Mechanism Of Decarboxylation Research Articles

The thermally induced decarboxylation mechanism of a mixed-oxidation state carboxylate-based iron metal-organic framework.

Investigations into a thermally generated decarboxylation mechanism for metal site activation and the generation of mesopores in a carboxylate iron-based MOF, PCN-250, have been conducted. PCN-250 exhibits an interesting oxidation state change during thermal treatment under inert atmospheres or vacuum conditions, transitioning from an Fe(iii)3 cluster to a Fe(ii)Fe(iii)2 cluster. To probe this redox event and discern a mechanism of activation, a combination of thermogravimetric analysis, gas sorption, scanning electron microscopy, 57Fe Mössbauer spectroscopy, gas chromatography-mass spectrometry, and X-ray diffraction studies were conducted. The results suggest that the iron-site activation occurs due to ligand decarboxylation above 200 °C. This is also consistent with the generation of a missing cluster mesoporous defect in the framework. The resulting mesoporous PCN-250 maintains high thermal stability, preserving crystallinity after multiple consecutive high-temperature regeneration cycles. Additionally, the thermally reduced PCN-250 shows improvements in the total uptake capacity of methane and CO2.

Synthesis of 2-Quinolinones via a Hypervalent Iodine(III)-Mediated Intramolecular Decarboxylative Heck-Type Reaction at Room Temperature.

A hypervalent iodine(III)-mediated intramolecular decarboxylative Heck-type reaction of 2-vinyl-phenyl oxamic acids has been developed. The unique ring-strain-enabled radical decarboxylation mechanism is preliminarily revealed. This protocol features metal-free reaction conditions and operational simplicity, allowing the lactamization of 2-vinylanilines using a readily accessible carbonyl source and the synthesis of various 2-quinolinones with excellent chemoselectivity at room temperature.

Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase.

The electron-rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We herein provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non-heme iron(II)-dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)-3-((carboxymethyl)amino)butanoic acid to (R)-3-isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, of which several members are critical for the virulence of pathogenic mycobacteria.

Isonitrile Formation by a Non‐Heme Iron(II)‐Dependent Oxidase/Decarboxylase

AbstractThe electron‐rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We herein provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non‐heme iron(II)‐dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)‐3‐((carboxymethyl)amino)butanoic acid to (R)‐3‐isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, of which several members are critical for the virulence of pathogenic mycobacteria.

Reversibility of the catalytic ketonization of carboxylic acids and of beta-keto acids decarboxylation

Decarboxylation of beta-keto acids in enzymatic and heterogeneous catalysis has been considered in the literature as an irreversible reaction due to a large positive entropy change. We report here experimental evidence for its reversibility in heterogeneous catalysis by solid metal oxide(s) surfaces. Ketones and carboxylic acids having 13C-labeled carbonyl group undergo 13C/12C exchange when heated in an autoclave in the presence of 12CO2 and ZrO2 catalyst. In the case of ketones, the carbonyl group exchange with CO2 serves as evidence for the reversibility of all steps of the catalytic mechanism of carboxylic acids ketonic decarboxylation, i.e. enolization, condensation, dehydration and decarboxylation.

Orotidine 5'-Monophosphate Decarboxylase: Probing the Limits of the Possible for Enzyme Catalysis.

ConspectusThe mystery associated with catalysis by what were once regarded as protein black boxes, diminished with the X-ray crystallographic determination of the three-dimensional structures of enzyme–substrate complexes. The report that several high-resolution X-ray crystal structures of orotidine 5′-monophosphate decarboxylase (OMPDC) failed to provide a consensus mechanism for enzyme-catalyzed decarboxylation of OMP to form uridine 5′-monophosphate, therefore, provoked a flurry of controversy. This controversy was fueled by the enormous 1023-fold rate acceleration for this enzyme, which had “jolted many biochemists’ assumptions about the catalytic potential of enzymes.” Our studies on the mechanism of action of OMPDC provide strong evidence that catalysis by this enzyme is not fundamentally different from less proficient catalysts, while highlighting important architectural elements that enable a peak level of performance. Many enzymes undergo substrate-induced protein conformational changes that trap their substrates in solvent occluded protein cages, but the conformational change induced by ligand binding to OMPDC is incredibly complex, as required to enable the development of 22 kcal/mol of stabilizing binding interactions with the phosphodianion and ribosyl substrate fragments of OMP. The binding energy from these fragments is utilized to activate OMPDC for catalysis of decarboxylation at the orotate fragment of OMP, through the creation of a tight, catalytically active, protein cage from the floppy, open, unliganded form of OMPDC. Such utilization of binding energy for ligand-driven conformational changes provides a general mechanism to obtain specificity in transition state binding. The rate enhancement that results from the binding of carbon acid substrates to enzymes is partly due to a reduction in the carbon acid pKa that is associated with ligand binding. The binding of UMP to OMPDC results in an unusually large >12 unit decrease in the pKa = 29 for abstraction of the C-6 substrate hydrogen, due to stabilization of an enzyme-bound vinyl carbanion, which is also an intermediate of OMPDC-catalyzed decarboxylation. The protein–ligand interactions operate to stabilize the vinyl carbanion at the enzyme active site compared to aqueous solution, rather than to stabilize the transition state for the concerted electrophilic displacement of CO2 by H+ that avoids formation of this reaction intermediate. There is evidence that OMPDC induces strain into the bound substrate. The interaction between the amide side chain of Gln-215 from the phosphodianion gripper loop and the hydroxymethylene side chain of Ser-154 from the pyrimidine umbrella of ScOMPDC position the amide side chain to interact with the phosphodianion of OMP. There are no direct stabilizing interactions between dianion gripper protein side chains Gln-215, Tyr-217, and Arg-235 and the pyrimidine ring at the decarboxylation transition state. Rather these side chains function solely to hold OMPDC in the catalytically active closed conformation. The hydrophobic side chains that line the active site of OMPDC in the region of the departing CO2 product may function to stabilize the decarboxylation transition state by providing hydrophobic solvation of this product.

Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase.

The utilization of CO2 as a carbon source for organic synthesis meets the urgent demand for more sustainability in the production of chemicals. Herein, we report on the enzyme‐catalyzed para‐carboxylation of catechols, employing 3,4‐dihydroxybenzoic acid decarboxylases (AroY) that belong to the UbiD enzyme family. Crystal structures and accompanying solution data confirmed that AroY utilizes the recently discovered prenylated FMN (prFMN) cofactor, and requires oxidative maturation to form the catalytically competent prFMNiminium species. This study reports on the in vitro reconstitution and activation of a prFMN‐dependent enzyme that is capable of directly carboxylating aromatic catechol substrates under ambient conditions. A reaction mechanism for the reversible decarboxylation involving an intermediate with a single covalent bond between a quinoid adduct and cofactor is proposed, which is distinct from the mechanism of prFMN‐associated 1,3‐dipolar cycloadditions in related enzymes.

OleB from Bacterial Hydrocarbon Biosynthesis Is a β-Lactone Decarboxylase That Shares Key Features with Haloalkane Dehalogenases.

OleB is an α/β-hydrolase found in bacteria that biosynthesize long-chain olefinic hydrocarbons, but its function has remained obscure. We report that OleB from the Gram-negative bacterium Xanthomonas campestris performs an unprecedented β-lactone decarboxylation reaction, to complete cis-olefin biosynthesis. OleB reactions monitored by 1H nuclear magnetic resonance spectroscopy revealed a selectivity for decarboxylating cis-β-lactones and no discernible activity with trans-β-lactones, consistent with the known configuration of pathway intermediates. Protein sequence analyses showed OleB proteins were most related to haloalkane dehalogenases (HLDs) and retained the canonical Asp-His-Asp catalytic triad of HLDs. Unexpectedly, it was determined that an understudied subfamily, denoted as HLD-III, is comprised mostly of OleB proteins encoded within oleABCD gene clusters, suggesting a misannotation. OleB from X. campestris showed very low dehalogenase activity only against haloalkane substrates with long alkyl chains. A haloalkane substrate mimic alkylated wild-type X. campestris OleB but not OleBD114A, implicating this residue as the active site nucleophile as in HLDs. A sequence-divergent OleB, found as part of a natural OleBC fusion and classified as an HLD-III, from the Gram-positive bacterium Micrococcus luteus was demonstrated to have the same activity, stereochemical preference, and dependence on the proposed Asp nucleophile. H218O studies with M. luteus OleBC suggested that the canonical alkyl-enzyme intermediate of HLDs is hydrolyzed differently by OleB enzymes, as 18O is not incorporated into the nucleophilic aspartic acid. This work defines a previously unrecognized reaction in nature, functionally identifies some HLD-III enzymes as β-lactone decarboxylases, and posits an enzymatic mechanism of β-lactone decarboxylation.

Ketone Formation from Carboxylic Acids by Ketonic Decarboxylation: The Exceptional Case of the Tertiary Carboxylic Acids.

For the reaction mechanism of the ketonic decarboxylation of two carboxylic acids, a β-keto acid is favored as key intermediate in many experimental and theoretical studies. Hydrogen atoms in the α-position are an indispensable requirement for the substrates to react by following this mechanism. However, isolated observations with tertiary carboxylic acids are not consistent with it and these are revisited and discussed herein. The experimental results obtained with pivalic acid indicate that the ketonic decarboxylation does not occur with this substrate. Instead, it is consumed in alternative reactions such as disintegration into isobutene, carbon monoxide, and water (retro-Koch reaction). In addition, the carboxylic acid is isomerized or loses carbon atoms, which converts the tertiary carboxylic acid into carboxylic acids bearing α-proton atoms. Hence, the latter are suitable to react through the β-keto acid pathway. A second substrate, 2,2,5,5-tetramethyladipic acid, reacted by following the same retro-Koch pathway. The primary product was the monocarboxylic acid 2,2,5-trimethyl-4-hexenoic acid (and its double bond isomer), which might be further transformed into a cyclic enone or a lactone. The ketonic decarboxylation product, 2,2,5,5-tetramethylcyclopentanone was observed in traces (<0.2 % yield). Therefore, it can be concluded that the observed experimental results further support the proposed mechanism for the ketonic decarboxylation via the β-keto acid intermediate.

The Enigmatic P450 Decarboxylase OleT Is Capable of, but Evolved To Frustrate, Oxygen Rebound Chemistry.

OleT is a cytochrome P450 enzyme that catalyzes the removal of carbon dioxide from variable chain length fatty acids to form 1-alkenes. In this work, we examine the binding and metabolic profile of OleT with shorter chain length (n ≤ 12) fatty acids that can form liquid transportation fuels. Transient kinetics and product analyses confirm that OleT capably activates hydrogen peroxide with shorter substrates to form the high-valent intermediate Compound I and largely performs C-C bond scission. However, the enzyme also produces fatty alcohol side products using the high-valent iron oxo chemistry commonly associated with insertion of oxygen into hydrocarbons. When presented with a short chain fatty acid that can initiate the formation of Compound I, OleT oxidizes the diagnostic probe molecules norcarane and methylcyclopropane in a manner that is reminiscent of reactions of many CYP hydroxylases with radical clock substrates. These data are consistent with a decarboxylation mechanism in which Compound I abstracts a substrate hydrogen atom in the initial step. Positioning of the incipient substrate radical is a crucial element in controlling the efficiency of activated OH rebound.

Investigating the Catalytic Molecular Details of Malonyl‐thioester Decarboxylating Enzymes

Decarboxylation reactions release the free energy necessary for carbon‐carbon bond formation in the biosynthesis of polyketides and fatty acids. Ketosynthases from fatty acid and polyketide synthases perform a decarboxylative Claisen‐condensation between an acyl‐thioester intermediate and a malonyl‐derived extender unit. However, the molecular details of decarboxylation and C‐C bond formation is not well understood. We are synthesizing and characterizing non‐hydrolyzable and non‐decarboxylatable substrate mimics to capture intermediate catalytic states via X‐ray crystallography. Capturing the substrate mimics in the active site of ketosynthases will yield insight into the mechanism of decarboxylation and polymerization of the two carbon units. Decarboxylation reactions are essentially non‐reversible and have various possible chemical mechanisms, which makes them difficult to study. Ketosynthases are also challenging to study due to their multiple substrates and need for protein‐protein interactions. Therefore, we have begun characterization of our substrate mimics with simpler systems, such as malonyl‐ and methylmalonyl‐CoA decarboxylases (MCD and MMCD), as a proof of principle. We have successfully crystallized E. coli MMCD and the bifunctional acyltransferase/decarboxylase, LnmK, with our substrate mimics. Our substrate mimics preserve the thioester carbonyl as a thioester, ester or amide and have a nitro or sulfonate moiety in place of the carboxylate. Structures of MMCD and LnmK with multiple bound substrate mimics reveals mechanistic insight into decarboxylation. While MMCD and LnmK have no sequence homology to ketosynthases, this study reveals that our substrate mimics indeed inhibit decarboxylation reactions. Therefore, we are beginning to apply this concept to ketosynthases from type III polyketide synthases.Support or Funding InformationFunding provided by the Department of Biochemistry at Purdue University

Influence of Solvent on Liquid Phase Hydrodeoxygenation of Furfural-Acetone Condensation Adduct using Ni/Al2O3-ZrO2 Catalysts

Influence of water and acidic protic solvent on hydrodeoxygenation (HDO) of the furfural-acetone adduct (FAA) over Ni/Al2O3-ZrO2 (NiAZ) catalysts were investigated. The HDO of FAA was carried out in a batch reactor at 150°C for 8 hours. The NiAZ catalysts were home-made catalysts which were prepared by wet impregnation method with 10 and 20% nickel loading. The HDO reaction of FAA using 10NiAZ in water at 150°C gave alkane and oxygenated hydrocarbons at 31.41% with selectivity over tridecane (C13) in 6.67%. On the other hand, a reaction using acetic acid:water (1:19 v/v) in similar reaction condition gave only oxygenated compounds and hydrocracking product (C8-C10). The formation of tridecane (C13) was proposed by hydrogenation of C=O and C=C followed by decarboxylation without hydrocracking process. The presence of water facilitated decarboxylation mechanism by stabilized dehydrogenated derivatives of FAA.

Study on the Mechanism of Catalytic Decarboxylation of Naphthenic Acid

Study on the Mechanism of Catalytic Decarboxylation of Naphthenic Acid

Metal-catalyzed Decarboxylative Fluoroalkylation Reactions.

Metal-catalyzed decarboxylative fluoroalkylation reactions enable the conversion of simple O-based substrates into biologically relevant fluorinated analogs. Herein, we present decarboxylative methods that facilitate the synthesis of trifluoromethyl- and difluoroketone-containing products. We highlight key mechanistic aspects that are critical for efficient catalysis, and that inspired our thinking while developing the reactions.

Deoxygenation of octanoic acid catalyzed by hollow spherical Ni/ZrO2

A series of Ni located on hollow spherical ZrO2 catalysts was prepared, and their catalytic performances for octanoic acid deoxygenation were investigated. The ZrO2 hollow spheres saturated by the water phase served as a nanoreactor that captured octanoic acid to react with Ni located inside a hollow spherical ZrO2. The complete conversion of octanoic acid deoxygenation could be achieved by migration of reactants and products in the water-oil biphasic phase. Oxygen vacancies on ZrO2 that resulted from calcination temperature improved the catalytic activity of deoxygenation. Propionic acid was taken as a model compound instead of octanoic acid in view of their same functional group (carboxyl), to study the mechanisms of hydrodeoxygenation, decarbonylation, and decarboxylation through density functional theory of calculations. The main reaction route was decarboxylation which was consistent with the experimental results.

Functional Study of Lysine Decarboxylases from Klebsiella pneumoniae in Escherichia coli and Application of Whole Cell Bioconversion for Cadaverine Production.

Klebsiella pneumoniae is a gram-negative, non-motile, rod-shaped, and encapsulated bacterium in the normal flora of the intestines, mouth, skin, and food, and has decarboxylation activity, which results in generation of diamines (cadaverine, agmatine, and putrescine). However, there is no specific information on the exact mechanism of decarboxylation in K. pnuemoniae. Specifically lysine decarboxylases that generate cadaverine with a wide range of applications has not been shown. Therefore, we performed a functional study of lysine decarboxylases. Enzymatic characteristics such as optimal pH, temperature, and substrates were examined by overexpressing and purifying CadA and LdcC. CadA and LdcC from K. pneumoniae had a preference for L-lysine, and an optimal reaction temperature of 37°C and an optimal pH of 7. Although the activity of purified CadA from K. pneumoniae was lower than that of CadA from E. coli, the activity of K. pneumoniae CadA in whole cell bioconversion was comparable to that of E. coli CadA, resulting in 90% lysine conversion to cadaverine with pyridoxal 5'-phosphate L-lysine.

ChemInform Abstract: One‐Pot Palladium(II)‐Catalyzed Synthesis of Fluorenones via Decarboxylative Cyclization.

AbstractThe reaction works with 1,1′‐biphenyl‐2‐carboxylic acids only.

Electrophilic and nucleophilic pathways in ligand oxide mediated reactions of phenylsulfinylacetic acids with oxo(salen)chromium(V) complexes

The mechanism of oxidative decarboxylation of phenylsulfinylacetic acids (PSAA) by oxo(salen)Cr(V)+ ion in the presence of ligand oxides has been studied spectrophotometrically in acetonitrile medium. Addition of ligand oxides (LO) causes a red shift in the λmax values of oxo(salen) complexes and an increase in absorbance with the concentration of LO along with a clear isobestic point. The reaction shows first-order dependence on oxo(salen)-chromium(V)+ ion and fractional-order dependence on PSAA and ligand oxide. Michaelis–Menten kinetics without kinetic saturation was observed for the reaction. The order of reactivity among the ligand oxides is picoline N-oxide>pyridine N-oxide>triphenylphosphine oxide. The low catalytic activity of TPPO was rationalized. Both electron-withdrawing and electron-donating substituents in the phenyl ring of PSAA facilitate the reaction rate. The Hammett plots are non-linear upward type with negative ρ value for electron-donating substituents, (ρ−=−0.740 to −4.10) and positive ρ value for electron-withdrawing substituents (ρ+=+0.057 to +0.886). Non-linear Hammett plot is explained by two possible mechanistic scenarios, electrophilic and nucleophilic attack of oxo(salen)chromium(V)+-LO adduct on PSAA as the substituent in PSAA is changed from electron-donating to electron-withdrawing. The linearity in the logk vs. Eox plot confirms single-electron transfer (SET) mechanism for PSAAs with electron-donating substituents.

A paradigm shift in rate determining step from single electron transfer between phenylsulfinylacetic acids and iron(III) polypyridyl complexes to nucleophilic attack of water to the produced sulfoxide radical cation: a non‐linear Hammett

Mechanism of oxidative decarboxylation of phenylsulfinylacetic acids (PSAAs) by iron(III) polypyridyl complexes in aqueous acetonitrile medium has been investigated spectrophotometrically. An initial intermediate formation between PSAA and [Fe(NN)3]3+ is confirmed from the observed Michaelis–Menten kinetics and fractional order dependence on PSAA. Significant rate retardation with concentration of [Fe(NN)3]3+ is rationalized on the basis of coordination of a water molecule at the carbon atom adjacent to the ring nitrogen of the metal polypyridyl complexes by nucleophilic attack at higher concentrations. Electron‐withdrawing and electron‐releasing substituents in PSAA facilitate the reaction and Hammett correlation gives an upward ‘V’ shaped curve. The apparent upward curvature is rationalized based on the change in the rate determining step from electron transfer to nucleophilic attack, by changing the substituents from electron‐releasing to electron‐withdrawing groups. Electron‐releasing substituents in PSAA accelerate the electron transfer from PSAA to the complex and also stabilize the intermediate through resonance interaction leading to negative reaction constants (ρ). Conversely, electron‐withdrawing groups, while retarding the electron transfer exert an accelerating effect on the nucleophilic attack of H2O which leading to low magnitude of ρ+ compared to high ρ− values of electron‐releasing groups. Marcus theory is applied, and a fair agreement is seen with the experimental values. Copyright © 2016 John Wiley &amp; Sons, Ltd.

Catalytic decarboxylation of non-edible oils over three-dimensional, mesoporous silica-supported Pd

Deoxygenation of fatty acids (oleic and stearic acids) and non-edible oil (jatropha oil) over Pd(1–5wt%) supported on two structurally different, three-dimensional, mesoporous silica (SBA-12 and SBA-16) catalysts was investigated. Pd/SBA-16 (cubic mesoporous structure with space group Im3¯m) showed higher catalytic activity than Pd/SBA-12 (hexagonal mesoporous structure with space group p63/mmc). The influence of reaction parameters like temperature, H2 pressure and Pd content as well as the nature of the feedstock on catalytic activity and product selectivity was studied. A temperature of above 320°C, reaction time of 5h and Pd content (on silica surface) of 3wt% enabled complete conversion of the fatty compounds into diesel-range hydrocarbons. Deoxygenation proceeded through hydrodeoxygenation and decarboxylation mechanisms when a saturated (stearic) acid was used as a feed while it advanced mainly through decarboxylation route when an unsaturated (oleic) acid was employed. Higher surface hydrophobicity and smaller size particles of Pd are the possible causes for the superior catalytic activity of Pd/SBA-16.