Kinetic Isotope Effect Studies Research Articles

Palladium-Catalyzed Oxidative Cyclization of O-Aryl Cyclic Vinylogous Esters: Synthesis of Benzofuran-Fused Cyclohexenones.

This study presents a method for synthesizing functionalized hydrodibenzofuran derivatives. Using palladium catalysis, O-aryl cyclic vinylogous esters undergo dehydrogenative intramolecular arylation at the vinylic carbon. Preliminary kinetic isotope effect studies suggest that the C(aryl)-H bond cleavage may be the rate-determining step.

Insights into C-H Activation Reactivity of Fe (IV)O Porphyrinoid Complexes: A Computational Investigation.

This work presents a detailed comparative analysis of C-H activations catalyzed by three different Fe(IV)O porphyrinoid complexes. The study considers the usual heme porphyrin (complex I) as the base compound, porphyrazine (complex II), which is obtained by replacing carbon with nitrogen at the meso position, and phthalocyanine (complex III), which is obtained through the peripheral benzoannulation of porphyrazine. The focus here is to explore the impact of bridging groups and peripheral functionalization in heme systems on reactivity. Factors such as distortion energy and electron acceptor orbitals significantly affect the overall reactivity. The effect of substitution on quantum mechanical tunneling, using H/D kinetic isotope effect studies, is also included. The results reveal a fascinating reactivity order: meso nitrogen substitution enhances reactivity, while additional benzo-annulation hinders reactivity, leading to the order complex II > complex I > complex III. In comparison to the usual Cpd I, which is Fe(IV)O-porphyrin π cation radical with an -SH axial ligand, complex II was found to be more reactive. The electron affinity of the Fe(IV)O complexes and the dissociation energy of the forming Fe(IV)O-H bond aligns with observed reactivity trend. These findings support the use of accessible iron frameworks derived from porphyrin in C-H activation processes.

Revealing OH species in situ generated on low-valence Cu sites for selective carbonyl oxidation

Catalytic oxidation through the transfer of lattice oxygen from metal oxides to reactants, namely the Mars-van Krevelen mechanism, has been widely reported. In this study, we evidence the overlooked oxidation route that features the in situ formation of surface OH species on Cu catalysts and its selective addition to the reactant carbonyl group. We observed that glucose oxidation to gluconic acid in air (21% O2) was favored on low-valence Cu sites according to X-ray spectroscopic analyses. Molecular O2 was activated in situ on Cu0/Cu+ forming localized, adsorbed hydroxyl radicals (*OH) which played the primary reactive oxygen species as confirmed by the kinetic isotope effect (KIE) study in D2O and in situ Raman experiments. Combined with DFT calculations, we proposed a mechanism of O2-to-*OH activation through the *OOH intermediate. The localized *OH exhibited higher selectivity toward glucose oxidation at C1HO to form gluconic acid (up to 91% selectivity), in comparison with free radicals in bulk environment that emerged from thermal, noncatalytic hydrogen peroxide decomposition (40% selectivity). The KIE measurements revealed a lower glucose oxidation rate in D2O than in H2O, highlighting the role of water (H2O/D2O) or its derivatives (e.g., *OH/*OD) in the rate-determining step. After proving the C1-H activation step kinetically irrelevant, we proposed the oxidation mechanism that was characterized by the rate-limiting addition of *OH to C1=O in glucose. Our findings advocate that by maneuvering the coverage and activity of surface *OH, high-performance oxidation of carbonyl compounds beyond biomass molecules can be achieved in water and air using nonprecious metal catalysts.

Atomically Isolated Pd Sites Promote Electrochemical CO Reduction to Acetate through a Protonation-Regulated Mechanism.

Electrochemical CO reduction reaction (CORR) offers a promising approach for sustainable acetate production, the promotion of which requires the control of multiple protonation steps. This paper describes the synthesis of atomically isolated Pd sites onto Cu nanoflakes to regulate the protonation of key intermediates. The Pd sites with moderate water activation capability are found to enhance the protonation of *CO at the neighboring Cu site to *COH, which is confirmed to be the rate-determining step through kinetic isotope effect studies. The formation of *COH-*CO is therefore promoted. Additionally, the Pd sites would preferentially protonate the C-OH group in *COH-*CO due to the spatial approximability and electronic modulation effects, generating *CCO for the selective formation of acetate. An acetate Faradaic efficiency of 59.5% is achieved at -0.78 V vs reversible hydrogen electrode (RHE), with a maximum partial current density of 286 mA cm-2 at -0.86 V vs RHE. The optimized catalyst also exhibits long-term stability for 500 h at 100 mA cm-2 in a membrane electrode assembly. This work reveals a new promoting mechanism for selective CORR with simultaneous tuning of the structural and electronic properties of the proton-supplying sites.

Mechanistic Analysis of 5-Hydroxy γ-Pyrones as Michael Acceptor Prodrugs.

Substituted 5-hydroxy γ-pyrones have shown promise as covalent inhibitor leads against cysteine proteases and transcription factors, but their hydrolytic instability has hindered optimization efforts. Previous mechanistic proposals have suggested that these molecules function as Michael acceptor prodrugs, releasing a leaving group to generate an o-quinone methide-like structure. Addition to this electrophile of either water or an active site cysteine was purported to lead to inhibitor hydrolysis or enzyme inhibition, respectively. Through the use of kinetic nuclear magnetic resonance experiments, Hammett analysis, kinetic isotope effect studies, and density functional theory calculations, our findings suggest that enzyme inhibition and hydrolysis proceed by distinct pathways and are differentially influenced by substituent electronics. This mechanistic revision helps enable a more rational optimization for this class of promising compounds.

Theoretical study of kinetic isotope effects for vacancy diffusion of impurity in solids

Theoretical study of kinetic isotope effects for vacancy diffusion of impurity in solids

Cobalt(II)-Catalyzed Synthesis of γ-Diketones from Aryl Alkenes and Its Utilization in the Synthesis of Various Heterocyclic Compounds.

An earth-abundant Co(II) salt-catalyzed mild and affordable synthetic route has been developed for the synthesis of industrially relevant 1,4-dicarbonyl compounds (or γ-diketones) via oxidative coupling between aryl alkenes and ketones (both cyclic and acyclic) using TBHP and DBU as the oxidant and base, respectively. 1,4-Dicarbonyl compounds are known to be synthesized using expensive metal catalysts, dual catalysts, or low-cost metal complexes combined with an additive or ligand template, which further needs to be synthesized. Herein, we report the synthesis of 1,4-dicarbonyl compounds using cobalt(II) acetate as a catalyst without any expensive co-catalyst or ligand templates. This methodology has a broad substrate scope with significant yields and good functional group tolerance. Generation of unsymmetrical 1,4-dicarbonyls at room temperature and its versatile synthetic expansion to produce synthetically and biologically valuable heterocyclic compounds are salient features of this novel methodology. In addition, various controlled experiments such as primary kinetic isotope effect study, Hammett analysis with variation of the nature of the substituents on the styrene ring, and theoretical calculations (density functional theory) unravel the mechanistic intricacies involved in this new, simple, and atom-economic methodology.

Noncovalent interaction with a spirobipyridine ligand enables efficient iridium-catalyzed C–H activation

Exploitation of noncovalent interactions for recognition of an organic substrate has received much attention for the design of metal catalysts in organic synthesis. The CH–π interaction is especially of interest for molecular recognition because both the C–H bonds and the π electrons are fundamental properties of organic molecules. However, because of their weak nature, these interactions have been less utilized for the control of organic reactions. We show here that the CH–π interaction can be used to kinetically accelerate catalytic C–H activation of arenes by directly recognizing the π-electrons of the arene substrates with a spirobipyridine ligand. Computation and a ligand kinetic isotope effect study provide evidence for the CH–π interaction between the ligand backbone and the arene substrate. The rational exploitation of weak noncovalent interactions between the ligand and the substrate will open new avenues for ligand design in catalysis.

Regio- and Diastereoselective Annulation of α,β-Unsaturated Aldimines with Alkenes via Allylic C(sp3)-H Activation by Rare-Earth Catalysts.

The [3 + 2] or [4 + 2] annulation of α,β-unsaturated aldimines with alkenes via β'- or γ-allylic C(sp3)-H activation is, in principle, an atom-efficient route for the synthesis of five- or six-membered-ring cycloalkylamines, which are important structural motifs in numerous natural products, bioactive molecules, and pharmaceuticals. However, such a transformation has remained undeveloped to date probably due to the lack of suitable catalysts. We report herein for the first time the regio- and diastereoselective [3 + 2] and [4 + 2] annulations of α,β-unsaturated imines with alkenes via allylic C(sp3)-H activation by half-sandwich rare-earth catalysts having different metal ion sizes. The reaction of α-methyl-substituted α,β-unsaturated aldimines with alkenes by a C5Me4SiMe3-ligated scandium catalyst took place in a trans-diastereoselective [3 + 2] annulation fashion via C(sp3)-H activation at the α-methyl group (β'-position), exclusively affording alkylidene-functionalized cyclopentylamines with excellent trans-diastereoselectivity. In contrast, the reaction of β-methyl-substituted α,β-unsaturated aldimines with alkenes by a C5Me5-ligated cerium catalyst proceeded in a cis-diastereoselective [4 + 2] annulation fashion via γ-allylic C(sp3)-H activation, selectively yielding multisubstituted 2-cyclohexenylamines with excellent cis-diastereoselectivity. The mechanistic details of these transformations have been elucidated by deuterium-labeling experiments, kinetic isotope effect studies, and the isolation and transformations of key reaction intermediates. This work offers an efficient and selective protocol for the synthesis of a new family of cycloalkylamine derivatives, featuring 100% atom efficiency, high regio- and diastereoselectivity, broad substrate scope, and an unprecedented reaction mechanism.

Anion-Bridged Dual Hydrogen Bond Enabled Concerted Addition of Phenol to Glycal.

A noncovalent organocatalytic concerted addition of phenol to glycal is developed for the stereoselective and regioselective construction of biologically important phenolic 2-deoxyglycosides, featuring wide substrate tolerance. The method relies on an anion-bridged dual hydrogen bond interaction which is experimentally proved by Nuclear Magnetic Resonance (NMR), Ultraviolet and visible (UV-vis), and fluorescence analysis. Experimental evidence including kinetic analysis, Kinetic Isotope Effect (KIE) studies, linear free energy relationship, Hammett plot, and density functional theory (DFT) calculations is provided for a concerted mechanism where a high-energy oxocarbenium ion is not formed. In addition, the potential utility of this method is further demonstrated by the synthesis of biologically active glycosylated flavones. The benchmarking studies demonstrate significant advances in this newly developed method compared to previous approaches.

4-Aldrithiol-based photometric assay for detection of methylthioalkylmalate synthase activity.

In Brassica plants, glucosinolates are a diverse class of natural products, of which aliphatic methionine-derived glucosinolates are the most abundant form. Their structural diversity comes from the elongation of some side-chains by up to 9 carbons, which, after the formation of the core glucosinolate structure, can undergo further chemical modifications. Methylthioalkylmalate synthase (MAMS) catalyzes the iterative elongation process for aliphatic methionine-derived glucosinolates. Most biochemical studies on MAMS have been performed using liquid chromatography/mass spectrometry (LC/MS)-based assays or high-performance liquid chromatography (HPLC)-based assays. The LC/MS- and HPLC-based methods are endpoint assays, which cannot be monitored in real time and require a laborious process for data collection. These analytical methods are inefficient for performing multiple enzymatic assays needed to determine steady-state kinetic parameters or for mechanistic evaluation of pH-dependence and kinetic isotope effect studies. Although the function of MAMS has long been defined, there is a gap in knowledge as it pertains to biochemical characterization of this plant enzyme. Part of this may be due to the lack of efficient methods that can be used for this type of research. This chapter describes a continuous photometric assay to track MAMS activity in real time using the 4-aldrithiol reagent for reaction detection.

Catalytic partial oxidation of methane over oxide-ion-conductive lanthanum silicate apatites.

A lanthanum silicate La9.33Si6O26 (LSO) crystallizes in an apatite-type structure and has been known as a promising oxide-ion conductor. Here, we report the activity of LSO for catalytic partial oxidation of methane (CPOX) to synthesis gas. The LSO catalyst demonstrated relatively high catalytic activity from 500 to 700 °C, with CH4 conversion reaching 22.1% at 700 °C while retaining moderate CO and H2 selectivities of 20-60%. Notably, LSO exhibited higher CPOX activity than non-apatite-type La2SiO5 despite their similar specific surface areas. The higher CPOX activity of LSO is likely attributed to its structural superiority involving mobile oxide ions in the crystal structure. The reaction kinetic study showed that the reaction orders for methane and oxygen in the CPOX reaction over the LSO catalyst were 0.69-0.73 and 0.08-0.21, respectively. Furthermore, the small contribution of adsorbed O species generated from gas-phase O2 molecules indicated that the lattice oxygen may be involved in the reaction mechanism. The kinetic isotope effect (KIE) study using a CD4 suggested that C-H bond breaking is the rate-determining step of CPOX over LSO.

Cu(II) Promoted C(sp3 )-H Activation in Unactivated Cycloalkanes: Oxo-Alkylation of Styrenes to Synthesize β-Disubstituted Ketones.

We report the Cu(II) catalyzed synthesis of β-disubstituted ketones from styrene via oxo-alkylation with unactivated cycloalkanes as the alkylating agent in presence of tert-butylhydroperoxide (TBHP) and 1-methylimidazole as oxidant and base respectively. β-disubstituted ketones are known to be synthesized by using either expensive Ru/Ir complexes, or low-cost metal complexes (e. g., Fe, Mn) with activated species like aldehyde, acid, alcohol, or phthalimide derivatives as the alkylating agent, however, use of unactivated cycloalkanes directly as the alkylating agent remains challenging. A wide range of aliphatic C-H substrates as well as various olefinic arenes and heteroarene (35 substrates including 14 new substrates) are well-tolerated in this method. Hammett analysis shed more light on the substitution effect in the olefinic part on the overall mechanism. Furthermore, the controlled experiments, kinetic isotope effect study, and theoretical calculations (DFT) enable us to gain deeper insight of mechanistic intricacies of this new simple and atom-economic methodology.

“Stepwise or concerted or a hybrid mechanism for berberine bridge enzyme?”: A computational mechanistic study by QM-MM and QM methods

Berberine bridge enzyme (BBE) is a plant-based amine oxidase that catalyzes conversion of (S)-reticuline into (S)-scoulerine using flavin as cofactor in a stereospecific way in an alkaloid biosynthesis pathway. Based on the active site enzyme variants, a concerted mechanism was proposed involving hydride transfer, proton transfer, and substrate cyclization processes in a single step. In this mechanism, Glu417 residue acts as the catalytic base which deprotonates the phenolic proton of the substrate while a hydride ion transfers from the substrate to flavin and the substrate cyclizes. However, based on solvent and substrate deuterium kinetic isotope effect studies, it was proposed that the oxidation process occurs in a stepwise fashion in which a hydride ion transfer from substrate to flavin first, then cyclization of the substrate occurs together with the proton transfer process. In this study, we formulated computational models to elucidate the oxidation mechanism of (S)-reticuline into (S)-scoulerine using the crystal structure of enzyme complexed with (S)-reticuline. Both QM and QM-MM calculations revealed that a hybrid of concerted and stepwise mechanisms might be operative during the catalysis. It was found that a concerted hydride-proton transfer processes occurs forming a reactive intermediate which subsequently cyclize without an energy barrier as a decoupled step.

Aerobic oxidation of alkyl aromatics to ketones catalyzed by biomimetic copper complex and N-hydroxyphthalimide (NHPI) under mild conditions

A galactose oxidase-like copper complex (CuIIL) (Ligand: N, N′-bis(2-hydroxy-3,5-di-tert-butylphenyl)-2,2′-diaminobiphenyl) was synthesized and used to catalyze the aerobic oxidation of alkyl aromatics to ketones in presence of N-hydroxyphthalimide (NHPI). The catalytic system exhibited excellent performance and tolerance under mild conditions. Mechanistic studies indicated that NHPI could be activated smoothly to generate phthalimide N-oxyl (PINO) radical in the presence of CuIIL. The kinetic isotope effect (KIE) studies showed that the generation of PINO radical was the rate-determining step.

Transition from Sequential to Concerted Proton-Coupled Electron Transfer of Water Oxidation on Semiconductor Photoanodes.

Accelerating proton transfer has been demonstrated as key to boosting water oxidation on semiconductor photoanodes. Herein, we study proton-coupled electron transfer (PCET) of water oxidation on five typical photoanodes [i.e., α-Fe2O3, BiVO4, TiO2, plasmonic Au/TiO2, and nickel-iron oxyhydroxide (Ni1-xFexOOH)-modified silicon (Si)] by combining the rate law analysis of H2O molecules with the H/D kinetic isotope effect (KIE) and operando spectroscopic studies. An unexpected and universal half-order kinetics is observed for the rate law analysis of H2O, referring to a sequential proton-electron transfer pathway, which is the rate-limiting factor that causes the sluggish water oxidation performance. Surface modification of the Ni1-xFexOOH electrocatalyst is observed to break this limitation and exhibits a normal first-order kinetics accompanied by much enhanced H/D KIE values, facilitating the turnover frequency of water oxidation by 1 order of magnitude. It is the first time that Ni1-xFexOOH is found to be a PCET modulator. The rate law analysis illustrates an effective strategy for modulating PCET kinetics of water oxidation on semiconductor surfaces.

Electrocatalytic Hydrogen Evolution using a Nickel-based Calixpyrrole Complex: Controlling the Secondary Coordination Sphere on an Electrode Surface.

Incorporating design elements from homogeneous catalysts to construct well defined active sites on electrode surfaces is a promising approach for developing next generation electrocatalysts for energy conversion reactions. Furthermore, if functionalities that control the electrode microenvironment could be integrated into these active sites it would be particularly appealing. In this context, a square planar nickel calixpyrrole complex, Ni(DPMDA) (DPMDA=2,2'-((diphenylmethylene)bis(1H-pyrrole-5,2-diyl))bis(methaneylylidene))bis(azaneylylidene))dianiline) with pendant amine groups is reported that forms a heterogeneous hydrogen evolution catalyst using anilinium tetrafluoroborate as the proton source. The supported Ni(DPMDA) catalyst was surprisingly stable and displayed fast reaction kinetics with turnover frequencies (TOF) up to 25,900 s-1 or 366,000 s-1 cm-2 . Kinetic isotope effect (KIE) studies revealed a KIE of 5.7, and this data, combined with Tafel slope analysis, suggested that a proton-coupled electron transfer (PCET) process involving the pendant amine groups was rate-limiting. While evidence of an outer-sphere reduction of the Ni(DPMDA) catalyst was observed, it is hypothesized that the control over the secondary coordination sphere provided by the pendant amines facilitated such high TOFs and enabled the PCET mechanism. The results reported herein provide insight into heterogeneous catalyst design and approaches for controlling the secondary coordination sphere on electrode surfaces.

Kinetic isotope effect study of N-6 methyladenosine chemical demethylation in bicarbonate-activated peroxide system.

N-6 methyladenosine is the most abundant nucleic acid modification in eukaryotes and plays a crucial role in gene regulation. The AlkB family of alpha-ketoglutarate-dependent dioxygenases is responsible for nucleic acid demethylation. Recent studies have discovered that a chemical demethylation system using hydrogen peroxide and ammonium bicarbonate can effectively demethylate nucleic acids. The addition of ferrous ammonium sulfate boosts the oxidation rate by forming a Fenton reagent with hydrogen peroxide. However, the specific mechanism and key steps of this process remain unclear. In this study, we investigate the influence of ferrous ammonium sulfate concentration on the kinetic isotope effect (KIE) of the chemical demethylation system using LC-MS. As the concentration of ferrous ions increases, the observed KIE decreases from 1.377 ± 0.020 to 1.120 ± 0.016, indicating a combination of the primary isotope effect and inverse α-secondary isotope effect with the ion pairing effect. We propose that the initial hydrogen extraction is the rate-limiting step and observe a tight transition state structure in the formation of the hm6A process through the analysis of KIE trends. The concentration-dependent KIE provides a novel perspective on the mechanism of chemical demethylation and offers a chemical model for enzyme-catalyzed demethylation.

Computational Insights on the Hydride and Proton Transfer Mechanisms of D-Arginine Dehydrogenase.

D-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is an amine oxidase which catalyzes the conversion of D-arginine into iminoarginine. It contains a non-covalent FAD cofactor that is involved in the oxidation mechanism. Based on substrate, solvent, and multiple kinetic isotope effects studies, a stepwise hydride transfer mechanism is proposed. It was shown that D-arginine binds to the active site of enzyme as α-amino group protonated, and it is deprotonated before a hydride ion is transferred from its α-C to FAD. Based on a mutagenesis study, it was concluded that a water molecule is the most likely catalytic base responsible from the deprotonation of α-amino group. In this study, we formulated computational models based on ONIOM method to elucidate the oxidation mechanism of D-arginine into iminoarginine using the crystal structure of enzyme complexed with iminoarginine. The calculations showed that Arg222, Arg305, Tyr249, Glu87, His 48, and two active site water molecules play key roles in binding and catalysis. Model systems showed that the deprotonation step occurs prior to hydride transfer step, and active site water molecule(s) may have participated in the deprotonation process.

Electrochemical Activation of Nitromethane to Construct Isoxazoline Aldoximes.

Activation of nitromethane to endow new reactivity is an interesting and meaningful but also challenging topic. Herein, we report an electrochemical activation of nitromethane to serve as both the heterocyclic skeleton and oxime sources for the construction of isoxazoline aldoximes. The isoxazoline aldoximes that are prepared by four steps with the reported strategy are synthesized in a single step from low-cost and readily available nitromethane and olefins with moderate to excellent yields under our electrochemical conditions. The reaction also takes advantage of high atom-economy and E-selectivity. Moreover, the mechanism is studied by control experiments, a kinetic isotope effect (KIE) study, cyclic voltammogram (CV) experiments, and density functional theory (DFT) calculations. The mechanistic results reveal that nitromethane may be activated under electrochemical conditions to deliver a 1,2,5-oxadiazole 2-oxide intermediate, which undergoes [3+2] cycloaddition with olefins to yield isoxazoline aldoximes.