Full Catalytic Cycle Research Articles

Elucidation of the noncovalent interactions driving enzyme activity guides branching enzyme engineering for α-glucan modification

Branching enzymes (BEs) confer to α-glucans, the primary energy-storage reservoir in nature, a variety of features, like slow digestion. The full catalytic cycle of BEs can be divided in six steps, namely two covalent catalytic steps involving glycosylation and transglycosylation, and four noncatalytic steps involving substrate binding and transfers (SBTs). Despite the ever-growing wealth of biochemical and structural information on BEs, clear mechanistic insights into SBTs from an industrial-performance perspective are still missing. Here, we report a Rhodothermus profundi BE (RpBE) endowed with twice as much enzymatic activity as the Rhodothermus obamensis BE currently used in industry. Furthermore, we focus on the SBTs for RpBE by means of large-scale computations supported by experiment. Engineering of the crucial positions responsible for the initial substrate-binding step improves enzymatic activity significantly, while offering a possibility to customize product types. In addition, we show that the high-efficiency substrate-transfer steps preceding glycosylation and transglycosylation are the main reason for the remarkable enzymatic activity of RpBE, suggestive of engineering directions for the BE family.

Quantum Chemical Modeling of the Full Catalytic Cycle for Selective Oxidation of Propane to Propene on the M1 Phase of Mo–Te–Nb–O Mixed-Metal Oxide Catalysts

Quantum Chemical Modeling of the Full Catalytic Cycle for Selective Oxidation of Propane to Propene on the M1 Phase of Mo–Te–Nb–O Mixed-Metal Oxide Catalysts

Directing-group-free strategy for the iodine-mediated regioselective dichalcogenation of indolines: understanding the full catalytic cycles

A metal-free catalytic method for the regioselective direct dehydrogenation–dichalcogenation of indolines. The reaction mechanism and regioselectivity have been elucidated via density functional theory studies.

Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO2 Fixation.

Crotonyl-CoA carboxylase/reductase (Ccr) is one of the fastest CO2 fixing enzymes and has become part of efficient artificial CO2-fixation pathways in vitro, paving the way for future applications. The underlying mechanism of its efficiency, however, is not yet completely understood. X-ray structures of different intermediates in the catalytic cycle reveal tetramers in a dimer of dimers configuration with two open and two closed active sites. Upon binding a substrate, this active site changes its conformation from the open state to the closed state. It is challenging to predict how these coupled conformational changes will alter the CO2 binding affinity to the reaction's active site. To determine whether the open or closed conformations of Ccr affect binding of CO2 to the active site, we performed all-atom molecular simulations of the various conformations of Ccr. The open conformation without a substrate showed the highest binding affinity. The CO2 binding sites are located near the catalytic relevant Asn81 and His365 residues and in an optimal position for CO2 fixation. Furthermore, they are unaffected by substrate binding, and CO2 molecules stay in these binding sites for a longer time. Longer times at these reactive binding sites facilitate CO2 fixation through the nucleophilic attack of the reactive enolate in the closed conformation. We previously demonstrated that the Asn81Leu variant cannot fix CO2. Simulations of the Asn81Leu variant explain the loss of activity through the removal of the Asn81 and His365 binding sites. Overall, our findings show that the conformational dynamics of the enzyme controls CO2 binding. Conformational changes in Ccr increase the level of CO2 in the open subunit before the substrate is bound, the active site closes, and the reaction starts. The full catalytic Ccr cycle alternates among CO2 addition, conformational change, and chemical reaction in the four subunits of the tetramer coordinated by communication between the two dimers.

Catalytic process of anhydro-N-acetylmuramic acid kinase from Pseudomonas aeruginosa

The bacterial cell envelope is the structure with which the bacterium engages with, and is protected from, its environment. Within this envelop is a conserved peptidoglycan polymer which confers shape and strength to the cell envelop. The enzymatic processes that build, remodel, and recycle the chemical components of this cross-linked polymer are preeminent targets of antibiotics and exploratory targets for emerging antibiotic structures. We report a comprehensive kinetic and structural analysis for one such enzyme, the Pseudomonas aeruginosa anhydro-N-acetylmuramic acid (anhNAM) kinase (AnmK). AnmK is an enzyme in the peptidoglycan-recycling pathway of this pathogen. It catalyzes the pairing of hydrolytic ring opening of anhNAM with concomitant ATP-dependent phosphoryl transfer. AnmK follows a random-sequential kinetic mechanism with respect to its anhNAM and ATP substrates. Crystallographic analyses of four distinct structures (apo AnmK, AnmK:AMPPNP, AnmK:AMPPNP:anhNAM, and AnmK:ATP:anhNAM) demonstrate that both substrates enter the active site independently in an ungated conformation of the substrate subsites, with protein loops acting as gates for anhNAM binding. Catalysis occurs within a closed conformational state for the enzyme. We observe this state crystallographically using ATP-mimetic molecules. A remarkable X-ray structure for dimeric AnmK sheds light on the precatalytic and postcatalytic ternary complexes. Computational simulations in conjunction with the high-resolution X-ray structures reveal the full catalytic cycle. We further report that a P.aeruginosa strain with disrupted anmK gene is more susceptible to the β-lactam imipenem compared to the WT strain. These observations position AnmK for understanding the nexus among peptidoglycan recycling, susceptibility to antibiotics, and bacterial virulence.

Valve turning towards on-cycle in cobalt-catalyzed Negishi-type cross-coupling

Ligands and additives are often utilized to stabilize low-valent catalytic metal species experimentally, while their role in suppressing metal deposition has been less studied. Herein, an on-cycle mechanism is reported for CoCl2bpy2 catalyzed Negishi-type cross-coupling. A full catalytic cycle of this kind of reaction was elucidated by multiple spectroscopic studies. The solvent and ligand were found to be essential for the generation of catalytic active Co(I) species, among which acetonitrile and bipyridine ligand are resistant to the disproportionation events of Co(I). Investigations, based on Quick-X-Ray Absorption Fine Structure (Q-XAFS) spectroscopy, Electron Paramagnetic Resonance (EPR), IR allied with DFT calculations, allow comprehensive mechanistic insights that establish the structural information of the catalytic active cobalt species along with the whole catalytic Co(I)/Co(III) cycle. Moreover, the acetonitrile and bipyridine system can be further extended to the acylation, allylation, and benzylation of aryl zinc reagents, which present a broad substrate scope with a catalytic amount of Co salt. Overall, this work provides a basic mechanistic perspective for designing cobalt-catalyzed cross-coupling reactions.

Evidence of redox cycling as a sub-mechanism in hydrogen production during ethanol steam reforming over La0.7Sr0.3MnO3-x perovskite oxide catalysts

Ethanol steam reforming (ESR) is of societal interest. In this work, experiments were conducted to ascertain if some of the H2 is produced by a redox cycle involving H2O filling oxygen vacancies over reducible oxide catalysts. Redox cycling experiments were performed over La0.7Sr0.3MnO3-x(100) in ultra-high vacuum. It was found that H2 was produced from redox cycling with alternating ethanol and water exposures over La0.7Sr0.3MnO3-x(100), with both half-cycles occurring at temperatures ≤800 K. In the first half-cycle, ethanol ‘directly’ reduced the surface to create oxygen vacancies (not by a CO intermediate), and in the second half-cycle water filled oxygen vacancies to make H2. The H2 production during the water exposure has a half-cycle turnover frequency of >3.2 × 10-2 molecules site-1 s−1 in the temperature range of 700–800 K, which is fast enough to be part of the ESR full catalytic cycle. Flowing both reactant gases together, ethanol and water, over La0.7Sr0.3MnO3-x(100) and La0.7Sr0.3MnO3-x powders significantly increases hydrogen production compared to pure ethanol. The results suggest that steady state ESR includes a sub-mechanism of ethanol ‘directly’ reducing the surface to create oxygen vacancy, and water filling oxygen vacancy to make some of the H2 by a Mars van Krevelen type mechanism.

Ultra-small Mo-Pt subnanoparticles enable CO2 hydrogenation at room temperature and atmospheric pressure.

We present a partially-oxidised bimetallic Mo-Pt subnanoparticle (Mo4Pt8Ox) enabling thermally-driven CO2 hydrogenation to CO at room temperature and atmospheric pressure. A mechanistic study explained the full catalytic cycle of the reaction from CO2 activation to catalyst reactivation. DFT calculations revealed that alloying with Mo lowers the activation barrier by weakening the CO adsorption. This finding could be a first step for low-energy CO2 conversion.

Rational Design of a Facially Coordinating P,N,N Ligand for Manganese-Catalysed Enantioselective Hydrogenation of Cyclic Ketones.

DFT calculations on the full catalytic cycle for manganese catalysed enantioselective hydrogenation of a selection of ketones have been carried out at the PBE0-D3PCM //RI-BP86PCM level. Mn complexes of an enantiomerically pure chiral P,N,N ligand have been found to be most reactive when adopting a facial coordination mode. The use of a new ligand with an ortho-substituted dimethylamino-pyridine motif has been calculated to completely transform the levels of enantioselectivity possible for the hydrogenation of cyclic ketones relative to the first-generation Mn catalysts. In silico evaluation of substrates has been used to identify those likely to be reduced with high enantiomer ratios (er), and others that would exhibit less selectivity; good agreements were then found in experiments. Various cyclic ketones and some acetophenone derivatives were hydrogenated with er's up to 99 : 1.

Rational Design of a Facially CoordinatingP,N,NLigand for Manganese‐Catalysed Enantioselective Hydrogenation of Cyclic Ketones

AbstractDFT calculations on the full catalytic cycle for manganese catalysed enantioselective hydrogenation of a selection of ketones have been carried out at the PBE0‐D3PCM//RI‐BP86PCMlevel. Mn complexes of an enantiomerically pure chiralP,N,Nligand have been found to be most reactive when adopting a facial coordination mode. The use of a new ligand with anortho‐substituted dimethylamino‐pyridine motif has been calculated to completely transform the levels of enantioselectivity possible for the hydrogenation of cyclic ketones relative to the first‐generation Mn catalysts.In silicoevaluation of substrates has been used to identify those likely to be reduced with high enantiomer ratios (er), and others that would exhibit less selectivity; good agreements were then found in experiments. Various cyclic ketones and some acetophenone derivatives were hydrogenated wither'sup to 99 : 1.

Mechanistic aspects of the Pd(OAc)n (n = 1–3) catalyzed ethylene acetoxylation: A density functional theory study

Vinyl acetate is a valuable industrial material used in the production of various polymers. The homogeneous Pd(OAc)n (n = 1–3) can catalyze ethylene acetoxylation to produce vinyl acetate. However, the reaction mechanism of Pd‐catalyzed formation of vinyl acetate remains unclear, especially in recognizing the active valence states of the Pd center. The full catalytic cycle of Pd‐catalyzed vinyl acetate formation includes ethylene‐acetate coupling, β‐H elimination, and catalyst regeneration. Based on the Wacker mechanism, two pathways were proposed for the ethylene‐acetate coupling, including a six‐membered ring mechanism through the attack of carbonyl oxygen (O2) of acetate, and a four‐membered ring mechanism through the attack of acetoxy oxygen (O1) of acetate on the coordinated ethylene. Our density functional theory (DFT) calculation shows that PdOAc cannot catalyze the acetoxylation of ethylene to form vinyl acetate due to the presence of a high energetic span. Pd(OAc)2 catalyzed reaction via the six‐membered mechanism is preferred, and the β‐H elimination is the rate‐determining step. For Pd(OAc)3, the six‐membered mechanism is favored as well, and the ethylene‐acetate coupling is the rate‐determining step. Overall, Pd(OAc)2 showed high activity (path a) toward the formation of vinyl acetate with a calculated TOF of 349 h−1.

Enantioselective Synthesis of α,β‐Unsaturated Aryl Lactams by Heck‐Matsuda and Heck‐Mizoroki Arylations of Enelactams

AbstractThe chiral aryl lactam nucleus is a common motif present in many bioactive natural products and the development of effective enantioselective methodologies for its preparation is of great interest. In this work, we report the synthesis of several enantioenriched aryl lactams in good yields and enantiomeric ratios using a combined strategy employing arenediazonium salts bearing electron‐withdrawing substituents, aryl iodides with electron‐donating substituents, and chiral N,N‐ligands. The chiral α,β‐unsaturated aryl lactams were obtained in yields of up to 78 % and enantiomeric ratios up to 95 : 5. Furthermore, this work demonstrates the use of chiral N,N‐ligands as a viable alternative to the phosphine‐based ligands in the enantioselective Heck‐Mizoroki reactions using aryl iodides. The origins of the enantioselectivity and the full catalytic cycle for the Heck‐Matsuda arylation of the enelactams were investigated through DFT calculations.

Transfer C–H borylation of alkenes under Rh(I) catalysis: Insight into the synthetic capacity, mechanism, and selectivity control

Transfer C–H borylation of alkenes bears the potential to unlock a range of attractive transformations for modular synthesis and late-stage derivatization of complex molecules. However, its scarce precedence and a limited mechanistic understanding hinders the development of practical synthetic protocols. Here, we report a Rh(I)-catalyzed transfer C–H borylation that is applicable to various terminal and internal alkenes and compatible with a plethora of functional groups, including often problematic motifs. The successful late-stage borylation of bioactive molecules, including derivatives of macrocyclic zearalenol and the drug brompheniramine, underscores its synthetic capacity. A thorough mechanistic investigation involving a series of catalytic and stoichiometric experiments as well as computational studies gave insight into the full catalytic cycle employing a β-boryl elimination, which is unprecedented for Rh-catalysis, and elucidated the features controlling the activity and the selectivity. This work sets the stage for the development of other hydrogen-for-functional group exchange reactions undergoing similar pathways.

Catalytic trajectory of a dimeric nonribosomal peptide synthetase subunit with an inserted epimerase domain

Nonribosomal peptide synthetases (NRPSs) are modular assembly-line megaenzymes that synthesize diverse metabolites with wide-ranging biological activities. The structural dynamics of synthetic elongation has remained unclear. Here, we present cryo-EM structures of PchE, an NRPS elongation module, in distinct conformations. The domain organization reveals a unique “H”-shaped head-to-tail dimeric architecture. The capture of both aryl and peptidyl carrier protein-tethered substrates and intermediates inside the heterocyclization domain and l-cysteinyl adenylate in the adenylation domain illustrates the catalytic and recognition residues. The multilevel structural transitions guided by the adenylation C-terminal subdomain in combination with the inserted epimerase and the conformational changes of the heterocyclization tunnel are controlled by two residues. Moreover, we visualized the direct structural dynamics of the full catalytic cycle from thiolation to epimerization. This study establishes the catalytic trajectory of PchE and sheds light on the rational re-engineering of domain-inserted dimeric NRPSs for the production of novel pharmaceutical agents.

A DFT Study on the Binuclear Copper(I)-Catalyzed Synthesis Mechanism of 1,2,3-Triazolo[1,5-c]Pyrimidine via Interrupted Click and Ketenimine Rearrangement.

In this paper, the mechanism of the full catalytic cycle for binuclear Cu(I)-catalyzed sulfonyl azide-alkyne cycloaddition reaction for the synthesis of triazolopyrimidines was rationalized by density functional theoretical (DFT) calculations. The computed reaction route consists of: (a) formation of dicopper intermediates, including C-H activation of terminal alkyne, 3+2 ring cycloaddition and ring-reducing reaction and transmetalation, (b) interrupted CuAAC reaction, including di-copper catalyzed ring-opening of 2H-azirines and C-C bond formation to generate the copper-triazoles and -ketenimines, (c) two-step C-N cross-coupling and following (d) multi-step hydrogen transfer by the hydrogen bonding chain of water to promote the C-N formation and another C-N cleavage through the removal of p-tolyl sulfonamides. Our DFT results indicate that the multi-step hydrogen transfer process is the rate-determining step along the potential energy surface profile. The explicit water model was used for systematic determination of barrier for C-C cross-coupling, C-N bond formation and cleavage, and p-tolylsulfonamide removal. A critical insight in the interrupted CuAAC reaction was proposed. Further prediction interprets H2 O hydrogen bond chain plays an important role in C-N bond formation and cleavage, and the removal of p-tolylsulfonamide. This may have fundamental guidance on the design of 1, 5-herterocyclic functionalized triazolopyrimidines via interrupted CuAAC rearrangement reaction, as well as hydrogen bond chain of water.

Mechanistic Insight into Pd(II)-Catalyzed Late-Stage Nondirected C(sp2)-H Cyanation of Toluene Using the Dual Ligands MPAA and Quinoxaline: A Density Functional Theory Investigation.

Density functional theory (DFT) calculations were performed to investigate the mechanism of Pd(II)-catalyzed late-stage nondirected C(sp2)-H cyanation of toluene. We confirmed the resting state and catalytic active species of this stoichiometric reaction, and we calculated the full catalytic cycle to obtain a favorable reaction pathway. The DFT calculation results indicate that the morphology of the active species is essential for the observed concerted metalation/deprotonation step. Although C-H activation is reversible in principle, it is the regioselectivity- or product-determining step. Our calculation results show that the regioselectivity is not only influenced by the electron effects but also by the potential steric repulsion interactions between the substrates and the specific geometry of the catalyst. Interestingly, the transmetalation process involves the largest overall change in free energy; thus, transmetalation is defined as the rate-determining step and turnover-determining step.

Efficient workflow for the investigation of the catalytic cycle of water oxidation catalysts: Combining GFN-xTB and density functional theory.

Photocatalytic water oxidation remains the bottleneck in many artificial photosynthesis devices. The efficiency of this challenging process is inherently linked to the thermodynamic and electronic properties of the chromophore and the water oxidation catalyst (WOC). Computational investigations can facilitate the search for favorable chromophore‐catalyst combinations. However, this remains a demanding task due to the requirements on the computational method that should be able to correctly describe different spin and oxidation states of the transition metal, the influence of solvation and the different rates of the charge transfer and water oxidation processes. To determine a suitable method with favorable cost/accuracy ratios, the full catalytic cycle of a molecular ruthenium based WOC is investigated using different computational methods, including density functional theory (DFT) with different functionals (GGA, Hybrid, Double Hybrid) as well as the semi‐empirical tight binding approach GFN‐xTB. A workflow with low computational cost is proposed that combines GFN‐xTB and DFT and provides reliable results. GFN‐xTB geometries and frequencies combined with single‐point DFT energies give free energy changes along the catalytic cycle that closely follow the full DFT results and show satisfactory agreement with experiment, while significantly decreasing the computational cost. This workflow allows for cost efficient determination of energetic, thermodynamic and dynamic properties of WOCs.

Palladium‐Catalyzed Regioselective and Stereospecific Ring‐Opening Suzuki‐Miyaura Arylative Cross‐Coupling of 2‐Arylazetidines with Arylboronic Acids

AbstractWe have developed a palladium‐catalyzed regioselective and enantiospecific ring‐opening Suzuki–Miyaura arylative cross‐coupling of N‐tosyl‐2‐arylazetidines to give enantioenriched 3,3‐diarylpropylamines. This reaction represents an example of transition‐metal‐catalyzed ring‐opening cross‐coupling using azetidines as a non‐classical alkyl electrophile. Density functional theory rationalized the mechanism of the full catalytic cycle, which consists of the selectivity‐determining ring opening of the azetidine, reaction with water, rate‐determining transmetalation, and reductive elimination. Transition states of the selectivity‐determining ring‐opening step were systematically determined by the multi‐component artificial force induced reaction (MC‐AFIR) method to explain the regioselectivity of the reaction.magnified image

Ensemble effects on allylic oxidation within explicit solvation environments.

Umbrella-sampling density functional theory molecular dynamics (DFT-MD) has been employed to study the full catalytic cycle of the allylic oxidation of cyclohexene using a Cu(ii) 7-amino-6-((2-hydroxybenzylidene)amino)quinoxalin-2-ol complex in acetonitrile to create cyclohexenone and H2O as products. After the initial H-atom abstraction step, two different reaction pathways have been identified that are distinguished by the participation of alkyl hydroperoxide (referred to as the "open" cycle) versus the methanol side-product (referred to as the "closed" cycle) within the catalyst recovery process. Importantly, both pathways involve dehydrogenation and re-hydrogenation of the -NH2 group bound to the Cu-site - a feature that is revealed from the ensemble sampling of configurations of the reactive species that are stabilized within the explicit solvent environment of the simulation. Estimation of the energy span from the experimental turnover frequency yields an approximate value of 22.7 kcal mol-1 at 350 K. Whereas the closed cycle value is predicted to be 26.2 kcal mol-1, the open cycle value at 16.5 kcal mol-1. Both pathways are further consistent with the equilibrium between Cu(ii) and Cu(iii) that has previously been observed. In comparison to prior static DFT calculations, the ensemble of both solute and solvent configurations has helped to reveal a breadth of processes that underpin the full catalytic cycle yielding a more comprehensive understanding of the importance of radical reactions and catalysis recovery.

Toward a Neutral Single-Component Amidinate Iodide Aluminum Catalyst for the CO2 Fixation into Cyclic Carbonates.

A new iodide aluminum complex ({AlI(κ4-naphbam)}, 3) supported by a tetradentate amidinate ligand derived from a naphthalene-1,8-bisamidine precursor (naphbamH, 1) was obtained in quantitative yield via reaction of the corresponding methyl aluminum complex ({AlMe(κ4-naphbam)}, 2) with 1 equiv of I2 in CH2Cl2 at room temperature. Complexes 2 and 3 were tested and found to be active as catalysts for the cyclic carbonate formation from epoxides at 80 °C and 1 bar of CO2 pressure. A first series of experiments were carried out with 1.5 mol % of the alkyl complex 2 and 1.5 mol % of tetrabutylammonium iodide (TBAI) as a cocatalyst; subsequently, the reactions were carried out with 1.5 mol % of iodide complex 3 as a single-component catalyst. Compound 3 is one of the first examples of a nonzwitterionic halide single-component aluminum catalyst producing cyclic carbonates. The full catalytic cycle with characterization of all minima and transition states was characterized by quantum chemistry calculations (QCCs) using density functional theory. QCCs on the reaction mechanism support a reaction pathway based on the exchange of the iodine contained in the catalyst by 1 equiv of epoxide, with subsequent attack of I- to the epoxide moiety producing the ring opening of the epoxide. QCCs triggered new insights for the design of more active halide catalysts in future explorations of the field.