Thiazolium C(2)-proton exchange: structure-reactivity correlations and the pKa of thiamin C(2)-H revisited

Pre-analytical challenges from adsorptive losses associated with thiamine analysis

Thiamine (vitamin B1) is an essential vitamin serving in its diphosphate form as a cofactor for enzymes in the citric acid cycle and pentose-phosphate pathways. Its concentration reported in the pM and nM range in environmental and clinical analyses prompted our consideration of the components used in pre-analytical processing, including the selection of filters, filter apparatuses, and sample vials. The seemingly innocuous use of glass fiber filters, glass filter flasks, and glass vials, ubiquitous in laboratory analysis of clinical and environmental samples, led to marked thiamine losses. 19.3 nM thiamine was recovered from a 100 nM standard following storage in glass autosampler vials and only 1 nM of thiamine was obtained in the filtrate of a 100 nM thiamine stock passed through a borosilicate glass fiber filter. We further observed a significant shift towards phosphorylated derivatives of thiamine when an equimolar mixture of thiamine, thiamine monophosphate, and thiamine diphosphate was stored in glass (most notably non-silanized glass, where a reduction of 54% of the thiamine peak area was observed) versus polypropylene autosampler vials. The selective losses of thiamine could lead to errors in interpreting the distribution of phosphorylated species in samples. Further, some loss of phosphorylated thiamine derivatives selectively to amber glass vials was observed relative to other glass vials. Our results suggest the use of polymeric filters (including nylon and cellulose acetate) and storage container materials (including polycarbonate and polypropylene) for thiamine handling. Losses to cellulose nitrate and polyethersulfone filters were far less substantial than to glass fiber filters, but were still notable given the low concentrations expected in samples. Thiamine losses were negated when thiamine was stored diluted in trichloroacetic acid or as thiochrome formed in situ, both of which are common practices, but not ubiquitous, in thiamine sample preparation.

Dynamic Protonation States Underlie Carbene Formation in ThDP-Dependent Enzymes: A Theoretical Study

The activation mechanism of thiamine diphosphate (ThDP) in enzymes has long been the subject of intense research and controversial discussion. Particularly contentious is the formation of a carbene intermediate, the first one observed in an enzyme. For the formation of the carbene to take place, both intramolecular and intermolecular proton transfer pathways have been proposed. However, the physiologically relevant pH of ThDP-dependent enzymes around neutrality does not seem to be suitable for the formation of such reactive chemical species. Herein, we investigate the general mechanism of activation of the ThDP cofactor in human transketolase (TKT), by means of electronic structure methods. We show that in the case of the human TKT, the carbene species is accessible through a pKa shift induced by the electrostatics of a neighboring histidine residue (H110), whose protonation state change modulates the pKa of ThDP and suppresses the latter by more than 6 pH units. Our findings highlight that ThDP enzymes activate the cofactor beyond simple geometric constraints and the canonical glutamate. Such observations in nature can pave the way for the design of biomimetic carbene catalysts and the engineering of tailored enzymatic carbenes.

Recent advances in sustainable N-heterocyclic carbene-Pd(II)-pyridine (PEPPSI) catalysts: A review

Various catalysts in homogeneous or heterogeneous catalysis deploy unconventional reaction pathways by lowering the activation energy (AE) barrier, controlling the selectivity, and creating environmental impact, thereby bringing about economic viability. Hence, the study of these methodologies is of immense interest. To develop a new chemistry, there is much scope for the invention of brilliant candidates that could effectively catalyze diverse reaction methodologies. The palladium-catalyzed reactions motivate interesting applications on various organic transformations under mild reaction conditions. Although phosphorous designed ligands or catalysts have been used, despite their expensiveness, sensitivity and other properties, there is the necessity of developing even better cross-coupling ligands or catalysts such as N-heterocyclic carbene (NHC)-based palladium complexes. These palladium-NHCs (Pd-NHC) are novel and universal nucleophilic entities that have come into light as the most successful class of catalysts in organometallic chemistry. In the same class, a specific category of palladium-NHCs such as palladium-pyridine enhanced pre-catalyst preparation by the stabilization initiation (palladium-PEPPSI) complexes, are emerging as versatile alternatives to phosphine containing palladium complexes for various cross-coupling reactions due to their excellent catalytic activity. Further to mention that NHCs are recently extensively used as ancillary ligands in organometallic chemistry, which includes industrial-related catalytic transformations due to strong σ-donors to metal centres. Apart from this, many NHC-metal complexes are the fascinating consideration in material science as probable metallo-pharmaceuticals. The current review offers a brief exploration of palladium-PEPPSI complexes over the past few years. Further, the synthesis of a variety of these types of catalysts, their applications in Suzuki-Miyaura, Buchwald-Hartwig, Sonogashira, Negishi couplings direct C2-arylation, O-C(O) cleavage, α-arylation/alkylation of carbonyl compounds and trans-amidation reactions via cross-coupling methodologies, which are covered. Additionally, reported recent developments on reusable heterogeneous PdPEPPSI complexes and their catalytic applications are being covered. Finally, the chiral Pd complexes and their asymmetric transformations are discussed.

The Role of the Fused Ring in Bicyclic Triazolium Organocatalysts: Kinetic, X-ray, and DFT Insights

Bicyclic triazolium scaffolds are widely employed in N-heterocyclic carbene (NHC) organocatalysis. While the incorporation of a fused ring was initially for synthetic utility in accessing chiral, modular triazolyl scaffolds, recent results highlight the potential for impact upon reaction outcome with the underpinning origins unclear. The common first step to all triazolium-catalyzed transformations is C(3)-H deprotonation to form the triazolylidene NHC. Herein, we report an analysis of the impact of size of the fused (5-, 6-, and 7-membered, n = 1, 2, and 3, respectively) ring on the C(3) proton transfer reactions of a series of bicyclic triazolium salts. Rate constants for the deuteroxide-catalyzed C(3)-H/D-exchange of triazolium salts, kDO, were significantly influenced by the size of the adjacent fused ring, with the kinetic acidity trend, or protofugalities, following the order kDO (n = 1) > kDO (n = 2) ≈ kDO (n = 3). Detailed analyses of X-ray diffraction (XRD) data for 20 triazolium salts (including 16 new structures) and of computational data for the corresponding triazolylidene NHCs provide insight on structural effects of alteration of fused ring size. In particular, changes in internal triazolyl NCN angle and positioning of the most proximal CH2 with variation in fused ring size are proposed to influence the experimental protofugality order.

N-Heterocyclic Carbene Organocatalysis: With or Without Carbenes?

In this work the mechanism of the aldehyde umpolung reactions, catalyzed by azolium cations in the presence of bases, was studied through computational methods. Next to the mechanism established by Breslow in the 1950s that takes effect through the formation of a free carbene, we have suggested that these processes can follow a concerted asynchronous path, in which the azolium cation directly reacts with the substrate, avoiding the formation of the carbene intermediate. We hereby show that substituting the azolium cation, and varying the base or the substrate do not affect the preference for the concerted reaction mechanism. The concerted path was found to exhibit low barriers also for the reactions of thiamine with model substrates, showing that this path might have biological relevance. The dominance of the concerted mechanism can be explained through the specific structure of the key transition state, avoiding the liberation of the highly reactive, and thus unstable carbene lone pair, whereas activating the substrate through hydrogen-bonding interactions. Polar and hydrogen-bonding solvents, as well as the presence of the counterions of the azolium salts facilitate the reaction through carbenes, bringing the barriers of the two reaction mechanisms closer, in many cases making the concerted path less favorable. Thus, our data show that by choosing the exact components in a reaction, the mechanism can be switched to occur with or without carbenes.

The Mechanism of N-Heterocyclic Carbene Organocatalysis through a Magnifying Glass

The term "N-Heterocyclic carbene organocatalysis" is often invoked in organic synthesis for reactions that are catalyzed by different azolium salts in the presence of bases. Although the mechanism of these reactions is considered today evident, a closer look into the details that have been collected throughout the last century reveals that there are many open questions and even contradictions in the field. Emerging new theoretical and experimental results offer solutions to these problems, because they show that through considering alternative reaction mechanisms a more consistent picture on the catalytic process can be obtained. These novel perspectives will be able to extend the scope of the reactions that we call today N-heterocyclic carbene organocatalysis.

The importance of N-heterocyclic carbene basicity in organocatalysis

This review highlights the importance of N-heterocyclic carbene (NHC) basicity for transformations in which NHCs are used as catalysts.

Origin of the Reductive Tricarboxylic Acid (rTCA) Cycle-Type CO2 Fixation: A Perspective

The reductive tricarboxylic acid (rTCA) cycle is among the most plausible candidates for the first autotrophic metabolism in the earliest life. Extant enzymes fixing CO₂ in this cycle contain cofactors at the catalytic centers, but it is unlikely that the protein/cofactor system emerged at once in a prebiotic process. Here, we discuss the feasibility of non-enzymatic cofactor-assisted drive of the rTCA reactions in the primitive Earth environments, particularly focusing on the acetyl-CoA conversion to pyruvate. Based on the energetic and mechanistic aspects of this reaction, we propose that the deep-sea hydrothermal vent environments with active electricity generation in the presence of various sulfide catalysts are a promising setting for it to progress. Our view supports the theory of an autotrophic origin of life from primordial carbon assimilation within a sulfide-rich hydrothermal vent.

Substituent Effects on Carbon Acidity in Aqueous Solution and at Enzyme Active Sites

Methods are described for the determination of pK_as for weak carbon acids in water. The application of these methods to the determination of the pK_as for a variety of carbon acids including nitriles, imidazolium cations, amino acids, peptides and their derivatives and, α-iminium cations is presented. The substituent effects on the acidity of these different classes of carbon acids are discussed; and, the relevance of these results to catalysis of the deprotonation of amino acids by enzymes and by pyridoxal 5'-phosphate is reviewed. The procedure for estimating the pK_a of uridine 5'-phosphate for C-6 deprotonation at the active site of orotidine 5'-phosphate decarboxylase is described, and the effect of a 5-F substituent on carbon acidity of the enzyme-bound substrate is discussed.

Ionic liquids are not innocent in Pd catalysis. C–H arylation of thiazolium and imidazolium ionic liquids with aryl halides

The ionic liquids bearing an aromatic vinylic C–H moiety are not innocent during Pd-catalyzed cross-coupling reactions of aryl halides. Palladium-catalyzed direct C–H arylation of thiazolium and imidazolium ionic liquids took place to give arylated ionic liquids.

Insights into the Thiamine Diphosphate Enzyme Activation Mechanism: Computational Model for Transketolase Using a Quantum Mechanical/Molecular Mechanical Method

We propose the first computational model for transketolase (TK), a thiamine diphosphate (ThDP)-dependent enzyme, using a quantum mechanical/molecular mechanical method on the basis of crystallographic TK structures from yeast and Escherichia coli, together with experimental kinetic data reported in the literature with wild-type and mutant TK. This model allowed us to define a new route for ThDP activation in the enzyme environment. We evidenced a strong interaction between ThDP and Glu418B of the TK active site, itself stabilized by Glu162A. The crucial point highlighted here is that deprotonation of ThDP C2 is not performed by ThDP N4' as reported in the literature, but by His481B, involving a HOH688A molecule bridge. Thus, ThDP N4' is converted from an amino form to an iminium form, ensuring the stabilization of the C2 carbanion or carbene. Finally, ThDP activation proceeds via an intermolecular process and not by an intramolecular one as reported in the literature. More generally, this proposed ThDP activation mechanism can be applied to some other ThDP-dependent enzymes and used to define the entire TK mechanism with donor and acceptor substrates more accurately.

Chemomimetic biocatalysis: exploiting the synthetic potential of cofactor-dependent enzymes to create new catalysts

Despite the astonishing breadth of enzymes in nature, no enzymes are known for many of the valuable catalytic transformations discovered by chemists. Recent work in enzyme design and evolution, however, gives us good reason to think that this will change. We describe a chemomimetic biocatalysis approach that draws from small-molecule catalysis and synthetic chemistry, enzymology, and molecular evolution to discover or create enzymes with non-natural reactivities. We illustrate how cofactor-dependent enzymes can be exploited to promote reactions first established with related chemical catalysts. The cofactors can be biological, or they can be non-biological to further expand catalytic possibilities. The ability of enzymes to amplify and precisely control the reactivity of their cofactors together with the ability to optimize non-natural reactivity by directed evolution promises to yield exceptional catalysts for challenging transformations that have no biological counterparts.

Lithium-stabilized nucleophilic addition of thiamin to a ketone provides an efficient route to mandelylthiamin, a critical pre-decarboxylation intermediate

Mandelylthiamin (MTh) is an accurate model of the covalent intermediate derived from the condensation of thiamin diphosphate and benzoylformate in benzoylformate decarboxylase. The properties and catalytic susceptibilities of mandelylthiamin are the subjects of considerable interest. However, the existing synthesis gives only trace amounts of the precursor to MTh as it is conducted under reversible conditions. An improved approach derives from the unique ability of lithium ions to drive to completion the otherwise unfavorable condensation of the conjugate base of thiamin and methyl benzoylformate. The unique efficiency of the condensation reaction in the presence of lithium ions is established in contrast to the effects of other Lewis acids. Interpretation of the pattern of the results indicates that the condensation of the ketone and thiamin is thermodynamically controlled. It is proposed that the addition of lithium ions displaces the equilibrium toward the product through formation of a stable lithium-alkoxide.

High-affinity host–guest complex of cucurbit[7]uril with a bis(thiazolium) salt

The stability of a bis(thiazolium) dication was improved upon inclusion by cucurbit[7]uril, as demonstrated by the slowed-down C(2)-H/D exchange.

Sweet siblings with different faces: the mechanisms of FBP and F6P aldolase, transaldolase, transketolase and phosphoketolase revisited in light of recent structural data

Nature has evolved different strategies for the reversible cleavage of ketose phosphosugars as essential metabolic reactions in all domains of life. Prominent examples are the Schiff-base forming class I FBP and F6P aldolase as well as transaldolase, which all exploit an active center lysine to reversibly cleave the C3-C4 bond of fructose-1,6-bisphosphate or fructose-6-phosphate to give two 3-carbon products (aldolase), or to shuttle 3-carbon units between various phosphosugars (transaldolase). In contrast, transketolase and phosphoketolase make use of the bioorganic cofactor thiamin diphosphate to cleave the preceding C2-C3 bond of ketose phosphates. While transketolase catalyzes the reversible transfer of 2-carbon ketol fragments in a reaction analogous to that of transaldolase, phosphoketolase forms acetyl phosphate as final product in a reaction that comprises ketol cleavage, dehydration and phosphorolysis. In this review, common and divergent catalytic principles of these enzymes will be discussed, mostly, but not exclusively, on the basis of crystallographic snapshots of catalysis. These studies in combination with mutagenesis and kinetic analysis not only delineated the stereochemical course of substrate binding and processing, but also identified key catalytic players acting at the various stages of the reaction. The structural basis for the different chemical fates and lifetimes of the central enamine intermediates in all five enzymes will be particularly discussed, in addition to the mechanisms of substrate cleavage, dehydration and ring-opening reactions of cyclic substrates. The observation of covalent enzymatic intermediates in hyperreactive conformations such as Schiff-bases with twisted double-bond linkages in transaldolase and physically distorted substrate-thiamin conjugates with elongated substrate bonds to be cleaved in transketolase, which probably epitomize a canonical feature of enzyme catalysis, will be also highlighted.

Progress in the experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations

Thiamin diphosphate (ThDP), the vitamin B1 coenzyme is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/carbene/C2-carbanion of the thiazolium ring and the C2α-carbanion/enamine, once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of several intermediates which are stable under acidic conditions, solid-state NMR and circular dichroism detection of the states of ionization and tautomerization of the 4'-aminopyrimidine moiety of ThDP in some of the intermediates. These methods also enabled in some cases determination of the rate-limiting step in the complex series of steps. This review is an update of a review with the same title published by the authors in 2005 in this Journal. Much progress has been made in the intervening decade in the identification of the intermediates and their application to gain additional mechanistic insight.

A thiamin-utilizing ribozyme decarboxylates a pyruvate-like substrate

Vitamins are hypothesized to be relics of an RNA world, and were probably participants in RNA-mediated primordial metabolism. If catalytic RNAs, or ribozymes, could harness vitamin cofactors to aid their function in a manner similar to protein enzymes, it would enable them to catalyse a much larger set of chemical reactions. The cofactor thiamin diphosphate, a derivative of vitamin B1 (thiamin), is used by enzymes to catalyse difficult metabolic reactions, including decarboxylation of stable α-keto acids such as pyruvate. Here, we report a ribozyme that uses free thiamin to decarboxylate a pyruvate-based suicide substrate (LnkPB). Thiamin conjugated to biotin was used to isolate catalytic individuals from a pool of random-sequence RNAs attached to LnkPB. Analysis of a stable guanosine adduct obtained via digestion of an RNA sequence (clone dc4) showed the expected decarboxylation product. The discovery of a prototypic thiamin-utilizing ribozyme has implications for the role of RNA in orchestrating early metabolic cycles.

Catalysis in Enzymatic Decarboxylations: Comparison of Selected Cofactor-dependent and Cofactor-independent Examples

This review is focused on three types of enzymes decarboxylating very different substrates: (1) Thiamin diphosphate (ThDP)-dependent enzymes reacting with 2-oxo acids; (2) Pyridoxal phosphate (PLP)-dependent enzymes reacting with α-amino acids; and (3) An enzyme with no known co-factors, orotidine 5'-monophosphate decarboxylase (OMPDC). While the first two classes have been much studied for many years, during the past decade studies of both classes have revealed novel mechanistic insight challenging accepted understanding. The enzyme OMPDC has posed a challenge to the enzymologist attempting to explain a 10¹⁷-fold rate acceleration in the absence of cofactors or even metal ions. A comparison of the available evidence on the three types of decarboxylases underlines some common features and more differences. The field of decarboxylases remains an interesting and challenging one for the mechanistic enzymologist notwithstanding the large amount of information already available.

Proton transfer from C-6 of uridine 5'-monophosphate catalyzed by orotidine 5'-monophosphate decarboxylase: formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent

The exchange for deuterium of the C-6 protons of uridine 5'-monophosphate (UMP) and 5-fluorouridine 5'-monophosphate (F-UMP) catalyzed by yeast orotidine 5'-monophosphate decarboxylase (ScOMPDC) at pD 6.5-9.3 and 25 °C was monitored by (1)H NMR spectroscopy. Deuterium exchange proceeds by proton transfer from C-6 of the bound nucleotide to the deprotonated side chain of Lys-93 to give the enzyme-bound vinyl carbanion. The pD-rate profiles for k(cat) give turnover numbers for deuterium exchange into enzyme-bound UMP and F-UMP of 1.2 × 10(-5) and 0.041 s(-1), respectively, so that the 5-fluoro substituent results in a 3400-fold increase in the first-order rate constant for deuterium exchange. The binding of UMP and F-UMP to ScOMPDC results in 0.5 and 1.4 unit decreases, respectively, in the pK(a) of the side chain of the catalytic base Lys-93, showing that these nucleotides bind preferentially to the deprotonated enzyme. We also report the first carbon acid pK(a) values for proton transfer from C-6 of uridine (pK(CH) = 28.8) and 5-fluorouridine (pK(CH) = 25.1) in aqueous solution. The stabilizing effects of the 5-fluoro substituent on C-6 carbanion formation in solution (5 kcal/mol) and at ScOMPDC (6 kcal/mol) are similar. The binding of UMP and F-UMP to ScOMPDC results in a greater than 5 × 10(9)-fold increase in the equilibrium constant for proton transfer from C-6, so that ScOMPDC stabilizes the bound vinyl carbanions, relative to the bound nucleotides, by at least 13 kcal/mol. The pD-rate profile for k(cat)/K(m) for deuterium exchange into F-UMP gives the intrinsic second-order rate constant for exchange catalyzed by the deprotonated enzyme as 2300 M(-1) s(-1). This was used to calculate a total rate acceleration for ScOMPDC-catalyzed deuterium exchange of 3 × 10(10) M(-1), which corresponds to a transition-state stabilization for deuterium exchange of 14 kcal/mol. We conclude that a large portion of the total transition-state stabilization for the decarboxylation of orotidine 5'-monophosphate can be accounted for by stabilization of the enzyme-bound vinyl carbanion intermediate of the stepwise reaction.

α,β-Unsaturated acyl azoliums from N-heterocyclic carbene catalyzed reactions: observation and mechanistic investigation

Catalytically generated acyl azoliums I and their α,β-unsaturated counterparts II are thought to be key reactive intermediates in a rapidly growing number of transformations promoted by N-heterocyclic carbene (NHC) catalysts.[1 ] Acyl azoliums are invoked in the postulated catalytic cycles of nearly all of the new NHC-catalyzed reactions of α-functionalized aldehydes reported since 2004, in which they are generally assumed to possess the reactivity of an activated carboxylic acid, that is, analogous to an activated ester.[2 ] In NHC-catalyzed processes, they are most often obtained through internal redox reactions of functionalized aldehydes but have also been prepared by oxidations of the Breslow intermediates[3 ] or additions to ketenes.[4 ] Acyl azoliums I are important intermediates in thiamine pyrophosphate (ThPP) dependent enzymatic reactions.[5 ] Townsend et al. have recently proposed that unsaturated acyl azolium III is the key intermediate in clavulanic acid biosynthesis;[6 ] despite careful efforts, III or its analogues II have never been characterized or independently synthesized. Here, we document the observation and characterization of α,β-unsaturated acyl azoliums 1 and 2 (Scheme 1 ) and demonstrate that their corresponding hemiacetals (1 ′ and 2 ”) are the kinetically important intermediates in both their acylation and annulation reactions.

Covalently bound substrate at the regulatory site of yeast pyruvate decarboxylases triggers allosteric enzyme activation

The mechanism by which the enzyme pyruvate decarboxylase from two yeast species is activated allosterically has been elucidated. A total of seven three-dimensional structures of the enzyme, of enzyme variants, or of enzyme complexes from two yeast species, three of them reported here for the first time, provide detailed atomic resolution snapshots along the activation coordinate. The prime event is the covalent binding of the substrate pyruvate to the side chain of cysteine 221, thus forming a thiohemiketal. This reaction causes the shift of a neighboring amino acid, which eventually leads to the rigidification of two otherwise flexible loops, one of which provides two histidine residues necessary to complete the enzymatically competent active site architecture. The structural data are complemented and supported by kinetic investigations and binding studies, providing a consistent picture of the structural changes occurring upon enzyme activation.

Reaction mechanisms of thiamin diphosphate enzymes: defining states of ionization and tautomerization of the cofactor at individual steps

We summarize the currently available information regarding the state of ionization and tautomerization of the 4'-aminopyrimidine ring of the thiamine diphosphate on enzymes requiring this coenzyme. This coenzyme forms a series of covalent intermediates with its substrates as an electrophilic catalyst, and the coenzyme itself also carries out intramolecular proton transfers, which is virtually unprecedented in coenzyme chemistry. An understanding of the state of ionization and tautomerization of the 4'-aminopyrimidine ring in each of these intermediates provides important details about proton movements during catalysis. CD spectroscopy, both steady-state and time-resolved, has proved crucial for obtaining this information because no other experimental method has provided such atomic detail so far.

Normal carbon acid referencing for protein amide hydrogen exchange

Measurement of the exchange kinetics for amide hydrogens along the protein backbone continues to offer valuable insights into structural stability and conformational dynamics. Since such studies routinely compare samples that differ in solution conditions or mechanical handling, normalization of the relative exchange rates can present a potentially significant source of experimental uncertainty. The carbon acids 1,3-dimethylimidazolium cation and thiomethylacetonitrile exhibit base catalyzed exchange rates similar to those of the slowly exchanging amides, under conditions typical for protein studies. With 13C enrichment at the acidic carbon position to facilitate selective observation, such carbon acids offer practical internal calibration of exchange.

Thiamin Deprotonation Mechanism. Carbanion Development Stabilized by the LUMOs of Thiazolium and Pyrimidylimine Working in Tandem and Release Governed by a H-Bond Switch

Our previous paper (J. Phys. Chem. A 2005, 109, 7606) using computed atomic charges, based on the quantum theory of atoms in molecules (QTAIM), on azolium models of thiamin diphosphate has shown that only sulfur acts as an effective electron sink in the formation of the thiamin carbanion intermediate. Herein we apply natural bond orbital (NBO) theory to the analysis of orbital contributions to canonical molecular orbitals (CMOs) of six abbreviated azolium analogs of the carbanion to better understand the unique function of sulfur. The NBO/CMO data provide a description of the origin of the first thiamin electron sink: sulfur performing in the sigma- and pi-orbitals of the transition state as well as in the carbanion, and its advantages due to low electronegativity and moderate size. At the next level of thiamin modeling, we include the six-membered pyrimidine ring to represent the prerequisite V-structure in the iminopyrimidine tautomeric form. This model is subjected to incremental deprotonation and MO decomposition. The 4'-pyrimidylimine moiety, in addition to being an internal base to abstract the C2 proton, also performs as the second electron sink. Thus, the LUMOs of the thiazolium and pyrimidylimine systems working in tandem stabilize the developing charges in these transient structures, with facilitation from their HOMOs. Further, the absence of detectable amounts of the C2 carbanion in 13C2-labeled thiamin-enzyme complex by NMR is explained. Both NBO analysis and the QTAIM topological electronic properties suggest the operation of a H-bonding scheme that leads to the formation of a cryptic C2 carbanion that is not accumulated. The shielding of the carbanion by the N4'-H hydrogen bond is weakened by N1'-H deprotonation. Consequently, prior return of the N1' proton to the nearby glutamate may be the switch for streaming a timed-release of the unstable C2 carbanion to the incoming substrate.

The guanine cation radical: investigation of deprotonation states by ESR and DFT

This work reports ESR studies that identify the favored site of deprotonation of the guanine cation radical (G*+) in an aqueous medium at 77 K. Using ESR and UV-visible spectroscopy, one-electron oxidized guanine is investigated in frozen aqueous D2O solutions of 2'-deoxyguanosine (dGuo) at low temperatures at various pHs at which the guanine cation radical, G*+ (pH 3-5), singly deprotonated species, G(-H)* (pH 7-9), and doubly deprotonated species, G(-2H)*- (pH > 11), are found. C-8-deuteration of dGuo to give 8-D-dGuo removes the major proton hyperfine coupling at C-8. This isolates the anisotropic nitrogen couplings for each of the three species and aids our analyses. These anisotropic nitrogen couplings were assigned to specific nitrogen sites by use of 15N-substituted derivatives at N1, N2, and N3 atoms in dGuo. Both ESR and UV-visible spectra are reported for each of the species: G*+, G(-H)*, and G(-2H)*-. The experimental anisotropic ESR hyperfine couplings are compared to those obtained from DFT calculations for the various tautomers of G(-H)*. Using the B3LYP/6-31G(d) method, the geometries and energies of G*+ and its singly deprotonated state in its two tautomeric forms, G(N1-H)* and G(N2-H)*, were investigated. In a nonhydrated state, G(N2-H)* is found to be more stable than G(N1-H)*, but on hydration with seven water molecules G(N1-H)* is found to be more stable than G(N2-H)*. The theoretically calculated hyperfine coupling constants (HFCCs) of G*+, G(N1-H)*, and G(-2H)*- match the experimentally observed HFCCs best on hydration with seven or more waters. For G(-2H)*-, the hyperfine coupling constant (HFCC) at the exocyclic nitrogen atom (N2) is especially sensitive to the number of hydrating water molecules; good agreement with experiment is not obtained until nine or 10 waters of hydration are included.

Reactions of endo-3-Diazotricyclo[3.2.1.02,4]oct-6-ene, a Potential Precursor for the Generation of a Neutral C8H8 Molecule with a Pyramidally Coordinated Carbon

endo-3-Diazotricyclo[3.2.1.0(2,4)]oct-6-ene (endo-6) has already been prepared in solution. According to B3LYP/6-311+G(d,p) computations, the corresponding carbene endo-7 easily produces the highly strained neutral C8H8 compound 4 comprising a pyramidally tetracoordinated carbon which then rearranges to bridgehead alkene 15 through a cascade of rearrangements. Nonplanar diazocyclopropane structures are predicted for endo- and exo-6. Furthermore, their ring-opened isomers 27 are the first representatives of a new class of non-Kekulé compounds, the diazoallyls.

Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids

The branched-chain amino acids are synthesized by plants, fungi and microorganisms, but not by animals. Therefore, the enzymes of this pathway are potential target sites for the development of antifungal agents, antimicrobials and herbicides. Most research has focused upon the first enzyme in this biosynthetic pathway, acetohydroxyacid synthase (AHAS) largely because it is the target site for many commercial herbicides. In this review we provide a brief overview of the important properties of each enzyme within the pathway and a detailed summary of the most recent AHAS research, against the perspective of work that has been carried out over the past 50 years.

Separation of thiamin and its phosphate esters by capillary zone electrophoresis and its application to the analysis of water-soluble vitamins

A capillary zone electrophoresis method for the separation and determination of thiamin and its phosphate esters (free thiamin, thiamin monophosphate, and thiamin pyrophosphate) was developed and optimized. The efficiency achieved with boric acid-sodium tetraborate decahydrate buffer (pH 8.24; 65-8 mM) at an applied potential of 30 kV gave the detection limit (S/N = 3) and the limit of quantitative measurement (S/N = 10) of thiamin and its phosphate esters ranging from 10(-4) to 6 x 10(-4) mM and from 6 x 10(-4) to 1.2 x 10(-3) mM, respectively. The effects of pH on separation and migration times of thiamin and its phosphate esters are described. The method was validated and applied to the quantitative determination of thiamin in commercial tablets containing both a massive and a normal dose of thiamin.

Experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations

Thiamin diphosphate (ThDP), the vitamin B1 coenzyme, is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/C2-carbanion of the thiazolium ring and the C2alpha-carbanion (or enamine) once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state (X-ray) methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of a several intermediates which are stable under acidic conditions, and circular dichroism detection of the 1',4'-imino tautomer of ThDP in some of the intermediates. Some of these methods also enable the investigator to determine the rate-limiting step in the complex series of steps.

Metal-ligand bifunctional catalysis for asymmetric hydrogenation

Chiral diphosphine/1,2-diamine-Ru(II) complexes catalyse the rapid, productive and enantioselective hydrogenation of simple ketones. The carbonyl-selective hydrogenation takes place via a non-classical metal-ligand bifunctional mechanism. The reduction of the C=O function occurs in the outer coordination sphere of an 18e trans-RuH2(diphosphine)(diamine) complex without interaction between the unsaturated moiety and the metallic centre. The Ru atom donates a hydride and the NH2 ligand delivers a proton through a pericyclic six-membered transition state, directly giving an alcoholic product without metal alkoxide formation. The enantiofaces of prochiral ketones are differentiated on the chiral molecular surface of the saturated RuH2 species. This asymmetric catalysis manifests the significance of 'kinetic' supramolecular chemistry.

On the importance of being zwitterionic: enzymatic catalysis of decarboxylation and deprotonation of cationic carbon

Carbanion ylides are strongly stabilized by electrostatic interactions between opposing charges at neighboring atoms and this stabilizing electrostatic interaction increases with decreasing dielectric constant of the medium through which the charges interact. Consequently, there is a large increase in the thermodynamic driving force, with decreasing dielectric constant of the reaction medium, for deprotonation of cationic carbon acids and decarboxylation to form related ylides. This favors catalysis of the formation of unstable ylides at enzyme active sites of low dielectric constant. A brief survey of enzymes that catalyze deprotonation of cationic carbon acids and related decarboxylation reactions shows catalysis generally occurs for substrates that are bound in a deep pocket on the protein, with an apparent dielectric constant that is much lower than for the solvent water. In several cases, proton transfer is to a catalytic residue that is relatively weakly solvated in water. We suggest that there is a strong advantage for evolution of protein catalysts that utilize weakly solvated basic side chains which are relatively easily buried in nonpolar active sites that are favorable for zwitterion formation.

Mechanism of asymmetric hydrogenation of ketones catalyzed by BINAP/1,2-diamine-rutheniumII complexes

Asymmetric hydrogenation of acetophenone with trans-RuH(eta(1)-BH(4))[(S)-tolbinap][(S,S)-dpen] (TolBINAP = 2,2'-bis(di-4-tolylphosphino)-1,1'-binaphthyl; DPEN = 1,2-diphenylethylenediamine) in 2-propanol gives (R)-phenylethanol in 82% ee. The reaction proceeds smoothly even at an atmospheric pressure of H(2) at room temperature and is further accelerated by addition of an alkaline base or a strong organic base. Most importantly, the hydrogenation rate is initially increased to a great extent with an increase in base molarity but subsequently decreases. Without a base, the rate is independent of H(2) pressure in the range of 1-16 atm, while in the presence of a base, the reaction is accelerated with increasing H(2) pressure. The extent of enantioselection is unaffected by hydrogen pressure, the presence or absence of base, the kind of base and coexisting metallic or organic cations, the nature of the solvent, or the substrate concentrations. The reaction with H(2)/(CH(3))(2)CHOH proceeds 50 times faster than that with D(2)/(CD(3))(2)CDOD in the absence of base, but the rate differs only by a factor of 2 in the presence of KO-t-C(4)H(9). These findings indicate that dual mechanisms are in operation, both of which are dependent on reaction conditions and involve heterolytic cleavage of H(2) to form a common reactive intermediate. The key [RuH(diphosphine)(diamine)](+) and its solvate complex have been detected by ESI-TOFMS and NMR spectroscopy. The hydrogenation of ketones is proposed to occur via a nonclassical metal-ligand bifunctional mechanism involving a chiral RuH(2)(diphosphine)(diamine), where a hydride on Ru and a proton of the NH(2) ligand are simultaneously transferred to the C=O function via a six-membered pericyclic transition state. The NH(2) unit in the diamine ligand plays a pivotal role in the catalysis. The reaction occurs in the outer coordination sphere of the 18e RuH(2) complex without C=O/metal interaction. The enantiofaces of prochiral aromatic ketones are kinetically differentiated on the molecular surface of the coordinatively saturated chiral RuH(2) intermediate rather than in a coordinatively unsaturated Ru template.

Dual catalytic apparatus of the thiamin diphosphate coenzyme: acid-base via the 1',4'-iminopyrimidine tautomer along with its electrophilic role

It was recently reported (Jordan, F.; Zhang, Z.; Sergienko, E. A. Bioorg. Chem. 2002, 30, 188-198) that addition to the E477Q active-center variant of yeast pyruvate decarboxylase of (a) pyruvate on a rapid-scan UV stopped-flow, or (b) acetaldehyde or benzoylformate on a circular dichroism (CD) instrument, generates a new band with lambda(max) near 300-310 nm. A chemical model demonstrated that the wavelength is appropriate to the 1',4'-iminopyrimidine tautomer of the 4'-aminopyrimidine ring in thiamin diphosphate. Herein, we report the formation of a new positive CD band centered at 305 nm when the Escherichia colipyruvate dehydrogenase complex first E1 subunit and its variants are exposed to phosphonolactylthiamin diphosphate, a stable analogue of the covalent adduct formed between the substrate pyruvate and the C2 atom of thiamin diphosphate. The behavior of this CD band, whether it suggests saturation of the enzyme by phosphonolactylthiamin diphosphate, or its very existence (the band is not seen with the E571A E1 variant, where E571 is hydrogen bonded to the N1' atom of the 4'-aminopyrimidine ring), as well as its position are consistent with its assignment to the 1',4'-imino thiamin diphosphate tautomer on the enzyme, chiral by virtue of its fixed V conformation. The mechanism of binding of phosphonolactylthiamin diphosphate closely resembles that of thiamin diphosphate itself.