B18-Core EXAFS
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Diamond Proposal Number(s):
[12746]
Abstract: Carbon-supported Pt-based nanoparticles are important electrocatalysts for energy conversion reactions such as the oxygen reduction reaction (ORR). Although this reaction has been extensively studied, the influence of factors such as the particle size and interparticle distance of the nanoparticle-based or nanosized electrocatalysts on the ORR activity and durability are not yet fully understood and often intertwined. This lack of understanding is mostly based on the limitation in the synthetic approaches of the electrocatalysts, which usually do not allow an independent variation of the particle size and interparticle distance. In the presented work, we succeeded to disentangle both factors using a “colloidal toolbox” approach and have demonstrated an effect of the interparticle distance on the electronic properties of the nanoparticle via operando electrochemical X-ray absorption spectroscopy (XAS).
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Jun 2021
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I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[16479]
Open Access
Abstract: In situ X-ray absorption and emission spectroscopies (XAS and XES) are used to provide details regarding the role of the accessibility and extent of redox activity of the Mn ions in determining the oxygen reduction activity of LaMnO3 and CaMnO3, with X-ray absorption near-edge structure (XANES) providing the average oxidation state, extended X-ray absorption fine structure (EXAFS) providing the local coordination environment, and XES providing the population ratios of the Mn2+, Mn3+, and Mn4+ sites as a function of the applied potential. For LaMnO3, XANES and XES show that Mn3+ is formed, but Mn4+ ions are retained, which leads to the 4e– reduction between 0.85 and 0.6 V. At more negative potentials, down to 0.2 V, EXAFS confirms an increase in oxygen vacancies as evidenced by changes in the Mn–O coordination distance and number, while XES shows that the Mn3+ to Mn4+ ratio increases. For CaMnO3, XANES and XES show the formation of both Mn3+ and Mn2+ as the potential is made more negative, with little retention of Mn4+ at 0.2 V. The EXAFS for CaMnO3 also indicates the formation of oxygen vacancies, but in contrast to LaMnO3, this is accompanied by loss of the perovskite structure leading to structural collapse. The results presented have implications in terms of understanding of both the pseudocapacitive response of Mn oxide electrocatalysts and the processes behind degradation of the activity of the materials.
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May 2021
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B18-Core EXAFS
I11-High Resolution Powder Diffraction
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Pu
Zhao
,
Lin
Ye
,
Guangchao
Li
,
Chen
Huang
,
Simson
Wu
,
Ping-Luen
Ho
,
Haokun
Wang
,
Tatchamapan
Yoskamtorn
,
Denis
Sheptyakov
,
Giannantonio
Cibin
,
Angus I.
Kirkland
,
Chiu C.
Tang
,
Anmin
Zheng
,
Wenjuan
Xue
,
Donghai
Mei
,
Kongkiat
Suriye
,
Shik Chi Edman
Tsang
Abstract: Synthesizing atomically dispersed synergistic active pairs is crucial yet challenging in developing highly active heterogeneous catalysts for various industrially important reactions. Here, a single molecular Re species is immobilized on the inner surface of a Y zeolite with Brønsted acid sites (BASs) within atomic proximity to form Re OMS–BAS active pairs for the efficient catalysis of olefin metathesis reactions (OMS: olefin metathesis site). The synergy within the active pairs is revealed by studying the coadsorption geometry of the olefin substrates over the active pairs by synchrotron X-ray and neutron powder diffraction. It is shown that the BAS not only facilitates olefin adsorption but also aligns the olefin molecule to the Re OMS for efficient intermediate formation. Consequently, for the cross-metathesis of ethene and trans-2-butene to propene, this catalyst shows high activity under mild reaction conditions without observable deactivation. The catalyst outperforms not only traditional ReOx-based catalysts but also the best industrially applicable WOx-based catalyst thus far that we discovered previously. The concept of using two isolated active sites of different functionalities within atomic proximity in a confined cavity can provide opportunities for designing synergistically catalytic materials.
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Mar 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[9948]
Open Access
Abstract: Cytochrome P450 CYP153AM.aq from Marinobacter aquaeolei serves as a model enzyme for the terminal (ω-) hydroxylation of medium- to long-chain fatty acids. We have engineered this enzyme using different mutagenesis approaches based on structure-sequence-alignments within the 3DM database and crystal structures of CYP153AM.aq and a homologue CYP153AP.sp. Applying these focused mutagenesis strategies and site-directed saturation mutagenesis, we created a variant that ω-hydroxylates octanoic acid. The M.aqRLT variant exhibited 151-fold improved catalytic efficiency and showed strongly improved substrate binding (25-fold reduced Km compared to the wild type). We then used molecular dynamics simulations to gain deeper insights into the dynamics of the protein. We found the tunnel modifications and the two loop regions showing greatly reduced flexibility in the engineered variant were the main features responsible for stabilizing the enzyme–substrate complex and enhancing the catalytic efficiency. Additionally, we showed that a previously known fatty acid anchor (Q129R) interacts significantly with the ligand to hold it in the reactive position, thereby boosting the activity of the variant M.aqRLT toward octanoic acid. The study demonstrates the significant effects of both substrate stabilization and the impact of enzyme flexibility on catalytic efficiency. These results could guide the future engineering of enzymes with deeply buried active sites to increase or even establish activities toward yet unknown types of substrates.
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Feb 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[13587]
Open Access
Abstract: Isoelectronic metal fluoride transition state analogue (TSA) complexes, MgF3– and AlF4–, have proven to be immensely useful in understanding mechanisms of biological motors utilizing phosphoryl transfer. Here we report a previously unobserved octahedral TSA complex, MgF3(H2O)−, in a 1.5 Å resolution Zika virus NS3 helicase crystal structure. 19F NMR provided independent validation and also the direct observation of conformational tightening resulting from ssRNA binding in solution. The TSA stabilizes the two conformations of motif V of the helicase that link ATP hydrolysis with mechanical work. DFT analysis further validated the MgF3(H2O)− species, indicating the significance of this TSA for studies of biological motors.
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Feb 2021
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Open Access
Abstract: The utilization of operando spectroscopy has allowed us to watch the dynamic nature of supported metal nanoparticles. However, the realization that subtle changes to environmental conditions affect the form of the catalyst necessitates that we assess the structure of the catalyst across the reactant/product gradient that exists across a fixed bed reactor. In this study, we have performed spatial profiling of a Pd/Al2O3 catalyst during NH3 oxidation, simultaneously collecting mass spectrometry and X-ray absorption spectroscopy data at discrete axial positions along the length of the catalyst bed. The spatial analysis has provided unique insights into the structure–activity relationships that govern selective NH3 oxidation—(i) our data is consistent with the presence of PdNx after the spectroscopic signatures for bulk PdNx disappear and that there is a direct correlation to the presence of this structure and the selectivity toward N2; (ii) at high temperatures, ≥400 °C, we propose that there are two simultaneous reaction pathways—the oxidation of NH3 to NOx by PdO and the subsequent catalytic reduction of NOx by NH3 to produce N2. The results in this study confirm the structural and catalytic diversity that exists during catalysis and the need for such an understanding if improvements to important emission control technologies, such as the selective catalytic oxidation of NH3, are to be made.
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Feb 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[12788]
Open Access
Abstract: The UbiD family of reversible (de)carboxylases depends on the recently discovered prenylated-FMN (prFMN) cofactor for activity. The model enzyme ferulic acid decarboxylase (Fdc1) decarboxylates unsaturated aliphatic acids via a reversible 1,3-cycloaddition process. Protein engineering has extended the Fdc1 substrate range to include (hetero)aromatic acids, although catalytic rates remain poor. This raises the question how efficient decarboxylation of (hetero)aromatic acids is achieved by other UbiD family members. Here, we show that the Pseudomonas aeruginosa virulence attenuation factor PA0254/HudA is a pyrrole-2-carboxylic acid decarboxylase. The crystal structure of the enzyme in the presence of the reversible inhibitor imidazole reveals a covalent prFMN–imidazole adduct is formed. Substrate screening reveals HudA and selected active site variants can accept a modest range of heteroaromatic compounds, including thiophene-2-carboxylic acid. Together with computational studies, our data suggests prFMN covalent catalysis occurs via electrophilic aromatic substitution and links HudA activity with the inhibitory effects of pyrrole-2-carboxylic acid on P. aeruginosa quorum sensing.
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Feb 2021
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B18-Core EXAFS
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Abstract: Four Mo-based catalysts were prepared via three different synthesis techniques supported on SiO2 and/or SBA-15. By means of complementary in situ characterization techniques, the carburization process and the final characteristics of these catalysts were investigated. Additionally, the four catalysts were evaluated for the activation of CO2 in the absence and presence of H2 (reverse water–gas shift, RWGS). The results suggest that CO2 reacts via a dissociation on the carbide surface, forming adsorbed oxygen surface species. Severe oxidation of the carbide into its oxidic phases (MoO2 or MoO3) only occurs at temperatures above 850 K in the presence of CO2. O2 dissociates on the carbide surface when introduced at low concentrations (1 vol %) at room temperature, but when exposed to higher concentrations, a strong exothermic bulk re-oxidation reaction occurs, forming MoO2. All four catalysts show high RWGS activity in terms of CO2 conversions with a minimum CO selectivity of 98% without any signs of bulk catalyst oxidation. Although minimal, the observed deactivation is suggested to be primarily due to phase changes between Mo2C allotropes (β-phase, oxycarbide, and η-phase) and/or sintering of the active phase.
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Jan 2021
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B18-Core EXAFS
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Abstract: This work describes the transformation of Pd species under reaction conditions to control the reactivity of heterogeneous catalysts, in which the real active sites for hydrogenation differ from simple Pd sites on a carbon nanofiber. Specifically, in the presence of C2H2/C2H4/H2 reaction mixtures, a permeable amorphous hydrocarbon overlayer is formed with simultaneous insertion of carbon atoms into the Pd lattice that drives the formation of low-coordinated Pd-carbide, thus providing more reactive Pd–Csub@Clayer sites (Csub: subsurface carbon; Clayer: carbon layer on the surface). The combination of these surface and subsurface effects hinders Pd-hydride, weakens ethylene adsorption confirmed by density functional theory (DFT) calculation, and thus improves catalytic behavior for selective hydrogenation of acetylene (93% ethylene selectivity at 100% conversion) with long-term stability. In the absence of hydrogen, a denser more crystalline overlayer is formed with severely restricted permeability, resulting in significantly lower activity. Moreover, by X-ray absorption spectroscopy (XAS) and in situ X-ray diffraction (XRD), it is demonstrated that different active sites dominate this catalytic reaction depending on the choice of adsorbate and exposure temperature. This work represents an alternative and arguably a simpler manner to design more reactive catalytic sites with the characteristics of long-term stability and facile preparation, which would enable promising industrial applications.
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Dec 2020
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Abstract: The enzyme (R)-3-hydroxybutyrate dehydrogenase (HBDH) catalyzes the enantioselective reduction of 3-oxocarboxylates to (R)-3-hydroxycarboxylates, the monomeric precursors of biodegradable polyesters. Despite its application in asymmetric reduction, which prompted several engineering attempts of this enzyme, the order of chemical events in the active site, their contributions to limit the reaction rate, and interactions between the enzyme and non-native 3-oxocarboxylates have not been explored. Here, a combination of kinetic isotope effects, protein crystallography, and quantum mechanics/molecular mechanics (QM/MM) calculations were employed to dissect the HBDH mechanism. Initial velocity patterns and primary deuterium kinetic isotope effects establish a steady-state ordered kinetic mechanism for acetoacetate reduction by a psychrophilic and a mesophilic HBDH, where hydride transfer is not rate limiting. Primary deuterium kinetic isotope effects on the reduction of 3-oxovalerate indicate that hydride transfer becomes more rate limiting with this non-native substrate. Solvent and multiple deuterium kinetic isotope effects suggest hydride and proton transfers occur in the same transition state. Crystal structures were solved for both enzymes complexed to NAD+:acetoacetate and NAD+:3-oxovalerate, illustrating the structural basis for the stereochemistry of the 3-hydroxycarboxylate products. QM/MM calculations using the crystal structures as a starting point predicted a higher activation energy for 3-oxovalerate reduction catalyzed by the mesophilic HBDH, in agreement with the higher reaction rate observed experimentally for the psychrophilic orthologue. Both transition states show concerted, albeit not synchronous, proton and hydride transfers to 3-oxovalerate. Setting the MM partial charges to zero results in identical reaction activation energies with both orthologues, suggesting the difference in activation energy between the reactions catalyzed by cold- and warm-adapted HBDHs arises from differential electrostatic stabilization of the transition state. Mutagenesis and phylogenetic analysis reveal the catalytic importance of His150 and Asn145 in the respective orthologues.
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Dec 2020
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