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At least 163 records · Page 9

Active Sites in the Dealuminated Beta Zeolite-Supported Cobalt Catalyst for Non-Oxidative Ethane Dehydrogenation

Dispersed metal species in siliceous zeolites have been actively studied for non-oxidative dehydrogenation of ethane (NDE). Fundamental insights into the dynamics of metal species in zeolites under reaction conditions have rarely been explored. Herein, we report an atomic level understanding of the dynamics and activity of cobalt (Co) sites in dealuminated Beta zeolite (DeAl-BEA) for NDE during induction and reaction conditions with extensive characterization techniques such as diffuse reflectance UV–vis, solid state nuclear magnetic resonance and X-ray photoelectron, X-ray diffraction along with in situ Fourier transform infrared and X-ray absorption spectroscopy. For a catalyst with 0.5 mass % Co loading, tetrahedral Co 2+ mononuclear sites, di-coordinated to the zeolite framework and with two silanol groups in vicinity (i.e., (≡SiO) 2 Co(HO–Si≡) 2 ), form upon exposure to hydrogen during induction and persist through the NDE reaction. Increasing the Co loading to 3.0 mass % yielded Co sites with similar electronic and coordination structures but slightly elongated Co–O bonds. Upon cooling to room temperature, the Co sites persisted in the same coordination environment, though the disappearance of a feature in the Co K-edge near-edge region revealed changes in the active site’s electronic structure coinciding with modest shifts in bond lengths. The electronic structure and activity of (≡SiO) 2 Co(HO–Si≡) 2 sites were studied comparatively to a few other hypothetical Co 2+ coordination structures, using electronic structure calculations and microkinetic simulations. The simulations showed that NDE is controlled by β-hydride elimination following C–H bond activation and that Co-sites possessing flexibility because of neighboring silanol defects are more active. Interestingly, dinuclear Co–O–Co sites (i.e., (≡SiO)Co(HO–Si≡) 2 –O–(HO–Si≡) 2 Co(≡SiO)) were more active than the mononuclear (≡SiO) 2 Co(HO–Si≡) 2 sites because of favorable hydrogen bonding with the vicinal silanol groups. In conclusion, the present study bridges the gap between the knowledge acquired by ex-situ characterizations and the active sites under the reaction conditions in alkane dehydrogenation chemistry.

36 MATERIALS SCIENCE↗

Intrinsically Conductive {pi}‑d Conjugated Layers with Co–N4 Active Sites for Efficient Nitrate Electrocatalysis and Zinc-Nitrate Batteries

Electrochemical synthesis of ammonia from nitrate has been extensively investigated as a potential alternative to the energy-intensive Haber-Bosch process. This approach not only operates under ambient conditions but also simultaneously removes nitrate contaminants while producing ammonia as a value-added product. However, the ongoing quest lies in designing an efficient electrocatalyst that achieves a high ammonia yield rate, high selectivity, and long-term stability. Herein, we report the outstanding performance of a Co–N4 coordinated π-d layered Co3(HITP)2 (HITP = 2,3,6,7,10,11-hexaiminotriphenylene) in nitrate electrocatalysis. The unique combination of abundant Co–N4 active sites and superior electrical conductivity enables significant electrocatalytic activity, delivering a maximum ammonia yield rate of 56.8 mg cm–2 h–1 at −0.8 V vs RHE and a Faradaic efficiency of ∼91% at −0.4 V vs RHE. Mechanistic analysis reveals that alkaline conditions accelerate water dissociation to generate adsorbed hydrogen intermediates (H*), which are utilized by Co–N4 sites to drive the stepwise hydrogenation of nitrate to ammonia while suppressing competing hydrogen evolution reaction (HER) pathways. Furthermore, integration of this catalyst into a zinc-nitrate battery resulted in a maximum power density of 5.3 mW cm–2 and an open-circuit potential of ∼1.45 V. These results highlight the potential of π-d conjugated Co–N4 materials as an efficient catalyst for both environmental remediation and energy conversion.

Namvar, shahrirar↗

Exploring the Role of the Central Carbide of the Nitrogenase Active-Site FeMo-cofactor through Targeted 13 C Labeling and ENDOR Spectroscopy

Mo-dependent nitrogenase is a major contributor to global biological N 2 reduction, which sustains life on Earth. Its multi-metallic active-site FeMo-cofactor (Fe 7 MoS 9 C-homocitrate) contains a carbide (C 4– ) centered within a trigonal prismatic CFe 6 core resembling the structural motif of the iron carbide, cementite. The role of the carbide in FeMo-cofactor binding and activation of substrates and inhibitors is unknown. Here, to explore this role, the carbide has been in effect selectively enriched with 13 C, which enables its detailed examination by ENDOR/ESEEM spectroscopies. 13 C-carbide ENDOR of the S = 3/2 resting state (E 0 ) is remarkable, with an extremely small isotropic hyperfine coupling constant, C a = +0.86 MHz. Turnover under high CO partial pressure generates the S = 1/2 hi-CO state, with two CO molecules bound to FeMo-cofactor. This conversion surprisingly leaves the small magnitude of the 13 C carbide isotropic hyperfine-coupling constant essentially unchanged, C a = –1.30 MHz. This indicates that both the E 0 and hi-CO states exhibit an exchange-coupling scheme with nearly cancelling contributions to C a from three spin-up and three spin-down carbide-bound Fe ions. In contrast, the anisotropichyperfine coupling constant undergoes a symmetry change upon conversion of E 0 to hi-CO that may be associated with bonding and coordination changes at Fe ions. In combination with the negligible difference between CFe 6 core structures of E 0 and hi-CO, these results suggest that in CO-inhibited hi-CO the dominant role of the FeMo-cofactor carbide is to maintain the core structure, rather than to facilitate inhibitor binding through changes in Fe-carbide covalency or tretching/breaking of carbide–Fe bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantification of active sites in yttrium containing dealuminated Beta zeolites during conversion of ethanol and acetaldehyde to butadiene

Here, in this work, yttrium containing dealuminated Beta zeolites (Y/deAlBeta) were synthesized and characterized by various spectroscopic techniques to improve understanding of ethanol upgrading over these materials. Characterization results indicate yttrium atoms partially condense with framework silanol nests formed during dealumination of parent Al-Beta supports. Active sites for conversion of ethanol and acetaldehyde to butadiene were quantified on a series of Y/deAlBeta catalysts (0.1–10 wt% yttrium) via ex situ chemisorption and transmission Fourier transformed infrared (FTIR) spectroscopy measurements by first measuring the integrated molar extinction coefficient (IMEC) for pyridine bound to Lewis acidic yttrium sites. In situ titrations with pyridine demonstrate that the number of sites quantified by ex situ chemisorption IR is quantitatively similar to the number of sites that catalyze butadiene formation, which varies (from 0.05 to 0.35) across the series of catalysts. In situ pyridine titrations impact butadiene site time yields (STY), but not crotonaldehyde STY, indicating that a distribution of yttrium sites is present, and that discrete yttrium site types participate in distinct steps in the pathway from ethanol to butadiene. Apparent kinetic parameters including activation energies and reaction orders were measured, these suggest differences in reactant (or reactant-derived intermediate) surface coverages result in higher STYs (per mol Y or per Lewis acidic Y site) for samples with low Y loadings relative to those with higher Y loadings. Isotopic labeling experiments evince the existence of other kinetically relevant steps in addition to the crotonaldehyde transformation to crotyl alcohol. Together, these findings provide further guidance into the heterogeneities in site structures in yttrium-containing zeolites and their relevance for the various steps in the pathway from ethanol to C 4 products useful for production of sustainable aviation fuel and renewable butadiene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing Active Sites in Cu x Pd y Cluster Catalysts by Machine-Learning-Assisted X-ray Absorption Spectroscopy

Size-selected clusters are important model catalysts because of their narrow size and compositional distributions, as well as enhanced activity and selectivity in many reactions. Still, their structure-activity relationships are, in general, elusive. The main reason is the difficulty in identifying and quantitatively characterizing the catalytic active site in the clusters when it is confined within subnanometric dimensions and under the continuous structural changes the clusters can undergo in reaction conditions. Using machine learning approaches for analysis of the operando X-ray absorption near-edge structure spectra, we obtained accurate speciation of the Cu x Pd y cluster types during the propane oxidation reaction and the structural information about each type. As a result, we elucidated the information about active species and relative roles of Cu and Pd in the clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases

An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. Here, we have utilized biotin–streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S 112 E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic Fe II complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S 112 E. Two aqua ligands complete the primary coordination sphere of the Fe II center with both involved in hydrogen bond networks within Sav. The corresponding Fe III protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The Fe III protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Elucidating the Active Site and the Role of Alkali Metals in Selective Hydrodeoxygenation of Phenols over Iron-Carbide-based Catalyst

In this study, iron-carbide-based catalysts have been explored in the selective hydrodeoxygenation (HDO) of phenol, aiming at elucidating the role of active site and alkali metal. Complementary characterization such as X-ray diffraction, X-ray photoelectron spectroscopy, high-resolution transmission electron microscopy, and scanning transmission electron microscopy coupled with electron energy loss spectroscopy, together with catalytic evaluations revealed a rapid structural reconstruction of iron carbide (Fe 3 C) catalysts, leading to a stable defective graphene-covered metallic Fe active phase (G@Fe) under reaction conditions. Further studies using different alkali metals (i.e., Na, K, and Cs) revealed that alkali metals showed negligible effect on the phase transformation of Fe 3 C. However, the reconstructed G@Fe doped with alkali metals inhibited the tautomerization, a facile reaction pathway to saturation of the aromatic ring, leading to enhanced selectivity to arene. The extent of inhibition of tautomerization or selectivity to arene was closely related to the degree of electron donation of alkali metal to Fe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring the Impact of Active Site Structure on the Conversion of Methane to Methanol in Cu‐Exchanged Zeolites

Abstract In the past, Cu‐oxo or ‐hydroxy clusters hosted in zeolites have been suggested to enable the selective conversion of methane to methanol, but the impact of the active site's stoichiometry and structure on methanol production is still poorly understood. Herein, we apply theoretical modeling in conjunction with experiments to study the impact of these two factors on partial methane oxidation in the Cu‐exchanged zeolite SSZ‐13. Phase diagrams developed from first‐principles suggest that Cu‐hydroxy or Cu‐oxo dimers are stabilized when O 2 or N 2 O are used to activate the catalyst, respectively. We confirm these predictions experimentally and determine that in a stepwise conversion process, Cu‐oxo dimers can convert twice as much methane to methanol compared to Cu‐hydroxyl dimers. Our theoretical models rationalize how Cu‐di‐oxo dimers can convert up to two methane molecules to methanol, while Cu‐di‐hydroxyl dimers can convert only one methane molecule to methanol per catalytic cycle. These findings imply that in Cu clusters, at least one oxo group or two hydroxyl groups are needed to convert one methane molecule to methanol per cycle. This simple structure–activity relationship allows to intuitively understand the potential of small oxygenated or hydroxylated transition metal clusters to convert methane to methanol.

Chemistry↗

Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex

CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1—Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.

59 BASIC BIOLOGICAL SCIENCES↗

Enhanced active-site electric field accelerates enzyme catalysis

In this study, the design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic catalysis can be leveraged to substantially improve a natural enzyme’s activity. We enhanced the active-site electric field in horse liver alcohol dehydrogenase by replacing the serine hydrogen-bond donor with threonine and replacing the catalytic Zn 2+ with Co 2+ . Based on the electric field enhancement, we make a quantitative prediction of rate acceleration—50-fold faster than the wild-type enzyme—which was in close agreement with experimental measurements. The effects of the hydrogen bonding and metal coordination, two distinct chemical forces, are described by a unified physical quantity—electric field, which is quantitative, and shown here to be additive and predictive. These results suggest a new design paradigm for both biological and non-biological catalysts.

59 BASIC BIOLOGICAL SCIENCES↗

A Theory-Guided X-ray Absorption Spectroscopy Approach for Identifying Active Sites in Atomically Dispersed Transition-Metal Catalysts

Atomically dispersed supported metal catalysts offer new properties and the benefits of maximized metal accessibility and utilization. The characterization of these materials, however, remains challenging. Using atomically dispersed platinum supported on crystalline MgO (chosen for its well-defined bonding sites) as a prototypical example, we demonstrate in this work how systematic density functional theory calculations for assessing all the potentially stable platinum sites, combined with automated analysis of extended X-ray absorption fine structure (EXAFS) spectra, leads to unbiased identification of isolated, surface-enveloped platinum cations as the catalytic species for CO oxidation. The catalyst has been characterized by atomic-resolution imaging and EXAFS and high-energy resolution fluorescence detection X-ray absorption near edge spectroscopy. The proposed platinum sites are in agreement with experiment. This theory-guided workflow leads to rigorously determined structural models and provides a more detailed picture of the structure of the catalytically active site than what is currently possible with conventional EXAFS analyses. As this approach is efficient and agnostic to the metal, support, and catalytic reaction, we posit that it will be of broad interest to the materials characterization and catalysis communities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The ever-evolving active site: transformation of single atoms to extended structures during the Rh-catalyzed reverse water–gas shift reaction

At low temperatures (< 400°C), single atoms of Rh supported on rutile TiO 2 (rTiO 2 ) are responsible for the formation of CO during the reverse water gas shift (RWGS), while methane production is associated with the Rh-TiO 2 interface due to the correlation between methane formation rates and the volume-averaged Rh nanoparticle diameter. As the temperature is increased to >540°C, there is a notable increase in CO selectivity and methane production rates tend towards zero. The time to reach zero depends on the temperature but independent of the initial Rh structure (single atoms and/or nanoparticles), which is controlled by the catalyst preparation method (wetness impregnation versus colloidal nanoparticles). At 600°C and > 4 h time on stream, the catalytic behaviour becomes completely agnostic to the initial Rh structure as well as weight loading, and the catalysts are highly selective for the reverse water gas-shift reaction. Post-reaction HR-TEM image analysis confirms Rh nanoparticles crystallize/order during the reaction; at 400°C, most of the Rh particles are disordered, while at 600°C, they are more ordered (i.e., development of defined faceting). Infrared spectroscopy of CO adsorption on Rh nanoparticles confirms the appearance of defined facets after annealing in nitrogen at high temperatures. Annealing the Rh/rTiO 2 catalysts prior to the RWGS reaction demonstrates the structural transformation of Rh depends only on time and temperature and not on reactant or product fugacity. Sites responsible for stabilizing Rh single atoms are no longer competent at higher temperatures, enabling their integration into existent nanoparticles. As the reaction temperature is increased to temperatures >540°C, the dominant active site for CO production evolves from single atoms to extended Rh structures.

36 MATERIALS SCIENCE↗

The nitrosoamphetamine metabolite is accommodated in the active site of human hemoglobin: Spectroscopy and crystal structure

Amphetamine-based (Amph) drugs are metabolized in humans to their hydroxylamine (AmphNHOH) and nitroso (AmphNO) derivatives. The latter metabolites are known to bind to the Fe centers of cytochrome P450 and other heme enzymes to inhibit their activities. Although these AmphNHOH/AmphNO metabolites are present in vivo, their interactions with the blood protein hemoglobin (Hb) and the muscle protein (Mb) have been largely discounted due to a perception that the relatively small heme active sites of Hb and Mb will not be able to accommodate the large AmphNO group. Here, we report the 2.15 Å resolution X-ray crystal structure of the AmphNO adduct of adult human hemoglobin as the Hb [ α -Fe III (H 2 O)][ β -Fe II (AmphNO)] derivative. We show that the binding of AmphNO to the β subunit is enabled by an E helix movement and stabilization of ligand binding by H-bonding with the distal His63 residue. We also observe an AmphNHOH group in the Xe2 pocket in close proximity to the α heme site in this derivative. Additionally, UV–vis spectroscopy was used to characterize this and related wt and mutant Mb adducts. Importantly, our X-ray crystal structure of this Hb-nitrosoamphetamine complex represents the first crystal structure of a wild-type heme protein adduct of any amphetamine metabolite. Our results provide a framework for further studies of AmphNHOH/AmphNO interactions with Hb and Mb as viable processes that potentially contribute to the overall biological inorganic chemistry of amphetamine drugs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and Reactivity of Binuclear Cu Active Sites in Cu-CHA Zeolites for Stoichiometric Partial Methane Oxidation to Methanol

Aluminosilicate zeolites exchanged with copper ions facilitate partial methane oxidation (PMO) to methanol in stoichiometric oxidation and reduction cycles, yet the identities of active Cu sites and details of the reaction mechanism remain debated. Here, we use the high-symmetry chabazite (CHA) zeolite framework as a model support to probe the relationship between bulk composition, Cu speciation, and response to various oxidizing and reducing treatments. Density functional theory and first-principles thermodynamics combined with statistical models reveal that Cu speciation and composition depend strongly on Al configuration and external gas conditions. Cu-CHA samples were synthesized to survey broad regions of Si/Al and Cu/Al composition space and framework Al proximity. Characterization by in situ X-ray absorption and UV–visible spectroscopy during exposure to different oxidation conditions reveal that the extent of Cu oxidation is sensitive to activation conditions and thus that both kinetic and thermodynamic factors influence Cu oxidizability in a given material. Similar characterizations during CO reduction reveal that CO titrates Cu 2+ in amounts suggesting the presence of both O- and O 2 -bridged species. In contrast, CH 4 and autoreduction (He) treatments reduce similar but smaller numbers of Cu sites than CO, implicating O 2 -bridged Cu dimers as a potential common intermediate in the former reduction pathways. Furthermore, a systematic increase in methanol yields (per Cu) in stoichiometric PMO cycles increase with the fraction of binuclear O x -bridged Cu sites suggests these species as active sites, as depicted in an updated PMO reaction mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site

As an approach towards unraveling the nitrogenase mechanism, we have studied the binding of CO to the activesite FeMo-cofactor. CO is not only an inhibitor of nitrogenase, but it is also a substrate, undergoing reduction to hydrocarbons (Fischer–Tropsch-type chemistry). The CC bond forming capabilities of nitrogenase suggest that multiple CO or COderived ligands bind to the active site. Herein, we report a crystal structure with two CO ligands coordinated to the FeMo-cofactor of the molybdenum nitrogenase at 1.33 resolution. In addition to the previously observed bridging CO ligand between Fe2 and Fe6 of the FeMo-cofactor, a new ligand binding mode is revealed through a second CO ligand coordinated terminally to Fe6. While the relevance of this state to nitrogenase-catalyzed reactions remains to be established, it highlights the privileged roles for Fe2 and Fe6 in ligand binding, with multiple coordination modes available depending on the ligand and reaction conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evidence of Atypical Structural Flexibility of the Active Site Surrounding of an [FeFe] Hydrogenase from Clostridium beijerinkii

[FeFe] hydrogenase from Clostridium beijerinkii (CbHydA1) is an unusual hydrogenase in that it can withstand prolonged exposure to O 2 by reversibly converting into an O 2 -protected, inactive state (Hinact). It has been indicated in the past that an atypical conformation of the “SC 367 CP” loop near the [2Fe] H portion of the six-iron active site (H-cluster) allows the Cys367 residue to adopt an “off-H + -pathway” orientation, promoting a facile transition of the cofactor to Hinact. Here, we investigated the electronic structure of the H-cluster in the oxidized state (H ox ) that directly converts to Hinact under oxidizing conditions and the related CO-inhibited state (H ox -CO). We demonstrate that both states exhibit two distinct forms in electron paramagnetic resonance (EPR) spectroscopy. The ratio between the two forms is pH-dependent but also sensitive to the buffer choice. Our IR and EPR analyses illustrate that the spectral heterogeneity is due to a perturbation of the coordination environment of the H-cluster’s [4Fe4S] H subcluster without affecting the [2Fe] H subcluster. Overall, we conclude that the observation of two spectral components per state is evidence of heterogeneity of the environment of the H-cluster likely associated with conformational mobility of the SCCP loop. Such flexibility may allow Cys367 to switch rapidly between off- and on-H + -pathway rotamers. Consequently, we believe such structural mobility may be the key to maintaining high enzymatic activity while allowing a facile transition to the O 2 -protected state.

08 HYDROGEN↗

Role of the Mobile Active Site Flap in IMP Dehydrogenase Inhibitor Binding

Inosine 5′-monophosphate dehydrogenase (IMPDH) is a promising antibiotic target. This enzyme catalyzes the NAD-dependent oxidation of inosine 5′-monophosphate (IMP) to xanthosine 5′-monophosphate (XMP), which is the rate-limiting step in guanine nucleotide biosynthesis. Bacterial IMPDH-specific inhibitors have been developed that bind to the NAD + site. These inhibitors display varied affinities to different bacterial IMPDHs that are not easily rationalized by X-ray crystal structures of enzyme–inhibitor complexes. Inspection of X-ray crystal structures of 25 enzyme–inhibitor complexes, including 10 newly described, suggested that a mobile active site flap may be a structural determinant of inhibitor potency. Saturation transfer difference NMR experiments also suggested that the flap may contact the inhibitors to varying extents in different IMPDHs. Flap residue Leu413 contacted some inhibitors but was not structured in the crystal structures of other inhibitor complexes. The substitution of Leu413 with Phe or Ala in Bacillus anthracis IMPDH had inhibitor-selective effects, suggesting residue 413 could be a structural determinant of affinity. Curiously, the Ala substitution increased the potency of most inhibitors, even those that contacted Leu413 in the crystal structures. Presteady-state and steady-state kinetics experiments showed that the Leu413Ala substitution had comparable effects on inhibitor binding to the noncovalent E·IMP complex and the covalent intermediate E-XMP*, suggesting that the flap had similar interactions in both complexes. These results demonstrate that contacts do not necessarily indicate favorable interactions, and poorly structured mobile regions should not be discounted when assessing binding determinants.

Conformation↗