I04-1-Macromolecular Crystallography (fixed wavelength)
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Marion
Schuller
,
Galen J.
Correy
,
Stefan
Gahbauer
,
Daren
Fearon
,
Taiasean
Wu
,
Roberto Efraín
Díaz
,
Iris D.
Young
,
Luan
Carvalho Martins
,
Dominique H.
Smith
,
Ursula
Schulze-Gahmen
,
Tristan W.
Owens
,
Ishan
Deshpande
,
Gregory E.
Merz
,
Aye C.
Thwin
,
Justin T.
Biel
,
Jessica K.
Peters
,
Michelle
Moritz
,
Nadia
Herrera
,
Huong T.
Kratochvil
,
Anthony
Aimon
,
James
Bennett
,
Jose
Brandao Neto
,
Aina E.
Cohen
,
Alexandre
Dias
,
Alice
Douangamath
,
Louise
Dunnett
,
Oleg
Fedorov
,
Matteo P.
Ferla
,
Martin R.
Fuchs
,
Tyler J.
Gorrie-Stone
,
James M.
Holton
,
Michael G.
Johnson
,
Tobias
Krojer
,
George
Meigs
,
Alisa J.
Powell
,
Johannes Gregor Matthias
Rack
,
Victor
Rangel
,
Silvia
Russi
,
Rachael E.
Skyner
,
Clyde A.
Smith
,
Alexei S.
Soares
,
Jennifer L.
Wierman
,
Kang
Zhu
,
Peter
O’brien
,
Natalia
Jura
,
Alan
Ashworth
,
John J.
Irwin
,
Michael C.
Thompson
,
Jason E.
Gestwicki
,
Frank
Von Delft
,
Brian K.
Shoichet
,
James S.
Fraser
,
Ivan
Ahel
Diamond Proposal Number(s):
[27001]
Open Access
Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate–ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
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Apr 2021
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I11-High Resolution Powder Diffraction
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Martin
Schroeder
,
Louis
Kimberley
,
Alena M.
Sheveleva
,
Jiangnan
Li
,
Joseph H.
Carter
,
Xinchen
Kang
,
Gemma L.
Smith
,
Xue
Han
,
Sarah J.
Day
,
Chiu C.
Tang
,
Floriana
Tuna
,
Eric J. L.
Mcinnes
,
Sihai
Yang
Abstract: Selective oxidation of benzylic C‐H compounds to ketones is important for the production of a wide range of fine chemicals, and is often achieved using toxic or precious metals catalysts. Here, we report the efficient oxidation of benzylic C‐H groups in a broad range of substrates under mild conditions over a robust metal‐organic framework material, MFM‐170, incorporating redox‐active [Cu2II(O2CR)4] paddlewheel nodes. A comprehensive investigation employing electron paramagnetic resonance (EPR) spectroscopy and synchrotron X‐ray diffraction has identified the critical role of the paddlewheel moiety in activating the oxidant tBuOOH (t‐butyl hydroperoxide) via partial reduction to [CuIICuI(O2CR)4] species.
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Apr 2021
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B21-High Throughput SAXS
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[14980, 19844]
Abstract: Ubiquitin-specific protease 1 (USP1) acts together with the cofactor UAF1 during DNA repair processes to specifically remove monoubiquitin signals. One substrate of the USP1−UAF1 complex is the monoubiquitinated FANCI−FANCD2 heterodimer, which is involved in the repair of DNA interstrand crosslinks via the Fanconi anemia pathway. Here we determine structures of human USP1−UAF1 with and without ubiquitin and bound to monoubiquitinated FANCI−FANCD2. The crystal structures of USP1−UAF1 reveal plasticity in USP1 and key differences to USP12−UAF1 and USP46−UAF1, two related proteases. A cryo-EM reconstruction of USP1−UAF1 in complex with monoubiquitinated FANCI−FANCD2 highlights a highly orchestrated deubiquitination process, with USP1−UAF1 driving conformational changes in the substrate. An extensive interface between UAF1 and FANCI, confirmed by mutagenesis and biochemical assays, provides a molecular explanation for the requirement of both proteins, despite neither being directly involved in catalysis. Overall, our data provide molecular details of USP1−UAF1 regulation and substrate recognition.
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Apr 2021
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I13-2-Diamond Manchester Imaging
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G. R.
Parker
,
D. S.
Eastwood
,
M.
Storm
,
K.
Vitharana
,
E. M.
Heatwole
,
I.
Lopez-Pulliam
,
R. M.
Broilo
,
P. M.
Dickson
,
A.
Martinez
,
Christoph
Rau
,
N. K.
Bourne
Diamond Proposal Number(s):
[15068, 16650, 18198]
Abstract: High-resolution synchrotron x-ray radiography with computed tomography is used to observe the evolution of porosity created by thermal exposure in two HMX-based polymer-bonded explosive compositions; LX-04 and BX-63. The measurements were made in situ, over an extended period of time, during which the samples were heated on a slow-rate thermal trajectory. The tests ended with thermal-runaway to ignition after which the samples were consumed by combustion. The primary means of damage appears to be from mechanical debonding of the HMX-binder interface with secondary contribution from chemical decomposition. Confinement and binder properties affect the amount of porosity and permeability that develops. Additionally, observations were made describing the emergence and structure of an internal ignition volume, the formation and transport of a pre-ignition melt layer, and how the early stages of combustion were affected by material morphology, mechanical confinement and melt. The contact angle between molten HMX and the fluoropolymer, Viton A, is also presented. For the first time we have time-resolved x-ray images of ignition in sufficient detail to verify the mechanism of cookoff in polymer-bonded explosive compositions.
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Apr 2021
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[22198]
Abstract: Solid state batteries have attracted extensive attention, but the lithium penetration through the solid electrolyte remains a critical barrier to commercialisation and is not yet fully understood. In this study, the 3D morphological evolution of cracks with deposited lithium were tracked as they penetrated through the solid electrolyte during repetitive plating. This is achieved by utilising in-situ synchrotron X-ray computed tomography with high spatial and temporal resolutions. Thin-sheet cracks were observed to penetrate the solid electrolyte without immediate short-circuiting of the cell. Changes in their width and volume were quantified. By calculating the volume of deposited lithium, it was found that the lithium was only partially filled in cracks, and its filling ratio quickly dropped from 94.95% after the 1st plating to ca. 20% after the 4th plating. The filling process was revealed through tracking the line profile of grayscale along cracks. It was found that lithium grew much more slowly than cracks, so that the cracks near the cathode side were largely hollow and the cell could continue to operate. The deposited lithium after short circuit was segmented and its distribution was visualised. DVC analysis was applied to map local high stress and strain, which aggregated along cracks and significantly increased at areas where new cracks formed.
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Apr 2021
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[19216]
Abstract: High-speed synchrotron tomography was used to investigate the nucleation and growth dynamics of Al13Fe4 intermetallic during solidification of an Al-5wt%Fe alloy, providing new insights into its formation process. The majority of Al13Fe4 intermetallics nucleated near the surface oxide of the specimen and a few nucleated at Al13Fe4 phase. Al13Fe4 crystals grew into a variety of shapes, including plate-like, hexagonal tabular, stair-like and V-shaped, which can be attributed to the crystal structure of this compound and its susceptibility to twinning. Hole-like defects filled with aluminium melt were observed within the intermetallics. Oriented particle attachment mechanism was proposed to explain the formation of the Al13Fe4 intermetallic, which needs further experiments and simulation to confirm.
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Apr 2021
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Karel
Saksl
,
Ildikó
Pethes
,
Pál
Jóvári
,
Zuzana
Molčanová
,
Juraj
Durisin
,
Beáta
Ballóková
,
László
Temleitner
,
Stefan
Michalik
,
Michaela
Sulikova
,
Katarína
Šuľová
,
Miloš
Fejercak
,
Dagmara
Varcholová
,
Rastislav
Motýľ
Abstract: Amorphous alloys consisting of elements present in the human body, such as magnesium, zinc and calcium, are currently extensively studied in order to utilize them as a material for biodegradable orthopaedic implants. amongst all Mg-Zn-Ca alloys investigated up to date, the Mg66Zn30Ca4 composition has the greatest potential for applications. Its critical casting thickness reaches a value of 5 mm, the compressive strength (716–854 MPa) is about 4 times the limit of human cortical bone while elastic modulus is (31 GPa) is only 3 times higher than that of human bone. During dissolution the alloy shows only marginal hydrogen evolution. Here we present a detailed, experiment-based structural investigation of Mg66Zn30Ca4. Structural and topological analysis of its atomic structure reveals a high number of predominantly icosahedral densely packed Zn-centred clusters. It is believed that the existence of these structural units is responsible for the suppression of internal diffusion and thus greatly improves glass formability.
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Apr 2021
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I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[23538]
Abstract: n this work the suitability of nanostructured ferrite materials with the general formula AFe2O4 (where A is a divalent cation) for photocatalytic applications is investigated. Spinel ferrite MgFe2O4 nanoparticles and macroporous CaFe2O4 sponge structures were produced by microwave-assisted syntheses in high-boiling organic solvents and subsequent calcination in air. The elemental composition of the products was monitored by energy dispersive X-ray spectroscopy and the synthesis procedures were optimized to ensure an ideal stoichiometry of the products. Phase purity of the products was confirmed by calcination studies combined with diffraction experiments and by a wide variety of spectroscopic techniques. The morphology of the ferrite materials is characterized by electron microscopy, gas physisorption and mercury intrusion porosimetry. Regarding the electronic band structure of ferrites, a vast dissent is found in published literature. This is addressed by a thorough characterization of the electronic structure using photoelectrochemical measurements, X-ray based spectroscopic techniques, and by a detailed interpretation of their optical absorption spectra. The determined band positions suggest that CaFe2O4 is suitable for photocatalytic hydrogen evolution under visible light, while MgFe2O4 is not. Nevertheless, both phases remain inactive in hydrogen evolution test reactions as well as other photocatalytic experiments. X-ray based spectroscopy suggests that the presence of a transition metal with d5 electronic configuration causes a strong discrepancy between the fundamental electronic band gap and the one determined by optical spectroscopy. The Fe3+ crystal field orbitals involved in the ligand-to-metal charge transfer excitations that are responsible for the absorption of visible light are highly localized at the Fe3+ centers. The weak orbital overlap causes a low mobility of excited charge carriers explaining the inactivity in photocatalysis. Additional to the optical and photocatalytic properties, the magnetism of the synthesized materials is investigated by Mössbauer spectroscopy and SQUID magnetometry. While CaFe2O4 exhibits antiferromagnetic behavior, the MgFe2O4 nanoparticles exhibit a tunable magnetization, that depends on crystallite size and cation inversion and is therefore adjustable by post-synthetic calcination. First attempts towards the synthesis of magnetic NiFe2O4 and MnFe2O4 nanoparticles were made, to extend the scope of magnetic nanoparticles that can be synthesized via the microwave-assisted reaction. Attempting to combine the optical and magnetic characteristics of ferrites with other chemical functionalities in a composite material, phase-pure MgFe2O4 nanoparticles were immobilized on functionalized, ordered-mesoporous SiO2 and organosilica host networks.
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Apr 2021
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Abstract: A main challenge in the enumeration of small-molecule chemical spaces for drug design is to quickly and accurately differentiate between possible and impossible molecules. Current approaches for screening enumerated molecules (e.g., 2D heuristics and 3D force fields) have not been able to achieve a balance between accuracy and speed. We have developed a new automated approach for fast and high-quality screening of small molecules, with the following steps: (1) for each molecule in the set, an ensemble of 2D descriptors as feature encoding is computed; (2) on a random small subset, classification (feasible/infeasible) targets via a 3D-based approach are generated; (3) a classification dataset with the computed features and targets is formed and a machine learning model for predicting the 3D approach’s decisions is trained; and (4) the trained model is used to screen the remainder of the enumerated set. Our approach is ≈8× (7.96× to 8.84×) faster than screening via 3D simulations without significantly sacrificing accuracy; while compared to 2D-based pruning rules, this approach is more accurate, with better coverage of known feasible molecules. Once the topological features and 3D conformer evaluation methods are established, the process can be fully automated, without any additional chemistry expertise.
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Apr 2021
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I15-1-X-ray Pair Distribution Function (XPDF)
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Jianwei
Zheng
,
Lilin
Lu
,
Konstantin
Lebedev
,
Simson
Wu
,
Pu
Zhao
,
Ian J.
Mcpherson
,
Tai-Sing
Wu
,
Ryuichi
Kato
,
Yiyang
Li
,
Ping-Luen
Ho
,
Guangchao
Li
,
Linlu
Bai
,
Jianhui
Sun
,
Dharmalingam
Prabhakaran
,
Robert A.
Taylor
,
Yun-Liang
Soo
,
Kazu
Suenaga
,
Shik Chi Edman
Tsang
Abstract: Current industrial production of ammonia from the Haber-Bosch process and its transport concomitantly produces a large quantity of CO2. Herein, we successfully synthesize inorganic-structure-based catalysts with [Fe-S2-Mo] motifs with a connecting structure similar to that of FeMoco (a cofactor of nitrogenase) by placing iron atoms on a single molecular layer of MoS2 at various loadings. This type of new catalytic material functionally mimics the nitrogenase to convert N2 to ammonia and hydrogen in water without adding any sacrificial agent under visible-light illumination. Using the elevated temperature boosts the ammonia yield and the energy efficiency by one order of magnitude. The solar-to-NH3 energy-conversion efficiency can be up to 0.24% at 270°C, which is the highest efficiency among all reported photocatalytic systems. This method of ammonia production and the photocatalytic materials may open up an exciting possibility for the decentralization of ammonia production for fertilizer provision to local farmlands using solar illumination.
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Apr 2021
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