Solvent Kinetic Isotope Effects Research Articles

Insights into the contrasting effects of sulfidation on dechlorination of chlorinated aliphatic hydrocarbons by zero-valent iron

Contrasting effects of sulfidation on contaminants reduction by zero-valent iron (ZVI) has been reported in literature but the underlying mechanisms remain unclear. Here, under well-controlled conditions, we compared the performance of ZVI and sulfidated ZVI (S-ZVI) toward a series of chlorinated compounds. Results revealed that, although S-ZVI was more reactive than ZVI toward hexachloroethane, pentachloroethane, tetrachloroethylene, and trichloroethene, sulfidation hindered the dechlorination of the other ten tested chlorinated aliphatics by a factor of 1.5–125. Moreover, S-ZVI may lead to an accumulation of toxic partially-dechlorinated products. Analogous to its effects on ZVI reactivity, sulfidation also exerted positive, negligible, or negative effects on the electron efficiency of ZVI. Solvent kinetic isotope effect analysis suggested that direct electron transfer rather than reaction with atomic hydrogen was the dominant reduction mechanism in S-ZVI system. Hence, the sulfidation enhancing effects could be expected only when direct electron transfer is the preferred reduction route for target contaminants. Furthermore, linear free energy relationships analysis indicated one-electron reduction potential could be used to predict the transformation of chlorinated ethanes by S-ZVI, whereas for chlorinated ethenes, their adsorption properties on S-ZVI determined the dechlorination process. All these findings may offer guidance for the decision-making regarding the application of S-ZVI.

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

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

Ten-Fold Solvent Kinetic Isotope Effect for the Nonradiative Relaxation of the Aqueous Ferrate(VI) Ion.

Hypervalent iron intermediates have been invoked in the catalytic cycles of many metalloproteins, and thus, it is crucial to understand how the coupling between such species and their environment can impact their chemical and physical properties in such contexts. In this work, we take advantage of the solvent kinetic isotope effect (SKIE) to gain insight into the nonradiative deactivation of electronic excited states of the aqueous ferrate(VI) ion. We observe an exceptionally large SKIE of 9.7 for the nanosecond-scale relaxation of the lowest energy triplet ligand field state to the ground state. Proton inventory studies demonstrate that a single solvent O-H bond is coupled to the ion during deactivation, likely due to the sparse vibrational structure of ferrate(VI). Such a mechanism is consistent with that reported for the deactivation of f-f excited states of aqueous trivalent lanthanides, which exhibit comparably large SKIE values. This phenomenon is ascribed entirely to dissipation of energy into a higher overtone of a solvent acceptor mode, as any impact on the apparent relaxation rate due to a change in solvent viscosity is negligible.

Experimental Evidence and Mechanistic Description of the Phenolic H-Transfer to the Cu2O2 Active Site of oxy-Tyrosinase.

Tyrosinase is a ubiquitous coupled binuclear copper enzyme that activates O2 toward the regioselective monooxygenation of monophenols to catechols via a mechanism that remains only partially defined. Here, we present new mechanistic insights into the initial steps of this monooxygenation reaction by employing a pre-steady-state, stopped-flow kinetics approach that allows for the direct measurement of the monooxygenation rates for a series of para-substituted monophenols by oxy-tyrosinase. The obtained biphasic Hammett plot and the associated solvent kinetic isotope effect values provide direct evidence for an initial H-transfer from the protonated phenolic substrate to the Cu2O2 core of oxy-tyrosinase. The correlation of these experimental results to quantum mechanics/molecular mechanics calculations provides a detailed mechanistic description of this H-transfer step. These new mechanistic insights revise and expand our fundamental understanding of Cu2O2 active sites in biology.

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

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

Tetrabromobisphenol A transformation by biochar supported post-sulfidated nanoscale zero-valent iron: Mechanistic insights from shell control and solvent kinetic isotope effects

Post-sulfidated nanoscale zero-valent iron with a controlled FeSX shell thickness deposited on biochar (S-nZVI/BC) was synthesized to degrade tetrabromobisphenol A (TBBPA). Detailed characterizations revealed that the increasing sulfidation degree altered shell thickness/morphology, S content/speciation/distribution, hydrophobicity, and electron transfer capacity. Meanwhile, the BC improved electron transfer capacity and hydrophobicity and inhibited the surface oxidation of S-nZVI. These properties endowed S-nZVI/BC with highly reactive (∼8.9–13.2 times) and selective (∼58.4–228.9 times) over nZVI/BC in TBBPA transformation. BC modification improved the reactivity and selectivity of S-nZVI by 1.77 and 1.96 times, respectively. The difference of S-nZVI/BC in reactivity was related to hydrophobicity and electron transfer, particularly FeSX shell thickness and morphology. Optimal shell thickness of ∼32 nm allowed the maximum association between Fe0 core and exterior FeSX, resulting in superior reactivity. A thicker shell with abundant networks increased the roughness but decreased the surface area and electron transfer. The higher [S/Fe]surface and [S/Fe]particle were conducive to the selectivity, and [S/Fe]particle was more influential than [S/Fe]surface on selectivity upon similar hydrophobicity. The solvent kinetic isotope effects (SKIEs) exhibited that increasing [S/Fe]dose tuned the relative contributions of atomic H and electron in TBBPA debromination but failed to alter the dominant debromination pathway (i.e., direct electron transfer) in (S)-nZVI/BC systems. Mechanism of electron transfer rather than atomic H contributed to higher selectivity. This work demonstrated that S-nZVI/BC was a prospective material for the remediation of TBBPA-contaminated groundwater.

Engineering C-C Bond Cleavage Activity into a P450 Monooxygenase Enzyme.

The cytochrome P450 (CYP) superfamily of heme monooxygenases has demonstrated ability to facilitate hydroxylation, desaturation, sulfoxidation, epoxidation, heteroatom dealkylation, and carbon-carbon bond formation and cleavage (lyase) reactions. Seeking to study the carbon-carbon cleavage reaction of α-hydroxy ketones in mechanistic detail using a microbial P450, we synthesized α-hydroxy ketone probes based on the physiological substrate for a well-characterized benzoic acid metabolizing P450, CYP199A4. After observing low activity with wild-type CYP199A4, subsequent assays with an F182L mutant demonstrated enzyme-dependent C-C bond cleavage toward one of the α-hydroxy ketones. This C-C cleavage reaction was subject to an inverse kinetic solvent isotope effect analogous to that observed in the lyase activity of the human P450 CYP17A1, suggesting the involvement of a species earlier than Compound I in the catalytic cycle. Co-crystallization of F182L-CYP199A4 with this α-hydroxy ketone showed that the substrate bound in the active site with a preference for the (S)-enantiomer in a position which could mimic the topology of the lyase reaction in CYP17A1. Molecular dynamics simulations with an oxy-ferrous model of CYP199A4 revealed a displacement of the substrate to allow for oxygen binding and the formation of the lyase transition state proposed for CYP17A1. This demonstration that a correctly positioned α-hydroxy ketone substrate can realize lyase activity with an unusual inverse solvent isotope effect in an engineered microbial system opens the door for further detailed biophysical and structural characterization of CYP catalytic intermediates.

Deuterium Solvent Kinetic Isotope Effect on Enzymatic Methyl Transfer Catalyzed by Catechol O-methyltransferase.

Catechol o-methyltransferase plays a key role in the metabolism of catecholamine neurotransmitters. At present, its catalytic mechanism, overall structure, and kinetic characteristics have been basically clarified, but few people have paid attention to the function of solvents on enzymatic methyl transfer reactions. The influence of solvents on enzymatic reactions has always been a fuzzy hot topic. In addition, as a well-studied typical methyltransferase, COMT is a good test bed for exploring the source of the solvent isotope effect, which is a powerful tool in enzymatic mechanism research. We have measured the kinetic parameters of methyl transfer catalyzed by COMT in both normal water (H2O) and heavy water (D2O) by high-performance liquid chromatography (HPLC) in the range of pL 6 ~ 11. The kinetic characteristics of COMT in H2O and D2O were significantly different under different pH/pD conditions. Significant solvent kinetic isotope effects (SKIE) were obtained, especially inverse solvent kinetic isotope effects (SKIE < 1) were observed in this methyl transfer reaction for the first time. Traditional factors which could interpret the solvent isotope effect were ruled out. It's suggested that the solvent might affect the overall conformation as well as the flexibility of protein through non-covalent forces, thus altering the catalytic activity of COMT and leading to the solvent isotope effect.

Solvent isotope effects in the catalytic cycle of P450 CYP17A1: Computational modeling of the hydroxylation and lyase reactions

The catalytic cycle of the cytochromes P450 (CYP) requires two electrons from a protein redox partner and two protons from water to generate the main catalytic intermediate, a ferryl-oxo complex with π-cation on the heme porphyrin ring, termed Compound 1. The protonation steps are at least partially rate-limiting, therefore the steady-state rates of P450 catalysis are usually slower in deuterated solvent (D2O) by a factor of 1.5–3. However, in several P450 systems a pronounced inverse kinetic solvent isotope effect (KSIE ∼0.4–0.7) is observed, where the reaction is faster in D2O. This raises an important mechanistic question: Is this inverse solvent isotope effect compatible with Compound 1 catalyzed reactions, or is it indicative of another catalytic intermediate being involved? In this communication we use exhaustive numerical modeling of the P450 steady-state kinetics to demonstrate that a significant inverse KSIE cannot be obtained for a pure Compound 1 driven catalytic cycle of P450. Rather, an alternative, protonation independent, catalytic intermediate needs to be introduced. This result is applicable to the broad spectrum of P450s in nature, but as an example we use the extensively documented inverse isotope effect in the human steroid biosynthetic P450 CYP17A1 where the involvement of a heme peroxo anion intermediate has been characterized. Based on this analysis, we show that the observation of an inverse KSIE can be used as a general mechanistic probe for reaction cycle intermediates in the cytochromes P450.

Changing the reaction pathway in TiO2 photocatalytic dehalogenation of halogenated aromatic pollutants by surface hydroxyl regulation.

Understanding the photocatalytic reductive dehalogenation mechanism of halogenated aromatic pollutants is of great research value. However, the proton source in the photocatalytic dehalogenation process of representative halogenated aromatic pollutants by TiO2 is not clear. In this study, the TiO2 surface was modified by hydrochloric acid, sodium hydroxide, and sodium fluoride to obtain TiO2 samples with different hydroxyl groups. It was found that the hydroxyl groups on the surface of TiO2 affects the sequence of proton and electron transfer in dehalogenation. The abundance of hydroxyl groups on the surface of TiO2 can accelerate the reductive dehalogenation process of representative halogenated aromatic pollutants. The kinetic solvent isotope effect was used to study the proton-coupled electron transfer process in the reaction. It shows that the enriching of protons on TiO2 bridging oxygen (bridging hydroxyl groups) is conducive to the rapid step of protonation of the reactant, and subsequent proton and electron transfer. On the contrary, the bridging hydroxyl groups can be removed by reacting with strongly basic sodium hydroxide and sodium ions can occupy the bridging oxygen. The substitution of bridging oxygen by fluorine ions can also lead to the destruction of bridge hydroxyl groups. Significantly, the absence of bridging hydroxyl groups on titanium dioxide will lead to the dehalogenation of representative halogenated aromatic pollutants initiated by electron transfer. This study is helpful to understand dehalogenation reaction paths catalyzed by TiO2.

Solvent Deuterium Isotope Effects of Substrate Reduction by Nitrogenase from Azotobacter vinelandii.

The mechanism of nitrogenase, the enzyme responsible for biological nitrogen fixation, has been of great interest for understanding the catalytic strategy utilized to reduce dinitrogen to ammonia under ambient temperatures and pressures. The reduction mechanism of nitrogenase is generally envisioned as involving multiple cycles of electron and proton transfers, with the known substrates requiring at least two cycles. Solvent kinetic isotope effect experiments, in which changes of reaction rates or product distribution are measured upon enrichment of solvent with heavy atom isotopes, have been valuable for deciphering the mechanism of complex enzymatic reactions involving proton or hydrogen transfer. We report the distribution of ethylene, dihydrogen, and methane isotopologue products measured from nitrogenase-catalyzed reductions of acetylene, protons, and cyanide, respectively, performed in varying levels of deuterium enrichment of the solvent. As has been noted previously, the total rate of product formation by nitrogenase is largely insensitive to the presence of D2O in the solvent. Nevertheless, the incorporation of H/D into products can be measured for these substrates that reflect solvent isotope effects on hydrogen atom transfers that are faster than the overall rate-determining step for nitrogenase. From these data, a minimal isotope effect is observed for acetylene reduction (1.4 ± 0.05), while the isotope effects for hydrogen and methane evolution are significantly higher at 4.2 ± 0.1 and 4.4 ± 0.1, respectively. These results indicate that there are pronounced differences in the sensitivity to isotopic substitution of the hydrogen atom transfer steps associated with the reduction of these substrates by nitrogenase.

Photoredox C(sp3)−C(sp3) Cross‐Dehydrogenative Coupling of Xanthene with β‐keto Moiety using MoS2 Quantum Dot (QD) Catalyst.

AbstractVisible light‐mediated Cross‐Dehydrogenative Coupling of Xanthene with β‐keto moieties has been developed using MoS2 Quantum Dot (QD) as a photoredox catalyst. Interesting features of this strategy includes circumventing the requisite of pre‐functionalized starting material, broad substrate scope, mild reaction condition, water as a solvent system, and recyclability of catalyst up to six cycles without loss of yield and selectivity. We have also enlightened the Kinetic Solvent Isotope Effect (KSIE) by scrutinizing the aspect of triplet‐to‐triplet photo energy transfer. The reductive quenching mechanism of QD photocatalyst has been endorsed by cyclic voltametric study.magnified image

Kinetic Solvent Isotope Effect in P450-Mediated Cyclization in Indolactams: Evidence for Branched Reactions and Guide for Their Modulation in Heterocycle Chemoenzymatic Synthesis

Kinetic Solvent Isotope Effect in P450-Mediated Cyclization in Indolactams: Evidence for Branched Reactions and Guide for Their Modulation in Heterocycle Chemoenzymatic Synthesis

Alkane Oxidation with H2O2 Catalyzed by Dicopper Complex with 6-hpa Ligand: Mechanistic Insights as Key Features for Methane Oxidation

Abstract Alkane oxidations with H2O2 catalyzed by copper complexes [Cu2(µ-OH)(6-hpa)]3+ (1) and [Cu(MeCN)(tpa)]2+ (2) were examined. In the oxidation of cyclohexane (CyH), cyclohexyl hydroperoxide (CyO2H) was formed as the first product and converted to cyclohexanol (CyOH) with PPh3. The turnover frequency (TOF/h) and turnover number (TON) of 1 are 150 and 1030, respectively. The kinetic studies showed that the product formation rate, d[CyO2H]/dt, is proportional to [1] and [H2O2], and partly to [Et3N] and [H2O]. Solvent kinetic isotope effect kH2O/kD2O was 2.2, showing that a H2O molecule is involved in the rate-limiting step. tert-BuO2H disturbs the formation of a di(hydroperoxo) intermediate [Cu2(O2H)2(6-hpa)]2+ to reduce the d[CyO2H]/dt. The active species [Cu2(O•)(O2•)(6-hpa)]2+ was detected by CSI MS. The inhibitory effects of a radical trap reagent DMPO and CO gas revealed that 1 suppresses the HO• formation. Methane oxidation with H2O2 catalyzed by 1, 2, and related complexes was conducted using a high-pressure reactor. Key features for the high catalytic activity of 1 in the methane oxidation are the complex-based active species [Cu2(O•)(O2•)(6-hpa)]2+ capable of cleaving the strong C-H bond of methane and the long catalyst life enabled by the suppression of the HO• formation.

Trinuclear Nickel Catalyst for Water Oxidation: Intramolecular Proton-Coupled Electron Transfer Triggered Trimetallic Cooperative O–O Bond Formation

Trinuclear Nickel Catalyst for Water Oxidation: Intramolecular Proton-Coupled Electron Transfer Triggered Trimetallic Cooperative O–O Bond Formation

Mechanistic studies of the solvolysis of alkanesulfonyl and arenesulfonyl halides.

There have been several studies on the solvolysis mechanisms for alkanesulfonyl chlorides (RSO2Cl) and arenesulfonyl chlorides (ArSO2Cl). The earlier of these studies were reviewed a little over thirty years ago by Gordon, Maskill and Ruasse (Chem. Soc. Rev. 1989, 18, 123–151) in a contribution entitled “Sulfonyl Transfer Reactions”. The present review will emphasize more recent contributions and, in particular, the application of the extended Grunwald–Winstein equation and kinetic solvent isotope effects to the solvolysis reactions. There is also an appreciable number of reports concerning the corresponding anhydrides with the chloride leaving group replaced by the appropriate sulfonate leaving group, concerning sulfamoyl chlorides (ZZ'NSO2Cl) with Z and Z' being alkyl or aryl and concerning the solvolysis of chlorosulfate esters (alkoxy- or aryloxysulfonyl chlorides), with the structures ROSO2Cl or ArOSO2Cl. The solvolyses of these additional types of sulfur(VI) substrates will be the topics of a future review.

Complexation and reduction of soil iron minerals by natural polyphenols enhance persulfate activation for the remediation of triphenyl phosphate (TPHP)-contaminated soil

Peroxydisulfate-based in-situ chemical oxidation (PDS-ISCO) is a promising technology for soil remediation. The weak potential of soil constituents for PDS decomposition results in the low degradation efficiency of soil contaminants. Herein, we propose a new soil remediation strategy by accelerating the activation efficiency of PDS using chelating and reducing reagents (CRs) to complex and reduce soil Fe-minerals. Experimental results demonstrated that the introduction of tea polyphenols (TP) into soil-PDS system could effectively improve the reduction of Fe-minerals and the degradation of triphenyl phosphate (TPHP) in soil. With increasing TP concentration from 0 to 40 mM, the degradation efficiency of TPHP increased from 10.8% to 58.6% in an upland soil (T1 soil). TP could directly complex and reduce the solid-phase Fe-minerals, leading to a significant increase of Fe(II) content, especially the insoluble Fe(II) content, which could further induce the PDS activation. Results of radical quenching experiments, electron paramagnetic resonance (EPR) analysis, and kinetic solvent isotope effect (KSIE) evaluation showed that sulfate radicals (SO4•−, especially surface-bound SO4•−), hydroxyl radicals (HO•, especially surface-bound HO•), and singlet oxygen (1O2) played major roles in TPHP degradation, with the estimated contributions of 39.03%, 43.99%, and 16.98%, respectively. The higher content of high active Fe fractions, such as amorphous Fe, the larger yields of Fe(II) species and TPHP degradation. Increased content of soil organic matter (SOM) and pH value from 2.5 to 8.0 may reduce TPHP degradation. The effects of inorganic anions and Mn-minerals, presented in natural soil, on TPHP degradation were very limited. Simulated in-situ soil remediation using soil column confirmed that this strategy is suitable for the large-scale remediation of contaminated soil.

A mechanistic study of thiol addition to N-phenylacrylamide.

Cysteine (Cys) residues contain a redox-sensitive thiol and are commonly found in enzyme active sites. In recent years, the presence of a reactive thiolate group on a protein has been exploited in the development of irreversible enzyme inhibitors as therapeutic agents. Many targeted covalent inhibitors (TCIs) are designed to covalently react with a specific Cys residue on a target protein active site, irreversibly modifying the target and inhibiting its normal function. The electrophilic warhead most commonly used in this way is the acrylamide functional group. Although the acrylamide group is well known for its ability to undergo thiol-addition reactions, very few studies have been conducted to elucidate the detailed mechanism of this reaction, which inspired us to conduct a thorough kinetic investigation. First, we developed a robust kinetic assay to accurately monitor reaction progress between N-phenylacrylamide (NPA) and a small library of alkyl thiols having widely varying pKa values. This allowed us to construct a Brønsted-type plot for the thiol addition reaction, revealing a βnucRS- value of 0.07 ± 0.04. We also studied the solvent kinetic isotope effects (SKIEs), pH dependence, and temperature dependence of the reaction, which showed that reaction has a relatively large negative ΔS‡, and a small ΔH‡. Computational studies provided a structure for the transition state that is consistent with the experimental data. All of these data are consistent with rate-limiting nucleophilic attack, followed by rapid protonation of the enolate, corresponding to the microscopic reverse of the E1revcb elimination mechanism.

The complete mechanism of an aldol condensation in water.

The base-catalyzed aldol condensation between benzaldehyde and p-acetylbenzoic acid in water shows an inverse solvent kinetic isotope effect, k3,D2O/k3,H2O, of 1.33 ± 0.03. The reaction is definitely faster in D2O. This is interpreted to mean that the rate-limiting step in a five-step mechanism is Step 5, the final elimination of hydroxide from the enolate intermediate, not the formation of that intermediate. This is the same result and the same conclusion as from earlier studies in aqueous acetonitrile and refutes a suggestion, based on computations, that the rate-limiting step would change in water. Those computations are criticized as implying impossibly large isotope effects.

Mechanistic implications of the solvent kinetic isotope effect in the hydrolysis of NaBH4

The sodium borohydride, NaBH4, hydrolysis mechanism is studied via the H2O/D2O kinetic isotope effect (KIE). This reaction is of importance as NaBH4 is considered as a hydrogen storage material. Nowadays, hydrogen is thought to be one of the most promising and efficient clean energy carriers. In order to control the rate of the hydrogen evolution reaction (HER), one has to understand the mechanism of its production. The H2O/D2O KIE of the reactions of NaBH4 and NaBD4 with water was studied in solutions containing a ratio of H2O/D2O = 1.00. The separation factor, α, of both reactions is α = 5.0 ± 1.0. The rate of the hydrolysis of BD4− in H2O is faster than that of BH4−. The results point out that the rate-determining step in all hydrolysis stages is the H–OH bond scission.