I11-High Resolution Powder Diffraction
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Tatchamapan
Yoskamtorn
,
Pu
Zhao
,
Xin-ping
Wu
,
Kirsty
Purchase
,
Fabio
Orlandi
,
Pascal
Manuel
,
James
Taylor
,
Yiyang
Li
,
Sarah
Day
,
Lin
Ye
,
Chiu C.
Tang
,
Yufei
Zhao
,
S. C. Edman
Tsang
Abstract: Understanding structural responses of metal–organic frameworks (MOFs) to external stimuli such as the inclusion of guest molecules and temperature/pressure has gained increasing attention in many applications, for example, manipulation and manifesto smart materials for gas storage, energy storage, controlled drug delivery, tunable mechanical properties, and molecular sensing, to name but a few. Herein, neutron and synchrotron diffractions along with Rietveld refinement and density functional theory calculations have been used to elucidate the responsive adsorption behaviors of defect-rich Zr-based MOFs upon the progressive incorporation of ammonia (NH3) and variable temperature. UiO-67 and UiO-bpydc containing biphenyl dicarboxylate and bipyridine dicarboxylate linkers, respectively, were selected, and the results establish the paramount influence of the functional linkers on their NH3 affinity, which leads to stimulus-tailoring properties such as gate-controlled porosity by dynamic linker flipping, disorder, and structural rigidity. Despite their structural similarities, we show for the first time the dramatic alteration of NH3 adsorption profiles when the phenyl groups are replaced by the bipyridine in the organic linker. These molecular controls stem from controlling the degree of H-bonding networks/distortions between the bipyridine scaffold and the adsorbed NH3 without significant change in pore volume and unit cell parameters. Temperature-dependent neutron diffraction also reveals the NH3-induced rotational motions of the organic linkers. We also demonstrate that the degree of structural flexibility of the functional linkers can critically be affected by the type and quantity of the small guest molecules. This strikes a delicate control in material properties at the molecular level.
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Feb 2021
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Ed
Daniel
,
Mirko M.
Maksimainen
,
Neil
Smith
,
Ville
Ratas
,
Ekaterina
Biterova
,
Sudarshan N.
Murthy
,
M. Tanvir
Rahman
,
Tiila-riikka
Kiema
,
Shruthi
Sridhar
,
Gabriele
Cordara
,
Subhadra
Dalwani
,
Rajaram
Venkatesan
,
Jaime
Prilusky
,
Orly
Dym
,
Lari
Lehtio
,
M. Kristian
Koski
,
Alun W.
Ashton
,
Joel L.
Sussman
,
Rikkert K.
Wierenga
Open Access
Abstract: The web-based IceBear software is a versatile tool to monitor the results of crystallization experiments and is designed to facilitate supervisor and student communications. It also records and tracks all relevant information from crystallization setup to PDB deposition in protein crystallography projects. Fully automated data collection is now possible at several synchrotrons, which means that the number of samples tested at the synchrotron is currently increasing rapidly. Therefore, the protein crystallography research communities at the University of Oulu, Weizmann Institute of Science and Diamond Light Source have joined forces to automate the uploading of sample metadata to the synchrotron. In IceBear, each crystal selected for data collection is given a unique sample name and a crystal page is generated. Subsequently, the metadata required for data collection are uploaded directly to the ISPyB synchrotron database by a shipment module, and for each sample a link to the relevant ISPyB page is stored. IceBear allows notes to be made for each sample during cryocooling treatment and during data collection, as well as in later steps of the structure determination. Protocols are also available to aid the recycling of pins, pucks and dewars when the dewar returns from the synchrotron. The IceBear database is organized around projects, and project members can easily access the crystallization and diffraction metadata for each sample, as well as any additional information that has been provided via the notes. The crystal page for each sample connects the crystallization, diffraction and structural information by providing links to the IceBear drop-viewer page and to the ISPyB data-collection page, as well as to the structure deposited in the Protein Data Bank.
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Feb 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Anka
Lucic
,
Philip
Hinchliffe
,
Tika R.
Malla
,
Catherine L.
Tooke
,
Jurgen
Brem
,
Karina
Calvopina
,
Christopher T.
Lohans
,
Patrick
Rabe
,
Michael A.
Mcdonough
,
Timothy
Armistead
,
Allen M.
Orville
,
James
Spencer
,
Christopher J.
Schofield
Diamond Proposal Number(s):
[17212, 23269, 18069]
Open Access
Abstract: Penems have demonstrated potential as antibacterials and β-lactamase inhibitors; however, their clinical use has been limited, especially in comparison with the structurally related carbapenems. Faropenem is an orally active antibiotic with a C2 tetrahydrofuran (THF) ring, which is resistant to hydrolysis by some β-lactamases. We report studies on the reactions of faropenem with carbapenem-hydrolysing β-lactamases, focusing on the class A serine β-lactamase KPC-2 and the metallo β-lactamases (MBLs) VIM-2 (a subclass B1 MBL) and L1 (a B3 MBL). Kinetic studies show that faropenem is a substrate for all three β-lactamases, though it is less efficiently hydrolysed by KPC-2. Crystallographic analyses on faropenem-derived complexes reveal the opening of the β-lactam ring with formation of an imine with KPC-2, VIM-2, and L1. In the cases of the KPC-2 and VIM-2 structures, the THF ring is opened to give an alkene, but with L1 the THF ring remains intact. Solution state studies, employing NMR, were performed on L1, KPC-2, VIM-2, VIM-1, NDM-1, OXA-23, OXA-10, and OXA-48. The solution results reveal, in all cases, formation of imine products in which the THF ring is opened; formation of a THF ring-closed imine product was only observed with VIM-1 and VIM-2. An enamine product with a closed THF ring was also observed in all cases, at varying levels. Combined with previous reports, the results exemplify the potential for different outcomes in the reactions of penems with MBLs and SBLs and imply further structure-activity relationship studies are worthwhile to optimise the interactions of penems with β-lactamases. They also exemplify how crystal structures of β-lactamase substrate/inhibitor complexes do not always reflect reaction outcomes in solution.
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Feb 2021
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B18-Core EXAFS
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Diamond Proposal Number(s):
[19850]
Open Access
Abstract: Hierarchically porous (HP) zeotype materials (possessing both micropores and mesopores) offer improved diffusional access to intra-framework active sites, analogous to mesoporous materials, yet retain the high selectivity of the microporous (MP) bulk. We have recently designed crystalline hierarchically porous silicoaluminophosphates (SAPOs) with enhanced mass-transport characteristics, which can lead to significant improvement in catalytic activity and catalyst lifetime. In this study, we have prepared PdAu bimetallic nanostructures supported on HP-SAPO frameworks by an incipient impregnation of metal precursors followed by H2 reduction at 300 °C, for the aerobic oxidation of benzyl alcohol to benzaldehyde. PdAu NPs supported on HP framework displayed significantly enhanced catalytic activities, when compared with their MP analogues, clearly highlighting the benefits of introducing hierarchical porosity in the SAPO support matrix.
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Feb 2021
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I11-High Resolution Powder Diffraction
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Abstract: The structure and reorientational dynamics of KB3H8 were studied by using quasielastic and inelastic neutron scattering, Raman spectroscopy, first-principles calculations, differential scanning calorimetry, and in situ synchrotron radiation powder X-ray diffraction. The results reveal the existence of a previously unknown polymorph in between the α′- and β-polymorphs. Furthermore, it was found that the [B3H8]− anion undergoes different reorientational motions in the three polymorphs α, α′, and β. In α-KB3H8, the [B3H8]− anion performs 3-fold rotations in the plane created by the three boron atoms, which changes to a 2-fold rotation around the C2 symmetry axis of the [B3H8]− anion upon transitioning to α′-KB3H8. After transitioning to β-KB3H8, the [B3H8]− anion performs 4-fold rotations in the plane created by the three boron atoms, which indicates that the local structure of β-KB3H8 deviates from the global cubic NaCl-type structure. The results also indicate that the high reorientational mobility of the [B3H8]− anion facilitates the K+ cation conductivity, since the 2-orders-of-magnitude increase in the anion reorientational mobility observed between 297 and 311 K coincides with a large increase in K+ conductivity.
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Feb 2021
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[9860]
Abstract: Osteogenesis imperfecta (OI or brittle bone disease) is a group of genetic disorders of the connective tissues caused mainly by mutations in the genes encoding collagen type I. Clinical manifestations of OI include skeletal fragility, bone deformities, and severe functional disabilities, such as hearing loss. Progressive hearing loss, usually beginning in childhood, affects approximately 70% of people with OI with more than half of the cases involving the inner ear. There is no cure for OI nor a treatment to ameliorate its corresponding hearing loss, and very little is known about the properties of OI ears. In this study, we investigate the morphology of the otic capsule and the cochlea in the inner ear of the oim mouse model of OI. High-resolution 3D images of 8-week old oim and WT inner ears were acquired using synchrotron microtomography. Volumetric morphometric measurements were conducted for the otic capsule, its intracortical canal network and osteocyte lacunae, and for the cochlear spiral ducts. Our results show that the morphology of the cochlea is preserved in the oim ears at 8 weeks of age but the otic capsule has a greater cortical thickness and altered intracortical bone porosity, with a larger number and volume density of highly branched canals in the oim otic capsule. These results portray a state of compromised bone quality in the otic capsule of the oim mice that may contribute to their hearing loss.
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Feb 2021
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I04-Macromolecular Crystallography
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Open Access
Abstract: The structures of the adducts formed upon reaction of the cytotoxic paddlewheel dirhodium complex [Rh2(μ-O2CCH3)4] with the model protein hen egg white lysozyme (HEWL) under different experimental conditions are reported. Results indicate that [Rh2(μ-O2CCH3)4] extensively reacts with HEWL:it in part breaks down, at variance with what happens in reactions with other proteins. A Rh center coordinates the side chains of Arg14 and His15. Dimeric Rh–Rh units with Rh–Rh distances between 2.3 and 2.5 Å are bound to the side chains of Asp18, Asp101, Asn93, and Lys96, while a dirhodium unit with a Rh–Rh distance of 3.2–3.4 Å binds the C-terminal carboxylate and the side chain of Lys13 at the interface between two symmetry-related molecules. An additional monometallic fragment binds the side chain of Lys33. These data, which are supported by replicated structural determinations, shed light on the reactivity of dirhodium tetracarboxylates with proteins, providing useful information for the design of new Rh-containing biomaterials with an array of potential applications in the field of catalysis or of medicinal chemistry and valuable insight into the mechanism of action of these potential anticancer agents.
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Feb 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Iain W.
Mcnae
,
James
Kinkead
,
Divya
Malik
,
Li-hsuan
Yen
,
Martin K.
Walker
,
Chris
Swain
,
Scott P.
Webster
,
Nick
Gray
,
Peter M.
Fernandes
,
Elmarie
Myburgh
,
Elizabeth
Blackburn
,
Ryan
Ritchie
,
Carol
Austin
,
Martin A.
Wear
,
Adrian J.
Highton
,
Andrew J.
Keats
,
Antonio
Vong
,
Jacqueline
Dornan
,
Jeremy C.
Mottram
,
Paul A. M.
Michels
,
Simon
Pettit
,
Malcolm D.
Walkinshaw
Diamond Proposal Number(s):
[9487, 13550]
Open Access
Abstract: The parasitic protist Trypanosoma brucei is the causative agent of Human African Trypanosomiasis, also known as sleeping sickness. The parasite enters the blood via the bite of the tsetse fly where it is wholly reliant on glycolysis for the production of ATP. Glycolytic enzymes have been regarded as challenging drug targets because of their highly conserved active sites and phosphorylated substrates. We describe the development of novel small molecule allosteric inhibitors of trypanosome phosphofructokinase (PFK) that block the glycolytic pathway resulting in very fast parasite kill times with no inhibition of human PFKs. The compounds cross the blood brain barrier and single day oral dosing cures parasitaemia in a stage 1 animal model of human African trypanosomiasis. This study demonstrates that it is possible to target glycolysis and additionally shows how differences in allosteric mechanisms may allow the development of species-specific inhibitors to tackle a range of proliferative or infectious diseases.
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Feb 2021
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I05-ARPES
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Simone M.
Kevy
,
Henriette E.
Lund
,
Laura
Wollesen
,
Kirstine J.
Dalgaard
,
Yu-te
Hsu
,
Steffen
Wiedmann
,
Marco
Bianchi
,
Ann Julie Utne
Holt
,
Davide
Curcio
,
Deepnarayan
Biswas
,
Alfred J. H.
Jones
,
Klara
Volckaert
,
Cephise
Cacho
,
Pavel
Dudin
,
Philip
Hofmann
,
Martin
Bremholm
Diamond Proposal Number(s):
[20218]
Abstract: The crystal structure, electronic structure, and transport properties of crystals with the nominal composition
Nb
0.25
Bi
2
Se
3
are investigated. X-ray diffraction reveals that the as-grown crystals display phase segregation and contain major contributions of BiSe and the superconducting misfit layer compound
(
Bi
Se
)
1.1
Nb
Se
2
. The inhomogeneous character of the samples is also reflected in the electronic structure and transport properties of different single crystals. Angle-resolved photoemission spectroscopy (ARPES) reveals an electronic structure that resembles poor-quality
Bi
2
Se
3
with an ill-defined topological surface state. High-quality topological surface states are instead observed when using a highly focused beam size, i.e., nanoARPES. While the superconducting transition temperature is found to vary between 2.5 and 3.5 K, the majority of the bulk single crystals does not exhibit a zero-resistance state suggesting filamentary superconductivity in the materials. Susceptibility measurements of the system together with the temperature dependence of the coherence length extracted from the upper critical field are consistent with conventional BCS superconductivity of a type II superconductor.
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Feb 2021
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I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[20552]
Open Access
Abstract: Most metallodrugs are prodrugs that can undergo ligand exchange and redox reactions in biological media. Here we have investigated the cellular stability of the anticancer complex [OsII[(η6‐p‐cymene)(RR/SS‐MePh‐DPEN)] [1] (MePh‐DPEN=tosyl‐diphenylethylenediamine) which catalyses the enantioselective reduction of pyruvate to lactate in cells. The introduction of a bromide tag at an unreactive site on a phenyl substituent of Ph‐DPEN allowed us to probe the fate of this ligand and Os in human cancer cells by a combination of X‐ray fluorescence (XRF) elemental mapping and inductively coupled plasma‐mass spectrometry (ICP‐MS). The BrPh‐DPEN ligand is readily displaced by reaction with endogenous thiols and translocated to the nucleus, whereas the Os fragment is exported from the cells. These data explain why the efficiency of catalysis is low, and suggests that it could be optimised by developing thiol resistant analogues. Moreover, this work also provides a new way for the delivery of ligands which are inactive when administered on their own.
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Feb 2021
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