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Low-temperature plasma catalysis holds promise for electrification of energy-intensive chemical processes such as methane reforming and ammonia synthesis.
O 2 is an attractive oxidant but it is also kinetically inert which limits its use in synthetic transformations. Metal–ligand cooperativity is a promising biomimetic strategy to activate O 2 for oxidative reactivity and catalysis.
Ion-transfer reactions in the presence of electric fields are ubiquitous in (bio/electro)chemical systems and catalysis, yet the impact of the electric field is poorly understood. Here, we use bipolar membranes (BPMs) to isolate electric-field-driven non-faradaic water dissociation (WD: H 2 O → H + + OH − ) on catalytic surfaces. We find the catalyst layer's ionic properties dictate both the transport and kinetic processes within the BPM. The role of these properties are explored via a series of membrane architectures, and catalyst poisoning experiments, and the corresponding current–voltage and impedance responses. Arrhenius analyses show that an acidic graphene-oxide (GO x ) catalyst layer gives rise to low interfacial H 2 O entropy in the heterojunction, illustrated via a >100 fold increase in the Arrhenius prefactor relative to baseline TiO 2 measurements. Furthermore, ∼50% of the applied driving force goes towards reducing the apparent enthalpic activation barrier in the case of GO x , while other metal-oxide catalysts have enthalpic barriers independent of driving force. This analysis demonstrates a new mechanistic understanding of WD, where local electric fields augment enthalpic transition-state barriers, and the local ionic environment facilitates field-driven ion transfer. Ultimately, these results present a new design space for designing ion-transfer catalytic processes, and ionic heterojunctions more broadly.
Significance Recent experiments have suggested that the energy released by a chemical reaction can propel its enzyme catalyst (for example, alkaline phosphatase). However, this topic remains controversial, partially due to the indirect and ensemble nature of existing measurements. Here, we used recently developed single-molecule approaches to monitor directly the motions of individual proteins in aqueous solution and find that single alkaline phosphatase enzymes do not diffuse faster under catalysis. Instead, we demonstrate that interactions between the fluorescent dye and the enzyme’s substrate can produce the signature of apparent diffusion enhancement in fluorescence correlation spectroscopy, the standard ensemble assay currently used to study enzyme diffusion and indicate that single-molecule approaches provide a more robust means to investigate diffusion at the nanoscale.
Abstract Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTHL1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a reduced activity on lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.
High-entropy materials with compositional and structural complexities introduce a transformative opportunity for catalysis.
Complementary XFEL methods reveal O 2 reaction intermediates and global protein dynamics during Isopenicillin N synthase catalysis.
Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.
Abstract Background Lignin peroxidases catalyze a variety of reactions, resulting in cleavage of both β-O-4′ ether bonds and C–C bonds in lignin, both of which are essential for depolymerizing lignin into fragments amendable to biological or chemical upgrading to valuable products. Studies of the specificity of lignin peroxidases to catalyze these various reactions and the role reaction conditions such as pH play have been limited by the lack of assays that allow quantification of specific bond-breaking events. The subsequent theoretical understanding of the underlying mechanisms by which pH modulates the activity of lignin peroxidases remains nascent. Here, we report on combined experimental and theoretical studies of the effect of pH on the enzyme-catalyzed cleavage of β-O-4′ ether bonds and of C–C bonds by a lignin peroxidase isozyme H8 from Phanerochaete chrysosporium and an acid stabilized variant of the same enzyme. Results Using a nanostructure initiator mass spectrometry assay that provides quantification of bond breaking in a phenolic model lignin dimer we found that catalysis of degradation of the dimer to products by an acid-stabilized variant of lignin peroxidase isozyme H8 increased from 38.4% at pH 5 to 92.5% at pH 2.6. At pH 2.6, the observed product distribution resulted from 65.5% β-O-4′ ether bond cleavage, 27.0% C α -C 1 carbon bond cleavage, and 3.6% C α -oxidation as by-product. Using ab initio molecular dynamic simulations and climbing-image Nudge Elastic Band based transition state searches, we suggest the effect of lower pH is via protonation of aliphatic hydroxyl groups under which extremely acidic conditions resulted in lower energetic barriers for bond-cleavages, particularly β-O-4′ bonds. Conclusion These coupled experimental results and theoretical explanations suggest pH is a key driving force for selective and efficient lignin peroxidase isozyme H8 catalyzed depolymerization of the phenolic lignin dimer and further suggest that engineering of lignin peroxidase isozyme H8 and other enzymes involved in lignin depolymerization should include targeting stability at low pH.
The Richard J. Kokes Travel Award program encourages student participation in the biennial North American Catalysis Society (NACS) Meetings. During NAM27 in 2022, 50 of the 111 students who received the Kokes Award were supported through this proposal, funded by the Department of Energy (DOE). The award covered a significant conference-related expense, that is the registration fees. Eligible students had to be enrolled in a North American university, present an oral or poster presentation, and contribute 2-4 hours to assist with meeting operations. While the program is open to undergraduate students, none were awarded in 2022. The selection process involved a comprehensive evaluation by external academic reviewers from NACS.
CCEI was founded in 2009 as a transformative catalysis center for energy innovation that combines fundamental science with technology transfer to address one of today’s most challenging problems: transforming lignocellulosic biomass into renewable transportation fuels and chemicals. Center members made significant progress toward solving this grand challenge by creating new heterogeneous catalysts and developing processes involving their use.
This report presents a technology case study reflecting one exemplary representative pathway for the conversion of lignocellulosic sugars to sustainable aviation fuels (SAF) via aqueous phase reforming (APR) catalysis, considered within a broader integrated biorefinery framework based on biochemical processing operations. While far from the only option for converting sugars to SAF, this pathway was selected as a case study here based on its relatively high technology maturity and simplistic processing approach (avoiding complex separations or other equipment scalability challenges), coupled with the potential for high fuel yields and favorable costs/carbon intensities with opportunities for further near-term optimization. The report considers key process integration and engineering design considerations for a modeled hypothetical, nth-plant commercial biorefinery, reflecting a number of processing options and parameters envisioned to be achievable as future goals. Resultant outputs from Aspen Plus process simulations are evaluated through techno-economic and life cycle analyses (TEA and LCA), including implications for marginal cost of CO2 abatement and inclusion of currently-applicable policy incentives. Moving beyond base case configurations, a number of alternative scenarios are also evaluated for their ability to further improve economics, greenhouse gas (GHG) emissions, and marginal cost of abatement, highlighting a path to achieve deep decarbonization goals of more than 70% GHG reduction for SAF (with the potential to reach net-negative carbon intensities in some cases) under reasonable fuel production costs. The report also highlights future opportunities and gaps for further research on this technology pathway.
The objective of this research program is to discover and develop new approaches for ab initio computational simulations of molecular motion. Specifically, this program aims to decipher the connection between the underlying electronic structure and the accordant molecular vibrations in reactive ions and radicals for renewable-energy purposes. Recent experimental progress in ion sources and optical spectroscopies has unearthed considerable new inner-sphere detail for these complexes, but the connection between these spectral signatures and mechanistic information often remains elusive, to the continued frustration of experimentalists. For this purpose, new anharmonic vibrational frequency methods, along with a publicly deployed software package, will be developed. Working closely with committed experimental collaborators, this conceptual and computational framework will be used to explain the results of new spectroscopy experiments, focusing specifically on the inner-shell mechanisms of renewable-energy catalysis. The oxidation half of catalytic water-splitting chemistry will be a central focus, along with fundamental studies of the manner in which strong ions and radicals activate solvent as a chemical species. The resulting products of the research program will include openly available software and algorithms for the ab initio simulation of challenging vibrational spectra, as well as critical mechanistic insight into energy-focused catalytic processes that are opaque to other existing analytical techniques.
The Catalysis Gordon Research Conference and Seminar took place from June 15, 2024 through June 21, 2024 at the Colby-Sawyer College in New London, New Hampshire.
In chemical industry controlling the activity and selectivity of a chemical conversion process is of immense importance. Traditionally, dissipation of thermal energy drives transformation of reactants, which may lead to formation of a variety of products; it remains a key challenge to design a process that dissociation and formation of specific chemical bonds can be triggered to form certain desirable products with very high selectivity, preferably at low temperatures. Introduction of light-sensitive solid materials into catalysis provides a powerful, alternate strategy for this purpose.
This project aimed to develop a fundamental understanding of the factors that dictate activity and selectivity during electrochemical partial oxidation of multi-carbon organic molecules derived from biomass. Value-adding selective conversions of alcohols to aldehydes, and aldehydes to carboxylic acids were considered, with the ultimate goal to establish general principles for controlling selectivity in organic oxidations. Specific aims involved the use of furfural (FF) and 5-hydoxymethyfurfural (HMF) as model systems and seek to develop knowledge for control of mechanisms that permit selective conversions between oxygenate functional groups with prevention or control of C-C cleavage steps. Another major focus of the work was in achieving these transformations in acidic conditions, which contrasts most existing work (done in base), but is crucial toward compatibility with common pretreatments used to generate small molecules from lignocellulose (e.g. acid hydrolysis or pyrolysis). The work involved well-defined catalyst material synthesis, comparative kinetics, and operando spectroscopies (PI Holewinski), supported by quantum chemical simulations (PI Janik), enabling progress toward efficient, acid-stable oxidation catalysis for biomass upgrading.
Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.
Acetone carboxylase (AC) from Xanthobacter autotrophicus is a 360 KDa α2β2γ2 heterohexamer that catalyzes the ATP-dependent formation of phosphorylated acetone and bicarbonate intermediates that react at Mn(II) metal active sites to form acetoacetate. Structural models of X. autotrophicus AC (XaAC) with and without nucleotides reveal that the binding and phosphorylation of the two substrates occurs ~40 Å from the Mn(II) active sites where acetoacetate is formed. Based on the crystal structures, a significant conformational change was proposed to open and close a tunnel that facilitates the passage of reaction intermediates between the sites for nucleotide binding and phosphorylation of substrates and Mn(II) sites of acetoacetate formation. We have employed electron paramagnetic resonance (EPR), kinetic assays, and hydrogen/deuterium exchange mass spectrometry (HDX-MS) of poised ligand-bound states and site-specific amino acid variants to complete an in-depth analysis of Mn(II) coordination and allosteric communication throughout the catalytic cycle. In contrast with the established paradigms for carboxylation, our analyses of XaAC suggested a carboxylate shift that couples both local and long-range structural transitions. Shifts in the coordination mode of a single carboxylic acid residue (αE89) mediate both catalysis proximal to a Mn(II) center and communication with an ATP active site in a separate subunit of a 180 kDa α2β2γ2 complex at a distance of 40 Å. This work demonstrates the power of combining structural models from X-ray crystallography with solution-phase spectroscopy and biophysical techniques to elucidate functional aspects of a multi-subunit enzyme.