similar to the 7.8 kcal/mol stabilization of the transition state for OMPDC-catalyzed decarboxylation of a truncated substrate analog by bound HPO(3)(2-). These results show that the intrinsic binding energy of phosphite dianion is used in the stabilization of the vinyl carbanion-like transition state common to the decarboxylation and deuterium exchange reactions.

Formation and Stability of a Vinyl Carbanion at the Active Site of Orotidine 5‘-Monophosphate Decarboxylase: pKa of the C-6 Proton of Enzyme-Bound UMP

We report that orotidine 5‘-monophosphate decarboxylase (OMPDC) catalyzes exchange of the C-6 proton of uridine 5‘-monophosphate (UMP) for deuterium from solvent in D2O at 25 °C and pD 7.0−9.3. Kinetic analysis of deuterium exchange gives pKa ≤ 22 for carbon deprotonation of enzyme-bound UMP, which is at least 10 units lower than that for deprotonation of an analogue of UMP in water. The observation of enzyme-catalyzed deuterium exchange via a stabilized carbanion provides convincing evidence for the decarboxylation of orotidine 5‘-monophosphate (OMP) by OMPDC to give the same carbanion intermediate. The data show that yeast OMPDC stabilizes the bound vinyl carbanion by at least 14 kcal/mol. We conclude that OMPDC also provides substantial stabilization of the late carbanion-like transition state for the decarboxylation of OMP, and that this transition state stabilization constitutes a large fraction, but probably not all, of the enormous 1017-fold enzymatic rate acceleration.

Intermediates and Transition States in Thiamin Diphosphate-Dependent Decarboxylases. A Kinetic and NMR Study on Wild-Type Indolepyruvate Decarboxylase and Variants Using Indolepyruvate, Benzoylformate, and Pyruvate as Substrates

The thiamin diphosphate (ThDP)-dependent enzyme indolepyruvate decarboxylase (IPDC) is involved in the biosynthetic pathway of the phytohormone 3-indoleacetic acid and catalyzes the nonoxidative decarboxylation of 3-indolepyruvate to 3-indoleacetaldehyde and carbon dioxide. The steady-state distribution of covalent ThDP intermediates of IPDC reacting with 3-indolepyruvate and the alternative substrates benzoylformate and pyruvate has been analyzed by (1)H NMR spectroscopy. For the first time, we are able to isolate and directly assign covalent intermediates of ThDP with aromatic substrates. The intermediate analysis of IPDC variants is used to infer the involvement of active site side chains and functional groups of the cofactor in distinct catalytic steps during turnover of the different substrates. As a result, three residues (glutamate 468, aspartate 29, and histidine 115) positioned perpendicular to the thiazolium moiety of ThDP are involved in binding of all substrates and decarboxylation of the respective tetrahedral ThDP-substrate adducts. Most likely, interactions of these side chains with the substrate-derived carboxylate account for an optimal orientation of the substrate and/or intermediate in the course of carbon-carbon ligation and decarboxylation supporting the suggested least-motion, maximum overlap mechanism. The active site residue glutamine 383, which is located at the opposite site of the thiazolium nucleus as the "carboxylate pocket" (formed by the Glu-Asp-His triad), is central to the substrate specificity of IPDC, probably through orbital alignment. The Glu51-cofactor proton shuttle is, conjointly with the Glu-Asp-His triad, involved in multiple proton transfer steps, including ylide generation, substrate binding, and product release. Studies with para-substituted benzoylformate substrates demonstrate that the electronic properties of the substrate affect the stabilization or destabilization of the carbanion intermediate or carbanion-like transition state and in that way alter the rate dependence on decarboxylation. In conclusion, general mechanistic principles of catalysis of ThDP-dependent enzymes are discussed.

Nucleophilic Addition to CC Bonds, Part X

A mechanistic model is presented for the base-catalyzed intramolecular cyclization of polycyclic unsaturated alcohols of type A to ethers D (Scheme 1). The alkoxide anion B is formed first in a fast acid-base equilibrium. For the subsequent reaction to D, a carbanion-like transition state C is proposed. This mechanism is in full agreement with our results regarding the influence of substituents on the regioselectivity and the rate of cyclization. We studied the effect of alkyl substituents in allylic position (alkylated endocylic olefinic alcohols 1–3) and, especially, at the exocyclic double bond (12–15). The fastest cyclization (krel=1) is 12→16, which proceeds via a primary carbanion-like transition state (E: R1=R2=H). The corresponding processes 13→17 and 14→17 are characterized by a less-stable secondary carbanion-like transtition state (E: R1=Me, R2=H, or vice versa) and are slower by a factor of 104. The slowest reaction (krel ca. 10−6) is the cyclization 15→18 via a tertiary carbanion-like transition state (E: R1=R2=Me).

Kinetics and mechanism of benzoylformate decarboxylase using 13C and solvent deuterium isotope effects on benzoylformate and benzoylformate analogues.

Benzoylformate decarboxylase (benzoylformate carboxy-lyase, BFD; EC 4.1.1.7) from Pseudomonas putida is a thiamine pyrophosphate (TPP) dependent enzyme which converts benzoylformate to benzaldehyde and carbon dioxide. The kinetics and mechanism of the benzoylformate decarboxylase reaction were studied by solvent deuterium and 13C kinetic isotope effects with benzoylformate and a series of substituted benzoylformates (pCH3O, pCH3, pCl, and mF). The reaction was found to have two partially rate-determining steps: initial tetrahedral adduct formation (D2O sensitive) and decarboxylation (13C sensitive). Solvent deuterium and 13C isotope effects indicate that electron-withdrawing substituents (pCl and mF) reduce the rate dependence upon decarboxylation such that decreased 13(V/K) effects are observed. Conversely, electron-donating substituents increase the rate dependence upon decarboxylation such that a larger 13(V/K) is seen while the D2O effects on V and V/K are not dramatically different from those for benzoylformate. All of the data are consistent with substituent stabilization or destabilization of the carbanionic intermediate (or carbanion-like transition state) formed during decarboxylation. Additional information regarding the mechanism of the enzymic reaction was obtained from pH studies on the reaction of benzoylformate and the binding of competitive inhibitors. These studies suggest that two enzymic bases are required to be in the correct protonation state (one protonated and one unprotonated) for optimal binding of substrate (or inhibitors).

Electrophilicity of perfluoroisobutylene and methyl perfluoromethacrylate

1. Interaction of m- and p-fluorophenylmagnesium bromide with perfluoroisobutylene or with methyl perfluoromethacrylate gives the corresponding arylperfluoroisobutylenes and methylα-trifluoromethyl-β-fluoro-β-arylacrylates. 2. Examination of the19F NMR spectra of substituted m- and p-fluorobenzenes reveals that the unsaturated units CF=C(CF3)X and trans-CH=CHX have a greater deshielding effect on the fluorine nucleus in C6H4F when X=CF3 than when X=CO2Me. 3. Extended Huckel and CNDO/2 calculations on methyl perfluoromethacrylate and perfluoroisobutylene reveal that the negative π-electron charge on the “central” carbon atom is more efficiently delocalized by the methoxycarbonyl group than the trifluoromethyl. 4. The higher electrophilicity of methyl perfluoromethacrylate relative to perfluoroisobutylene stems from the greater ability of the alkoxycarbonyl group to stabilize the intermediate carbanion or the carbanion-like transition state in the reaction with the nucleophile.

Isomerisation of β-epoxy sulfones

The base-catalyzed isomerisation of β-epoxy sulfones to γ-hydroxy αβ-unsaturated sulfones was shown by kinetic data, isotope effect and stereochemistry to involve an intramolecular synfacial 1-3 hydrogen migration with carbanion-like transition state.

Primary isotope effects and mechanism of base initiated β-elimination reactions of di-(p-nitrophenyl)fluoroethanes

The second-order rate constants have been determined for the β-elimination reactions of 2,2-di-(p-nitrophenyl)-1,1,1-trifluoroethane, 2,2-di-(p-nitrophenyl)-1-fluoroethane, and their β-deuterated analogues with sodium methoxide in methanol. The primary isotope effects and activation parameters for these reactions are reported. It is suggested that the trifluoro-compound reacts via the pre-equilibrium carbanion mechanism (ElcB)R and that the monofluoro compound follows the E2 mechanism via a carbanion-like transition state.

The carbanion mechanism of olefin-forming elimination. Part V. Evidence from linear free energy relationships for E1cB dehydrochlorination of 1,1-diaryl-2,2,2-trichloroethanes

Rate constants for dehydrochlorination of the title compounds by NaOMe in MeOH may be fitted to the Brøonsted equation appropriate to carbanion formation from hydrocarbons in the same medium. The identity of elimination and carbanion formation rates provides further evidence for the operation of an ‘irreversible’E1cB mechanism in the dehydrochlorination. A basicity function approach leads to the same mechanistic conclusion. The high Hammett ρ values (2–3) for eliminations in OR––ROH (R = Me and But) are diagnostic of a carbanion-like transition state, and consideration of the effect of base strength on ρ leads to the conclusion that stronger bases cause the proton to be more extensively transferred at the transition state, contrary to predictions based on the Hammond postulate.