E1cB Mechanism Research Articles

Synthesis of Stilbenes by Cyanide/Base-Mediated Coupling of Benzylic Chlorides and Alcohols

AbstractA straightforward procedure has been developed for the direct synthesis of stilbenes from benzylic chlorides and alcohols. The transformation employs a two-step one-pot protocol where the benzylic chloride is first subjected to a substitution with potassium cyanide in o-xylene. Without workup, the resulting arylacetonitrile is then reacted directly with the benzylic alcohol and potassium tert-butoxide to generate the stilbene framework. The condensation has been performed with a variety of commercially available benzylic chlorides and alcohols to afford substituted stilbenes as the pure E-isomers. A kinetic isotope effect of 5.2 has been measured for the overall transformation when comparing benzyl alcohol and α,α-d 2-benzyl alcohol. The release of cyanide during the final elimination to stilbene has been confirmed by a picrate test. Thus, the potassium tert-butoxide-mediated elimination of cyanide is believed to proceed by an E1cB mechanism where the deprotonation reaction constitutes the rate-determining step.

Exploring the Substrate-Assisted Dehydration of Chorismate Catalyzed by Dehydratase MqnA from QM/MM Calculations: The Role of Pocket Residues and the Hydrolysis Mechanism of N17D Mutant.

MqnA is the first enzyme on the futalosine pathway to menaquinone, which catalyzes the dehydration of chorismate to yield 3-enolpyruvyl-benzoate (3-EPB). MqnA is also the only chorismate dehydratase known so far. In this work, based on the recently determined crystal structures, we constructed the enzyme-substrate complex models and conducted quantum mechanics/molecular mechanics (QM/MM) calculations to elucidate the reaction details of MqnA and the critical roles of pocket residues. The calculation results confirm that the MqnA-catalyzed dehydration of chorismate follows the substrate-assisted E1cb mechanism, in which the enol carboxylate in the side chain of the substrate is responsible for deprotonating the C3 of chorismate. This proton transfer process is much slower than C4-OH departure. Calculations on different mutants reveal that S86 and N17 are important for anchoring the enol carboxylate of the substrate in a favorable conformation to extract the C3-proton. The strong H-bonds formed between the enol carboxylate of chorismate and S86/N17 play a key role in stabilizing the reaction intermediate. Consistent with the experimental observations, our calculations demonstrate that the MqnA N17D mutant also shows hydrolase activity and the typical enzyme-catalyzed hydrolysis mechanism is elucidated. The protonated D17 is responsible for saturating the methylene group of chorismate to start the hydrolysis reaction. The orientation of the carboxyl group of D17 is key in determining MqnA to be a dehydratase or hydrolase.

Comprehensive study on selective dehydrochlorination of 2-chloro-3,3,3-trifluoropropene over carbon-based catalysts and catalyst deactivation

3,3,3-trifluoropropyne (HFY-2223tz) is a novel refrigerant with great physicochemical properties. Though preparation of HFY-2223tz from halogenated olefins is theoretically effective, it remains great challenges for dehydrohalogenation from halogenated olefins, limiting the detailed knowledge. Here, we established a facile investigation to explore the gas-phase dehydrochlorination reaction of 2‑chloro-3,3,3-trifluoropropene (HCFO-1233xf) over various halides (Na, K, Rb, Cs) supported active carbon (AC) catalysts. The CsF was concluded as the optimal active component with best dehydrochlorination selectivity and conversion of HCFO-1233xf. The CO2-TPD results illustrated that dehydrochlorination of HCFO-1233xf proceeded through E1cB mechanism. Mechanism study revealed the evolution of side-products including (Z/E)-1,3,3,3-tetrafluoropropylene, 2,3,3,3-tetrafluoropropylene, (Z/E)-1‑chloro‑3,3,3-trifluoroproene, and 3,3,3-trifluoroprop-1-ene, etc. However, observable deactivation of CsF catalyst was noticed, which, according to combined XRD and XPS results and density functional theory (DFT) calculations, was attributed to the F/Cl exchange between HCFO-1233xf and catalyst, leading to rapid fluorine consumption. This work thus provides basic knowledge about heterogeneous catalytic synthesis of HFY-2223tz from dehydrohalogenation of halogenated olefins.

Hajos-Parrish-Eder-Sauer-Wiechert reaction: The definitive reaction mechanism deciphered by DFT calculations

The use of (S)-proline as a catalyst for intramolecular aldol reactions pioneered by Hajos, Parrish, Eder, Sauer and Wiechert paved the way for modern organocatalysis, which earned MacMillan and List the Nobel Prize in Chemistry in 2021. The work reported herein shed light on mechanistic aspects regarding the “prototypal” H-P-E-S-W reaction that, up to date, are unclear. The DFT calculations determined i) the mechanism of the dehydration step of the ketol intermediate that proceeds via an E1cB (elimination, unimolecular, conjugate base) mechanism; ii) the rate-determining steps (RDS) of the H-P-E-S-W reaction that correspond to enamine formation and dehydration; iii) the catalytic role of the water molecule formed during the reaction, that behaves as a proton shuttle during the enamine and CC bond formation and determines a significant lowering of the activation barriers.

Use of glycerol, waste glycerol from biodiesel production and other protic solvents in bioactive α,β-unsaturated ketones synthesis

Glycerol is the main co-product from biodiesel production and has been recognized as a sustainable solvent. Herein, we used glycerol and waste glycerol in synthesis of two bioactive α,β-unsaturated ketones (E,E)-1,5-diphenylpenta-2,4-dien-1-one (1) and (E,E)-2,6-dibenzylidenecyclohexanone (2), using aldol mono- and di-condensation reactions, respectively. Crude yield values were calculated from product mass after precipitation and drying. Purity was measured by High Performance Liquid Chromatography with Photodiode Array (HPLC-PAD) using analytical curves and reference compounds. Glycerol and waste glycerol were able to furnish 1 and 2 in higher crude yields and HPLC-PAD purities values than other protic solvents (ethanol, methanol, PEG-400 and water). In order to investigate reasons of glycerol efficiency when compared to water efficiency, we performed computational calculations using Density Functional Theory (DFT). Theoretical predictions confirmed the E1cB mechanism, as well as favourable energy barrier using glycerol in comparison to water, corroborating their sustainable properties. In addition, waste glycerol from corn and sunflower oil transesterifications were used in the synthesis of 1 and 2 for four recycles, displaying good crude yields and HPLC-purities.

Application of E1cB Elimination in Asymmetric Organocatalytic Cascade Reactions To Construct Polyheterocyclic Compounds.

By introducing a carbon functionality at 2-position of chromane, the formal asymmetric functionalization of the 3-position of 2-substituted chromane has been realized via a highly chemo-, regio-, and stereoselective organocatalytic cascade reaction in a sequential one-pot manner involving an E1cB mechanism governed ring-opening process. Critical to our success was the design of a chiral dipeptide-based bifunctional acid-base organocatalyst, which exhibited high catalytic activity at low catalyst loading (1-0.1 mol %), leading to biologically interesting polyheterocyclic compounds.

Menaquinone Biosynthesis: Biochemical and Structural Studies of Chorismate Dehydratase.

Menaquinone (MK, vitamin K) is a lipid-soluble quinone that participates in the bacterial electron transport chain. In mammalian cells, vitamin K functions as an essential vitamin for the activation of several proteins involved in blood clotting and bone metabolism. MqnA is the first enzyme on the futalosine-dependent pathway to menaquinone and catalyzes the aromatization of chorismate by water loss. Here we report biochemical and structural studies of MqnA. These studies suggest that the dehydration reaction proceeds by a variant of the E1cb mechanism in which deprotonation is slower than water loss and that the enol carboxylate of the substrate is serving as the base.

The mechanism and kinetics of methyl isobutyl ketone synthesis from acetone over ion-exchanged hydroxyapatite

The synthesis of methyl isobutyl ketone (MIBK) can be carried out by the condensation of acetone in the presence of hydrogen over a supported metal catalyst. Previous studies have shown that hydroxyapatite is an excellent catalyst for condensation reactions. The present investigation was undertaken in order to elucidate the reaction mechanism and site requirements for acetone coupling to MIBK over a physical mixture of hydroxyapatite and Pd/SiO2. The reaction is found to proceed by consecutive aldol addition to form diacetone alcohol (DAA), dehydration of DAA to mesityl oxide (MO), and hydrogenation of MO to MIBK. The products formed by feeding DAA and MO reveal that aldol addition of acetone is rapid and reversible, and that the subsequent dehydration of DAA is rate-limiting. Pyridine and CO2 titration show that aldol dehydration occurs over basic sites via an E1cB mechanism. A series of cation-substituted hydroxyapatite samples were prepared by ion-exchange to further investigate the role of acid-base strength on catalyst performance. Characterization of these samples by PXRD, BET, ICP-OES, XPS, CO2-TPD, and Raman spectroscopy demonstrated that the exchange procedure used does not affect the bulk properties of hydroxyapatite. DFT calculations reveal that in addition to affecting the Lewis acidity/basicity of the support, the size of the cation plays a significant role in the chemistry: cations that are too large (Ba2+) or too small (Mg2+) adversely affect reaction rates due to excessive stabilization of intermediate species. Strontium-exchanged hydroxyapatite was found to be the most active catalyst because it promoted α-hydrogen abstraction and CO bond cleavage of DAA efficiently.

Dehydrochlorination of 1, 1, 2-trichloroethane over SiO2-supported alkali and transition metal catalysts: Tunable selectivity controlled by the acid - base properties of the catalysts

Dehydrochlorination of 1, 1, 2-trichloroethane was performed on SiO2 supported alkali metal (Na. K, Cs) and transition metal (Mn, Ni, Zn) catalysts. The surface basicity or acidity of the catalyst exerted great influence on catalytic behaviors. The catalysts with higher amount of base or acid sites resulted in higher activity due to more adsorption sites for reactant. The basic catalysts (Cs/SiO2 and K/SiO2) tended to form vinylidene chloride with a selectivity up to 80 %; the neutral catalysts (Na/SiO2 and SiO2) tended to form 1, 2-dichloroethene with a selectivity up to about 80 %; the acidic catalysts (Zn/SiO2, Mn/SiO2 and Ni/SiO2) tended to form 1, 2-dichloroethene with a selectivity up to 96 %. Proposed reaction mechanisms included an E1cb mechanism with a carbanion intermediate on the basic catalysts, an E2 concerted mechanism on the neutral catalysts, and an E1 mechanism with a carbonium intermediate on the acidic catalysts.

Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins

AbstractThe uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3′‐deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine‐5′‐aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3′‐deoxy pacidamycin moiety with the synthetic anti‐retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.

Kinetic Study and Mechanism Hydrolysis of 4‐Bromo‐3,5 dimethylphenyl N‐methylcarbamate in Aqueous Media

ABSTRACTDegradation via hydrolysis is among the main transformation pathways and particularly for N‐methylcarbamates. Carbamate pesticide hydrolysis is known to proceed through alkaline catalysis, with reaction of the hydroxide ion with the carbonyl function or with abstraction of hydrogen in the α position with respect to the carbonyl. This reaction leads to the formation of methylamine and corresponding phenol. In this respect, the reaction kinetics of 4‐bromo‐3,5‐dimethylphenyl N‐methylcarbamate (BDMC) hydrolysis have been investigated in alkaline solution using a spectrophotometric technique and reversed phase liquid chromatography. The kinetic constants were determined following a proposed pseudo–first‐order kinetic model. The positive activation entropy ΔS≠ = +35.73 J mol−1 K−1 and the absence of general base catalysis indicated an unimolecular elimination conjugate base (E1cB) hydrolytic mechanism involving the formation of methyl isocyanate. This result was confirmed by the fact that BDMC fits well into brönsted and Hammett lines, obtained for a series of substituted N‐methylcarbamate whose decomposition in aqueous media was established to follow an E1cB mechanism.

X-Ray snapshots of a pyridoxal enzyme: a catalytic mechanism involving concerted [1,5]-hydrogen sigmatropy in methionine \u03b3-lyase

Pyridoxal 5′-phosphate (PLP)-enzymes are essentially involved in amino acid and amine metabolism of a wide variety of organisms. Despite their extensive biochemical studies, there are little evidence and structural data to comprehensively elaborate the catalytic mechanism. We obtained X-ray snapshots of l-methionine γ-lyase from Entamoeba histolytica (EhMGL), a PLP-enzyme catalyzing the γ-elimination reaction of methionine. Here, we suggest a catalytic mechanism of EhMGL by using the X-ray snapshots covering all stages of this multistep catalysis reaction. Initial formation of a Michaelis complex is followed by the migration of double bond from the C4′=Nα–Cα moiety in an intermediate PLP-methionine imine to C4′–Nα=Cα in pyridoxamine 5′-phosphate (PMP)-α,β-dehydromethionine imine without intervention of a putative quinonoid intermediate. The enzyme can facilitate the subsequent γ-elimination of methanethiol by the possible general acid-base catalysis of Tyr108 for the E1cB mechanism, enabling to form the ene-imine C4′–Nα=Cα–Cβ=Cγ structure with the s-cis conformation, which is prerequisite for the non-enzymatic symmetry-allowed suprafacial [1,5]-hydrogen shift to complete the catalytic cycle by releasing α-ketobutyrate. The mechanism based on the X-ray snapshots is consistent with the reactivity of MGL toward methionine analogues. The generality of such a mechanism involving non-enzymatic concerted reaction in other PLP enzymes is discussed.

New Mechanism Proposed for the Base-Catalyzed Urea⁻Formaldehyde Condensation Reactions: A Theoretical Study.

Base-catalyzed urea–formaldehyde condensation reactions were investigated by using a quantum chemistry method. It was found that monomethylolurea or N,N’-dimethylolurea can produce the methyleneurea intermediate (–HN–CO–N=CH2) with the catalysis of base. The E1cb (unimolecular elimination of conjugate base) mechanism was identified for the formation of such an intermediate. The potential energy barrier was theoretically predicted to be 59.6 kJ/mol for the E1cb step, which is about half of that of previously proposed SN2 (bimolecular nucleophilic substitution) mechanism. In the subsequentcondensation reactions, Michael addition reactions that lead to different condensed structures can occur between the methyleneurea intermediate and the anions produced from methylolureas under alkaline conditions. Based on the theoretical calculations on the kinetics and thermodynamics of the selected reactions, the competitive formations of methylene linkages, ether linkages and uron were discussed in combination with our previous experimental observations.

Kinetics and Mechanism of Degradation of Aqueous Promecarb Insecticide Studied by UV Spectrophotometry and HPLC

The present paper deals with the degradation mechanism of the insecticide promecarb, or 3-isopropyl-5-methylphenyl- N-methylcarbamate, in aqueous media. The reaction kinetics have been investigated using UV spectrophotometry and reversed phase HPLC. The determination of 3-isopropyl-5-methylphenol as the main product of promecarb hydrolysis gives evidence for the significant reactivity of this insecticide in alkaline solution. The rate constants were determined following a proposed first-order kinetic model. The positive activation entropy obtained Δ S≠= +66.82 J mol−1K−1and the absence of general basic catalysis indicates an E1cB mechanism involving unimolecular collapse of the promecarb via a methylisocyanate intermediate. These results were confirmed by the fact that promecarb fits well into Brønsted and Hammett plots obtained for a series of substituted N-methylcarbamates for which the decomposition in aqueous media was established to follow an E1cB mechanism.

Site-Directed Chemical Mutations on Abzymes: Large Rate Accelerations in the Catalysis by Exchanging the Functionalized Small Nonprotein Components.

Taking advantage of antibody molecules to generate tailor-made binding sites, we propose a new class of protein modifications, termed as "site-directed chemical mutation." In this modification, chemically synthesized catalytic components with a variety of steric and electronic properties can be noncovalently and nongenetically incorporated into specific sites in antibody molecules to induce enzymatic activity. Two catalytic antibodies, 25E2 and 27C1, possess antigen-combining sites which bind catalytic components and act as apoproteins in catalytic reactions. By simply exchanging these components, antibodies 25E2 and 27C1 can catalyze a wide range of chemical transformations including acyl-transfer, β-elimination, aldol, and decarboxylation reactions. Although both antibodies were generated with the same hapten, phosphonate diester 1, they showed different catalytic activity. When phenylacetic acid 4 was used as the catalytic component, 25E2 efficiently catalyzed the elimination reaction of β-haloketone 2, whereas 27C1 showed no catalytic activity. In this work, we focused on the β-elimination reaction and examined the site-directed chemical mutation of 27C1 to induce activity and elucidate the catalytic mechanism. Molecular models showed that the cationic guanidyl group of ArgH52 in 27C1 makes a hydrogen bond with the P═O oxygen in the hapten. This suggested that during β-elimination, ArgH52 of 27C1 would form a salt bridge with the carboxylate of 4, thus destroying reactivity. Therefore, we utilized site-directed chemical mutation to change the charge properties of the catalytic components. When amine components 7-10 were used, 27C1 efficiently catalyzed the β-elimination reaction. It is noteworthy that chemical mutation with secondary amine 8 provided extremely high activity, with a rate acceleration [(kcat/Km 2)/kuncat] of 1 000 000. This catalytic activity likely arises from the proximity effect, plus general-base catalysis associated the electrostatic interactions. In 27C1, the cationic guanidyl group of ArgH52 is spatially close to the nitrogen of the amine components. In this microenvironment, the intrinsic pKa of the amine is perturbed and shifts to a lower pKa, which efficiently abstracts the α-proton during the reaction. This mechanism is consistent with the observed kinetic isotope effect (E2 or E1cB mechanism). Thus, site-directed chemical mutation provides a better understanding of enzyme functions and opens new avenues in biocatalyst research.

The Synthesis of Ketone‐Derived Enamides by Elimination of HCN from Cyanoamides

Treatment of easily available ketone‐derived cyanoamides with NaOtBu leads to enamides in a simple, scalable, and inexpensive one‐step operation in good yield. Enamides not stabilized by conjugation or by inclusion in a ring can also be prepared. An E1cB mechanism consistent with all results and observations, is proposed. The Z geometry of the product enamide is highly favoured, and the regioselectivity can be directed by one′s choice of protecting group.

Ring-Closing Metathesis Reactions of Acyloxysulfones: Synthesis of γ-Alkylidene Butenolides

An acyloxysulfone ring-closing metathesis/sulfone elimination sequence has been developed for the preparation of various γ-alkylidene butenolides. The elimination is proposed to proceed via an E1cb mechanism leading to (<i>Z</i>)-γ-alkylidene butenolides as the major products.

Elimination Reactions of Aryl Furylacetates Promoted by R2NH-R2NH2+in 70 mol% MeCN(aq). Effects of β-Aryl on the Ketene-Forming Transition-State

, the effect of the β-aryl group on the ketene-formingelimination was assessed.Key Words : Elimination, E2 and E1cb Mechanism, β–Aryl Group effectIntroductionExtensive studies of the structure-reactivity relationshipsin the ketene-forming elimination reactions have led to thequalitative understanding of the relationship between thereactant structure and the mechanism.

Kinetic study by UV Spectrophotometry of Carzol degradation in aqueous medium

This paper deals with the kinetic hydrolysis in aqueous media of Carzol or (E) 3-dimethylamino- methyleneaminophenyl-N-methylcarbamate hydrochloride. The Carzol is a bifunctional compound which belongs to the chemical families formamidine and carbamate. This work is carried out by UV Spectrophotometry. The successive determination of 3-aminophenyl-N-methylcarbamate and 3-aminophenol, as the mainproducts of the formamidine and the carbamate groups of Carzol hydrolysis gives evidence for the significant reactivity of this insecticide-acaricide in aqueous media. The obtained negative activation entropy ΔS≠= - 32.39 J mol-1K-1 indicates a BAC2 mechanism involving bimolecular collapse of the formamidine group of Carzol. While, the obtained positive activation entropy ΔS≠= +100.24J mol-1 K-1and the absence of basic general catalysis indicate an E1cB mechanism involving unimolecular collapse of the carbamate group of Carzol via a methylisocyanate intermediate.

The reaction mechanism of UDP-GlcNAc 5,6-dehydratase: a quantum mechanical/molecular mechanical (QM/MM) study

UDP-GlcNAc 5,6-dehydratase (TunA), a particular member of the short-chain dehydrogenase/reductase family, catalyzes the bioconversion of UDP-GlcNAc to UDP-6-deoxy-GlcNAc-5,6-ene. To elucidate the detailed mechanism of TunA, combined quantum mechanical/molecular mechanical calculations have been performed. The calculation results reveal that the TunA-catalyzed process follows a three-step sequential mechanism, including oxidation, dehydration and reduction. The oxidation step is calculated to be rate limiting and undergoes a concerted but asynchronous mechanism with an energy barrier of 21.6 kcal/mol. The dehydration step proceeds via the E1cB mechanism involving proton transfer and departure of hydroxyl group. Our calculation results show that the key residue Glu121 is ideally situated in the active site and serves as the general base and then as acid to take part in the elimination of water. The residue Cys120 is confirmed to play an important role in maintaining the active pocket arrangement. As the reverse process of the oxidation reaction, the reduction step follows the same concerted asynchronous mechanism, but the hydride transfer is prior to proton transfer.