Secondary Kinetic Isotope Effects Research Articles

Cationic Effect on the Equilibria and Kinetics of the Excited-State Proton Transfer Reaction of a Photoacid in Aqueous Solutions.

Dissolved ions have a significant effect on the chemical equilibria and kinetics in aqueous solutions by changing the physical properties and hydrogen bond network of water. In this work, the ionic effects on the excited-state proton transfer (ESPT) reactions of Coumarin 183 (C183) in aqueous ionic solutions are comprehensively studied in terms of p Ka, p Ka*, activation energies, and kinetic isotope effect (KIE). The acid dissociation constants (p Ka and p Ka*) of C183 on the ground and excited states are determined by UV-visible absorption and steady-state fluorescence spectroscopy. The activation energies ( Ea) and KIE for the ESPT reaction of C183 are directly obtained by time-resolved fluorescence spectroscopy. The changes in p Ka, p Ka*, Ea, and KIE values of C183 are found to be dependent on the charge density of cations. The secondary KIE is more substantially influenced by the dissolved ions than the primary KIE. Furthermore, the ionic effects on the equilibrium (p Ka and p Ka*) and kinetic ( Ea and KIE) parameters of C183 are found to be well-explained by the free-energy reactivity relation. Our current results are very important in understanding the ionic effects on the equilibria and ESPT kinetics of photoacids in aqueous ionic solutions.

Thermal Rate Coefficients and Kinetic Isotope Effects for the Reaction OH + CH4 → H2O + CH3 on an ab Initio-Based Potential Energy Surface.

Thermal rate coefficients for the title reaction and its various isotopologues are computed using a tunneling-corrected transition-state theory on a global potential energy surface recently developed by fitting a large number of high-level ab initio points. The calculated rate coefficients are found to agree well with the measured ones in a wide temperature range, validating the accuracy of the potential energy surface. Strong non-Arrhenius effects are found at low temperatures. In addition, the calculations reproduced the primary and secondary kinetic isotope effects. These results confirm the strong influence of tunneling to this heavy-light-heavy hydrogen abstraction reaction.

Heavy Atom Secondary Kinetic Isotope Effect on H-Tunneling.

Although frequently employed, heavy atom kinetic isotope effects (KIE) have not been reported for quantum mechanical tunneling reactions. Here we examine the secondary KIE through 13C-substitution of the carbene atom in methylhydroxycarbene (H3C-C̈-OH) in its [1,2]H-tunneling shift reaction to acetaldehyde (H3C-CHO). Our study employs matrix-isolation IR spectroscopy in various inert gases and quantum chemical computations. Depending on the choice of the matrix host gas, the KIE varies within a range of 1.0 in xenon to 1.4 in neon. A KIE of 1.1 was computed using the Wentzel-Kramers-Brillouin (WKB) CVT/SCT, and instanton approaches for the gas phase at the B3LYP/cc-pVTZ level of theory. Computations with explicit consideration of the noble gas environment indicate that the surrounding atoms influence the tunneling reaction barrier height and width. The tunneling half-lives computed with the WKB approach are in good agreement with the experimental results in the different noble gases.

Tunnelling and the kinetic isotope effect in [formula omitted]: An application of semiclassical transition state theory

One-dimensional semiclassical transition state theory is applied to study the rate constants of the CH3+CH4 reaction and its hydrogen-substituted isotopic analogues. This requires calculation of vibrational frequencies at the reactant, product and transition states, and the anharmonic constants of the reaction coordinate at the transition state. The reactions studied have a hindered rotor vibration at the transition states, whose behaviour is approximated using two methods. The results show very good agreement to experimental and other theoretical results. The three reactions studied allow evaluation of both primary and secondary kinetic isotope effects in the title reaction.

Kinetic Isotope Effects and Transition State Structure for Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase from Plasmodium falciparum.

Plasmodium falciparum parasites are purine auxotrophs that rely exclusively on the salvage of preformed purines from their human hosts to supply the requirement for purine nucleotides. Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) catalyzes the freely reversible Mg2+-dependent conversion of 6-oxopurine bases to their respective nucleotides and inorganic pyrophosphate. The phosphoribosyl group is derived from 5-phospho-α-d-ribosyl 1-pyrophosphate (PRPP). The enzyme from malaria parasites (PfHGXPRT) is essential as hypoxanthine is the major precursor in purine metabolism. We used specific heavy atom labels in PRPP and hypoxanthine to measure primary (1-14C and 9-15N) and secondary (1-3H and 7-15N) intrinsic kinetic isotope effect (KIE) values for PfHGXPRT. Intrinsic isotope effects contain information for understanding enzymatic transition state properties. The transition state of PfHGXPRT was explored by matching KIE values predicted from quantum mechanical calculations to the intrinsic values determined experimentally. This approach provides information about PfHGXPRT transition state bond lengths, geometry, and atomic charge distribution. The transition state structure of PfHGXPRT was determined in the physiological direction of addition of ribose 5-phosphate to hypoxanthine by overcoming the chemical instability of PRPP. The transition state for PfHGXPRT forms nucleotides through a well-developed and near-symmetrical DN*AN, SN1-like transition state.

Secondary Deuterium Kinetic Isotope Effects in Phospha‐Michael Addition of Tertiary Phosphines to Electron‐Deficient Alkenes

AbstractFor the reaction of PPh3 with isotopomeric acrylonitriles in acetic acid solvent, replacement of H by D on the position α to the CN group unexpectedly produced normal secondary kinetic isotope effects (KIEs). These effects were interpreted on the basis of the known vibrational‐rotational coupling between two lowest vibrational modes of acrylonitrile, the in‐plane and out‐of‐plane C–C≡N bendings. For isotopomeric acrylonitriles this coupling leads to the difference in zero‐point energies (ZPEs) for the in‐plane C–C≡N bending, which defines the reaction coordinate during rate‐determining protonation of zwitterionic intermediate at heteroatom by acetic acid. Observation of these effects became possible due to dynamic behavior of the zwitterion, whose lifetime appears to be comparable with the time of the in‐plane bending. The untypical origin of secondary KIEs observed for acrylonitrile was evidenced by the absence of such effect for 2‐d‐acrylamide. Steric isotope effects for the reaction of d15‐PPh3 with a range of electron‐deficient alkenes revealed a significant increase in steric strain in transition state for nucleophilic attack step, when a substituent is introduced to the β‐position of the alkene.

Glycosyl Cations versus Allylic Cations in Spontaneous and Enzymatic Hydrolysis.

Enzymatic prenyl and glycosyl transfer are seemingly unrelated reactions that yield molecules and protein modifications with disparate biological functions. However, both reactions employ diphosphate-activated donors and each proceed via cationic species: allylic cations and oxocarbenium ions, respectively. In this study, we explore the relationship between these processes by preparing valienyl ethers to serve as glycoside mimics that are capable of allylic rather than oxocarbenium cation stabilization. Rate constants for spontaneous hydrolysis of aryl glycosides and their analogous valienyl ethers were found to be almost identical, as were the corresponding activation enthalpies and entropies. This close similarity extended to the associated secondary kinetic isotope effects (KIEs), indicating very similar transition state stabilities and structures. Screening a library of over 100 β-glucosidases identified a number of enzymes that catalyze hydrolysis of these valienyl ethers with kcat values up to 20 s-1. Detailed analysis of one such enzyme showed that ether hydrolysis occurs via the analogous mechanisms found for glycosides, and through a very similar transition state. This suggests that the generally lower rates of enzymatic cleavage of the cyclitol ethers reflects evolutionary specialization of these enzymes toward glycosides rather than inherent reactivity differences.

Modeling 3D-CSIA data: Carbon, chlorine, and hydrogen isotope fractionation during reductive dechlorination of TCE to ethene

Reactive transport modeling of multi-element, compound-specific isotope analysis (CSIA) data has great potential to quantify sequential microbial reductive dechlorination (SRD) and alternative pathways such as oxidation, in support of remediation of chlorinated solvents in groundwater. As a key step towards this goal, a model was developed that simulates simultaneous carbon, chlorine, and hydrogen isotope fractionation during SRD of trichloroethene, via cis-1,2-dichloroethene (and trans-DCE as minor pathway), and vinyl chloride to ethene, following Monod kinetics. A simple correction term for individual isotope/isotopologue rates avoided multi-element isotopologue modeling. The model was successfully validated with data from a mixed culture Dehalococcoides microcosm. Simulation of Cl-CSIA required incorporation of secondary kinetic isotope effects (SKIEs). Assuming a limited degree of intramolecular heterogeneity of δ37Cl in TCE decreased the magnitudes of SKIEs required at the non-reacting Cl positions, without compromising the goodness of model fit, whereas a good fit of a model involving intramolecular CCl bond competition required an unlikely degree of intramolecular heterogeneity. Simulation of H-CSIA required SKIEs in H atoms originally present in the reacting compounds, especially for TCE, together with imprints of strongly depleted δ2H during protonation in the products. Scenario modeling illustrates the potential of H-CSIA for source apportionment.

Exploring the substrate selectivity of human sEH and M. tuberculosis EHB using QM/MM

The mechanisms of human soluble epoxide hydrolase (sEH) and the corresponding epoxide hydrolase enzyme from Mycobacterium tuberculosis (EHB) are studied computationally, using the quantum mechanics/molecular mechanics (QM/MM) method. To do this, we modeled the alkylation and the hydrolysis steps of three substrates: trans-1,3-diphenylpropene oxide, trans-stilbene oxide and cis-stilbene oxide. Studying the regioselectivity for trans-1,3-diphenylpropene oxide, we determined that both enzymes prefer ring opening via attack on the benzylic carbon. In agreement with experimental studies, our computations show that the rate-limiting step is hydrolysis of the ester intermediate, with reaction barriers of approximately 13 to 18 kcal/mol. Using the barrier energies of this rate-limiting step, the three epoxides were ranked in order of reactivity. Though the reactivity order was correctly predicted for sEH, the predicted order for EHB did not correspond to experimental observations. Next, the electrostatic contributions of individual residues on the barrier height of the rate-limiting step were also studied. This revealed several residues important for catalysis. The secondary tritium kinetic isotope effect for the alkylation step was determined using a cluster model for the active site of sEH. The calculated value was 1.27, suggesting a late transition state for the rate-limiting step. Finally, we analyzed the reactivity trends using reactivity indicators from conceptual density functional theory, allowing us to identify ease of electron transfer as the primary driving force for the reaction.

Phenol-Induced O-O Bond Cleavage in a Low-Spin Heme-Peroxo-Copper Complex: Implications for O2 Reduction in Heme-Copper Oxidases.

This study evaluates the reaction of a biomimetic heme-peroxo-copper complex, {[(DCHIm)(F8)FeIII]-(O22-)-[CuII(AN)]}+ (1), with a phenolic substrate, involving a net H-atom abstraction to cleave the bridging peroxo O-O bond that produces FeIV═O, CuII-OH, and phenoxyl radical moieties, analogous to the chemistry carried out in heme-copper oxidases (HCOs). A 3D potential energy surface generated for this reaction reveals two possible reaction pathways: one involves nearly complete proton transfer (PT) from the phenol to the peroxo ligand before the barrier; the other involves O-O homolysis, where the phenol remains H-bonding to the peroxo OCu in the transition state (TS) and transfers the H+ after the barrier. In both mechanisms, electron transfer (ET) from phenol occurs after the PT (and after the barrier); therefore, only the interaction with the H+ is involved in lowering the O-O cleavage barrier. The relative barriers depend on covalency (which governs ET from Fe), and therefore vary with DFT functional. However, as these mechanisms differ by the amount of PT at the TS, kinetic isotope experiments were conducted to determine which mechanism is active. It is found that the phenolic proton exhibits a secondary kinetic isotope effect, consistent with the calculations for the H-bonded O-O homolysis mechanism. The consequences of these findings are discussed in relation to O-O cleavage in HCOs, supporting a model in which a peroxo intermediate serves as the active H+ acceptor, and both the H+ and e- required for O-O cleavage derive from the cross-linked Tyr residue present at the active site.

Organocatalysts Fold To Generate an Active Site Pocket for the Mannich Reaction

Catalysts containing urea, thiourea, and tertiary amine groups fold into a three-dimensional organized structure in solution both in the absence as well as in the presence of substrates or substrate analogues, as indicated by solution NMR and computational studies. These foldamer catalysts promote Mannich reactions with both aliphatic and aromatic imines and malonate esters. Hammett plot and secondary kinetic isotope effects provide evidence for the C–C bond forming event as the turnover-limiting step of the Mannich reaction. Computational studies suggest two viable pathways for the C–C bond formation step, differing in the activation modes of the malonate and imine substrates. The results show that the foldamer catalysts may promote C–C bond formation with an aliphatic substrate bearing a cyclohexyl group by enhanced binding of the substrates by dispersion interactions, but these interactions are largely absent with a simpler catalyst. Additional control experiments demonstrate the ability of simple thio...

Thermal decomposition reaction in ethanol solution of deuterated acetone cyclic diperoxide and acetone diperoxide. Secondary inverse isotopic effect

The characterization by mass spectrometry and the kinetic study of the thermal decomposition reaction of deuterated acetone diperoxide (dACDP) was studied in ethanol in the 140-165 oC temperature range. The comparison with the non deuterated species (ACDP) was also made. The kinetic behavior observed for both compounds follows a pseudo first order kinetic law up to at least 86 % peroxide conversions. It could be observed that under the established experimental conditions, the dACDP decomposes ca. 1.2 times faster than the ACDP. The activation parameters were calculated for both peroxides and allowed to postulate a single process initial step, the unimolecular thermal decomposition through the O-O bond cleavage to form an intermediate biradical. The products of the acetone derived peroxides thermal decomposition support a radical-based decomposition mechanism. The changes in kinetic parameters between dACDP and ACDP were justified attending to differences in ring substituents sizes. A secondary inverse kinetic isotope effect is observed (kH/kD <1).

Dynamical barrier and isotope effects in the simplest substitution reaction via Walden inversion mechanism

Reactions occurring at a carbon atom through the Walden inversion mechanism are one of the most important and useful classes of reactions in chemistry. Here we report an accurate theoretical study of the simplest reaction of that type: the H+CH4 substitution reaction and its isotope analogues. It is found that the reaction threshold versus collision energy is considerably higher than the barrier height. The reaction exhibits a strong normal secondary isotope effect on the cross-sections measured above the reaction threshold, and a small but reverse secondary kinetic isotope effect at room temperature. Detailed analysis reveals that the reaction proceeds along a path with a higher barrier height instead of the minimum-energy path because the umbrella angle of the non-reacting methyl group cannot change synchronously with the other reaction coordinates during the reaction due to insufficient energy transfer from the translational motion to the umbrella mode.

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.

Rate coefficients and kinetic isotope effects of the abstraction reaction of H atoms from methylsilane

ABSTRACTThermal rate constants for chemical reactions using improved canonical variational transition state theory (ICVT) with small-curvature tunnelling (SCT) contributions in a temperature range 180–2000 K are reported. The general procedure is used with high-quality ab initio computations and semi-classical reaction probabilities along the minimum energy path (MEP). The approach is based on a vibrational adiabatic reaction path and is applied to the multiple-channel hydrogen abstraction reaction H + SiH3CH3 → products and its isotopically substituted variants. All the degrees of freedom are optimised and harmonic vibrational frequencies and zero-point energies are calculated at the MP2 level with the cc-pVTZ basis set. Single-point energies are calculated at a higher level of theory; CCSD(T)-F12a/VTZ-F12. ICVT/SCT rate constants show that the quantum tunnelling contributions at low temperatures are relatively important and the H-abstraction channel from SiH3 group of SiH3CH3 is the major pathway. The total rate constants are given by the following expression: ktot(ICVT/SCT) = 2.29 10−18 T2.42 exp(−350.9/T) cm3 molec−1 s−1. These calculated rates are in agreement with the available experiments. The ICVT/SCT method is further exploited to predict primary and secondary kinetic isotope effects, respectively).

Synthesis of site-specifically 13C labeled linoleic acids

Soybean lipoxygenase-1 (SLO-1) catalyzes the C–H abstraction from the reactive carbon (C-11) in linoleic acid as the first and rate-determining step in the formation of alkylhydroperoxides. While previous labeling strategies have focused on deuterium labeling to ascertain the primary and secondary kinetic isotope effects for this reaction, there is an emerging interest and need for selectively enriched 13C isotopologues. In this Letter, we present synthetic strategies for site-specific 13C labeled linoleic acid substrates. We take advantage of a Corey–Fuchs formyl to terminal 13C-labeled alkyne conversion, using 13CBr4 as the labeling source, to reduce the number of steps from a previous fatty acid 13C synthetic labeling approach. The labeled linoleic acid substrates are useful as nuclear tunneling markers and for extracting active site geometries of the enzyme–substrate complex in lipoxygenase.

Carbon kinetic isotope effects at natural abundances during iron-catalyzed photolytic cleavage of C[sbnd]C bonds in aqueous phase α,ω-dicarboxylic acids

Carbon kinetic isotope effects (KIEs) at natural abundances during photolysis of Fe3+-oxalato, malonato, and succinato complexes in aqueous solution were studied to identify the CC bond cleaving mechanism of Fe3+-oxalato complexes under sunlight irradiation. Observed overall KIEs were 5.9‰, 11.5‰, and 8.4‰, respectively. This variation is inconsistent with secondary carbon KIEs for the FeO bond cleavage, but consistent with primary carbon KIEs for sequential cleavage of FeO and CC bonds. Position-specific probability of 13C content estimated KIEs of 5.9‰, 17.2‰, and 17‰ for 12C13C bond cleavage, respectively, indicating the different KIEs for carboxyl-carboxyl and methyl-carboxyl cleavage.

Secondary kinetic deuterium isotope effects. The CC cleavage of labeled tetramethylethylenediamine radical cations—Who gets to keep the electron?

The simple cleavage of the C–C bond in tetramethylethylenediamine molecular ions yields two fragments that are identical but for the positions of the charge and radical; nonetheless, the reactions of deuterium labeled analogs are accompanied by substantial secondary kinetic isotope effects. The underlying transition state zero-point vibrational energy differences depend particularly on the properties of the incipient radicals rather than on those of the charge-retaining products. The α-secondary effects arise primarily from vibrations related to deformation of the product –CH2N– and –CD2N– groups when the reactant is labeled at the central C–C bond, whereas CH/CD stretching vibrations are the origin of the γ-secondary effects observed for reactants with labeled methyl groups. These zero-point energy differences are mainly due to hyperconjugative interactions (Bohlmann shifts) and do not reflect bonding changes in the transition state; the secondary isotope effects on the dissociation of protonated amine dimers have a similar origin.

Computational Replication of the Primary Isotope Dependence of Secondary Kinetic Isotope Effects in Solution Hydride-Transfer Reactions: Supporting the Isotopically Different Tunneling Ready State Conformations.

We recently reported a study of the steric effect on the 1° isotope dependence of 2° KIEs for several hydride-transfer reactions in solution (J. Am. Chem. Soc. 2015, 137, 6653). The unusual 2° KIEs decrease as the 1° isotope changes from H to D, and more in the sterically hindered systems. These were explained in terms of a more crowded tunneling ready state (TRS) conformation in D-tunneling, which has a shorter donor-acceptor distance (DAD) than in H-tunneling. To examine the isotopic DAD difference explanation, in this paper, following an activated motion-assisted H-tunneling model that requires a shorter DAD in a heavier isotope transfer process, we computed the 2° KIEs at various H/D positions at different DADs (2.9 Å to 3.5 Å) for the hydride-transfer reactions from 2-propanol to the xanthylium and thioxanthylium ions (Xn(+) and TXn(+)) and their 9-phenyl substituted derivatives (Ph(T)Xn(+)). The calculated 2° KIEs match the experiments and the calculated DAD effect on the 2° KIEs fits the observed 1° isotope effect on the 2° KIEs. These support the motion-assisted H-tunneling model and the isotopically different TRS conformations. Furthermore, it was found that the TRS of the sterically hindered Ph(T)Xn(+) system does not possess a longer DAD than that of the (T)Xn(+) system. This predicts a no larger 1° KIE in the former system than in the latter. The observed 1° KIE order is, however, contrary to the prediction. This implicates the stronger DAD-compression vibrations coupled to the bulky Ph(T)Xn(+) reaction coordinate.

Mechanism of the Novel Prenylated Flavin-Containing Enzyme Ferulic Acid Decarboxylase Probed by Isotope Effects and Linear Free-Energy Relationships.

Ferulic acid decarboxylase from Saccharomyces cerevisiae catalyzes the decarboxylation of phenylacrylic acid to form styrene using a newly described prenylated flavin mononucleotide cofactor. A mechanism has been proposed, involving an unprecedented 1,3-dipolar cyclo-addition of the prenylated flavin with the α═β bond of the substrate that serves to activate the substrate toward decarboxylation. We measured a combination of secondary deuterium kinetic isotope effects (KIEs) at the α- and β-positions of phenylacrylic acid together with solvent deuterium KIEs. The solvent KIE is 3.3 on Vmax/KM but is close to unity on Vmax, indicating that proton transfer to the product occurs before the rate-determining step. The secondary KIEs are normal at both the α- and β-positions but vary in magnitude depending on whether the reaction is performed in H2O or D2O. In D2O, the enzyme catalyzed the exchange of deuterium into styrene; this reaction was dependent on the presence of bicarbonate. This observation implies that CO2 release must occur after protonation of the product. Further information was obtained from a linear free-energy analysis of the reaction through the use of a range of para- and meta-substituted phenylacrylic acids. Log(kcat/KM) for the reaction correlated well with the Hammett σ(-) parameter with ρ = -0.39 ± 0.03; r(2) = 0.93. The negative ρ value and secondary isotope effects are consistent with the rate-determining step being the formation of styrene from the prenylated flavin-product adduct through a cyclo-elimination reaction.