Normal Kinetic Isotope Effect Research Articles

Kinetic Isotope Effects During Reduction of Fe(III) to Fe(II): Large Normal and Inverse Isotope Effects for Abiotic Reduction and Smaller Fractionations by Phytoplankton in Culture

AbstractIron stable isotopes (δ56Fe) are a useful tool for studying Earth processes, many of which involve redox transformations between Fe(III) and Fe(II). Here, we present two related experimental efforts, a study of the kinetic isotope effects (KIEs) associated with the reduction of Fe(III)‐ethylenediaminetetraacetic acid (EDTA) to Fe(II), and measurements of the biological fractionation of Fe isotopes by phytoplankton in culture. Reductants tested were ascorbate, hydroxylamine, Mn(II), dithionite, and photoreduction at pH between 5 and 9 and temperatures from 0 to 100°C. Isotope fractionations were very large, and included both normal and inverse KIEs, ranging from −4‰ to +5‰. Experiments were reproducible, yielding similar results for triplicate experiments run concurrently and for experiments run weeks apart. However, fractionations were not predictable, without a clear relationship to reaction rate, temperature, pH, or the reductant used. Acquisition of Fe by eukaryotic phytoplankton also often involves the reduction of Fe(III) to Fe(II). Several species of diatoms and a coccolithophore were tested for Fe isotope fractionation in culture using EDTA, NTA, and DFB as Fe(III) chelating ligands, yielding fractionations from −1.3‰ to +0.6‰. Biological isotope effects were also unpredictable, showing no clear relationship to species, growth rate, or Fe concentration. Variability in Fe isotope fractionation observed in culture may be explained in part by the sensitivity of KIEs. This work has implications for the industrial purification of isotopes, interpretation of natural δ56Fe, and the use of Fe isotopes as a tracer Fe source and biological processes in the ocean and other natural systems.

Compound-specific, intra-molecular, and clumped 13C fractionations in the thermal generation and decomposition of ethane and propane: A DFT and kinetic investigation

The distribution of stable isotopes in organic compounds within geochemical systems reflects the reactions they undergo, which are often kinetically governed and can be elucidated through quantification based on first principles: employing quantum chemical simulations to derive energy barriers and kinetic isotope effects (KIEs), followed by kinetic calculations using these parameters. In this paper, the distribution of 13C in hydrocarbon gases during the thermal generation and decomposition of ethane and propane has been addressed. The work is based on abundant and systematic isotopic data, including the compound- and position-specific 13C compositions, recent improvements in kinetic networks in hydrocarbon generation, and state-of-the-art quantum chemical methods that can process organic geochemical systems involving solid phases. Density Functional Theory computations validate the carbonium path of hydrocarbon generation and the free-radical path of their decomposition under geological conditions. The first step of each path (alkyl sidechain protonation for generation and hydrogen abstraction for decomposition) is the rate-limiting step and determines the 13C fractionations of gaseous hydrocarbons, with the reaction rate constrained by the concentration or accessibility of the active species (hydrated protons and surface free radicals in the two paths, respectively). Alkyl protonation has normal 13C KIEs, but hydrogen abstraction on the surfaces of solid organic matter has inverse ones (substituting 12C by 13C accelerates the reaction). These inverse KIEs explain three isotopic phenomena in gaseous hydrocarbons in their late thermal evolution: 1) the depletion of 13C in ethane and propane accompanied by their decreased fraction in hydrocarbon gases (isotope “rollover”); 2) the reversed 13C sequence with carbon number (δ13Cmethane > δ13Cethane > δ13Cpropane); and 3) the depletion of 13C in the center carbon atoms of residual propane. Isotopic fractionation between gaseous hydrocarbons upon generation is evaluated using the Successive Random Chain-Scission model. The covariation of δ13C in alkanes shows a depletion in CH4 compared with the values expected from the reciprocal of the carbon numbers, indicating that this deviation may be intrinsic instead of mixing with microbial methane. The comparison of intramolecular 13C fractionation of propane between computational and observed data suggests the contribution of isoprenoids at the beginning of the generation, in addition to isotopic homogenization between the center and end carbon atoms through the ring closure of intermediate cations. The 13C–13C clumping exhibits a weak KIE in both the generation and decomposition of ethane; the clumping is essentially stochastically governed. This work demonstrates how first-principle calculations can provide significant insights into the details of geochemical reactions governing the isotopic distributions.

Effects of pH-dependent speciation on the photolytic degradation mechanism of phosphonates

Phosphonates, commonly used as strong metal chelating agents in household and industrial products, partially persist through water treatment processes, releasing significant amounts into the environment and raise concerns about potential environmental impacts. This study investigated effects of pH-dependent speciation of phosphonates on their photolysis by a medium-pressure mercury lamp in aqueous solution under ambient air conditions. Different species of aminotrimethylphosphonic acid (ATMP), and its most important transformation products iminodimethylphosphonic acid(IDMP) and aminomethylphosphonic acid(AMPA) were analyzed by liquid chromatography in combination with isotope ratio (CSIA) and high resolution mass spectrometry. UV radiation (<320 nm) was required for the photolytic degradation of ATMP, IDMP, and AMPA, and their photolysis was influenced by pH-dependent speciation. Degradation rate constant of ATMP was affected by pH, but a direct correlation between kobs and pH was not found. In contrast, IDMP and AMPA exhibited a direct correlation between pH and kobs during photolysis. CSIA revealed an inverse carbon kinetic isotope effect (KIE) for ATMP, while a normal carbon KIE was observed for IDMP and AMPA. Quantum chemical calculations supported degradation pathway interpretation and KIE understanding. Energy barrier calculations distinguished N-C vs C-P bond cleavage, favoring N-C cleavage on average, consistent with observed transformation products. Further calculations, considering possible transition states, provide first promising hints for elucidation of present KIEs.

Inverse kinetic isotope effect of proton and deuteron permeation through pyridinic N-doped graphene

Graphene is becoming an increasingly popular platform for developing high-efficiency hydrogen isotope separation technologies operated at room temperature. However, its performance can be strongly affected by contributions from atomic defects. Understanding the influence of defects on the hydrogen isotope selectivity of graphene is thus imperative but remains elusive. In this work, we investigated the electrically driven proton/deuteron permeation through nitrogen-doped graphene membranes with varying N concentrations and configurations. The results show that N-doping significantly enhances the proton and deuteron permeability of graphene (by one order of magnitude). More importantly, deuterons are found to permeate faster through pyridinic N-containing defects than protons, demonstrating a pronounced inverse kinetic isotope effect (KIE) with kH/kD of 0.75. Conversely, pyrrolic N-containing defects exhibit a normal KIE (kH/kD = 1.56). The exclusive contribution of the pyridinic N to the inverse KIE is confirmed by the reversed KIE factor of the pyridinic N-dominated sample subjected to modification. Theoretical calculations indicate that the explicit dependence of KIE on N configuration originates from the different leading mechanisms of proton/deuteron permeation through these N-containing defects, which is governed by the size and the chemisorption imparted by defects. These findings provide fundamental insights into the correlation between defect characteristics and proton/deuteron transport in graphene, and contribute to developing economical hydrogen isotope separation technologies through the defect engineering of graphene.

Microenvironment regulation of Ru(bda)L2 catalyst incorporated in metal-organic framework for effective photo-driven water oxidation

A Ru(bda)L2 molecular catalyst (H2bda = 2,2′-bipyridine-6,6′-dicarboxylic acid, L represents ligands) was incorporated into a UiO-66 metal-organic framework (MOF) as isolating sites for chemical- and photo-driven water oxidation with the water nucleophilic attack mechanism. An impressive turn-over number of 566 was obtained for photo-driven water oxidation in the phosphate buffer saline, which was nearly 20 times that of the homogenous counterpart in the presence of ruthenium tris(bipyridine) and sodium persulfate. Infrared spectroscopy, X-ray diffraction and X-ray spectroscopy techniques were used to characterize the composition and structure of the catalysts. Kinetic isotope effect (KIE), proton inventory experiment and proton nuclear magnetic resonance were conducted to understand the photo-driven O2 evolution mechanism. It was observed that the protons participated in O2 evolution with a normal KIE value, and the uptake of phosphates by UiO-66 matrix improved the affinity towards H2O via hydrogen bonding. The high O2 output and the limited photosensitizer oxidative decomposition in PBS suggest that the phosphate acted as a proton mediator to assist proton and/or proton-couple electron transfer through a hydrogen-bonded network of water molecules. This study uses a heterogenous matrix to emulate an enzyme-like microenvironment capable of achieving efficient artificial photosynthesis.

Probing the Free Energy Landscape of Organophotoredox-Catalyzed Anti-Markovnikov Hydrofunctionalization of Alkenes.

Experimental 13C kinetic isotope effects (KIEs) provide unprecedented mechanistic insight into three intermolecular anti-Markovnikov alkene hydrofunctionalization reactions─hydroesterification, hydroamination, and hydroetherification─enabled by organophotoredox catalysis. All three reactions are found to proceed via initial oxidation of the model alkenes to form a radical cation intermediate, followed by sequential nucleophilic attack and hydrogen-atom transfer to deliver the hydrofunctionalized product. A normal 13C KIE on the olefinic carbon that undergoes nucleophilic attack provides qualitative evidence for rate-limiting nucleophilic attack in all three reactions. Comparison to predicted 13C KIE values obtained from density functional theory (DFT) calculations for this step reveals that alkene oxidation has partial rate-limiting influence in hydroesterification and hydroamination, while the nucleophilic attack is solely rate-limiting in the hydroetherification reaction. The basic additive (2,6-lutidine) activates the nucleophile via deprotonation and is an integral part of the transition state for nucleophilic attack on the radical cation, providing an important design principle for the development of asymmetric versions of these reactions. A more electron-rich pyridine base (2,6-dimethoxypyridine) exhibits considerable rate enhancements in both inter- and intramolecular hydrofunctionalization reactions.

Mechanism and Origin of Remote Stereocontrol in the Organocatalytic Enantioselective Formal C(sp2)-H Alkylation Using Nitroalkanes as Alkylating Agents.

Experimental 13C kinetic isotope effects (KIEs) and density functional theory (DFT) calculations are used to evaluate the mechanism and origin of enantioselectivity in the formal C(sp2)-H alkylative desymmetrization of cyclopentene-1,3-diones using nitroalkanes as the alkylating agent. An unusual combination of an inverse (∼0.980) and a normal (∼1.033) KIE is observed on the bond-forming carbon atoms of the cyclopentene-1,3-dione and nitroalkane, respectively. These data provide strong support for a mechanism involving reversible carbon-carbon bond formation followed by rate- and enantioselectivity-determining nitro group elimination. The theoretical free-energy profile and the predicted KIEs indicate that this elimination event occurs via an E1cB pathway. The origin of remote stereocontrol is evaluated by distortion-interaction and SAPT0 analyses of the E1cB transition states leading to both enantiomers.

Carboxylate Catalyzed Isomerization of β,γ-Unsaturated N-Acetylcysteamine Thioesters.

We demonstrate herein the capacity of simple carboxylate salts – tetrametylammonium and tetramethylguanidinium pivalate – to act as catalysts in the isomerization of β,γ‐unsaturated thioesters to α,β‐unsaturated thioesters. The carboxylate catalysts gave reaction rates comparable to those obtained with DBU, but with fewer side reactions. The reaction exhibits a normal secondary kinetic isotope effect (k 1H/k 1D=1.065±0.026) with a β,γ‐deuterated substrate. Computational analysis of the mechanism provides a similar value (k 1H/k 1D=1.05) with a mechanism where γ‐reprotonation of the enolate intermediate is rate determining.

Hydride Transfer Mechanism of Enzymatic Sugar Nucleotide C2 Epimerization Probed with a Loose-Fit CDP-Glucose Substrate.

Transient oxidation–reduction through hydride transfer with tightly bound NAD coenzyme is used by a large class of sugar nucleotide epimerases to promote configurational inversion of carbon stereocenters in carbohydrate substrates. A requirement for the epimerases to coordinate hydride abstraction and re-addition with substrate rotation in the binding pocket poses a challenge for dynamical protein conformational selection linked to enzyme catalysis. Here, we studied the thermophilic C2 epimerase from Thermodesulfatator atlanticus (TaCPa2E) in combination with a slow CDP-glucose substrate (kcat ≈ 1.0 min–1; 60 °C) to explore the sensitivity of the enzymatic hydride transfer toward environmental fluctuations affected by temperature (20–80 °C). We determined noncompetitive primary kinetic isotope effects (KIE) due to 2H at the glucose C2 and showed that a normal KIE on the kcat (Dkcat) reflects isotope sensitivity of the hydrogen abstraction to enzyme-NAD+ in a rate-limiting transient oxidation. The Dkcat peaked at 40 °C was 6.1 and decreased to 2.1 at low (20 °C) and 3.3 at high temperature (80 °C). The temperature profiles for kcat with the 1H and 2H substrate showed a decrease in the rate below a dynamically important breakpoint (∼40 °C), suggesting an equilibrium shift to an impaired conformational landscape relevant for catalysis in the low-temperature region. Full Marcus-like model fits of the rate and KIE profiles provided evidence for a high-temperature reaction via low-frequency conformational sampling associated with a broad distribution of hydride donor–acceptor distances (long-distance population centered at 3.31 ± 0.02 Å), only poorly suitable for quantum mechanical tunneling. Collectively, dynamical characteristics of TaCPa2E-catalyzed hydride transfer during transient oxidation of CDP-glucose reveal important analogies to mechanistically simpler enzymes such as alcohol dehydrogenase and dihydrofolate reductase. A loose-fit substrate (in TaCPa2E) resembles structural variants of these enzymes by extensive dynamical sampling to balance conformational flexibility and catalytic efficiency.

Isotope effects at the origin of life: Fingerprints of the Strecker synthesis

Strecker synthesis creates α-amino acids from prebiotically plausible substrates (cyanide, ammonia, and aldehydes) and is widely hypothesized to be a key mechanism in the chemistry that led to life on Earth and on other planets. To better constrain the synthetic environments and precursors of abiotic α-amino acids, and to determine unique signatures of abiogenic amino acids, we measured the molecular-averaged and site-specific carbon and nitrogen isotope effects for the Strecker synthesis of alanine. The reaction steps of the Strecker synthesis can be divided into two groups: an initial series of reversible amination and nitrile-addition reactions (‘equilibration’) and a second series of irreversible hydrolysis reactions (‘hydrolysis’). The equilibration of cyanide, acetaldehyde, and ammonia with the intermediate, α-aminopropionitrile (α-APN), has a measured 55.1‰ equilibrium nitrogen isotope effect between the 15N-rich amine nitrogen in α-aminopropionitrile and the 15N-poor ammonia and a 20.0‰ equilibrium carbon isotope effect between the 13C-poor C-2 site in α-aminopropionitrile and the 13C-rich carbonyl carbon in acetaldehyde. The first irreversible hydrolysis step is inferred to have an up to 10‰ normal carbon fractionation (i.e., faster for 12C, slower for 13C) for the whole molecule, but it also has one or more side reactions that deplete the reactive α-APN reservoir by up to 15‰. The second hydrolysis step has a 15.4‰ normal kinetic isotope effect on the amide (C-1) site of alaninamide, which becomes the carboxyl site of alanine. Other α-amino acids will likely experience similar nitrogen isotope fractionations between ammonia and their amine sites, and similar carbon isotope fractionations between the carbonyl carbon in reactant aldehydes or ketones and the intermediate α-aminonitrile, and between cyanide and the carboxyl site. Therefore, these isotope effects allow us to predict the carbon and nitrogen isotopic contents and intramolecular structures of α-amino acids formed by Strecker synthesis based on their substrates’ isotopic compositions, or to infer the isotopic compositions of substrates from which amino acids formed, for example in the case of the amino-acid-rich carbonaceous chondrites. The site-specific C and N isotopic compositions of amino acids formed by Strecker chemistry contrast with those typical of terrestrial biosynthetic amino acids, so these data also provide a means of discriminating between biogenic and abiogenic α-amino acids.

Chemistry and Isotope Fractionation of Divalent Mercury during Aqueous Reduction Mediated by Selected Oxygenated Organic Ligands.

We have investigated the chemistry and Hg isotope fractionation during the aqueous reduction of HgII by oxalic acid, p-quinone, quinol, and anthraquinone-2,6-disulfonate (AQDS), a derivate of anthraquinone (AQ) that is found in secondary organic aerosols (SOA) and building blocks of natural organic matter (NOM). Each reaction was examined for the effects of light, pH, and dissolved O2. Using an excess of ligand, UVB photolysis of HgII was seen to follow pseudo-first-order kinetics, with the highest rate of ∼10-3 s-1 observed for AQDS and oxalic acid. Mass-dependent fractionation (MDF) occurs by the normal kinetic isotope effect (KIE). Only the oxalate ion, rather than oxalic acid, is photoreactive when present in HgC2O4, which decomposes via two separate pathways distinguishable by isotope anomalies. Upon UVB photolysis, only the reduction mediated by AQDS results in a large odd number mass-independent fractionation (odd-MIF) signified by enrichment of odd isotopes in the reactant. Consistent with the rate, MDF, and odd-MIF reported for fulvic acid, our AQDS result confirms previous assumptions that quinones control HgII reduction in NOM-rich waters. Given the magnitude of odd-MIF triggered via a radical pair mechanism and the significant rate in the presence of air, reduction of HgII by photoproducts of AQDS may help explain the positive odd-MIF observed in ambient aerosols depleted of HgII.

Insertion products in the reaction of carbonyl oxide Criegee intermediates with acids: Chloro(hydroperoxy)methane formation from reaction of CH2OO with HCl and DCl

The reactions of carbonyl oxide Criegee intermediates with acids proceed predominantly by an insertion mechanism. We characterise the products from one of the simplest reactions of carbonyl oxides with inorganic acids, CH2OO + hydrogen chloride, which occurs via a 1,2-insertion in the H–Cl bond. Reactions of both HCl and DCl isotopologues yield product signal at the mass of the insertion product chloro(hydroperoxy)methane and a dissociative ionisation peak at the mass of the protonated (or deuteronated) Criegee intermediate. The isotopic composition of the insertion product has been measured for reaction mixtures where both HCl isotopologues are present, and the H/D ratio of the product is consistently higher (by a factor of 1.6 ± 0.3) than that of the reactants. This isotope selectivity in the products has smaller uncertainty than the ratio of measured rate coefficients and suggests a normal (k H > k D) kinetic isotope effect in the reaction. Theoretical kinetics calculations predict a small normal kinetic isotope effect for the overall reaction (k H / k D = 1.35 at 20 Torr N2 and k H / k D = 1.2 at 1 atm N2) but predict a substantial inverse kinetic isotope effect (k D > k H) for the stabilisation fraction, in disagreement with the experimental observation.

Enzymatic Δ1-Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism

Δ1-Dehydrogenation of 3-ketosteroids catalyzed by flavin adenine dinucleotide (FAD)-dependent 3-ketosteroid dehydrogenases (Δ1-KSTD) is a crucial step in steroid degradation and synthesis of several steroid drugs. The catalytic mechanism assumes the formation of a double bond in two steps, proton abstraction by tyrosyl ion, and a rate-limiting hydride transfer to FAD. This hypothesis was never verified by quantum-mechanical studies despite contradictory results from the kinetic isotope effect (KIE) reported in 1960 by Jerussi and Ringold [Biochemistry 1965, 4 (10)]. In this paper, we present results that reconcile the mechanistic hypothesis with experimental evidence. Quantum mechanics/molecular mechanics molecular dynamics simulations show that the proposed mechanism is indeed the most probable, but barriers associated with substrate activation (13.4–16.3 kcal·mol–1) and hydride transfer (15.5–18.0 kcal·mol–1) are very close (1.7–2.1 kcal·mol–1), which explains normal KIE values for steroids labeled either at C1 or C2 atoms. We confirm that tyrosyl ion acting as the catalytic base is indeed necessary for efficient activation of the steroid. We explain the lower value of the observed KIE (1.5–3.5) by the nature of the free energy surface, the presence of diffusion limitation, and to a smaller extent, conformational changes of the enzyme upon substrate binding. Finally, we confirm the Ping-Pong bi–bi kinetics of the whole Δ1-dehydrogenation and demonstrate that substrate binding, steroid dehydrogenation, and enzyme reoxidation proceed at comparable rates.

Rapid kinetics reveal surprising flavin chemistry in bifurcating electron transfer flavoprotein from Acidaminococcus fermentans

Electron bifurcation uses free energy from exergonic redox reactions to power endergonic reactions. β-FAD of the electron transfer flavoprotein (EtfAB) from the anaerobic bacterium Acidaminococcus fermentans bifurcates the electrons of NADH, sending one to the low-potential ferredoxin and the other to the high-potential α-FAD semiquinone (α-FAD•−). The resultant α-FAD hydroquinone (α-FADH−) transfers one electron further to butyryl-CoA dehydrogenase (Bcd); two such transfers enable Bcd to reduce crotonyl-CoA to butyryl-CoA. To get insight into the mechanism of these intricate reactions, we constructed an artificial reaction only with EtfAB containing α-FAD or α-FAD•− to monitor formation of α-FAD•− or α-FADH−, respectively, using stopped flow kinetic measurements. In the presence of α-FAD, we observed that NADH transferred a hydride to β-FAD at a rate of 920 s−1, yielding the charge–transfer complex NAD+:β-FADH− with an absorbance maximum at 650 nm. β-FADH− bifurcated one electron to α-FAD and the other electron to α-FAD of a second EtfAB molecule, forming two stable α-FAD•−. With α-FAD•−, the reduction of β-FAD with NADH was 1500 times slower. Reduction of β-FAD in the presence of α-FAD displayed a normal kinetic isotope effect (KIE) of 2.1, whereas the KIE was inverted in the presence of α-FAD•−. These data indicate that a nearby radical (14 Å apart) slows the rate of a hydride transfer and inverts the KIE. This unanticipated flavin chemistry is not restricted to Etf–Bcd but certainly occurs in other bifurcating Etfs found in anaerobic bacteria and archaea.

Quantum Effects on H2 Diffusion in Zeolite RHO: Inverse Kinetic Isotope Effect for Sieving.

We use canonical variational theory (CVT) with small-curvature tunneling (SCT) contributions to investigate quantum effects on the H2 diffusion process in the pure-silica zeolite RHO. At low temperature we find an inverse kinetic isotopic sieving effect in that the heavier isotopic species diffuses faster than the lighter one. Three quantum effects contribute to this kinetic isotope effect (KIE). The first one is quantum mechanical tunneling; this-on its own-would lead to a normal kinetic isotopic sieving effect, in which lighter diprotium diffuses faster than dideuterium. The second factor, which we find to dominate in the present case, is zero-point energy (ZPE). Deuterium has a lower ZPE, which leads to a smaller effective barrier for tunneling because the transition state has a larger ZPE than the precursor stable state; this results in an inverse KIE. The third factor, the thermal vibrational energy (computed from the quantized vibrational partition function), also favors a normal KIE, but it is outweighed by the ZPE effect. The vibrations of the zeolite host framework are found to play an important role at low temperatures, and our calculations consider up to 7296 degrees of freedom at the equilibrium structure and the saddle point and up to 221 degrees of freedom along the reaction path. The importance of quantum considerations on the dynamics is elucidated by comparison to a purely classical treatment.

Isotope heterogeneity in ethyltoluenes from Australian condensates, and their stable carbon site-specific isotope analysis

Low-molecular-weight (LMW) aromatic compounds from petroleum fluids have not been widely studied for fluid-source correlations due to their volatility and their relatively low abundances in source rocks. However, LMW aromatics are important components in fluids, including condensates which lack biomarkers (molecular fossils typically used for correlation studies). Here, we have investigated the distribution of ethyltoluenes (o-ET, m-ET and p-ET; ortho, meta and para, respectively) in fluvial-deltaic condensates which contain relatively high abundances of the meta-isomer. The meta-selectivity found in these petroleum fluids is consistent with a mineral catalytic effect on the molecular distribution of these compounds, as it occurs during the clay-catalyzed synthesis of ethyltoluenes. Isomers differ up to 6‰ in δ13C values. Condensates from the Northern Carnarvon Basin, North West Shelf of Australia (NWS), have been analyzed by compound specific isotope analysis (CSIA) by GC-ir-MS, and site-specific isotope analysis (SSIA) using a Q-Exactive-GC Orbitrap™-based mass spectrometer. The SSIA revealed a 13C enrichment at the methyl end of the ethyl branch of m-ET, following a normal kinetic isotope effect during thermal maturation (cleavage). Continuous development of this first SSIA application will make possible high resolution analysis of light aromatics to outline the evolution of the organic matter to hydrocarbons in petroleum systems.

Active-Site Glu165 Activation in Triosephosphate Isomerase and Its Deprotonation Kinetics.

Triosephosphate isomerase (TIM) catalyzes the interconversion between dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP) via an enediol(ate) intermediate. The active-site residue Glu165 serves as the catalytic base during catalysis. It abstracts a proton from C1 carbon of DHAP to form the reaction intermediate and donates a proton to C2 carbon of the intermediate to form product GAP. Our difference Fourier transform infrared spectroscopy studies on the yeast TIM (YeTIM)/phosphate complex revealed a C═O stretch band at 1706 cm-1 from the protonated Glu165 carboxyl group at pH 7.5, indicating that the p Ka of the catalytic base is increased by >3.0 pH units upon phosphate binding, and that the Glu165 carboxyl environment in the complex is still hydrophilic in spite of the increased p Ka. Hence, the results show that the binding of the phosphodianion group is part of the activation mechanism which involves the p Ka elevation of the catalytic base Glu165. The deprotonation kinetics of Glu165 in the μs to ms time range were determined via infrared (IR) T-jump studies on the YeTIM/phosphate and ("heavy enzyme") [U-13C,-15N]YeTIM/phosphate complexes. The slower deprotonation kinetics in the ms time scale is due to phosphate dissociation modulated by the loop motion, which slows down by enzyme mass increase to show a normal heavy enzyme kinetic isotope effect (KIE) ∼1.2 (i.e., slower rate in the heavy enzyme). The faster deprotonation kinetics in the tens of μs time scale is assigned to temperature-induced p Ka decrease, while phosphate is still bound, and it shows an inverse heavy enzyme KIE ∼0.89 (faster rate in the heavy enzyme). The IR static and T-jump spectroscopy provides atomic-level resolution of the catalytic mechanism because of its ability to directly observe the bond breaking/forming process.

Fischer-Tropsch synthesis: Using deuterium tracer coupled with kinetic approach to study the kinetic isotopic effects of iron, cobalt and ruthenium catalysts

Deuterium tracer studies coupled with kinetic approach were developed to accurately determine the kinetic isotopic effects (KIE) for the CO hydrogenation and the formations of CO2, CH4 and light hydrocarbons (C2-C4) over iron, cobalt and ruthenium catalysts. Pronounced inverse kinetic isotope effects (IKIE) (kco,H/kco,D = 0.64–0.66) over the Fe and Co catalysts and a moderate IKIE (kco,H/kco,D = ∼0.8) on the Ru catalysts for the CO hydrogenation were obtained under typical FTS conditions. The IKIE was also found in CH4 formation, but the Co and Ru catalysts showed stronger IKIE than the Fe catalysts (kCH4/kCD4 = 0.6 vs 0.87). Regardless of catalyst type, only a minor normal KIE for the CO2 formation was obtained (kCO2, H/kCO2, D ˜ 1.1). The IKIE was found on various light 1-olefins and n-paraffin hydrocarbons as well. All the IKIEs can be explained by thermodynamic and kinetic isotope effects. The results suggested that deuterium was involved in quasi-equilibrated and hydrogenation steps that determined KIE. However, the Fe, Co and Ru catalysts showed different deuterium isotopic effect for the hydrocarbon selectivity. Deuterium promoted chain growth, thus lowered CH4 and light hydrocarbons selectivities and enhanced C5+ selectivity on both the Fe and Co catalysts; while it enhanced the hydrogenation rate to the low hydrocarbons and suppressed the formation of heavier hydrocarbons on the Ru catalysts.

18O Kinetic Isotope Effects Reveal an Associative Transition State for Phosphite Dehydrogenase Catalyzed Phosphoryl Transfer.

Phosphite dehydrogenase (PTDH) catalyzes an unusual phosphoryl transfer reaction in which water displaces a hydride leaving group. Despite extensive effort, it remains unclear whether PTDH catalysis proceeds via an associative or dissociative mechanism. Here, primary 2H and secondary 18O kinetic isotope effects (KIEs) were determined and used together with computation to characterize the transition state (TS) catalyzed by a thermostable PTDH (17X-PTDH). The large, normal 18O KIEs suggest an associative mechanism. Various transition state structures were computed within a model of the enzyme active site and 2H and 18O KIEs were predicted to evaluate the accuracy of each TS. This analysis suggests that 17X-PTDH catalyzes an associative process with little leaving group displacement and extensive nucleophilic participation. This tight TS is likely a consequence of the extremely poor leaving group requiring significant P-O bond formation to expel the hydride. This finding contrasts with the dissociative TSs in most phosphoryl transfer reactions from phosphate mono- and diesters.

D/H control of chemical kinetics in water solutions under low deuterium concentrations

Variations in the isotopic composition drastically changes properties of molecules. This also applies to H2O, one of the most indispensable substances on Earth. Here we investigated physical, chemical and biological characteristics of deuterium depleted water (0.5 mM HDO) compared to water with natural deuterium content (16 mM HDO) and heavy water D2O. Reaction systems of different organization levels were probed: molecular (galactose mutarotation), supramolecular (destabilase-lysozyme activity), two-phase heterogenic (suspension of slightly water-soluble active pharmaceutical ingredients), and living cells (unicellular biosensor S. ambigua lifespan). We have shown that the mutarotation rate constant for the l-galactose was 2-fold less than that for the D-isomer over the whole temperature range without dependence on HDO concentration in low values, whereas the first-order mutarotation kinetics was not observed for l-galactose in heavy water. Interestingly, the initial rate of lysozyme activity of destabilase-lysozyme increased two-fold in deuterium-depleted water whereas there was no activity change in heavy water. In suspension system, the dissolution kinetics of active pharmaceutical ingredients conformed with the normal kinetic isotope effect when kH/kD > 1. This confirms the important role of variations in the solvent (water) isotopic composition in the dissolution process acceleration. However, the most important isotope effect was observed in the living cells, where the rate constant for the processes of irreversible S. ambigua cell transition (from an active state to an immobilized state) increased up to 800 times under deuterium depletion.