Rate of Enolate Formation Is Not Very Sensitive to the Hydrogen Bonding Ability of Donors to Carboxyl Oxygen Lone Pair Acceptors; A Ramification of the Principle of Non-Perfect Synchronization for General-Base-Catalyzed Enolate Formation

Capturing the free energy of transition state stabilization: insights from the inhibition of mandelate racemase

Mandelate racemase (MR) catalyses the Mg²⁺-dependent interconversion of (R)- and (S)-mandelate. To effect catalysis, MR stabilizes the altered substrate in the transition state (TS) by approximately 26 kcal mol^-1 (-ΔG_tx), such that the upper limit of the virtual dissociation constant of the enzyme-TS complex is 2 × 10^-19 M. Designing TS analogue inhibitors that capture a significant amount of ΔG_tx for binding presents a challenge since there are a limited number of protein binding determinants that interact with the substrate and the structural simplicity of mandelate constrains the number of possible isostructural variations. Indeed, current intermediate/TS analogue inhibitors of MR capture less than or equal to 30% of ΔG_tx because they fail to fully capitalize on electrostatic interactions with the metal ion, and the strength and number of all available electrostatic and H-bond interactions with binding determinants present at the TS. Surprisingly, phenylboronic acid (PBA), 2-formyl-PBA, and para-chloro-PBA capture 31-38% of ΔG_tx. The boronic acid group interacts with the Mg²⁺ ion and multiple binding determinants that effect TS stabilization. Inhibitors capable of forming multiple interactions can exploit the cooperative interactions that contribute to optimum binding of the TS. Hence, maximizing interactions with multiple binding determinants is integral to effective TS analogue inhibitor design. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

The role of Brønsted base basicity in estimating carbon acidity at enzyme active sites: a caveat

Many enzymes catalyze the abstraction of a proton from a carbon acid substrate to initiate a variety of reactions; however, the development of a complete quantitative description of enzyme-catalyzed heterolytic cleavage of a C-H bond remains a challenge to enzymologists. To determine the pK value for such substrates bound at the active site, recent studies have estimated the equilibrium for formation of the deprotonated intermediate at the active site, however, accurate knowledge of the pK of the conjugate acid of the Brønsted base catalyst (BH⁺) is also required. Herein, it is shown that using the value of pK of the enzyme-substrate complex can underestimate the value of pK by an amount between zero and pδ, where pδ is the change in basicity of BH⁺ upon going from the enzyme-substrate complex to the enzyme-intermediate complex.

Rate-Driving Force Relationships in the Multisite Proton-Coupled Electron Transfer Activation of Ketones

Here we present a detailed kinetic study of the multisite proton-coupled electron transfer (MS-PCET) activations of aryl ketones using a variety of Brønsted acids and excited-state Ir(III)-based electron donors. A simple method is described for simultaneously extracting both the hydrogen-bonding equilibrium constants and the rate constants for the PCET event from deconvolution of the luminescence quenching data. These experiments confirm that these activations occur in a concerted fashion, wherein the proton and electron are transferred to the ketone substrate in a single elementary step. The rates constants for the PCET events were linearly correlated with their driving forces over a range of nearly 19 kcal/mol. However, the slope of the rate-driving force relationship deviated significantly from expectations based on Marcus theory. A rationalization for this observation is proposed based on the principle of non-perfect synchronization, wherein factors that serve to stabilize the product are only partially realized at the transition state. A discussion of the relevance of these findings to the applications of MS-PCET in organic synthesis is also presented.

New Insight into and Characterization of the Aqueous Metal-Enol(ate) Complexes of (Acetonedicarboxylato)copper

Nearly 50 years have passed since the classic studies by Larson and Lister [Larson D. W.; Lister M. W.Can. J. Chem.1968, 46, 823]and Hay and Leong [Hay R. W.; Leong K. N.J. Chem. Soc. A1971, 0, 3639]on the copper-catalyzed decarboxylation of acetonedicarboxylic acid (H₃Acdica). Although the authors laid the foundations for what we know about this reaction; still very little information exists regarding the underlying aqueous metal-enol(ate)s of (acetonedicarboxylato)copper. In this study, UV-visible titrations revealed three pK values, pK _[Cu(H2A)], pK _[Cu(HA)], and pK _[Cu(A)]. We associated the first two with ionization of α-carbon CH₂ groups in [Cu^II(H₂Acdica)_keto]¹⁺ and [Cu^II(HAcdica)_keto]⁰ to form unstable metal-enolates, {[Cu^II(HAcdica)_enolate]} and {[Cu^II(Acdica)_enolate]}, which through β-carbonyl oxygen protonation can form metal-enols [Cu^II(H₂Acdica)_enol]¹⁺ and [Cu^II(HAcdica)_enol]⁰. The square-planar Cu^II center (electron paramagnetic resonance results) plays a dual role of stabilizing negative electron density at the β-carbonyl oxygen and as an electron sink in [[Cu^I(HAcdica)_enolate]⁰]^‡ and [[Cu^I(Acdica)_enolate]^1-]^‡ (confirmed through cyclic voltammetry as two single 1e ^- transfers). The π → π* transition associated with [Cu^II(HAcdica)_enol]⁰ was used to determine pK _[Cu(A)] (deprotonation of enol OH) and enolization rate constant (stopped-flow spectroscopy) but also exhibited a time-dependent decrease in absorbance (on the order of min^-1), suggesting a new method to possibly obtain experimental values for the estimated "k _CuL" decarboxylation rate constant of metal-enolate [CuL]^1- calculated by Larson and Lister. On the basis of our results, we postulate that decarboxylation takes place primarily through {[Cu^II(HAcdica)_enolate]} and [Cu^II(HAcdica)_enol]⁰. These results add to our understanding of aqueous metal-enol(ate)s, which contain underlying Cu^II/I redox chemistry, "active methylenes" and enol tautomers and enolate anions, which play roles in many catalytic reactions of interdisciplinary importance.

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

While the strict definition of supramolecular chemistry is "chemistry beyond the molecule", meaning having a focus on non-covalent interactions, the field is primarily associated with the creation of synthetic receptors and self-assembly. For synthetic ease, the receptors and assemblies routinely possess a high degree of symmetry, which lends them an aspect of aesthetic beauty. Pictures of electron orbitals similarly can be seen as akin to works of art. This similarity was an early draw for me to the fields of supramolecular chemistry and molecular orbital theory, because I grew up in a household filled with art. In addition to art, my childhood was filled with repairing and constructing mechanical entities, such as internal combustion motors, where many components work together to achieve a function. Analogously, the field of supramolecular chemistry creates systems of high complexity that achieve functions or perform tasks. Therefore, in retrospect a career in supramolecular chemistry appears to be simply an extension of childhood hobbies involving art and auto-mechanics.

Cornus mas (Linnaeus) Novel Devised Medicinal Preparations: Bactericidal Effect against Staphylococcus aureus and Pseudomonas aeruginosa

The medicinal properties of Cornus mas L. (=Cornus mascula L.), Cornaceae, are well described in Hippocratian documents, and recent research provides experimental evidence for some of these properties. However, the chemical components of Cornus mas L. that may be of pharmaceutical importance are relatively unstable. In this respect a novel methodology for plant nutrient element extraction that provides favorable conditions for simultaneous stabilization of such fragile and unstable structures has been devised. Using this methodology, medicinal preparations derived from Cornus mas L. fresh fruits, proved to possess significant antimicrobial activity selective against S. aureus and P. aeruginosa. This effect became apparent with the addition of sodium bromide in the extraction procedure and varied with the ion availability during extraction. The identification of novel agents with potent antimicrobial activity against these species is of medical importance to overcome the problem of universal antibiotic resistance.

The distal effect of electron-withdrawing groups and hydrogen bonding on the stability of peptide enolates

Relative gas-phase carbon acidities have been computed for a series of acetamides, diketopiperazines, and linear dipeptides. The results show that N-electron-withdrawing substituents, protonation, and hydrogen bonding at amide nitrogen in these systems increase the acidity of both a C-H proton adjacent to the amide carbonyl and that of one proximal to the amide nitrogen. There is a good correlation between the magnitudes of the increases at the two positions, but the extent of the increase for the distal C-H adjacent to the carbonyl is greater than that for the proximal C-H, in most cases by a factor of about two. The effects on the stability of the distal enolate are shown to result from predominantly inductive affects. The size of these effects is such that protonation and hydrogen bonding at nitrogen increase the acidity of the distal C-H to almost the same extent as seen for the analogous interactions at the carbonyl oxygen. The effect is also seen in solution, where the computed aqueous pK(a) values are greater for the C-H adjacent to the amide carbonyl, by up to 13 units, and where preliminary experimental studies have shown that N-acetylation of an amide increases the rate of hydrogen-deuterium exchange via formation of the corresponding distal enolate by more than 3 orders of magnitude above the rates of exchange via the proximal enolate, of the nonacetylated amide and of diisopropylketone. The results also indicate that hydrogen bonding to amide nitrogen could be as important as bonding to oxygen in enzyme-catalyzed cleavage of alpha-C-H bonds.

Proton transfers in aromatic systems: How aromatic is the transition state?

The question as to what extent aromaticity in a reactant or product is expressed in the transition state of a reaction has only recently received serious attention. Inasmuch as aromaticity is related to resonance, one might expect that, in a reaction that leads to aromatic products, its development at the transition state should lag behind bond changes as is invariably the case for the development of resonance in reactions that lead to delocalized products. However, recent experimental and computational studies on proton transfers from carbon acids suggest the opposite behavior, i.e., the development of aromaticity at the transition state ismoreadvanced than the proton transfer. The evidence for this claim is based on the determination of intrinsic barriers that show a decrease with increasing aromaticity. According to the Principle of Nonperfect Synchronization (PNS), this decrease in the intrinsic barrier implies a disproportionately large amount of aromatic stabilization of the transition state. Additional evidence for the high degree of transition state aromaticity comes from the calculation of aromaticity indices such as HOMA, NICS, and the Bird Index. Possible reasons why the degree to which aromaticity and resonance are expressed at the transition state is different are discussed.

Electrophilic coordination catalysis: a summary of previous thought and a new angle of analysis

One of the most common, and yet least well understood, enzymatic transformations is proton abstraction from activated carbon acids such as carbonyls. Understanding the mechanism for these proton abstractions is basic to a good understanding of enzyme function. Significant controversy has arisen over the means by which a given enzyme might facilitate these deprotonations. Creating small molecule mimics of enzymes and physical organic studies that model enzymes are good approaches to probing mechanistic enzymology. This Account details a number of molecular recognition and physical organic studies, both from our laboratory and others, dealing with the elucidation of this quandary. Our analysis launches from an examination of the active sites and proposed mechanism of several enzyme-catalyzed deprotonations of carbon acids. This analysis highlights the geometries of the hydrogen bonds found at the enzyme active sites. We find evidence to support pi-oriented hydrogen bonding, rather than lone pair oriented hydrogen bonding. Our observations prompted us to study the stereochemistry of hydrogen bonding that activates carbonyl alpha-carbons to deprotonation. The results from our own thermodynamic, kinetics, and computational studies, all of which are reviewed herein, suggest that an unanticipated level of intermediate stabilization occurs via an electrophilic interaction through the pi-molecular orbital as opposed to traditional lone pair directed coordination. We do not postulate that hydrogen bonding to pi-systems is intrinsically stronger than to lone pairs, but rather that there is a greater change in bond strength during deprotonation when the hydrogen bonds are oriented at the pi-system. Through these studies, we conclude that many enzymes preferentially activate their carbon acid substrates through an electrophilic coordination directed towards the pi-bond of the carbonyl rather than the conventional lone pair directed model.

Does aromaticity in a reaction product increase or decrease the intrinsic barrier? Kinetics of the reversible deprotonation of benzofuran-3(2H)-one and benzothiophene-3(2H)-one

A kinetic study of the reversible deprotonation of benzofuran-3(2H)-one (3H-O) and benzothiophene-3(2H)-one (3H-S) by amines and hydroxide ion in water at 25 degrees C is reported. The respective conjugate bases, 3--O and 3--S, represent benzofuran and benzothiophene derivatives, respectively, and thus are aromatic. The main question addressed in this paper is whether this aromaticity has the effect of enhancing or lowering intrinsic barriers to proton transfer. These intrinsic barriers were either determined from Brønsted plots for the reactions with amines or calculated on the basis of the Marcus equation for the reaction with OH-; they were found to be lower for the more highly aromatic benzothiophene derivative, indicating that aromaticity lowers the intrinsic barrier. It is shown that the reduction in the intrinsic barrier is not an artifact of other factors such as inductive, steric, resonance, polarizability, and pi-donor effects, although these factors affect the intrinsic barriers in a major way. Our results imply that aromatic stabilization of the transition state is ahead of proton transfer; this contrasts with simple resonance effects, which typically lag behind proton transfer at the transition state, thereby increasing intrinsic barriers.

Kinetics of proton transfer from benzo[b]-2,3-dihydrofuran-2-one and benzo[b]-2,3-dihydrothiophene-2-one. Effect of anion aromaticity on intrinsic barriers

Rates of the reversible deprotonation of benzo[b]-2,3-dihydrofuran-2-one (6H-O) and benzo[b]-2,3-dihydrothiophene-2-one (6H-S) by OH-, primary aliphatic amines, secondary alicyclic amines, and carboxylate ions have been determined in water at 25 degrees C. As noted earlier by Kresge and Meng, 6H-S (pKa = 8.82) is considerably more acidic than 6H-O (pKa = 11.68), which mainly reflects the greater aromatic stabilization of the conjugate base of 6H-S (thiophene derivative) compared to that of 6H-O (furan derivative). The main focus of this paper is to assess how the difference in the aromaticity of the two enolate ions affects the intrinsic barrier to the proton transfer. These intrinsic barriers were determined from Brønsted plots for the reactions with the amines and carboxylate ions or calculated on the basis of the Marcus equation for the reactions with OH-. They are consistently somewhat higher for the reactions of 6H-S than for the reactions of 6H-O, implying that the aromaticity in the anion enhances the intrinsic barrier. This contrasts with a previous report on the deprotonation of some cyclic rhenium Fischer-type carbene complexes where the reaction that leads to the most aromatic conjugate base (thiophene derivative) has a lower intrinsic barrier than the reaction that leads to the less aromatic furan analogue. We are offering a detailed analysis of other potential factors that may affect the intrinsic barriers and which could explain these contradictory results.