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Rate enhancements in sulfoxidation reactions are often associated with a change in mechanism. Kinetic studies of sulfoxidation reactions by a series of Mn IV –oxo complexes reveal large rate changes while retaining an oxygen-atom transfer mechanism.
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
Lignin condensation reactions are hard to avoid or control during separation, which is a deterrent to lignin isolation and post-conversation, especially for the full utilization of lignocelluloses. Selective protection of β-aryl ether linkages in the isolation process is crucial to lignin valorization. Herein, a two-step acid/alkali separation method assisted with l-cysteine for eucalyptus lignin separation is developed, and the isolated L -cysteine lignins (LCLs) are comprehensively characterized by 2D NMR, 31 P NMR, thioacidolysis, etc. Compared to the two-step control treatment, a much higher β-O-4 content is preserved without reducing the separation efficiency assisted by L -cysteine, which is also significantly higher than alkali lignin and kraft lignin. The results of hydrogenolysis show that LCLs generate a much higher monomer yield than that of control sample. Structural analysis of LCLs suggests that lignin condensation reaction, to some extent, is suppressed by adding L -cysteine during the two-step acid/alkali separation. Further, mechanistic studies using dimeric model compound reveals that L -cysteine may be the α-carbon protective agent in the two-step separation. The role of L -cysteine in the two-step lignin isolation method provides novel insights to the selective fractionation of lignin from biomass, especially for the full valorization of lignocellulosic biomass.
We developed a catalytic platform to convert simple hydrocarbon feedstocks into valuable, tunable materials by leveraging nickel-catalyzed difunctionalization of cyclic dienes to access a novel class of cyclic alkene monomers. These monomers undergo ring-opening metathesis polymerization (ROMP) to yield sequence-controlled polymers with defined stereochemistry. Through mechanistic studies and catalyst optimization, we established a scalable, gram-level synthesis for selective diarylation, and expanded the reaction scope to include arylalkylation through rationally tuning the organoboron coupling partner. The resulting polymers were systematically studied to understand how steric, electronic, and stereochemical features influence polymerization behavior and bulk material properties. Functionalized derivatives bearing sulfonated groups were explored as proton-exchange membranes, and chemical recycling pathways were developed to recover monomers from the final materials. This work bridges small-molecule catalysis and macromolecular design, enabling access to tunable, recyclable polymers from abundant hydrocarbon starting materials.
The broad, long-term goal of the research is to provide insight into the mechanism of novel carboxylation and electron bifurcation reactions as paradigms to study how enzyme utilized protein conformational change to protect reactive intermediates and/or control the pathway in a catalytic cycle. catalyzed by enzymes involved in bacterial alkene, ketone, and epoxide metabolism. We are examining two paradigms in which conformational change is a key mechanistic feature of 1) protecting reaction intermediates that are sensitive to breakdown in the presence of water and 2) directing electron flow in reactions that split electron pairs along two pathways in reactions that fine tune metabolic efficiency in microbial metabolism. Both paradigms are of key importance in defining the molecular determinants of reactions relevant to CO 2 capture and fuel upcycling. In the first paradigm the compounds acetone and bicarbonate are activated by the addition of phosphate creating reaction intermediates (phosphoenolacetone and carboxyphosphate) that are very sensitive to breakdown in the presence of water. We are studying the mechanism of how the enzyme protects these reactive intermediates from water by encapsulating them upon their formation within a hydrophobic protein channel leading to an enzyme active site approximately 40 Å away. In the second paradigm, we are examining how the direction of electron transfer reactions can be modulated through protein conformational change that alters either the difference driving force or distance or both between electron transfer pathways in enzymes that catalyze electron bifurcation. We are using a combination of enzyme kinetics, mass spectrometry, spectroscopy, and structural analysis through X-ray diffraction and scattering methods to characterize the mechanism of conformational changes along the catalytic path. Within the context of the mission of the Department of Energy and the core activities of the Energy Biosciences, the results obtained in the study will reveal new insights into the fundamentals of novel carboxylation / CO 2 capture chemical transformations and electron transfer reactions that equate to biological fuel upcycling.
Electric fields play a key role in enzymatic catalysis and can enhance reaction rates by 100,000-fold, but the same rate enhancements have yet to be achieved in thermochemical heterogeneous catalysis. In this work, we probe the influence of catalyst potential and interfacial electric fields on heterogeneous Brønsted acid catalysis. We observed that variations in applied potential of ~380 mV led to a 100,000-fold rate enhancement for 1-methylcyclopentanol dehydration, which was catalyzed by carbon-supported phosphotungstic acid. Mechanistic studies support a model in which the interfacial electrostatic potential drop drives quasi-equilibrated proton transfer to the adsorbed substrate prior to rate-limiting C–O bond cleavage. Large increases in rate with potential were also observed for the same reaction catalyzed by Ti/TiO y H x and for the Friedel Crafts acylation of anisole with acetic anhydride by carbon-supported phosphotungstic acid.
Dilute Pd-in-Au alloys are valuable materials for selectively hydrogenating alkynes and isomerizing alkenes. By diluting Pd in a Au host, the selectivity toward semihydrogenated alkene isomers can be significantly enhanced and the unfavorable overhydrogenation to alkanes is suppressed. However, a detailed mechanistic study on the origin of the enhanced alkene selectivity over dilute alloy catalysts is still missing. Here, we combine experiment and theory to unravel the reaction mechanism, identifying rate-limiting and selectivity-controlling steps in 1-hexene hydrogenation over dilute Pd-in-Au catalysts. Using isotope-exchange hydrogenation experiments, we show that 1-hexene and hydrogen over a bimetallic Pd4Au96 in silica catalyst preferentially form 1-hexene isomers, (trans and cis) 2- and 3-hexene and only a small amounts of hexane. The reaction is consistent with a Horiuti–Polanyi mechanism, similar to a monometallic Pd nanoparticle catalyst. Computation of the free-energy profiles for 1-hexene hydrogenation and isomerization over a single Pd atom in a Au surface using first principles calculations indicated that the isomerization of 1-hexene to 2-hexene is energetically favorable due to the relatively large barrier for H2 dissociation preventing hydrogenation to n-hexane. Microkinetic modeling established that H2 dissociation on the single-atom Pd sites and H spillover from these sites onto the Au host are rate-limiting and key in steering the selectivity of dilute Pd-in-Au alloys toward the hexene isomers. Furthermore, the mechanistic insights from this study contribute to the rational design of optimized dilute alloy catalysts for selective alkene isomerization.
Excessive carbon dioxide (CO 2 ) emissions by combustion of fossil fuels are linked to global warming and rapid climate change. One promising route to lowering the concentration of CO 2 in the atmosphere is to reduce it to useful small molecules via photoelectrocatalytic hydrogenation, which would enable solar energy storage with a zero-carbon emission cycle and perform a more efficient separation of the photogenerated electron and hole pair than pure photocatalysis. Indeed, photoelectrocatalytic CO 2 reduction has been an intense focus of research. Using the density functional theory (DFT), we studied the CO 2 reduction reaction on the defective anatase TiO 2 (101) surface, at both the solvent/catalyst and the electrolyte/catalyst interfaces. The analysis of the electronic structure of the surface shows a contrast between the solvent/catalyst and the electrolyte/catalyst interfaces, which results in the two corresponding catalytic cycles being distinct. Furthermore, our study explains at the electronic and mechanistic levels why methanol is the main product in the presence of the electrolyte and why the overpotential is not only controlled by the reaction process but also by the diffusion process.
CO 2 is an abundant C 1 feedstock for fuel and chemical synthesis. We have previously demonstrated experimentally a stepwise insertion of CO 2 into a [Cu 2 H 2 ] core via a solid–gas in crystallo reaction, forming formate species that are unstable and inaccessible under solution-phase conditions. This work elucidates how structural confinement within the crystal lattice enables such selective reactivity. In particular, co-crystallized tetrahydrofuran molecules induce site asymmetry around the [Cu 2 H 2 ] unit, modulating both the local electronic environment and CO 2 diffusion pathways. Using a multiscale computational approach that combines classical molecular mechanics, hybrid quantum mechanics/molecular mechanics molecular dynamics, and enhanced-sampling free energy calculations, we demonstrate how site asymmetry affects CO 2 binding affinities and reaction pathways. These results provide detailed mechanistic insight into CO 2 insertion and hydride transfer, highlighting key differences between crystal- and solution-phase pathways and offering a general framework for understanding how lattice confinement shapes chemical reactivity.
Methane represents 34% of U.S. energy consumption and is a major greenhouse gas related to the global carbon cycle and energy production. However, current industrial practices significantly increase atmospheric methane levels, necessitating a deeper understanding of its biosynthesis and oxidation. Methyl-coenzyme M reductase (MCR) is central to biological methane metabolism, catalyzing the final step of methanogenesis and the first step in anaerobic methane oxidation. It is also a key target for strategies to capture and transform methane into value-added chemicals.The active site of MCR is a buried Ni-based cofactor only accessible by the substrates via a 50 Å long tunnel. Although the Ni(I) state is required to initiate catalysis, capturing this state remains a challenge for the current structural techniques. Recent advances in structural biology using X-ray Free-Electron Laser serial crystallography have provided insights into MCR's inactive Ni(II) state at room temperature and show promise for capturing its active Ni(I) form.Our team has established several critical aspects of the MCR mechanism using a combination of experimental and computational studies. MCR uses CH 3 -SCoM and CoBSH as substrates, producing methane and a disulfide product CoMSSCoB. Kinetic analysis showed that productive substrate binding requires CH 3 -SCoM to bind first, inducing conformational changes that optimize the active site for subsequent CoBSH binding. Following substrate binding, four proposed methane production/oxidation mechanisms were examined, establishing whether the reaction proceeds through an organometallic methyl-nickel(III), methyl anion ion, or methyl radical intermediate. Experimental measurements using CoBSH analogs successfully slowed the reaction, allowing for mechanistic insight that demonstrated the methyl radical pathway, where the initial interactions involve homolytic cleavage of the methyl-sulfur bond, generating a methyl radical that quickly abstracts the thiol hydrogen atom of CoBSH to form methane. Computational studies further confirmed that, compared to other mechanisms, the methyl radical mechanism is thermodynamically more favorable and accessible under physiological conditions.Spectroscopic and computational studies challenged the conventional understanding of substrate binding in MCR by proposing an alternative positioning of CH 3 -SCoM and CoMSSCoB in the active site pocket. The research suggested that CH 3 -SCoM (substrate) and CoMSSCoB (product) bind via their sulfonate groups to the Ni(I) center of cofactor F 430 . This binding allows for the reaction without substrate reorganization in the pocket but would require a long-range electron transfer. Altogether, the work summarized in this review reflects our current understanding of the enzyme's catalytic mechanism and structural dynamics. This is essential for developing efficient methane conversion technologies that could mitigate its environmental impact while harnessing energy-storage properties.
The huge scale of plastic waste generation and its environmental consequences drive the demands for catalytic plastic upcycling processes. Here, we report efficient polypropylene (PP) hydro-conversion over Ru and Ni supported on a sol-gel anatase TiO 2 (TiO 2 -A-SG). A small number of Brønsted acid sites on TiO 2 -A-SG enables hydrocracking, improving efficiency, steering the selectivity towards high-valued C 4-20 , and allowing more isomerization, compared to Ru-based monofunctional hydrogenolysis catalysts. The relative contribution of hydrocracking increases with lower hydrogen partial pressure, more branched substrates, and lower Ru loading. Ni/TiO 2 -A-SG exhibits superior hydrocracking activity and selectivity to Ni on conventional Brønsted-acidic supports, particularly zeolites. Further, mechanistic studies shows fast isomerization and sequential ß-scissions caused by strong polymer-catalyst interaction and fast cracking with abundant 3 C. This favors C 4-12 formation and prevents secondary reactions. This work demonstrated a novel, highly efficient noble-metal-free catalyst for plastic waste upcycling, while advancing the mechanistic understanding of polyolefin hydro-conversion.
Abstract Hemoproteins have recently emerged as promising biocatalysts for new-to-nature carbene transfer reactions. However, mechanistic understanding of the interplay between productive and unproductive pathways in these processes is limited. Using spectroscopic, structural, and computational methods, we investigate the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. These studies shed light on the nature and kinetics of key catalytic steps in this reaction, including the formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the cyclopropanation mechanism. Our analyses further reveal the existence of a complex mechanistic manifold for this reaction that includes a competing pathway resulting in the formation of an N-bound carbene adduct of the heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species can regenerate the active biocatalyst, constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings offer a valuable framework for both mechanistic analysis and design of hemoprotein-catalyzed carbene transfer reactions.
Nonprecious metal heterogeneous catalysts composed of first-row transition metals incorporated into nitrogen-doped carbon matrices (M-N-Cs) have been studied for decades as leading alternatives to Pt for the electrocatalytic O 2 reduction reaction (ORR). More recently, similar M-N-C catalysts have been shown to catalyze the aerobic oxidation of organic molecules. Here, this Focus Review highlights mechanistic similarities and distinctions between these two reaction classes and then surveys the aerobic oxidation reactions catalyzed by M-N-Cs. As the active-site structures and kinetic properties of M-N-C aerobic oxidation catalysts have not been extensively studied, the array of tools and methods used to characterize ORR catalysts are presented with the goal of supporting further advances in the field of aerobic oxidation.
In this study, Quantum Chemical (QC) calculations, utilizing Density Functional Theory (DFT), were performed to investigate the mechanistic aspects of the chemoselective catalyzed reaction of [Cp*Rh(bpy)H] + with the biomimetic NAD + analogues, N-benzylnicotinamide triflate, 1, and β-nicotinamide ribose-5'-methyl phosphate, 2, in the conversion to their 1,4-NADH analogues, 1,4-dihydro-N-benzylnicotinamide, 4, and β-1,4-dihydronicotinamide-5'-ribose methyl phosphate, 5. This reaction was in tandem with the 1,4-NADH dependent HLADH-Zn(II)- catalyzed reduction of achiral ketones to chiral S-alcohols. The [Cp*Rh(bpy)H] + complex, and not its equilibrium tautomer, [η 4 -Cp*HRh(bpy)] + , was found to control the hydride transfer during the biomimetic NAD + /1,4-NADH conversion, through the non-covalent interactions of the biomimetic co-factors with [Cp*Rh(bpy)H] + . The thermodynamics and kinetics for the chiral reduction of the Zn(II) bound ketones, 2-pentanone and 4-phenyl-2-butanone, with co-factor, 4, catalyzed by Zn(SCH 3 ) 2 (Imidazole), a core model of the Zn(II)-based catalytic center of HLADH, was also investigated by the evaluation of two possible reaction pathways: (1) formation of a ZnH from the C4-H hydride transfer of co-factor, 4, followed by reaction of the postulated ZnH with the bound 2-pentanone or 4-phenyl-2-butanone substrate, and (2), the direct C4-H transfer to the bound achiral ketone substrates, to provide the dominant chiral alcohols, S-2-pentanol or S-4-phenyl-2-butanol. The latter pathway was found most viable, and DFT calculations also revealed an essential η 2 -coordination of the 5,6 double bond of co-factor, 4, to the HLADH-Zn(II) metal ion center, upon imidazole decomplexation, providing an asymmetric differentiation of S-η 2 -5,6-1,4-NADH-Zn(II) binding. A proposed new paradigm for the Zn(II)'s non-innocent role in the HLADH-Zn(II) biocatalysis reduction mechanism, for enantioselective hydride transfer to a Zn(II) bound ketone, providing S-alcohols.
Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F 430 . The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C–S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni–thiol interaction between Ni(II)–MCR and inhibitor CoMSH, a Ni(I)–thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)–disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)–sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)–N/O complex, not Ni(I)–S. These studies rule out direct Ni(I)–sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)–sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.
Drimenol synthase fromAquimarina spongiae(AsDMS) is a highly unusual chimera that integrates two distinct, sequential isoprenoid processing activities within a single polypeptide chain. AsDMS catalyzes the class II cyclization of farnesyl diphosphate (FPP) to form drimenyl diphosphate, which then undergoes enzyme-catalyzed hydrolysis to yield drimenol, a bioactive sesquiterpene alcohol with antifungal and anticancer properties. Here, we report the X-ray crystal structures of AsDMS and its complex with a sesquiterpene thiol. The AsDMS structure exhibits a didomain architecture consisting of a terpene cyclase β domain and a haloacid dehalogenase-like phosphatase domain, with two distinct active sites located on opposite sides of the protein. Mechanistic studies show that dephosphorylation of the drimenyl diphosphate intermediate proceeds through stepwise hydrolysis such that two equivalents of inorganic phosphate rather than inorganic pyrophosphate are coproducts of the reaction sequence. When the AsDMS reaction is performed in H 2 18 O, 18 O is not incorporated into drimenol, indicating that the hydroxyl oxygen of drimenol originates from the prenyl oxygen of FPP rather than a water molecule from bulk solution. These results correct a mechanistic proposal previously advanced by another group. Surprisingly, AsDMS exhibits substrate promiscuity, catalyzing the conversion of the slowly reactive substrate mimic farnesyl-S-thiolodiphosphate into cyclic and linear sesquiterpene products. Structural and mechanistic insights gained from AsDMS illustrate the functional diversity of terpene biosynthetic enzymes and provide a foundation for engineering “designer cyclase” assemblies capable of generating a wide variety of terpenoid products.
Reactive organic fluid - mineral interactions at elevated temperatures contribute to the evolution of planetary matter. One of the less studied but important transformations in this regard involves the reactions of formic acid with naturally occurring clays such as sodium montmorillonite. To advance a mechanistic understanding of these interactions, we use ReaxFF reactive molecular dynamics simulations in conjunction with infrared (IR) spectroscopy and X-ray scattering experiments to investigate the speciation behavior of water-formic acid mixtures on sodium montmorillonite interfaces at 473 K and 1 atm. Using a newly developed reactive forcefield, we show that the experimental IR spectra of unreacted and reacted mixture can be accurately reproduced by ReaxFF/MD. We further benchmark the simulation predictions of sodium carbonate and bicarbonate formation in the clay interlayers using Small and Wide-Angle X-ray Scattering measurements. Subsequently, leveraging the benchmarked forcefield, we interrogate the pathway of speciation reactions with emphasis on carbonate, formate, and hydroxide groups elucidating the energetics, transition states, intermediates, and preferred products. Further, we also delineate the differences in reactivities and catalytic effects of clay edges, facets, and interlayers owing to their local chemical environments, which have far reaching consequences in their speciation behavior. The experimental and simulation approaches described in this study and the transferable forcefields can be applied translationally to advance the science of clay-fluid interactions for several applications including subsurface fluid storage and recovery and clay-pollutant dynamics.
The highly reactive gaseous ion [B 12 Br 11 ] – is a metal-free closed-shell anion which spontaneously forms covalent bonds with hydrocarbon molecules, including alkanes. Herein, we systematically investigate the reaction mechanism for binding of [B 12 Br 11 ] – to the five hexane isomers yielding [B 12 Br 11 (C 6 H 14 )] – , as well as to cyclohexane and several hexene isomers (yielding [B 12 Br 11 (C 6 H 12 )] – ) using collision-induced dissociation (CID), infrared photodissociation spectroscopy (IRPD) and computational methods. CID of the different [B 12 Br 11 (C 6 H 14 )] – ions results in distinct fragmentation patterns dependent on the structure of the hexane isomer. Further, the observed fragmentation reactions provide insights into the addition mechanism of [B 12 Br 11 ] – to hexane. Based on the observed CID patterns, we identified that either B–C bond formation through heterolytic C–C or C–H bond cleavages or B–H bond formation through heterolytic C–H cleavage occur dependent on the structure of the hexane isomer. Meanwhile, we observe identical CID spectra of adducts originating from isomers of C 6 H 12 . Spectroscopic investigations of adducts of 1-hexene and cyclohexane indicate the same product structure with an open C 6 chain. Computational investigations evidenced that low lying transition states are present, which enable a ring opening reaction of cyclohexane when binding to [B 12 Br 11 ] – .