Specific Base Catalysis Research Articles

Specific base catalysis by yeast alcohol dehydrogenase I with substitutions of histidine-48 by glutamate or serine residues in the proton relay system

His-48 in yeast alcohol dehydrogenase I (His 51 in horse liver alcohol dehydrogenase) is a highly conserved residue in the active sites of many alcohol dehydrogenases. The imidazole group of His-48 may participate in base catalysis of proton transfer as it is linked by hydrogen bonds through the 2′-hydroxyl group of the nicotinamide ribose and the hydroxyl group of Thr-45 to the hydroxyl group of the alcohol bound to the catalytic zinc. In this study, His-48 was substituted with a glutamic acid residue to determine if a carboxylate could replace imidazole or to a serine residue to determine if the exposure of the 2′-hydroxyl group of the ribose to solvent would allow proton transfer to water without base catalysis. At pH 7.3, the H48E substitution increases affinity for NAD+ and NADH 17- or 2.6-fold, but decreases catalytic efficiency (V/Km) on ethanol by 70-fold and on acetaldehyde by 6-fold relative to wild-type enzyme. The H48S substitution increases affinity for coenzymes by 2-fold and decreases (V/Km) on ethanol and acetaldehyde only by ∼3-fold. The substituted enzymes show substrate deuterium isotope (H/D) effects of 3–4 for turnover number (V1) and catalytic efficiency (V1/Kb) for ethanol oxidation, indicating that hydrogen transfer is partially rate-limiting and suggesting a somewhat more random mechanism for binding of ethanol and NAD+. For reduction of acetaldehyde, the deuterium isotope effects are small, and the kinetic mechanism appears to be ordered for binding of NADH first and acetaldehyde next. The pH dependencies for H48E and H48S ADHs can be described by a mechanism with pK values of about 6–7 and 9. However, the pH dependencies for oxidation of ethanol and butanol by the H48S enzyme are also simply described by a straight line, with slopes of log V1/Kb against pH of 0.37 or 0.43, respectively. The linear dependence apparently represents catalysis by hydroxide that has a low activity coefficient due to the protein environment, or to a kinetically complex proton transfer. The effects of the substitutions of His-48 show that this residue contributes to catalysis, although many dehydrogenases also have other residues.

Base-catalyzed hydrolysis of spectinomycin in aqueous solutions: Kinetics and mechanisms

Hydrolysis plays an imperative role in the abiotic transformation process of antibiotics in aqueous solutions. However, little information is available on the hydrolysis process of spectinomycin (an aminocyclitol antibiotic). This study systematically investigated the spectinomycin hydrolysis kinetics and mechanisms under different pH via experiments and density functional theory (DFT) computation. Hydrolysis was first conducted in a pure water system under pH of 4.0–9.0 and temperature of 25 °C, 50 °C and 70 °C, respectively. Results showed that hydrolysis was highly dependent on pH and temperature. When pH > 6.0, spectinomycin hydrolysis was accelerated by the catalysis of OH−. Meanwhile, the hydrolysis rate increased with the elevation of temperature. Then, for the reference of the practical environment, the general base-catalyzed hydrolysis and mechanisms were studied under environmental pH 6.0–8.0 and 25 °C. DFT calculation demonstrated that base-catalyzed hydrolysis of spectinomycin could be more thermodynamically and kinetically favorable based on the lower Gibbs free energies of reaction and Gibbs free energies of activation. Further, instead of specific base catalysis (OH−), the general base catalysis (e.g., phosphate buffer) was also found to promote hydrolysis efficiency. The antibacterial activity and ecotoxicities of the hydrolysis product were analyzed to be lower than the precursor, thereby decreasing the environmental impact of spectinomycin.

Mechanistic Study of the Peroxyoxalate System in Completely Aqueous Carbonate Buffer.

The peroxyoxalate reaction is one of the most efficient chemiluminescence transformations, with emission quantum yields of up to 50%; additionally, it is widely utilized in analytical and bioanalytical assays. Although the real reason for its extremely high efficiency is still not yet understood, the mechanism of this transformation has been well elucidated in anhydrous medium. Contrarily, only few mechanistic studies have been performed in aqueous media, which would be of great importance for its application in biological systems. We report here our experimental results of the peroxyoxalate reaction in completely aqueous carbonate buffer, using fluorescein as chemiluminescence activator. The kinetics are very fast in the used basic conditions (pH>9); despite this, reproducible kinetic results were obtained. The reaction proceeds by specific base catalysis, with rate-limiting attack of hydrogen peroxide anion to the oxalic ester, in competition with ester hydrolysis by hydroxide ion. Emission quantum yields increase with the hydrogen peroxide concentration up to an optimal concentration of 10mmol L-1 . The infinite singlet quantum yield of (5.8±0.2)×10-7 is much lower than in anhydrous medium; however, it is similar to quantum yields measured before in partially aqueous media.

Mechanistic Studies on the Salicylate-Catalyzed Peroxyoxalate Chemiluminescence in Aqueous Medium.

The peroxyoxalate reaction is one of the most efficient chemiluminescence transformations known and the onlysystem occurring by an intermolecular chemically initiated electron exchange luminescence (CIEEL) mechanism with confirmed high quantum yields. The peroxyoxalate chemiluminescence (PO-CL) is mainly studied in anhydrous organic medium; however, for bioanalytical application, it should be performed in aqueous media. In the present work, we study the peroxyoxalate system in a binary 1,2-dimethoxyethane/water mixture with bis(2,4,6-trichlorophenyl) oxalate (TCPO), bis(4-methylphenyl) oxalate (BMePO) and bis[2-(methoxycarbonyl)phenyl] oxalate (DMO), catalyzed by sodium salicylate, in the presence of rhodamine 6G as activator. Reproducible kinetic results are obtained for all systems; emission decay rate constants depend on the salicylate as well as hydrogen peroxide concentration, and the occurrence of a specific base catalysis is verified. Although singlet quantum yields determined are lower than in anhydrous media in comparable conditions, they are still considerably high and adequate for analytical applications. The highest singlet quantum yields are obtained for the "ecologically friendly" derivative DMO indicating that this derivative might be the most adequate substrate for the use of the peroxyoxalate system in bioanalytical applications.

Kinetic studies on 2,6-lutidine catalyzed peroxyoxalate chemiluminescence in organic and aqueous medium: Evidence for general base catalysis

The peroxyoxalate reaction, base catalyzed perhydrolysis of activated aromatic oxalate esters in the presence of chemiluminescence activators, has widespread analytical and bioanalytical applications and is one of the most efficient chemiluminescence transformations known. We report here a kinetic study on this reaction using 2,6-lutidine as catalyst in organic (1,2-dimethoxyethane) and aqueous medium. In both media, experimental conditions can be designed which lead to reproducible results important for analytical applications. Observed rate constants (determined by observing the light emission intensity as well as absorbance variation due to phenol releases) show dependence on both the 2,6-lutidine and the hydrogen peroxide concentration, indicating their participation in the rate-limiting step of the transformation. The rate constants obtained from these kinetic studies proved to be at least one order of magnitude higher in water than in 1,2-dimethoxyethane as solvent. Kinetic experiments designed to distinguish between three different types of catalysis (nucleophilic, specific base and general base catalysis) clearly indicate that the role of 2,6-lutidine in this reaction is as general base catalyst in water as well as most likely in organic medium.

The decomposition of triphenylimidazole-para-acetate follows specific base catalysis and can be conveniently followed by fluorescence.

The kinetics of the decomposition reaction of 4-(4,5-diphenyl-1H-imidazol-2-yl)phenyl acetate (1) in basic alcoholic media was investigated, using a simple fluorescence (FL) spectrophotometric procedure. The process was conveniently studied using FL, since the triphenylimidazole-derived ester 1 and its reaction products (the corresponding phenol 2 and phenolate 2- ) are all highly fluorescent (ΦFL >37%). By carefully selecting excitation and emission wavelengths, observed rate constants k1 in the order of 10-3 to 10-2 s-1 were obtained from either reactant consumption (λex =300nm, λem =400nm) or product formation (λex =350nm, λem =475nm); these were shown to be kinetically equivalent. Intensity-decay time profiles also gave a residual FL intensity parameter, shown to be associated to the distribution of produced species 2 and 2- , according to the basicity of the medium. Studying the reaction in both methanol (MeOH) and isopropanol (iPrOH), upon addition of HO- , provided evidence that the solvent's conjugate base is the active nucleophilic species. When different bases were used (tBuO- , HO- , DBU and TEA), bimolecular rate constants kbim ranging from 4.5 to 6.5Lmol-1 s-1 were obtained, which proved to be non-dependent on the base pKaH , suggesting specific base catalysis for the decomposition of 1 in alcoholic media.

Effect of ionic liquids on the kinetics and quantum efficiency of peroxyoxalate chemiluminescence in aqueous media

Although the peroxyoxalate reaction is widely used in diverse analytical and bioanalytical applications, only a few mechanistic studies were published on this reaction in aqueous media. We report here a kinetic study on this reaction in aqueous borate buffer, in the absence and presence of imidazole-based ionic liquids (ILs). The ILs employed were 1-butyl-3-methylimidazolium tetrafluoroborate (BMIBF4), 1-allyl-3-methylimidazolium chloride (AMICl) and 1-allyl-3-methylimidazolium acetate (AMIAc). The dependence of the emission intensity decay rate constants (kobs) on the hydrogen peroxide and borate buffer concentrations indicated that the reaction in this medium occurs by specific base catalysis and the reactive species is the hydroperoxy anion. The presence of the ILs results in an increase in the yields of singlet-excited states. In comparison, increasing the concentration of simple electrolytes, e.g., NaCl, tetra(n-butyl)ammonium chloride and acetate resulted in larger rate constants and smaller chemiluminescence quantum yields than those observed in aqueous buffer in the absence of these electrolytes. Correlation of the singlet quantum yields with the viscosity and empirical polarity of the aqueous IL solutions indicates that medium polarity is the more important parameter for chemiexcitation. In summary, our results indicate that the peroxyoxalate reaction can be conducted in essentially aqueous media; the presence of ILs increases the emission quantum yield, with a possible improvement in the detection limits of analytical applications.

Mechanistic model for the firefly luciferin regeneration in biomimetic conditions: a model for the in vivo process?

The emission of light by fireflies involves the enzymatic oxidation of firefly luciferin and ends up in the formation of 2-cyano-6-hydroxybenzothiazole, and this is recycled back to luciferin by condensation with cysteine. In this work, we suggest a mechanism for this transformation that operates under mild conditions that are similar to in vivo environments (i.e. biomimetic); the rate-determining step consists of an intermolecular nucleophilic attack from the cysteine thiolate on the nitrile, catalysed by a specific base, followed by a complex sequence of intramolecular reactions which are highly dependent on the medium pH.

Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+).

Solvent D2O and (18)O kinetic isotope effects on RNA 2'-O-transphosphorylation catalyzed by Zn(2+) demonstrate an altered transition state relative to specific base catalysis. A recent model from DFT calculations involving inner sphere coordination to the non-bridging and leaving group oxygens is consistent with the data.

Studies of 1-Amino-2,2-difluorocyclopropane-1-carboxylic Acid: Mechanism of Decomposition and Inhibition of 1-Aminocyclopropane-1-carboxylic Acid Deaminase.

1-Amino-2,2-difluorocyclopropane-1-carboxylic acid (DFACC) is of interest in the study of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase due to the increased reactivity of its cyclopropyl functionality. It is shown that DFACC is unstable under near-physiological conditions where it primarily decomposes via specific-base catalysis to 3-fluoro-2-oxobut-3-enoic acid with a rate constant of 0.18 ± 0.01 min(-1). Upon incubation with ACC deaminase, DFACC is found to be a slow-dissociating inhibitor of ACC deaminase with submicromolar affinity.

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data.

Kinetics and Mechanism of the Base-Catalyzed Rearrangement and Hydrolysis of Ezetimibe

The pH-rate profile of the pseudo-first-order rate constants for the rearrangement and hydrolysis of Ezetimibe giving (2R,3R,6S)-N,6-bis(4-fluorophenyl)-2-(4-hydroxyphenyl)-3,4,5,6-tetrahydro-2H-pyran-3-carboxamide (2) as the main product at pH of less than 12.5 and the mixture of 2 and 5-(4-fluorophenyl)-5-hydroxy-2-[(4-fluorophenylamino)-(4-hydroxyphenyl)methyl]-pentanoic acid (3) at pH of more than 12.5 in aqueous tertiary amine buffers and in sodium hydroxide solutions at ionic strength I = 0.1 mol L(-1) (KCl) and at 39 °C is reported. No buffer catalysis was observed and only specific base catalysis is involved. The pH-rate profile is more complex than the pH-rate profiles for the hydrolysis of simple β-lactams and it contains several breaks. Up to pH 9, the log k(obs) linearly increases with pH, but between pH 9 and 11 a distinct break downwards occurs and the values of log k(obs) slightly decrease with increasing pH of the medium. At pH of approximately 13, another break upwards occurs that corresponds to the formation of compound 3 that is slowly converted to (2R,3R,6S)-6-(4-fluorophenyl)-2-(4-hydroxyphenyl)-3,4,5,6-tetrahydro-2H-pyran-3-carboxylic acid (4). The kinetics of base-catalyzed hydrolysis of structurally similar azetidinone is also discussed.

An experimental and theoretical study of the mechanism of cleavage of an RNA-model phosphate diester by mononuclear Zn(II) complexes

Kinetic investigations and density functional theory calculations were used to explore the mechanism of the cleavage of the RNA analogue 2-hydroxypropyl-p-nitrophenyl phosphate promoted by mononuclear Zn(II) complexes of polyamine ligands, focusing the attention on the attack of the 2′-hydroxyl to the phosphorous atom. The results obtained indicate that mononuclear complexes of tridentate polyamine ligands are more reactive than the tetradentate ones notwithstanding similar Lewis acidity. Three reaction pathways were found corresponding to the three reaction mechanisms so far proposed: general base catalysis by a metal coordinated species, specific base catalysis and specific base catalysis involving coordination of the 2′-hydroxyl to the metal ion. The three mechanisms have similar reaction barriers with a slightly lower one for the general base catalysis one. Among the two specific base catalysis mechanisms, which are in agreement with previous experimental observation of low isotopic solvent kinetic effects for the reaction, the one involving metal coordination of the substrate alcoholic group appears the more likely and is also capable to explain the higher activity of mononuclear complexes of triamine ligands compared with tetramine ones.

PH-Dependent Molecular Behaviors of a New Potential Color Additive: 4{[6-(1-carboxyethyl)-2-hydroxy -1-naphthyl]diazenyl}-3,5- dinitro Benzoic Acid

Phenyl azo hydroxynaphthalene (PAHNP) is the pharmacophore in certain color additives (e.g. sunset yellow, FD & C yellow No. 6) approved for use in human foods, drugs and cosmetics. The azo compound, 4{[6-(1-carboxyethyl)-2-hydroxy -1-naphthyl] diazenyl}-3,5-dinitrobenzoic acid (AZ-03) is a new, non-genotoxic, PAHNP analog, in a mono-azo chemical library. Process understanding of pH dependent behaviors of the highly functionalized molecule, is a critical aid to its identification. Absorption spectra of a fixed concentration of AZ-03 [3.30 x 10-5 M] in buffer solutions of varied pH were recorded. Spectra overlay suggested isosbestic point exists around 520 nm. Absorbance measurements of solutions (1.10 x 10-5 M) of pH 7, 10 and 11 were taken at 522, 524, 526 and 528 nm. Relative contribuiton of variables to overall variance was; wavelength (7%, p = 0.16), pH of media (57%, p < 0.0001), interaction between pH and wavelength (7%, p = 0.46, 2-way ANOVA, Bonferroni test). The probability that signal difference across pH was due to chance was 4 times greater at 522 nm (p=0.29) relative to 524 nm (p=0.08, 1-way ANOVA). The orange, unionized specie and violet, ionized specie both exhibited intense absorption, with molar absorptivities of 14,600 (490 nm) and 12,800 (550 nm) [L mol-1 cm-1 ] respectively. AZ-03 was degraded by pseudo first-order kinetics in alkaline medium by specific-base catalysis. It was shown with some statistical rigor that the dye exhibits isosbestic point at 522 nm . Base-catalyzed degradation gave a non-linear and diagnostic rate-pH profile. These findings could aid precise authentication of this potential color additive, and thus facilitate further understanding and studies of its solution chemistry.

Dinuclear Zn(II) Complex Catalyzed Phosphodiester Cleavage Proceeds via a Concerted Mechanism: A Density Functional Theory Study

Density functional theory (DFT) calculations were used to study the mechanism for the cleavage reaction of the RNA analogue HpPNP (HpPNP = 2-hydroxypropyl-4-nitrophenyl phosphate) catalyzed by the dinuclear Zn(II) complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (Zn(2)(L(2)O)). We present a binding mode in which each terminal phosphoryl oxygen atom binds to one zinc center, respectively, and the nucleophilic 2-hydroxypropyl group coordinates to one of the zinc ions, while the hydroxide from deprotonation of a water molecule coordinates to the other zinc ion. Our calculations found a concerted mechanism for the HpPNP cleavage with a 16.5 kcal/mol reaction barrier. An alternative proposed stepwise mechanism through a pentavalent oxyphosphorane dianion reaction intermediate for the HpPNP cleavage was found to be less feasible with a significantly higher energy barrier. In this stepwise mechanism, the deprotonation of the nucleophilic 2-hydroxypropyl group is accompanied with nucleophilic attack in the rate-determining step. Calculations of the nucleophile (18)O kinetic isotope effect (KIE) and leaving (18)O KIE for the concerted mechanism are in reasonably good agreement with the experimental values. Our results indicate a specific-base catalysis mechanism takes place in which the deprotonation of the nucleophilic 2-hydroxypropyl group occurs in a pre-equilibrium step followed by a nucleophilic attack on the phosphorus center. Detailed comparison of the geometric and electronic structure for the HpPNP cleavage reaction mechanisms in the presence/absence of catalyst revealed that the catalyst significantly altered the determining-step transition state to become far more associative or tight, that is, bond formation to the nucleophile was remarkably more advanced than leaving group bond fission in the catalyzed mechanism. Our results are consistent with and provide a reliable interpretation for the experimental observations that suggest the reaction occurs by a concerted mechanism (see Humphry, T.; Iyer, S.; Iranzo, O.; Morrow, J. R.; Richard, J. P.; Paneth, P.; Hengge, A. C. J. Am. Chem. Soc. 2008, 130, 17858-17866) and has a specific-base catalysis character (see Yang, M.-Y.; Iranzo, O.; Richard, J. P.; Morrow, J. R. J. Am. Chem. Soc. 2005, 127, 1064-1065).

Basic hydrolysis of quinolinyl N,N‐dimethylcarbamates: a two‐step mechanism

AbstractThe reactivity of 6‐quinolinyl and 8‐quinolinyl N,N‐dimethylcarbamates was examined in several aqueous basic media. A quadratic dependence was observed for the constant rates upon hydroxide concentration for both compounds, which is a typical behaviour of a mechanism involving a base‐catalysed deprotonation of the tetrahedral intermediate with the formation of a dianion at high concentrations of hydroxide ion, while at lower concentrations a specific‐base catalysed addition–elimination mechanism seems to be predominant. The reactivity of 8‐quinolinyl N,N‐dimethylcarbamate was also studied in several amine buffers, showing specific base catalysis. The reactivity of 6‐quinolinyl N,N‐dimethylcarbamate was studied in H2O and in D2O and the solvent isotope effect supports the proposal of a mechanism involving a specific‐base hydrolysis. All results confirm the existence of a mechanism with a rate determining step involving the substrate anion and a second mole of hydroxide ion. This mechanism was so far unknown for carbamate reactivity, being only known to occur with amides. Copyright © 2011 John Wiley & Sons, Ltd.

Dual Reactivity of Hydroxy- and Methoxy- Substitutedo-Quinone Methides in Aqueous Solutions: Hydration versus Tautomerization.

4-Hydroxy-6-methylene-2,4-cyclohexadien-1-one (1) and 4-methoxy-6-methylene-2,4-cyclohexadien-1-one (2) were generated by efficient (Φ = 0.3) photodehydration of 2-(hydroxymethyl)benzene-1,4-diol (3a) and 2-(hydroxymethyl)-4-methoxyphenol (4a), respectively. o-Quinone methides 1 and 2 can be quantitatively trapped as Diels-Alder adducts with ethyl vinyl ether or intercepted by good nucleophiles, such as azide ion (k(N3)(1) = 3.15 × 10(4) M(-1) s(-1) and k(N3)(2) = 3.30 × 10(4) M(-1) s(-1)). In aqueous solution, o-quinone methide 2 rapidly adds water to regenerate starting material (τ(H(2)O)(2) = 7.8 ms at 25 °C). This reaction is catalyzed by specific acid (k(H(+))(2) = 8.37 × 10(3) s(-1) M(-1)) and specific base (k(OH(-))(2) = 1.08 × 10(4) s(-1) M(-1)) but shows no significant general acid/base catalysis. In sharp contrast, o-quinone methide 1 decays (τ(H(2)O)(1) = 3.3 ms at 25 °C) via two competing pathways: nucleophilic hydration to form starting material 3a and tautomerization to produce methyl-p-benzoquinone. The disappearance of 1 shows not only specific acid (k(H(+))(1) = 3.30 × 10(4) s(-1) M(-1)) and specific base catalysis (k(OH(-))(1) = 3.51 × 10(4) s(-1) M(-1)) but pronounced catalysis by general acids and bases as well. The o-quinone methides 1 and 2 were also generated by the photolysis of 2-(ethoxymethyl)benzene-1,4-diol (3b) and 2-(ethoxymethyl)-4-methoxyphenol (4b), as well as from (2,5-dihydroxy-1-phenyl)methyl- (3c) and (2-hydroxy-5-methoxy-1-phenyl)methyltrimethylammonium iodides (4c). Short-lived (τ(25°)(C) ≈ 20 μs) precursors of o-quinone methides 1 and 2 were detected in the laser flash photolysis of 3a,b and 4a,b. On the basis of their reactivity, benzoxete structures have been assigned to these intermediates.

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.

Telling It Like It Is: Teaching Mechanisms in Organic Chemistry

In this article I support and extend the ideas presented by J. Brent Friesen in his article Saying What You Mean; Teaching Mechanisms in Organic Chemistry (JCE November, 2008). I emphasize “telling the truth” about proton transfers. The truth is that in aqueous acid most reactions are subject to specific acid catalysis: the only kinetically significant proton donor is hydronium ion, and the only kinetically significant proton acceptor is water. Similarly, in aqueous base most reactions are subject to specific base catalysis: the only kinetically significant proton donor is water, and the only kinetically significant proton acceptor is hydroxide ion.

Kinetic studies of the degradation of an aminopenicillin antibiotic (amoxicillin trihydrate) in aqueous solution using heat conduction microcalorimetry

Recent developments in isothermal microcalorimetry allow the direct determination of kinetic and thermodynamic parameters for slow reactions from studies conducted at appropriate temperatures and under designated environmental control. The degradation kinetics of amoxicillin trihydrate has been investigated as a function of pH (1-10) and temperature (303.15-318.15 K) at 0.5 M ionic strength using heat conduction microcalorimetry. Equations were developed incorporating calorimetric accessible data, rate constants and change in enthalpy, which showed that the degradation of amoxicillin trihydrate in aqueous solution followed pseudo-first-order kinetics under our experimental conditions. The enthalpy of degradation reaction was found to be exothermic in nature. The values of the rate constant k for individual steps were determined from the values of the overall rate constants at different pH. Energy of activation of overall reaction as a function of pH and for individual rate constants was determined. The log k-pH profiles indicated specific-acid and specific-base catalysis and there were inflection points near pH 3 and pH 7 corresponding to the pKa1 and pKa2 values. Quantitatively, there was good correlation between calorimetric determined half-life (t1/2) and the literature value in the acidic region determined by other methods at 310.15 K. The presence of a beta-lactam ring and of an alpha-amino group in the C-6 side chain played a critical role in the degradation of amoxicillin trihydrate and the zwitterionic form of the drug was found to be more stable.