Kinetic Isotope Effect Measurements Research Articles

A Reactive Manganese(IV)–Hydroxide Complex: A Missing Intermediate in Hydrogen Atom Transfer by High-Valent Metal-Oxo Porphyrinoid Compounds

High-valent metal-hydroxide species are invoked as critical intermediates in both catalytic, metal-mediated O2 activation (e.g., by Fe porphyrin in Cytochrome P450) and O2 production (e.g., by the Mn cluster in Photosystem II). However, well-characterized mononuclear MIV(OH) complexes remain a rarity. Herein we describe the synthesis of MnIV(OH)(ttppc) (3) (ttppc = tris(2,4,6-triphenylphenyl) corrole), which has been characterized by X-ray diffraction (XRD). The large steric encumbrance of the ttppc ligand allowed for isolation of 3. The complexes MnV(O)(ttppc) (4) and MnIII(H2O)(ttppc) (1·H2O) were also synthesized and structurally characterized, providing a series of Mn complexes related only by the transfer of hydrogen atoms. Both 3 and 4 abstract an H atom from the O-H bond of 2,4-di- tert-butylphenol (2,4-DTBP) to give a radical coupling product in good yield (3 = 90(2)%, 4 = 91(5)%). Complex 3 reacts with 2,4-DTBP with a rate constant of k2 = 2.73(12) × 104 M-1 s-1, which is ∼3 orders of magnitude larger than 4 ( k2 = 17.4(1) M-1 s-1). Reaction of 3 with a series of para-substituted 2,6-di- tert-butylphenol derivatives (4-X-2,6-DTBP; X = OMe, Me, tBu, H) gives rate constants in the range k2 = 510(10)-36(1.4) M-1 s-1 and led to Hammett and Marcus plot correlations. Together with kinetic isotope effect measurements, it is concluded that O-H cleavage occurs by a concerted H atom transfer (HAT) mechanism and that the MnIV(OH) complex is a much more powerful H atom abstractor than the higher-valent MnV(O) complex, or even some FeIV(O) complexes.

Hydrogenated Blue Titania for Efficient Solar to Chemical Conversions: Preparation, Characterization, and Reaction Mechanism of CO2 Reduction

Here we report a facile low-temperature solvothermal method by using Li-dissolved ethanediamine to prepare uniform hydrogenated blue H-TiO2–x with wide spectrum response. H-TiO2–x possesses a distinct crystalline core–amorphous shell structure (TiO2@TiO2–x) with numerous oxygen vacancies and doped H in the amorphous shell. Efficient solar to chemical energy conversions, likely photocatalytic reduction of CO2, degradation of contaminants, and H2 generation from water splitting can be achieved over this blue titania. Notably, the optimized H-TiO2–x(200) shows high activity of CH4 formation at a rate of 16.2 μmol g–1 h–1 and a selectivity of 79% under full solar irradiation. The kinetic isotope effects measurements reveal that the cleavage of the C═O bond from CO2 rather than the O–H bond from H2O is the rate-determining step in CH4 formation. Meanwhile, in situ diffuse reflectance infrared Fourier transform spectroscopy shows the existence of the key intermediate CO2– species. The formation of intermediate ...

Molecular Iridium Complexes in Metal-Organic Frameworks Catalyze CO2 Hydrogenation via Concerted Proton and Hydride Transfer.

Molecular iridium catalysts immobilized in metal-organic frameworks (MOFs) were positioned in the condensing chamber of a Soxhlet extractor for efficient CO2 hydrogenation. Droplets of hot water seeped through the MOF catalyst to create dynamic gas/liquid interfaces which maximize the contact of CO2, H2, H2O, and the catalyst to achieve a high turnover frequency of 410 h-1 under atmospheric pressure and at 85 °C. H/D kinetic isotope effect measurements and density functional theory calculations revealed concerted proton-hydride transfer in the rate-determining step of CO2 hydrogenation, which was difficult to unravel in homogeneous reactions due to base-catalyzed H/D exchange.

The Transition-State Structure for Human MAT2A from Isotope Effects

Human methionine S-adenosyltransferase (MAT2A) catalyzes the formation of S-adenosylmethionine (SAM) from ATP and methionine. Synthetic lethal genetic analysis has identified MAT2A as an anticancer target in tumor cells lacking expression of 5'-methylthioadenosine phosphorylase (MTAP). Approximately 15% of human cancers are MTAP-/-. The remainder can be rendered MTAP- through MTAP inhibitors. We used kinetic isotope effect (KIE), commitment factor (Cf), and binding isotope effect (BIE) measurements combined with quantum mechanical (QM) calculations to solve the transition state structure of human MAT2A. The reaction is characterized by an advanced SN2 transition state. The bond forming from the nucleophilic methionine sulfur to the 5'-C of ATP is 2.03 Å at the transition state (bond order of 0.67). Departure of the leaving group triphosphate of ATP is well advanced and forms a 2.32 Å bond between the 5'-C of ATP and the oxygen of the triphosphate (bond order of 0.23). Interaction of MAT2A with its MAT2B regulatory subunit causes no change in the intrinsic KIEs, indicating the same transition state structure. The transition state for MAT2A is more advanced along the reaction coordinate (more product-like) than that from the near-symmetrical transition state of methionine adenosyltransferase from E.coli.

Triazolylidene Iridium Complexes for Highly Efficient and Versatile Transfer Hydrogenation of C═O, C═N, and C═C Bonds and for Acceptorless Alcohol Oxidation.

A set of iridium(I) and iridium(III) complexes is reported with triazolylidene ligands that contain pendant benzoxazole, thiazole, and methyl ether groups as potentially chelating donor sites. The bonding mode of these groups was identified by NMR spectroscopy and X-ray structure analysis. The complexes were evaluated as catalyst precursors in transfer hydrogenation and in acceptorless alcohol oxidation. High-valent iridium(III) complexes were identified as the most active precursors for the oxidative alcohol dehydrogenation, while a low-valent iridium(I) complex with a methyl ether functionality was most active in reductive transfer hydrogenation. This catalyst precursor is highly versatile and efficiently hydrogenates ketones, aldehydes, imines, allylic alcohols, and most notably also unpolarized olefins, a notoriously difficult substrate for transfer hydrogenation. Turnover frequencies up to 260 h-1 were recorded for olefin hydrogenation, whereas hydrogen transfer to ketones and aldehydes reached maximum turnover frequencies greater than 2000 h-1. Mechanistic investigations using a combination of isotope labeling experiments, kinetic isotope effect measurements, and Hammett parameter correlations indicate that the turnover-limiting step is hydride transfer from the metal to the substrate in transfer hydrogenation, while in alcohol dehydrogenation, the limiting step is substrate coordination to the metal center.

Isotope Studies in Oxidation of Propane over Vanadium Oxide

AbstractThe oxidation of propane has been studied over silica‐supported vanadium oxide and polycrystalline, bulk MoVTeNb oxide with M1 structure. Temperature‐programmed reaction experiments were performed, and the reactivity of propane molecules labeled with deuterium and 13C, respectively, was analyzed under steady‐state conditions. The measurement of kinetic isotope effects reveals fundamental differences in the activation of propane over the two catalysts. The reaction network of consecutive and parallel reactions of the formed propylene is comparable. However, oxygen insertion into the CHO group of acrolein under formation of acrylic acid is faster over M1 than oxidation at the CH2 group and decarbonylation to acetaldehyde. In contrast, the latter process is preferred over silica‐supported vanadium oxide resulting in lower selectivity to unsaturated oxygenates.

Selective Metal–Organic Framework Catalysis of Glucose to 5-Hydroxymethylfurfural Using Phosphate-Modified NU-1000

This manuscript demonstrates the synthesis of selective Lewis-acid sites in a metal–organic framework (MOF) for glucose transformation to 5-hydroxymethylfurfural (HMF). These sites are synthesized via partial phosphate modification of zirconia-cluster nodes in MOF NU-1000, which titrates strong Lewis-acid sites that would lead to undesired side reactions. Our mechanistic study using isotope tracer analysis and kinetic isotope effect measurements reveals that an isomerization–dehydration mechanism mainly occurs on the MOF catalyst, where fructose is an intermediate. This mechanism suggests that dilute concentrations are favorable in order to suppress undesired intermolecular condensation of glucose/fructose/HMF and maximize HMF yield. We demonstrate both high yield and selectivity of HMF formation of 64% with the MOF catalyst, at an initial glucose concentration of 1 mM in water/2-propanol. In stark contrast, similar partial phosphate modification of a bulk zirconia yields a catalyst that exhibits poor HMF...

Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase

Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assistedsynthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction.KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD). The KIE on reduction of p-nitrobenzoic acid (p-NBA) also indicates hydride transfer, and requires revision of prior computational mechanisms. Our mechanistic information provided a structural restraint for the orientation of bound substrate, placing the nitro group closer to the flavin N5 in the pocket that binds the amide of NADH. KIEs show that solvent provides a proton, enabling accommodation of different nitro group placements, consistent with the broad repertoire of NR.

Mechanistic Model for Enantioselective Intramolecular Alkene Cyanoamidation via Palladium-Catalyzed C-CN Bond Activation.

We studied key aspects of the mechanism of Pd-catalyzed C-CN bond activation and intramolecular enantioselective alkene cyanoamidation. An Abboud-Abraham-Kamlet-Taft (AAKT) linear solvation energy relationship (LSER) model for enantioselectivity was established. We investigated the impact of Lewis acid (BPh3), Lewis base (DMPU), and no additives. BPh3 additive led to diminished enantioselectivity and differing results in 13CN crossover experiments, initial rate kinetics, and natural abundance 12C/13C kinetic isotope effect measurements. We propose two catalytic mechanisms to account for our experimental results. We propose that the DMPU/nonadditive pathway passes through a κ2-phosphoramidite-stabilized Pd+ intermediate, resulting in high enantioselectivity. BPh3 prevents the dissociation of CN-, leading to a less rigid κ2-phosphoramidite-neutral Pd intermediate.

Measurement of Kinetic Isotope Effects by Continuously Monitoring Isotopologue Ratios Using NMR Spectroscopy.

Nuclear magnetic spectroscopic (NMR) methods are discussed for the measurement of heavy atom (13C, 18O, 15N) and secondary deuterium kinetic isotope effects. The discussion focuses primarily on the NMR methods that enable the measurement of quantitative spectra and not on methods to make labeled substrates. Two main techniques are considered: single-point determinations on natural abundance material and the continuous monitoring of isotopically enriched materials. The second method is described in more detail, and we include a discussion of the current state of instrumentation and computer programs for data acquisition and analysis.

Measurement of Kinetic Isotope Effects in an Enzyme-Catalyzed Reaction by Continuous-Flow Mass Spectrometry.

Kinetic isotope effects (KIEs) provide powerful probes of the mechanisms of enzyme-catalyzed reactions. In this chapter, we describe the use of continuous-flow mass spectrometry to determine the deuterium KIE for the enzyme N-acetylpolyamine oxidase based on the ratio of labeled and unlabeled products in mass spectra of whole reaction mixtures.

Measurement and Prediction of Chlorine Kinetic Isotope Effects in Enzymatic Systems.

Approaches to determine chlorine kinetic isotope effects (Cl-KIEs) on enzymatic dehalogenations are discussed and illustrated by representative examples. Three aspects are considered. First methodology for experimental measurement of Cl-KIEs, with stress being on FAB-IRMS technique developed in our laboratory, is described. Subsequently, we concentrate our discussion on the consequences of reaction complexity in the interpretation of experimental values, a problem especially important in cases of polychlorinated reactants. The most fruitful studies of enzymatic dehalogenations by Cl-KIEs require their theoretical evaluation, hence the computational focus of the second part of this chapter.

Sensitive and Accurate 13C Kinetic Isotope Effect Measurements Enabled by Polarization Transfer.

Polarization transfer is demonstrated as a sensitive technique for the measurement of isotopic fractionation of protonated carbons at natural abundance. This method allows kinetic isotope effects (KIEs) to be determined with substantially less material or shorter acquisition time compared with traditional experiments. Computations quantitatively reproduce the KIEs in a Diels-Alder reaction and a catalytic glycosylation. The glycosylation is shown to occur by an effectively concerted mechanism.

Plasmonic Au@Pd Nanoparticles Supported on a Basic Metal–Organic Framework: Synergic Boosting of H2 Production from Formic Acid

We report synergistic catalysis of plasmonic Au@Pd nanoparticles supported on titanium-doped zirconium-based amine-functionalized metal–organic frameworks (MOFs) (UiO-66(Zr100–xTix)) for boosting room-temperature hydrogen production from formic acid (HCOOH) under visible light irradiation. Our results revealed that the electronically promoted Pd sites by the localized surface plasmon resonance (LSPR) effect of Au as well as doping of amine functionality in the MOFs with titanium ions play crucial roles in achieving exceptional catalytic performance. Remarkably, a high H2 production rate of 42000 mL h–1 g–1 (Pd) with high a turnover frequency (TOF) of 200 h–1 based on Pd was obtained under visible light irradiation. Kinetic isotope effect (KIE) measurements demonstrated that dissociations of O–H and C–H bonds of formic acid, which are two important steps for hydrogen production from HCOOH, are individually facilitated by the assistance of amine groups within MOFs and active electron-rich Pd sites induced b...

13C kinetic isotope effects on the reaction of a flavin amine oxidase determined from whole molecule isotope effects

A large number of flavoproteins catalyze the oxidation of amines. Because of the importance of these enzymes in metabolism, their mechanisms have previously been studied using deuterium, nitrogen, and solvent isotope effects. While these results have been valuable for computational studies to distinguish among proposed mechanisms, a measure of the change at the reacting carbon has been lacking. We describe here the measurement of a 13C kinetic isotope effect for a representative amine oxidase, polyamine oxidase. The isotope effect was determined by analysis of the isotopic composition of the unlabeled substrate, N, N’-dibenzyl-1,4-diaminopropane, to obtain a pH-independent value of 1.025. The availability of a 13C isotope effect for flavoprotein-catalyzed amine oxidation provides the first measure of the change in bond order at the carbon involved in this carbon-hydrogen bond cleavage and will be of value to understanding the transition state structure for this class of enzymes.

C2-Oxyanion Neighboring Group Participation: Transition State Structure for the Hydroxide-Promoted Hydrolysis of 4-Nitrophenyl α-d-Mannopyranoside.

The hydroxide-catalyzed hydrolysis of aryl 1,2-trans-glycosides proceeds through a mechanism involving neighboring group participation by a C2-oxyanion and rate-limiting formation of a 1,2-anhydro sugar (oxirane) intermediate. The transition state for the hydroxide-catalyzed hydrolysis of 4-nitrophenyl α-d-mannopyranoside in aqueous media has been studied by the use of multiple kinetic isotope effect (KIE) measurements in conjunction with ab initio theoretical methods. The experimental KIEs are C1-2H (1.112 ± 0.004), C2-2H (1.045 ± 0.005), anomeric 1-13C (1.026 ± 0.006), C2-13C (0.999 ± 0.005), leaving group oxygen 2-18O (1.040 ± 0.012), and C2-18O (1.044 ± 0.006). The transition state for the hydrolysis reaction was modeled computationally using the experimental KIE values as constraints. Taken together, the reported kinetic isotope effects and computational modeling are consistent with the reaction mechanism involving rate-limiting formation of a transient oxirane intermediate that opens in water to give α-d-mannopyranose. The transition state has significant nucleophilic participation by the C2-alkoxide, an essentially cleaved glycosidic bond, and a slight shortening of the endocyclic C1-O5 bond. The TS is late, consistent with the large, normal C2-18O isotope effect.

Correction to "Mechanism of the Iron(II)-Catalyzed Hydrosilylation of Ketones: Activation of Iron Carboxylate Precatalysts and Reaction Pathways of the Active Catalyst".

A detailed mechanistic study of the catalytic hydrosilylation of ketones with the highly active and enantioselective iron(II) boxmi complexes as catalysts (up to >99% ee) was carried out to elucidate the pathways for precatalyst activation and the mechanism for the iron-catalyzed hydrosilylation. Carboxylate precatalysts were found to be activated by reduction of the carboxylate ligand to the corresponding alkoxide followed by entering the catalytic cycle for the iron-catalyzed hydrosilylation. An Eyring-type analysis of the temperature dependence of the enantiomeric ratio established a linear relationship of ln(S/R) and T–1, indicating a single selectivity-determining step over the whole temperature range from −40 to +65 °C (ΔΔG‡sel, 233 K = 9 ± 1 kJ/mol). The rate law as well as activation parameters for the rate-determining step were derived and complemented by a Hammett analysis, radical clock experiments, kinetic isotope effect (KIE) measurements (kH/kD = 3.0 ± 0.2), the isolation of the catalyticall...

Mechanism of the Iron(II)-Catalyzed Hydrosilylation of Ketones: Activation of Iron Carboxylate Precatalysts and Reaction Pathways of the Active Catalyst.

A detailed mechanistic study of the catalytic hydrosilylation of ketones with the highly active and enantioselective iron(II) boxmi complexes as catalysts (up to >99% ee) was carried out to elucidate the pathways for precatalyst activation and the mechanism for the iron-catalyzed hydrosilylation. Carboxylate precatalysts were found to be activated by reduction of the carboxylate ligand to the corresponding alkoxide followed by entering the catalytic cycle for the iron-catalyzed hydrosilylation. An Eyring-type analysis of the temperature dependence of the enantiomeric ratio established a linear relationship of ln(S/R) and T(-1), indicating a single selectivity-determining step over the whole temperature range from -40 to +65 °C (ΔΔG(‡)sel,233K = 9 ± 1 kJ/mol). The rate law as well as activation parameters for the rate-determining step were derived and complemented by a Hammett analysis, radical clock experiments, kinetic isotope effect (KIE) measurements (kH/kD = 3.0 ± 0.2), the isolation of the catalytically active alkoxide intermediate, and DFT-modeling of the whole reaction sequence. The proposed reaction mechanism is characterized by a rate-determining σ-bond metathesis of an alkoxide complex with the silane, subsequent coordination of the ketone to the iron hydride complex, and insertion of the ketone into the Fe-H bond to regenerate the alkoxide complex.

Experimental and Computational Evidence for a Loose Transition State in Phosphoroimidazolide Hydrolysis.

Phosphoroimidazolides play a critical role in several enzymatic phosphoryl transfer reactions and have been studied extensively as activated monomers for nonenzymatic nucleic acid replication, but the detailed mechanisms of these phosphoryl transfer reactions remain elusive. Some aspects of the mechanism can be deduced by studying the hydrolysis reaction, a simpler system that is amenable to a thorough mechanistic treatment. Here we characterize the transition state of phosphoroimidazolide hydrolysis by kinetic isotope effect (KIE) and linear free energy relationship (LFER) measurements, and theoretical calculations. The KIE and LFER observations are best explained by calculated loose transition structures with extensive scissile bond cleavage. These three-dimensional models of the transition state provide the basis for future mechanistic investigations of phosphoroimidazolide reactions.

Transition State Structure of RNA Depurination by Saporin L3.

Saporin L3 from the leaves of the common soapwort is a catalyst for hydrolytic depurination of adenine from RNA. Saporin L3 is a type 1 ribosome inactivating protein (RIP) composed only of a catalytic domain. Other RIPs have been used in immunotoxin cancer therapy, but off-target effects have limited their development. In the current study, we use transition state theory to understand the chemical mechanism and transition state structure of saporin L3. In favorable cases, transition state structures guide the design of transition state analogues as inhibitors. Kinetic isotope effects (KIEs) were determined for an A14C mutant of saporin L3. To permit KIE measurements, small stem-loop RNAs that contain an AGGG tetraloop structure were enzymatically synthesized with the single adenylate bearing specific isotopic substitutions. KIEs were measured and corrected for forward commitment to obtain intrinsic values. A model of the transition state structure for depurination of stem-loop RNA (5'-GGGAGGGCCC-3') by saporin L3 was determined by matching KIE values predicted via quantum chemical calculations to a family of intrinsic KIEs. This model indicates saporin L3 displays a late transition state with the N-ribosidic bond to the adenine nearly cleaved, and the attacking water nucleophile weakly bonded to the ribosyl anomeric carbon. The transition state retains partial ribocation character, a feature common to most N-ribosyl transferases. However, the transition state geometry for saporin L3 is distinct from ricin A-chain, the only other RIP whose transition state is known.