Kinetic Solvent Deuterium Isotope Effects Research Articles

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination.

Kinetic studies on the intramolecular hydroamination of protected variants of 2,2-diphenylpent-4-en-1-amine were carried out under a variety of conditions with cationic gold catalysts supported by phosphine ligands. The impact of ligand on gold, protecting group on nitrogen, and solvent and additive on reaction rates was determined. The most effective reactions utilized more Lewis basic ureas, and more electron-withdrawing phosphines. A DCM/alcohol cooperative effect was quantified, and a continuum of isotope effects was measured with low KIE's in the absence of deuterated alcoholic solvent, increasing to large solvent KIE's when comparing reactions in pure MeOH to those in pure MeOH-d4. The effects are interpreted both within the context of a classic gold π-activation/protodeauration mechanism and a general acid-catalyzed mechanism without intermediate gold alkyls.

Substrate Electronics Dominate the Rate of Reductive Dehalogenation Promoted by the Flavin-Dependent Iodotyrosine Deiodinase.

Iodotyrosine deiodinase (IYD) is unusual in its reliance on flavin to promote reductive dehalogenation of halotyrosines under aerobic conditions. Applications of this activity can be envisioned for bioremediation, but expansion of its specificity requires an understanding of the mechanistic steps that limit the rate of turnover. Key processes capable of controlling steady-state turnover have now been evaluated and described in this study. While proton transfer is necessary for converting the electron-rich substrate into an electrophilic intermediate suitable for reduction, kinetic solvent deuterium isotope effects suggest that this process does not contribute to the overall efficiency of catalysis under neutral conditions. Similarly, reconstituting IYD with flavin analogues demonstrates that a change in reduction potential by as much as 132 mV affects kcat by less than 3-fold. Furthermore, kcat/Km does not correlate with reduction potential and indicates that electron transfer is also not rate determining. Catalytic efficiency is most sensitive to the electronic nature of its substrates. Electron-donating substituents on the ortho position of iodotyrosine stimulate catalysis and conversely electron-withdrawing substituents suppress catalysis. Effects on kcat and kcat/Km range from 22- to 100-fold and fit a linear free-energy correlation with a ρ ranging from -2.1 to -2.8 for human and bacterial IYD. These values are consistent with a rate-determining process of stabilizing the electrophilic and nonaromatic intermediate poised for reduction. Future engineering can now focus on efforts to stabilize this electrophilic intermediate over a broad series of phenolic substrates that are targeted for removal from our environment.

The Mechanism of Cleavage and Isomerisation of RNA Promoted by an Efficient Dinuclear Zn2+ Complex

The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.

Kinetic Isotope Effects for RNA Cleavage by 2′-O- Transphosphorylation: Nucleophilic Activation by Specific Base

To better understand the interactions between catalysts and transition states during RNA strand cleavage, primary (18)O kinetic isotope effects (KIEs) and solvent D(2)O isotope effects were measured to probe the mechanism of base-catalyzed 2'-O-transphosphorylation of the RNA dinucleotide 5'-UpG-3'. The observed (18)O KIEs for the nucleophilic 2'-O and in the 5'-O leaving group at pH 14 are both large relative to reactions of phosphodiesters with good leaving groups, indicating that the reaction catalyzed by hydroxide has a transition state (TS) with advanced phosphorus-oxygen bond fission to the leaving group ((18)k(LG) = 1.034 +/- 0.004) and phosphorus-nucleophile bond formation ((18)k(NUC) = 0.984 +/- 0.004). A breakpoint in the pH dependence of the 2'-O-transphosphorylation rate to a pH independent phase above pH 13 has been attributed to the pK(a) of the 2'-OH nucleophile. A smaller nucleophile KIE is observed at pH 12 ((18)k(NUC) = 0.995 +/- 0.004) that is interpreted as the combined effect of the equilibrium isotope effect (ca. 1.02) on deprotonation of the 2'-hydroxyl nucleophile and the intrinsic KIE on the nucleophilic addition step (ca. 0.981). An alternative mechanism in which the hydroxide ion acts as a general base is considered unlikely given the lack of a solvent deuterium isotope effect above the breakpoint in the pH versus rate profile. These results represent the first direct analysis of the transition state for RNA strand cleavage. The primary (18)O KIE results and the lack of a kinetic solvent deuterium isotope effect together provide strong evidence for a late transition state and 2'-O nucleophile activation by specific base catalysis.

Transesterification of an RNA model in buffer solutions in H2O and D2O

AbstractTransesterification of a phosphodiester bond of RNA models has been studied in various buffer solutions, under neutral and slightly alkaline conditions in H2O and D2O. The results show that imidazole is the only buffer system where a clear buffer catalysis on the cleavage of a phosphodiester bond is observed. The rate enhancement in sulphonic acid buffers is smaller, and a sulphonate base, particularly, is inactive as a catalyst. The rate‐enhancing effect of imidazole is, however, catalytic, and the catalytic inactivity of sulphonate buffers can be attributed to their structure and/or charge. The catalysis by imidazole is a complex system which, in addition to first‐order reactions, involves a process that shows a second‐order dependence in imidazole concentration. The latter reaction becomes significant in acidic imidazole buffers (pH < pKa), as the buffer concentration increases. The kinetic solvent deuterium isotope effect kH/kD, referring to first‐order catalysis by imidazole base, is 2.3 ± 0.3. That referring to second‐order catalysis is most probably much larger, but an accurate value could not be obtained. Copyright © 2007 John Wiley & Sons, Ltd.

Kinetic solvent deuterium isotope effect in transesterification of RNA models

Abstract2‐Methylbenzimidazole ribonucleoside arylphosphates (1a,b) and alkylphosphates (2a,b) were synthesized as RNA model compounds containing a minimised number of exchangeable protons. Intramolecular transesterification of these substrates was studied in H2O and D2O solutions over a wide pL range and apparent kinetic solvent deuterium isotope effects of the alkaline cleavage of both substrates and of the cleavage and isomerisation of 2a under neutral and acidic conditions were determined. The observed k/k of 4.9 obtained for the alkaline cleavage of the arylphosphate 1b can be primarily attributed to the ΔpK of the attacking nucleophile. The alkyl leaving group in 2a brings about an additional 1.5‐fold isotope effect (k/k of 7.1 observed), which, considering the pL–dependence of the reaction, can not be explained by a process involving a proton transfer. Differences in solvation of the transition state are tentatively suggested as a source of the difference. In contrast to alkaline cleavage, under neutral and acidic conditions the cleavage and isomerisation of 2a showed no apparent solvent isotope effect. Several examples found in the literature show that intramolecular proton transfer from phosphate to the leaving group in pre‐equilibria may not necessarily result in an observable solvent isotope effect. This may also explain the results obtained in the present work, since intramolecular proton transfer processes take place in transesterification reactions of 2a under neutral and acidic conditions. Relevance of the results obtained in the base catalysed cleavage to hammerhead ribozyme reaction is briefly discussed. Copyright © 2004 John Wiley & Sons, Ltd.

Multiple isotope effects as a probe of proton and hydride transfer in the 6-phosphogluconate dehydrogenase reaction.

Primary solvent deuterium, primary substrate deuterium, multiple solvent deuterium/substrate deuterium, and multiple solvent deuterium/13C isotope effects on V/K6PG have been measured for the Candida utilis and sheep liver 6-phosphogluconate dehydrogenases (6PGDH). Proton inventory data suggest the presence of a significant medium effect in a step preceding hydride transfer and the presence of a kinetic solvent deuterium isotope effect on hydride transfer. Multiple isotope effect data confirm the presence of multiple solvent deuterium sensitive steps, likely including a conformational change preceding hydride transfer, hydride transfer, and decarboxylation.

Mechanism of Hydrolysis of Isopropenyl Glucopyranosides. Spectroscopic Evidence Concerning the Greater Reactivity of the alpha Anomer.

The mechanism of hydrolysis of isopropenyl alpha- and beta-glucopyranosides (1 and 2, respectively) has been studied by temperature-dependent reaction kinetics, stereochemical analysis of products by (1)H NMR, solvent (18)O- and (2)H-labeling experiments, kinetic solvent deuterium isotope effects, and alpha-values for general acid catalysis. Compounds 1 and 2 are the first vinyl acetals to be shown to undergo hydrolysis exclusively by cleavage of the vinyl ether and not the acetal C-O bond. While both glucopyranosides undergo irreversible, rate-limiting C-protonation, 1 hydrolyzes approximately four times faster than 2 and has an enthalpy of activation that is 5.8 kcal mol(-)(1) lower than that of 2, suggesting that 1 is kinetically more basic than 2. Spectroscopic evidence indicates that conjugation of the glycosidic oxygen with the alkenyl double bond is greater in 1 than in 2, probably because of steric or conformational constraints.

Intramolecular assistance of cis/trans isomerization of the histidine-proline moiety.

Peptidyl-prolyl cis/trans isomerization is a slow conformational interconversion in the polypeptide backbone that is frequently rate-limiting in refolding of proteins and is thought to play a role in cellular restructuring of proteins. In order to probe the influence of positively charged amino acids located in sequence segments adjacent to proline, the rotational barriers of Arg-Pro- and His-Pro-containing peptides were determined by isomer-specific proteolysis and dynamic NMR spectroscopy for Suc-Ala-His-Pro-Phe-NH-Np, Ac-Ala-Arg-Pro-Ala-Lys-NH2, Ac-Ala-His-Pro-Ala-Lys-NH2, angiotensin III, thyrotropin-releasing hormone (TRH), and [His(3-Me)2]TRH in aqueous solution. In contrast to the guanidinium group of arginine, the protonated side chain of histidine preceding proline led to an acceleration of the prolyl isomerization up to 10-fold relative to the unprotonated state. Both arginine and histidine residues succeeding proline in an amino acid sequence proved to be ineffective. Under basic and acidic conditions the kinetic solvent deuterium isotope effects Kc-->tH20/Kc-->tD20 for angiotensin III were 1.0 +/- 0.1 and 2.0 +/- 0.1, respectively. The results are interpreted in terms of intramolecular general acid catalysis of prolyl bond rotation by the imidazolium group that is without precedent in intermolecular catalysis.

Kinetic solvent deuterium isotope effect on the oxygenation of N,N-dimethylaniline with the pig liver microsomal fad-containing monooxygenase

Both the maximum velocity and the Michaelis constant of the oxygenation of N,N-dimethylaniline with the pig liver microsomal FAD-containing monooxygenase (EC 1.14.13.8) to N,N-dimethylaniline N-oxide appear 1.7 folds greater in aqueous buffer solution of pH 7.4 than those in deuterium oxide buffer solution of pD 7.4.

Mechanism of Decarboxylation of p-Aminosalicylic Acid

The rate of decarboxylation of p-aminosalicylic acid (1) in aqueous solutions was studied at 25°C (μ=0.5) as a function of pH and buffer concentration. A pH-rate profile was generated by using the rate constants extrapolated to zero buffer concentration. The profile was bell-shaped, with the maximum rate of decarboxylation near the isoelectric pH. The rate constants obtained in buffered solutions indicated general acid catalysis. Bronsted behavior appeared to be adhered to. The two ionization constants of 1 were determined spectrophotometrically at 25°C and at an ionic strength of 0.5. An HPLC method was used to characterize the degradation products of the reaction. Kinetic solvent deuterium isotope effects were studied to further confirm the mechanism of decarboxylation. Below pH 7.0, the mechanism of 1 decarboxylation is the rate controlling proton attack on the carbon-alpha to the carboxylic acid group of 1 anion and the ampholyte, followed by the rapid decarboxylation of the formed intermediate.

Relation of the transition-state structure for the water-catalyzed hydrolysis of 1-acetylimidazolium ion to solvent hydrophobicity: proton inventories in water-acetonitrile mixtures

The transition-state structure for the water-catalyzed hydrolysis of 1-acetylimidazolium ion has been probed in solvent systems which may mimic the hydrophobic nature of an enzyme's active site. The kinetic solvent deuterium isotope effects, k/sub H/sub 2/O//k/sub D/sub 2/O/, are 2.58, 2.49, and 2.10 in water, in 0.5 vol fraction of acetonitrile in water and 0.9 vol fraction of acetonitrile in water, respectively. The proton inventory investigations suggest all three solvent systems entertain a transition-state structure composed of a catalytic proton bridge between the reorganizing substrate and a water molecule acting as a general-base catalyst. A compression of the transition-state structure in the solvent system containing the largest amount of acetonitrile is suggested to be responsible for the diminished kinetic solvent deuterium isotope effect. The reaction has been shown to be second order with respect to water.

Kinetic deuterium solvent isotope effects on the general acid-catalysed dissociation of metal cryptates

The dissociation of metal ions from cryptate complexes is subject to general acid catalysis in a number of cases. The dissociation of Ca(2,2,2)2+ has been studied in the presence of HCl and several carboxylic acids as catalysts, and kinetic solvent isotope effects measured for the HCl- and CH3CO2H-catalysed dissociation. The observation of general acid catalysis, combined with relatively large isotope effects (2.4 and 2.7, respectively), are consistent with a rate-determining proton transfer in the dissociation reaction. The H+-catalysed dissociation of Ag(2,2,2)+ shows a lower, but still significant, isotope effect (1.9) and most likely also involves a rate-determining proton transfer step. Li(2,1,1)+ shows somewhat different behaviour in that the apparent catalytic constant for acid catalysed dissociation decreases with increasing buffer concentration. The results are shown to be in quantitative accord with a reaction scheme involving protonation of Li(2,1,1)+ followed by competitive dissociation of Li+ from Li(2,1,1)H2+ and deprotonation by A– of Li(2,1,1)H2+ to give (2,1,1)H+ or regenerate Li(2,1,1)+, respectively. Kinetic solvent deuterium isotope effects for the protonation and deprotonation–dissociation steps are close to unity.

Oxygen exchange between oxo-anions and water in basic media: molybdate(2–) and tungstate(2–)

The 18O-exchange reaction between [MoO4]2– and [WO4]2– respectively and water has been investigated in alkaline solutions at constant total concentration of ionic equivalents J= 1.0 mol dm–3(Na[ClO4]). Over the range 3 × 10– 3⩽[OH–]⩽ 1.5 × 10–l mol dm–3 at 5 °C ([MoO4]2–) and 2 × 10–3⩽[OH–]⩽7.5 × 10–3 mol dm–3 at 1 °C ([WO4]2–) the exchange occurs by spontaneous and hydroxide-ion catalyzed paths (X = MO or W) according to the rate equation (i). The rate constants extrapolated at 25 °C are k0= 0.33 s–l and k1= 2.22 dm3R/[XO42–]T=k0+k1[OH–](i) mol–1 s–1 for [MoO4]2– and k0= 0.44 s–l and k1= 273 dm3 mol–l s–l for [WO4]2–. The following activation parameters were obtained: ΔHo:‡= 62.8 ± 2.5 kJ mol–1ΔS0‡=–43.5 ± 9.0 J K–l mol–1, ΔH1‡= 70.3 ± 5.0 kJ mol–l, and ΔS1‡=–2.5 ± 13.0 J K–l mol–l([MoO4]2–); and ΔH0‡= 29.25 ± 3.22 kJ mol–l, ΔSo†=–153.55 ± 11.30 J K–l mol–1, ΔH1‡= 71.1 ± 8.0 kJ mol–l. ΔS1‡= 40.2 ± 28.9 J K–l mol–l([WO4]2–). The values for the kinetic solvent deuterium-isotope effects k0H/k0D= 3.6 and k1H/k1D= 2.3 (5 °C, [MoO4]2–) and k0H/k0d= 3.0 and k1H/k1D= 1.7 (1 °C, [WO4]2–), indicate proton transfer in the rate-determining step. The mechanisms of the spontaneous paths are described as solvent-assisted oxygen dissociations with association between H2O and [XO4]2– playing an important role, whereas the [OH]–- dependent paths are tentatively viewed associative reaction between [OH]– and [XO4]2–.

KINETICS, MEDIUM, AND DEUTERIUM ISOTOPE EFFECTS IN THE ALKALINE DECOMPOSITION OF QUATERNARY PHOSPHONIUM SALTS III1Tetraphenylphosphonium Chloride in Dimethylsulphoxide-Water Mixtures

Abstract The reaction between tetraphenylphosphonium chloride and hydroxide or deuteroxide anions was studied kinetically in a series of dimethylsulphoxide-water mixtures at several temperatures. The rate is first-order in the phosphonium cation and second-order in the hydroxide or deuteroxide anions. The reaction shows a dramatic increase in rate, up to about 1010 times, as the DMSO content is increased. The rate enhancement is attributed to a considerable drop in activation energy affected not only through an increased desolvation of reactant anions, but also through an increase in solvation of the transition state, brought about by gradual addition of DMSO. The kinetic solvent deuterium isotope effect in 60% DMSO-40% D2O is strongly dependent on temperature. The rate constant in the latter solvent mixture is represented by k i = 11.9 e −12700/RT l 2 mole−2 sec−1 as compared to k i = 19.0 e −22500/RT l 2 mole−2 sec−1 in the corresponding 60% DMSO-H2O mixture. The thermodynamic parameters of activation s...

Kinetic solvent deuterium isotope effects on the micellar-catalyzed hydrolysis of trisubstituted phosphate esters

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetic solvent deuterium isotope effects on the micellar-catalyzed hydrolysis of trisubstituted phosphate estersClifford A. Bunton and Simon DiazCite this: J. Org. Chem. 1976, 41, 1, 33–36Publication Date (Print):January 1, 1976Publication History Published online1 May 2002Published inissue 1 January 1976https://doi.org/10.1021/jo00863a007RIGHTS & PERMISSIONSArticle Views112Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (473 KB) Get e-Alerts Get e-Alerts

Oxygen exchange between iodate and water: catalysis by hydrogen and hydroxide lons

The 18O-exchange reaction between iodate ions and water has been investigated using a rapid chemical-quenching technique. Over the range 2.1 < pH < 12.5 the exchange occurs by hydrogen- and hydroxide-ion catalysed paths according to the rate law (i). At 5 ° C and I= 1.0 mol dm–3(Li[ClO4]) the rate constants are k0 < 0.01 s–1, R/[IO3–]=k0+k1[H+]+k2[H+]2+k3[OH–](i)k1=(3.20 ± 0.11)× 103 dm3 mol–1 s–1, k2=(1.38 ± 0.24)× 105 dm6 mol–2 s–1 and k3=(2.49 ± 0.16)× 102 dm3 mol–1 s–1 respectively. Activation parameters from data at 5–25 °C are ΔH1‡= 61.5 ± 3.8 kJ mol–1,ΔS1‡= 43.1 ± 13.0 J K–1 mol–1, ΔH3‡= 47.4 ± 1.7 kJ mol–1, and ΔS3‡=–28.3 ± 5.9 J K–1 mol–1. The following values for the kinetic solvent deuterium-isotope effect were obtained (5 °C) : klH/klD= 2.1, k2H/k2D= 0.49, and k3H/k3D= 1.7. The normal isotope effect suggests proton transfer as the rate-determining steps corresponding to k1 and k3, whereas the inverse isotope effect on k2 can be explained by a rapid acid–base pre-equilibrium. These results provide further evidence for associative substitution mechanisms with iodine(V).

Zur theorie der α-ketosa¨uren: Mechanismus der enolisierung einiger brenztraubensa¨ureamide

The mechanism of enolisation of pyruvamide is discussed by the influence of substituents on the kinetic CH 3-acidity, by general base-catalysis of enolisation, by the enthalpy and entropy of activation and primary kinetic and kinetic solvent deuterium isotope effects respectively. A Bro¨nsted coefficient β = 0·71 has been obtained in the general base catalysis of pyruvdiethylamide enolisation. The effect of car☐ylsubstituents on the kinetic CH 3-acidity is produced not only by an inductive mechanism. The importance of solvent structure is demonstrated by a strong negative entropy of activation for the H 2O-catalysed reaction. In the H 2O-catalysed enolisation of pyruvdiethylamide a large kinetic deuterium solvent isotope effect k o H 2O /k o D 2O = 2·39) was obtained at 25°C. In contrast, when hydroxid is the catalyst, the primary kinetic deuterium isotope effect is unusually low (k H/k D = 3·5). Thus, in comparison to other keto compounds, a different mechanism of enolisation for the pyruvic acid derivatives must be postulated. Some aspects of this mechanism are discussed in the paper.

Some properties of reactions catalyzed by pig brain NAD glycohydrolase

Some aspects of pig brain NADase-catalyzed hydrolysis of NAD have been examined employing a partially purified enzyme and a titrimetric assay for enzyme activity. In accord with previous observations, this enzyme was observed to be catalytically active toward a number of NAD analogs and toward both NMN and nicotinamide nucleoside. It is subject to competitive inhibition by nicotinamide. Employing the natural substrate, the reaction velocity is observed to be rather insensitive to changes in pH, diminishing some fourfold as the pH is lowered from 9 to 4. The kinetic solvent deuterium isotope effect, V H2 o V D2 o , increases from 1.5 at pH 8.7 to 2.5 at pH 7.7. The pig brain NADase-catalyzed reaction is subject to marked inhibition by dithiothreitol resulting from rapid inactivation of the enzyme. Treatment of the inactivated enzyme with thiols has not resulted in reactivation of the enzyme.