E01-JEM ARM 200CF
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Michael
Bowker
,
Naomi
Lawes
,
Isla
Gow
,
James
Hayward
,
Jonathan
Ruiz Esquius
,
Nia
Richards
,
Louise R.
Smith
,
Thomas J. A.
Slater
,
Thomas E.
Davies
,
Nicholas F.
Dummer
,
Lara
Kabalan
,
Andrew
Logsdail
,
Richard C.
Catlow
,
Stuart
Taylor
,
Graham J
Hutchings
Diamond Proposal Number(s):
[27530]
Open Access
Abstract: The rise in atmospheric CO2 concentration and the concomitant rise in global surface temperature have prompted massive research effort in designing catalytic routes to utilize CO2 as a feedstock. Prime among these is the hydrogenation of CO2 to make methanol, which is a key commodity chemical intermediate, a hydrogen storage molecule, and a possible future fuel for transport sectors that cannot be electrified. Pd/ZnO has been identified as an effective candidate as a catalyst for this reaction, yet there has been no attempt to gain a fundamental understanding of how this catalyst works and more importantly to establish specific design criteria for CO2 hydrogenation catalysts. Here, we show that Pd/ZnO catalysts have the same metal particle composition, irrespective of the different synthesis procedures and types of ZnO used here. We demonstrate that all of these Pd/ZnO catalysts exhibit the same activity trend. In all cases, the β-PdZn 1:1 alloy is produced and dictates the catalysis. This conclusion is further supported by the relationship between conversion and selectivity and their small variation with ZnO surface area in the range 6–80 m2g–1. Without alloying with Zn, Pd is a reverse water-gas shift catalyst and when supported on alumina and silica is much less active for CO2 conversion to methanol than on ZnO. Our approach is applicable to the discovery and design of improved catalysts for CO2 hydrogenation and will aid future catalyst discovery.
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Apr 2022
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B18-Core EXAFS
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Peng
Tang
,
Hyeon Jeong
Lee
,
Kevin
Hurlbutt
,
Po-Yuan
Huang
,
Sudarshan
Narayanan
,
Chenbo
Wang
,
Diego
Gianolio
,
Rosa
Arrigo
,
Jun
Chen
,
Jamie H.
Warner
,
Mauro
Pasta
Diamond Proposal Number(s):
[26066]
Abstract: Platinum single-site catalysts (SSCs) are a promising technology for the production of hydrogen from clean energy sources. They have high activity and maximal platinum-atom utilization. However, the bonding environment of platinum during operation is poorly understood. In this work, we present a mechanistic study of platinum SSCs using operando, synchrotron-X-ray absorption spectroscopy. We synthesize an atomically dispersed platinum complex with aniline and chloride ligands onto graphene and characterize it with ex-situ electron microscopy, X-ray diffractometry, X-ray photoelectron spectroscopy, X-ray absorption near-edge structure spectroscopy (XANES), and extended X-ray absorption fine structure spectroscopy (EXAFS). Then, by operando EXAFS and XANES, we show that as a negatively biased potential is applied, the Pt–N bonds break first followed by the Pt–Cl bonds. The platinum is reduced from platinum(II) to metallic platinum(0) by the onset of the hydrogen-evolution reaction at 0 V. Furthermore, we observe an increase in Pt–Pt bonding, indicating the formation of platinum agglomerates. Together, these results indicate that while aniline is used to prepare platinum SSCs, the single-site complexes are decomposed and platinum agglomerates at operating potentials. This work is an important contribution to the understanding of the evolution of bonding environment in SSCs and provides some molecular insights into how platinum agglomeration causes the deactivation of SSCs over time.
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Feb 2022
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[17773, 24447]
Abstract: Understanding the factors that underpin the enormous catalytic proficiencies of enzymes is fundamental to catalysis and enzyme design. Enzymes are, in part, able to achieve high catalytic proficiencies by utilizing the binding energy derived from nonreacting portions of the substrate. In particular, enzymes with substrates containing a nonreacting phosphodianion group coordinated in a distal site have been suggested to exploit this binding energy primarily to facilitate a conformational change from an open inactive form to a closed active form, rather than to either induce ground state destabilization or stabilize the transition state. However, detailed structural evidence for the model is limited. Here, we use β-phosphoglucomutase (βPGM) to investigate the relationship between binding a phosphodianion group in a distal site, the adoption of a closed enzyme form, and catalytic proficiency. βPGM catalyzes the isomerization of β-glucose 1-phosphate to glucose 6-phosphate via phosphoryl transfer reactions in the proximal site, while coordinating a phosphodianion group of the substrate(s) in a distal site. βPGM has one of the largest catalytic proficiencies measured and undergoes significant domain closure during its catalytic cycle. We find that side chain substitution at the distal site results in decreased substrate binding that destabilizes the closed active form but is not sufficient to preclude the adoption of a fully closed, near-transition state conformation. Furthermore, we reveal that binding of a phosphodianion group in the distal site stimulates domain closure even in the absence of a transferring phosphoryl group in the proximal site, explaining the previously reported β-glucose 1-phosphate inhibition. Finally, our results support a trend whereby enzymes with high catalytic proficiencies involving phosphorylated substrates exhibit a greater requirement to stabilize the closed active form.
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Feb 2022
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E01-JEM ARM 200CF
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Rosa
Arrigo
,
Raoul
Blume
,
Verena
Streibel
,
Chiara
Genovese
,
Alberto
Roldan
,
Manfred E.
Schuster
,
Claudio
Ampelli
,
Siglinda
Perathoner
,
Juan J.
Velasco Vélez
,
Michael
Hävecker
,
Axel
Knop-Gericke
,
Robert
Schlögl
,
Gabriele
Centi
Open Access
Abstract: Surface-sensitive ambient pressure X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy combined with an electrocatalytic reactivity study, multilength-scale electron microscopy, and theoretical modeling provide insights into the gas-phase selective reduction of carbon dioxide to isopropanol on a nitrogen-doped carbon-supported iron oxyhydroxide electrocatalyst. Dissolved atomic carbon forms at relevant potentials for carbon dioxide reduction from the reduction of carbon monoxide chemisorbed on the surface of the ferrihydrite-like phase. Theoretical modeling reveals that the ferrihydrite structure allows vicinal chemisorbed carbon monoxide in the appropriate geometrical arrangement for coupling. Based on our observations, we suggest a mechanism of three-carbon-atom product formation, which involves the intermediate formation of atomic carbon that undergoes hydrogenation in the presence of hydrogen cations upon cathodic polarization. This mechanism is effective only in the case of thin ferrihydrite-like nanostructures coordinated at the edge planes of the graphitic support, where nitrogen edge sites stabilize these species and lower the overpotential for the reaction. Larger ferrihydrite-like nanoparticles are ineffective for electron transport.
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Dec 2021
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B22-Multimode InfraRed imaging And Microspectroscopy
I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[22298]
Abstract: Unwanted N2O formation is a problem that has been noted in selective catalytic reduction (SCR) where copper zeolite catalysts are utilized. With its immense global warming potential and long-term stability, elevated atmospheric N2O has already been identified as a future challenge in the war on climate change. This paper explores the phenomenon of N2O formation during NH3-SCR over Cu-SSZ-13 catalysts, which are currently commercialized in automotive emissions control systems, and proposes a link between N2O production and the local copper environment found within the zeolite. To achieve this, a comparison is made between two Cu-SSZ-13 samples with different copper co-ordinations produced via different synthesis methods. A combination of synchrotron X-ray absorption near-edge spectroscopy, UV–vis, Raman, and density functional theory (DFT) is used to characterize the nature of copper species present within each sample. Synchrotron IR microspectroscopy is then used to compare their behavior during SCR under operando conditions and monitor the evolution of nitrate intermediates, which, along with further DFT, informs a mechanistic model for nitrate decomposition pathways. Increased N2O production is seen in the Cu-SSZ-13 sample postulated to contain a linear Cu species, providing an important correlation between the catalytic behavior of Cu-zeolites and the nature of their metal ion loading and speciation.
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Oct 2021
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I03-Macromolecular Crystallography
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Klara
Markova
,
Antonin
Kunka
,
Klaudia
Chmelova
,
Martin
Havlasek
,
Petra
Babkova
,
Sérgio M.
Marques
,
Michal
Vasina
,
Joan
Planas-Iglesias
,
Radka
Chaloupkova
,
David
Bednar
,
Zbynek
Prokop
,
Jiri
Damborsky
,
Martin
Marek
Abstract: The functionality of an enzyme depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric α/β-hydrolase enzyme (Tm = 73.5 °C; ΔTm > 23 °C) affected the protein folding energy landscape. The introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded soluble domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations might (i) activate cryptic hinge-loop regions and (ii) establish secondary interfaces, where they make extensive noncovalent interactions between the intertwined protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from small-angle X-ray scattering (SAXS) and cross-linking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain swapping occurs exclusively in vivo. Crucially, the swapped-dimers exhibited advantageous catalytic properties such as an increased catalytic rate and elimination of substrate inhibition. These findings provide additional enzyme engineering avenues for next-generation biocatalysts.
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Oct 2021
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E01-JEM ARM 200CF
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Diamond Proposal Number(s):
[26559]
Open Access
Abstract: State of the art electrocatalysts for the hydrogen evolution reaction (HER) are based on metal nanoparticles (NPs). It has been shown that the localized surface plasmon resonance (LSPR) excitation in plasmonic NPs can be harvested to accelerate a variety of molecular transformations. This enables the utilization of visible light as an energy input to enhance HER performances. However, most metals that are active toward the HER do not support LSPR excitation in the visible or near-IR ranges. We describe herein the synthesis of gold–rhodium core–shell nanoflowers (Au@Rh NFs) that are composed of a core made up of spherical Au NPs and shells containing Rh branches. The Au@Rh NFs were employed as a model system to probe how the LSPR excitation from Au NPs can lead to an enhancement in the HER performance for Rh. Our data demonstrate that the LSPR excitation at 533 nm (and 405 nm) leads to an improvement in the HER performance of Rh, which depends on the morphological features of the Au@Rh NFs, offering opportunities for optimization of the catalytic performance. Control experiments indicate that this improvement originates from the stronger interaction of Au@Rh NFs with H2O molecules at the surface, leading to an icelike configuration, which facilitated the HER under LSPR excitation.
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Oct 2021
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[20221]
Open Access
Abstract: Unspecific peroxygenases (UPOs) are glycosylated fungal enzymes that can selectively oxidize C–H bonds. UPOs employ hydrogen peroxide as the oxygen donor and reductant. With such an easy-to-handle cosubstrate and without the need for a reducing agent, UPOs are emerging as convenient oxidative biocatalysts. Here, an unspecific peroxygenase from Hypoxylon sp. EC38 (HspUPO) was identified in an activity-based screen of six putative peroxygenase enzymes that were heterologously expressed in Pichia pastoris. The enzyme was found to tolerate selected organic solvents such as acetonitrile and acetone. HspUPO is a versatile catalyst performing various reactions, such as the oxidation of prim- and sec-alcohols, epoxidations, and hydroxylations. Semipreparative biotransformations were demonstrated for the nonenantioselective oxidation of racemic 1-phenylethanol rac-1b (TON = 13 000), giving the product with 88% isolated yield, and the oxidation of indole 6a to give indigo 6b (TON = 2800) with 98% isolated yield. HspUPO features a compact and rigid three-dimensional conformation that wraps around the heme and defines a funnel-shaped tunnel that leads to the heme iron from the protein surface. The tunnel extends along a distance of about 12 Å with a fairly constant diameter in its innermost segment. Its surface comprises both hydrophobic and hydrophilic groups for dealing with substrates of variable polarities. The structural investigation of several protein–ligand complexes revealed that the active site of HspUPO is accessible to molecules of varying bulkiness with minimal or no conformational changes, explaining the relatively broad substrate scope of the enzyme. With its convenient expression system, robust operational properties, relatively small size, well-defined structural features, and diverse reaction scope, HspUPO is an exploitable candidate for peroxygenase-based biocatalysis.
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Sep 2021
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B23-Circular Dichroism
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Christopher D.
Fage
,
Simone
Kosol
,
Matthew
Jenner
,
Carl
Öster
,
Angelo
Gallo
,
Milda
Kaniusaite
,
Roman
Steinbach
,
Michael
Staniforth
,
Vasilios G.
Stavros
,
Mohamed A.
Marahiel
,
Max J.
Cryle
,
Józef R.
Lewandowski
Diamond Proposal Number(s):
[16655]
Open Access
Abstract: Nonribosomal peptides are a structurally diverse and bioactive class of natural products constructed by multidomain enzymatic assembly lines known as nonribosomal peptide synthetases (NRPSs). While the core catalytic domains and even entire protein subunits of NRPSs have been structurally elucidated, little biophysical work has been reported on the docking domains that promote interactions—and thus transfer of biosynthetic intermediates—between subunits. In the present study, we closely examine the COM domains that mediate COMmunication between donor epimerization (E) and acceptor condensation (C) domains found at the termini of NRPS subunits. Through a combination of X-ray crystallography, circular dichroism spectroscopy, solution- and solid-state NMR spectroscopy, and molecular dynamics (MD) simulations, we provide direct evidence for an intrinsically disordered donor COM region that folds into a dynamic helical motif upon binding to a suitable acceptor. Furthermore, our NMR titration and carbene footprinting experiments illuminate the residues involved at the COM interaction interface, and our MD simulations demonstrate folding consistent with experimental data. Although our results lend credence to the previously proposed helix-hand mode of interaction, they also underscore the importance of viewing COM interfaces as dynamic ensembles rather than single rigid structures and suggest that engineering experiments should account for the interactions which transiently guide folding in addition to those which stabilize the final complex. Through activity assays and affinity measurements, we further substantiate the role of the donor COM region in binding the acceptor C domain and implicate this short motif as readily transposable for noncognate domain crosstalk. Finally, our bioinformatics analyses show that COM domains are widespread in natural product pathways and function at interfaces beyond the canonical type described above, setting a high priority for thorough characterization of these docking domains. Our findings lay the groundwork for future attempts to rationally engineer NRPS domain–domain interactions with the ultimate goal of generating bioactive molecules.
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Aug 2021
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I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[19800]
Open Access
Abstract: ω-Transaminases (ω-TA) are attractive biocatalysts for the production of chiral amines from prochiral ketones via asymmetric synthesis. However, the substrate scope of ω-TAs is usually limited due to steric hindrance at the active site pockets. We explored a protein engineering strategy using computational design to expand the substrate scope of an (S)-selective ω-TA from Pseudomonas jessenii (PjTA-R6) toward the production of bulky amines. PjTA-R6 is attractive for use in applied biocatalysis due to its thermostability, tolerance to organic solvents, and acceptance of high concentrations of isopropylamine as amino donor. PjTA-R6 showed no detectable activity for the synthesis of six bicyclic or bulky amines targeted in this study. Six small libraries composed of 7–18 variants each were separately designed via computational methods and tested in the laboratory for ketone to amine conversion. In each library, the vast majority of the variants displayed the desired activity, and of the 40 different designs, 38 produced the target amine in good yield with >99% enantiomeric excess. This shows that the substrate scope and enantioselectivity of PjTA mutants could be predicted in silico with high accuracy. The single mutant W58G showed the best performance in the synthesis of five structurally similar bulky amines containing the indan and tetralin moieties. The best variant for the other bulky amine, 1-phenylbutylamine, was the triple mutant W58M + F86L + R417L, indicating that Trp58 is a key residue in the large binding pocket for PjTA-R6 redesign. Crystal structures of the two best variants confirmed the computationally predicted structures. The results show that computational design can be an efficient approach to rapidly expand the substrate scope of ω-TAs to produce enantiopure bulky amines.
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Aug 2021
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