Secondary Kinetic Isotope Effects Research Articles

Structural Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects of the NADH/NAD+ Model Reactions in Acetonitrile: Charge-Transfer Complex Tightness Is a Key.

It has recently frequently been found that the kinetic isotope effect (KIE) is independent of temperature (T) in H-tunneling reactions in enzymes but becomes dependent on T in their mutants. Many enzymologists found that the trend is related to different donor-acceptor distances (DADs) at tunneling-ready states (TRSs), which could be sampled by protein dynamics. That is, a more rigid system of densely populated short DADs gives rise to a weaker T dependence of KIEs. Theoreticians have attempted to develop H-tunneling theories to explain the observations, but none have been universally accepted. It is reasonable to assume that the DAD sampling concept, if it exists, applies to the H-transfer reactions in solution, as well. In this work, we designed NADH/NAD+ model reactions to investigate their structural effects on the T dependence of hydride KIEs in acetonitrile. Hammett correlations together with N-CH3/CD3 secondary KIEs were used to provide the electronic structure of the TRSs and thus the rigidity of their charge-transfer complexation vibrations. In all three pairs of reactions, a weaker T dependence of KIEs always corresponds to a steeper Hammett slope on the substituted hydride acceptors. It was found that a tighter/rigid charge-transfer complexation system corresponds with a weaker T dependence of KIEs, consistent with the observations in enzymes.

Impact of Catalyst Deuteration on the Reactivity of Chiral Phase-Transfer Organocatalysts.

Site-specifically deuterated organocatalysts were prepared and found to show improved reactivity over the non-deuterated analogs. Two privileged C2-symmetric chiral binaphthyl-modified tetraalkylammonium salts were selected for this study. The stability of these phase-transfer catalysts was generally improved by site-specific deuteration, though the degree of improvement was structure-dependent. In particular, a large secondary kinetic isotope effect was observed for the tetradeuterated phase-transfer catalyst. The performance of these deuterated catalysts in the asymmetric catalytic alkylation of amino acid derivatives was better than that of non-deuterated analogs at low catalyst loadings. The results suggest that catalyst-deuteration is a promising strategy for enhancing the stability and performance of organocatalysts.

Stepwise photoassisted decomposition of carbohydrates to H2

Stepwise photoassisted decomposition of carbohydrates to H2

Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.

Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand cleavage through 2'-O-transphosphorylation, provoking the question of whether protein and RNA enzymes facilitate mechanisms that pass through the same or distinct transition states. Here, we report the primary and secondary 18O kinetic isotope effects for hepatitis delta virus ribozyme catalysis that reveal a dissociative, metaphosphate-like transition state in stark contrast to the late, associative transition states observed for reactions catalyzed by specific base, Zn2+ ions, or ribonuclease A. This new information provides evidence for a discrete ribozyme active site design that modulates the RNA cleavage pathway to pass through an altered transition state.

Correlation of temperature dependence of hydride kinetic isotope effects with donor-acceptor distances in two solvents of different polarities.

Recently observed nearly temperature (T)-independent kinetic isotope effects (KIEs) in wild-type enzymes and T-dependent KIEs in variants were used to suggest that H-tunneling in enzymes is assisted by the fast protein vibrations that help sample short donor-acceptor distances (DADs). This supports the recently proposed role of protein vibrations in DAD sampling catalysis. However, use of T-dependence of KIEs to suggest DAD sampling associated with protein vibrations is debated. We have formulated a hypothesis regarding the correlation and designed experiments in solution to investigate it. The hypothesis is, a more rigid system with shorter DADTRS's at the tunneling ready states (TRSs) gives rise to a weaker T-dependence of KIEs, i.e., a smaller ΔEa (= EaD - EaH). In a former work, the solvent effects of acetonitrile versus chloroform on the ΔEa of NADH/NAD+ model reactions were determined, and the DADPRC's of the productive reactant complexes (PRCs) were computed to substitute the DADTRS for the DADTRS-ΔEa correlation study. A smaller ΔEa was found in the more polar acetonitrile where the positively charged PRC is better solvated and has a shorter DADPRC, indirectly supporting the hypothesis. In this work, the TRS structures of different DADTRS's for the hydride tunneling reaction from 1,3-dimethyl-2-phenylimidazoline to 10-methylacridinium were computed. The N-CH3/CD3 secondary KIEs on both reactants were calculated and fitted to the observed values to find the DADTRS order in both solutions. It was found that the equilibrium DADTRS is shorter in acetonitrile than in chloroform. Results directly support the DADTRS-ΔEa correlation hypothesis as well as the explanation that links T-dependence of KIEs to DAD sampling catalysis in enzymes.

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.

New Insights and Predictions into Complex Homogeneous Reactions Enabled by Computational Chemistry in Synergy with Experiments: Isotopes and Mechanisms

ConspectusHomogeneous catalysis and biocatalysis have been widely applied in synthetic, medicinal, and energy chemistry as well as synthetic biology. Driven by developments of new computational chemistry methods and better computer hardware, computational chemistry has become an essentially indispensable mechanistic "instrument" to help understand structures and decipher reaction mechanisms in catalysis. In addition, synergy between computational and experimental chemistry deepens our mechanistic understanding, which further promotes the rational design of new catalysts. In this Account, we summarize new or deeper mechanistic insights (including isotope, dispersion, and dynamical effects) into several complex homogeneous reactions from our systematic computational studies along with subsequent experimental studies by different groups. Apart from uncovering new mechanisms in some reactions, a few computational predictions (such as excited-state heavy-atom tunneling, steric-controlled enantioswitching, and a new geminal addition mechanism) based on our mechanistic insights were further verified by ensuing experiments.The Zimmerman group developed a photoinduced triplet di-π-methane rearrangement to form cyclopropane derivatives. Recently, our computational study predicted the first excited-state heavy-atom (carbon) quantum tunneling in one triplet di-π-methane rearrangement, in which the reaction rates and 12C/13C kinetic isotope effects (KIEs) can be enhanced by quantum tunneling at low temperatures. This unprecedented excited-state heavy-atom tunneling in a photoinduced reaction has recently been verified by an experimental 12C/13C KIE study by the Singleton group. Such combined computational and experimental studies should open up opportunities to discover more rare excited-state heavy-atom tunneling in other photoinduced reactions. In addition, we found unexpectedly large secondary KIE values in the five-coordinate Fe(III)-catalyzed hetero-Diels-Alder pathway, even with substantial C-C bond formation, due to the non-negligible equilibrium isotope effect (EIE) derived from altered metal coordination. Therefore, these KIE values cannot reliably reflect transition-state structures for the five-coordinate metal pathway. Furthermore, our density functional theory (DFT) quasi-classical molecular dynamics (MD) simulations demonstrated that the coordination mode and/or spin state of the iron metal as well as an electric field can affect the dynamics of this reaction (e.g., the dynamically stepwise process, the entrance/exit reaction channels).Moreover, we unveiled a new reaction mechanism to account for the uncommon Ru(II)-catalyzed geminal-addition semihydrogenation and hydroboration of silyl alkynes. Our proposed key gem-Ru(II)-carbene intermediates derived from double migrations on the same alkyne carbon were verified by crossover experiments. Additionally, our DFT MD simulations suggested that the first hydrogen migration transition-state structures may directly and quickly form the key gem-Ru-carbene structures, thereby "bypassing" the second migration step. Furthermore, our extensive study revealed the origin of the enantioselectivity of the Cu(I)-catalyzed 1,3-dipolar cycloaddition of azomethine ylides with β-substituted alkenyl bicyclic heteroarenes enabled by dual coordination of both substrates. Such mechanistic insights promoted our computational predictions of the enantioselectivity reversal for the corresponding monocyclic heteroarene substrates and the regiospecific addition to the less reactive internal C═C bond of one diene substrate. These predictions were proven by our experimental collaborators. Finally, our mechanistic insights into a few other reactions are also presented. Overall, we hope that these interactive computational and experimental studies enrich our mechanistic understanding and aid in reaction development.

Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition.

To analyze the impact of various technical details on the results of quantum mechanical (QM)/molecular mechanical (MM) enzyme simulations, including the QM region size, catechol-O-methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The results show that key equilibrium and kinetic properties for methyl transfer in COMT exhibit limited variations with respect to the size of the QM region, which ranges from ∼100 to ∼500 atoms in this study. With extensive sampling, local and global structural characteristics of the enzyme are largely conserved across the studied QM regions, while the nature of the transition state (e.g., secondary kinetic isotope effect) and reaction exergonicity are largely maintained. Deviations in the free energy profile with different QM region sizes are similar in magnitude to those observed with changes in other simulation protocols, such as different initial enzyme conformations and boundary conditions. Electronic structural properties, such as the covariance matrix of residual charge fluctuations, appear to exhibit rather long-range correlations, especially when the peptide backbone is included in the QM region; this observation holds when a range-separated DFT approach is used as the QM region, suggesting that delocalization error is unlikely the origin. Overall, the analyses suggest that multiple simulation details determine the results of QM/MM enzyme simulations with comparable contributions.

Improved Efficiency and Stability of Red Phosphorescent Organic Light-Emitting Diodes via Selective Deuteration

The secondary kinetic isotope effects (KIEs) of red phosphorescent Ir(III) complexes and the corresponding devices have been investigated. The selective deuterated red emitters show negligible influence on the luminescent spectra, but have positive effects on the quantum efficiencies and stabilities in the devices. As secondary KIEs predicted, the photolysis coinciding with the electrolysis of the deuterated complexes in the devices, measured via decreasing of luminescent intensity, are reduced in rate. An about 33% increase of the device working lifetime could be readily obtained with the strategy of selective deuteration on the emitter complexes. The findings demonstrate the importance of the isotopic effect on the performance improvement of organic light emitting devices and will also trigger the study on organic optoelectronic materials via isotopic tools.

Accurate Single-Molecule Kinetic Isotope Effects.

An accurate single-molecule kinetic isotope effect (sm-KIE) was applied to circumvent the inherent limitation of conventional ensemble KIE by using graphene-molecule-graphene single-molecule junctions. In situ monitoring of the single-molecule reaction trajectories in real time with high temporal resolution has the capability to characterize the deeper information brought by KIE. The C-O bond cleavage and the C-C bond formation of the transition state (TS) were observed in the Claisen rearrangement through the secondary kinetic isotope effect, demonstrating the high detection sensitivity and accuracy of this method. More interestingly, this sm-KIE can be used to determine TS structures under different electric fields, revealing the multidimensional regulation of the TS. The detection and manipulation of the TS provide a broad perspective to understand and optimize chemical reactions and biomimetic progress.

Hydrogen/Deuterium Transfer from Anisole to Methoxy Radicals: A Theoretical Study of a Deuterium-Labeled Drug Model.

Recently, deuterium-labeled drugs, such as deutetrabenazine, have attracted considerable attention. Consequently, understanding the reaction mechanisms of deuterium-labeled drugs is crucial, both fundamentally and for real applications. To understand the mechanisms of H- and D-transfer reactions, in this study, we used deuterated anisole as a deutetrabenazine model and computationally considered the nuclear quantum effects of protons, deuterons, and electrons. We demonstrated that geometrical differences exist in the partially and fully deuterated methoxy groups and hydrogen-bonded structures of intermediates and transition states due to the H/D isotope effect. The observed geometrical features and electronic structures are ascribable to the different nuclear quantum effects of protons and deuterons. Primary and secondary kinetic isotope effects (KIEs) were calculated for H- and D-transfer reactions from deuterated and undeuterated anisole, with the calculated primary KIEs in good agreement with the corresponding experimental data. These results reveal that the nuclear quantum effects of protons and deuterons need to be considered when analyzing the reaction mechanisms of H- and D-transfer reactions and that a theoretical approach that directly includes nuclear quantum effects is a powerful tool for the analysis of H/D isotope effects in H- and D-transfer reactions.

Secondary kinetic deuterium isotope effects on unimolecular cleavage reactions: Zero-point vibrational energy and qualitative RRKM theory.

Secondary kinetic isotope effects arise as the result of transition-state zero-point vibrational energy differences. Unimolecular simple cleavage reactions of gas-phase ions in mass spectrometers allow detailed studies of isotope effects on competing reactions, particularly when examined in intramolecular competition experiments where interpretation requires very few simplifying assumptions. The zero-point energy differences reflect changes of isotope sensitive vibrational properties, and both α- and β-secondary deuterium isotope effects are related to the sp 3 → sp 2 hybridization changes that accompany bond cleavage. Deuterium substitution three bonds or more removed from the bond broken also gives rise to isotope effects, but their origin is less easily interpreted. The magnitude and variation of the observed effects depend not only on zero-point energy differences; a number of additional factors play a role. The influence of the critical energy, the excess energy, the size of the reactant, and the presence of competing reactions can be rationalized within a simple, qualitative RRKM framework. The distinction between kinetic and thermodynamic isotope effects is not always obvious.

Asymmetric Organocatalyzed Aza-Henry Reaction of Hydrazones: Experimental and Computational Studies.

The first asymmetric catalyzed aza-Henry reaction of hydrazones is presented. In this process, quinine was used as the catalyst to synthesize different alkyl substituted β-nitrohydrazides with ee up to 77 %. This ee was improved up to 94 % by a further recrystallization and the opposite enantiomer can be obtained by using quinidine as the catalyst, opening exciting possibilities in fields in which the control of chirality is vital, such as the pharmaceutical industry. Additionally, experimental and ab initio studies were performed to understand the reaction mechanism. The experimental results revealed an unexpected secondary kinetic isotope effect (KIE) that is explained by the calculated reaction pathway, which shows that the protonation of the initial hydrazone and the C-C bond forming reaction occur during a concerted process. This concerted mechanism makes the catalysis conceptually different to traditional base-promoted Henry and aza-Henry reactions.

Kinetic Isotope Effects Quantify pH-Sensitive Water Dynamics at the Pt Electrode Interface.

The pH-dependent kinetics of the hydrogen oxidation and evolution reactions (HERs and HORs) remain a fundamental conundrum in modern electrochemistry. Recent efforts have focused on the impact of the interfacial water network on the reaction kinetics. In this work, we quantify the importance of interfacial water dynamics on the overall hydrogen reaction kinetics with kinetic isotope effect (KIE) voltammetry experiments on single-crystal Pt(111) and Pt(110). Our results find a surface-sensitive KIE for both the HER and the HOR that is measurable in base but not in acid. Remarkably, the HOR in KOD on Pt(111) yields a KIE of up to 3.4 at moderate overpotentials, greater than any expected secondary KIE values, yet the HOR in DClO4 yields no measurable KIE. These results provide direct evidence that solvent dynamics play a crucial role in the alkaline but not in the acidic hydrogen reactions, thus reinforcing the importance of "beyond adsorption" phenomena in modern electrocatalysis.

Thermal rate coefficients and kinetic isotope effects of the reaction HO + H2O → H2O + OH

Hydrogen-transfer reactions take place in a wide range of chemically active environments. In this work, thermal rate coefficients of the prototypical hydrogen-transfer reaction HO + H2O → H2O + OH and its various isotopologues are computed using both tunneling-corrected transition state and quasi-classical trajectory methods on a recently developed global potential energy surface. On the one hand, the calculated rate coefficients and kinetic isotope effects agree well with available experimental results, indicating the high fidelity of the potential energy surface. On the other hand, the observed normal primary and inverse secondary kinetic isotope effects appear to be prevalent in hydrogen abstraction reactions, which are rationalized by the change of classical and adiabatic minimum energy paths. In addition, there exists strong non-Arrhenius behavior at low temperatures due to the significant quantum tunneling effect.

Imbalanced Transition States from α-H/D and Remote β-Type N-CH/D Secondary Kinetic Isotope Effects on the NADH/NAD+ Analogues in Their Hydride Tunneling Reactions in Solution.

The α-H/D (if available) and remote β-type N-CH3/CD3 2° kinetic isotope effects (KIEs) on 10-methylacridine (MAH), 9,10-dimethylacridine (DMAH), 1,3-dimethyl-2-phenylbenzimidazoline (DMPBIH) and on the oxidized forms MA+ and DMA+, in their hydride transfer reactions with several hydride acceptors/donors in acetonitrile, were determined. The corresponding equilibrium isotope effects (EIEs) were computed. Hammett correlations of several closely related hydride transfer reactions were constructed using the literature data. The α-2° KIEs on both MAH and MA+ are inflated relative to the semiclassical prediction on the basis of the KIE/EIE comparison and Hammond's postulate. This together with previously published unusual 1° and 2° KIE behaviors strongly suggest a H-tunneling mechanism. By comparing with the EIEs, the α-2° KIEs were used to analyze the rehybridization of the reaction center C and the N-CH3/CD3 2° KIEs to calculate the charge distribution on the structure containing N during H-tunneling. The rehybridization appears to lag behind the charge development in the donor moiety. The charge distribution at the tunneling ready transition state is in agreement with the Hammett correlations; the donor is product-like, and the acceptor is reactant-like, indicative of a partial negative charge borne by the "in-flight" nucleus being "hydridic" in character. Results were compared with the α-2° KIEs on NADH/NAD+ and the Hammett correlations in closely related enzymes. The comparison implicates that the H-tunneling probability would be enhanced by these enzymes.

Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4'-O-Nucleotidyltransferase.

This work is focused on mechanistic studies of the transfer of an adenylyl group (Adenoside-5′-monophosfate) from adenosine 5′-triphosphate (ATP) to a OH-4′ hydroxyl group of an antibiotic. Using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques, we study the substrate and base-assisted mechanisms of the inactivation process of kanamycin A (KAN) catalyzed by 4′-O-Nucleotidyltransferase [ANT(4′)], an active enzyme against almost all aminoglycoside antibiotics. Free energy surfaces, obtained with Free Energy Perturbation methods at the M06-2X/MM level of theory, show that the most favorable reaction path presents a barrier of 12.2 kcal·mol−1 that corresponds to the concerted activation of O4′ from KAN by Glu145. In addition, the primary and secondary 18O kinetic isotope effects (KIEs) have been computed for bridge O3α, and non-bridge O1α, O2α, and O5′ atoms of ATP. The observed normal 1°-KIE of 1.2% and 2°-KIE of 0.07% for the Glu145-assisted mechanism are in very good agreement with experimentally measured data. Additionally, based on the obtained results, the role of electrostatic and compression effects in enzymatic catalysis is discussed.

Recent advances in studying the mechanism of phospha-Michael addition of tertiary phosphines to electron-deficient alkenes on the basis of kinetic isotope effects

The previously proposed mechanism for phospha-Michael addition of tertiary phosphines to electron-deficient alkenes has been amended according to the secondary kinetic isotope effects provided by α-deuterated activated alkenes. The data obtained have shown that rate-determining protonation of intermediate phosphonium zwitterion proceeds not directly at its carbanionic center but first at a heteroatom of the attached electron-withdrawing group, with subsequent isomerization of the enolic/eniminic intermediate to stable keto-/cyanophosphonium product.

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.

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.