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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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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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[20431, 22317]
Abstract: Electron ptychography is a 4-D STEM phase-contrast imaging technique with applications to light-element and beam-sensitive materials. Although the electron dose (electrons incident per unit area on the sample) is the primary figure of merit for imaging beam-sensitive materials, it is also necessary to consider the contrast transfer properties of the imaging technique. Here, we explore the contrast transfer properties of electron ptychography. The contrast transfer of focused-probe, non-iterative electron ptychography using the single-side-band (SSB) method is demonstrated experimentally. The band-pass nature of the phase-contrast transfer function (PCTF) for SSB ptychography places strict limitations on the probe convergence semi-angles required to resolve specific sample features with high contrast. The PCTF of the extended ptychographic iterative engine (ePIE) is broader than that for SSB ptychography, although when both high and low spatial frequencies are transferred, band-pass filtering is required to remove image artefacts. Normalisation of the transfer function with respect to the noise level shows that the transfer window is increased while avoiding noise amplification. Avoiding algorithms containing deconvolution steps may also increase the dose-efficiency of ptychographic phase reconstructions.
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Feb 2021
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I20-EDE-Energy Dispersive EXAFS (EDE)
I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[17574]
Open Access
Abstract: Deep eutectic solvents (DES) and their hydrated mixtures are used for solvothermal routes towards greener functional nanomaterials. Here we present the first static structural and in situ studies of the formation of iron oxide (hematite) nanoparticles in a DES of choline chloride[thin space (1/6-em)]:[thin space (1/6-em)]urea where xurea = 0.67 (aka. reline) as an exemplar solvothermal reaction, and observe the effects of water on the reaction. The initial speciation of Fe3+ in DES solutions was measured using extended X-ray absorption fine structure (EXAFS), while the atomistic structure of the mixture was resolved from neutron and X-ray diffraction and empirical potential structure refinement (EPSR) modelling. The reaction was monitored using in situ small-angle neutron scattering (SANS), to determine mesoscale changes, and EXAFS, to determine local rearrangements of order around iron ions. It is shown that iron salts form an octahedral [Fe(L)3(Cl)3] complex where (L) represents various O-containing ligands. Solubilised Fe3+ induced subtle structural rearrangements in the DES due to abstraction of chloride into complexes and distortion of H-bonding around complexes. EXAFS suggests the complex forms [–O–Fe–O–] oligomers by reaction with the products of thermal hydrolysis of urea, and is thus pseudo-zero-order in iron. In the hydrated DES, the reaction, nucleation and growth proceeds rapidly, whereas in the pure DES, the reaction initially proceeds quickly, but suddenly slows after 5000 s. In situ SANS and static small-angle X-ray scattering (SAXS) experiments reveal that nanoparticles spontaneously nucleate after 5000 s of reaction time in the pure DES before slow growth. Contrast effects observed in SANS measurements suggest that hydrated DES preferentially form 1D particle morphologies because of choline selectively capping surface crystal facets to direct growth along certain axes, whereas capping is restricted by the solvent structure in the pure DES.
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Jan 2021
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[23269]
Abstract: The acyl carrier protein (ACP) is an indispensable component of both fatty acid and polyketide synthases and is primarily responsible for delivering acyl intermediates to enzymatic partners. At present, increasing numbers of multidomain ACPs have been discovered with roles in molecular recognition of trans-acting enzymatic partners as well as increasing metabolic flux. Further structural information is required to provide insight into their function, yet to date, the only high-resolution structure of this class to be determined is that of the doublet ACP (two continuous ACP domains) from mupirocin synthase. Here we report the solution nuclear magnetic resonance (NMR) structure of the doublet ACP domains from PigH (PigH ACP1-ACP2), which is an enzyme that catalyzes the formation of the bipyrrolic intermediate of prodigiosin, a potent anticancer compound with a variety of biological activities. The PigH ACP1-ACP2 structure shows each ACP domain consists of three conserved helices connected by a linker that is partially restricted by interactions with the ACP1 domain. Analysis of the holo (4′-phosphopantetheine, 4′-PP) form of PigH ACP1-ACP2 by NMR revealed conformational exchange found predominantly in the ACP2 domain reflecting the inherent plasticity of this ACP. Furthermore, ensemble models obtained from SAXS data reveal two distinct conformers, bent and extended, of both apo (unmodified) and holo PigH ACP1-ACP2 mediated by the central linker. The bent conformer appears to be a result of linker–ACP1 interactions detected by NMR and might be important for intradomain communication during the biosynthesis. These results provide new insights into the behavior of the interdomain linker of multiple ACP domains that may modulate protein–protein interactions. This is likely to become an increasingly important consideration for metabolic engineering in prodigiosin and other related biosynthetic pathways.
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Jan 2021
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B18-Core EXAFS
I20-Scanning-X-ray spectroscopy (XAS/XES)
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V.
Celorrio
,
D. J.
Fermin
,
L.
Calvillo
,
A.
Leach
,
H.
Huang
,
G.
Granozzi
,
J. A.
Alonso
,
A.
Aguadero
,
R. M.
Pinacca
,
A. E.
Russell
,
D.
Tiwari
Diamond Proposal Number(s):
[10306, 15151, 16479]
Abstract: Oxygen electrocatalysis at transition metal oxides is one of the key challenges underpinning electrochemical energy conversion systems, involving a delicate interplay of the bulk electronic structure and surface coordination of the active sites. In this work, we investigate for the first time the structure–activity relationship of A2RuMnO7 (A = Dy3+, Ho3+, and Er3+) nanoparticles, demonstrating how orbital mixing of Ru, Mn, and O promotes high density of states at the appropriate energy range for oxygen electrocatalysis. The bulk structure and surface composition of these multicomponent pyrochlores are investigated by high-resolution transmission electron microscopy, X-ray diffraction, X-ray absorption spectroscopy, X-ray emission spectroscopy (XES), and X-ray photoemission spectroscopy (XPS). The materials exhibit high phase purity (cubic fcc with a space group Fd3̅m) in which variations in M–O bonds length are less than 1% upon replacing the A-site lanthanide. XES and XPS show that the mean oxidation state at the Mn-site as well as the nanoparticle surface composition was slightly affected by the lanthanide. The pyrochlore nanoparticles are significantly more active than the binary RuO2 and MnO2 toward the 4-electron oxygen reduction reaction in alkaline solutions. Interestingly, normalization of kinetic parameters by the number density of electroactive sites concludes that Dy2RuMnO7 shows twice higher activity than benchmark materials such as LaMnO3. Analysis of the electrochemical profiles supported by density functional theory calculations reveals that the origin of the enhanced catalytic activity is linked to the mixing of Ru and Mn d-orbitals and O p-orbitals at the conduction band which strongly overlap with the formal redox energy of O2 in solution. The activity enhancement strongly manifests in the case of Dy2RuMnO7 where the Ru/Mn ratio is closer to 1 in comparison with the Ho3+ and Er3+ analogs. These electronic effects are discussed in the context of the Gerischer formalism for electron transfer at the semiconductor/electrolyte junctions.
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Jan 2021
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Nathan David
Wright
,
Patrick
Collins
,
Lizbe
Koekemoer
,
Tobias
Krojer
,
Romain
Talon
,
Elliot
Nelson
,
Mingda
Ye
,
Radoslaw
Nowak
,
Joseph
Newman
,
Jia Tsing
Ng
,
Nick
Mitrovic
,
Helton
Wiggers
,
Frank
Von Delft
Open Access
Abstract: Despite the tremendous success of X-ray cryo-crystallography in recent decades, the transfer of crystals from the drops in which they are grown to diffractometer sample mounts remains a manual process in almost all laboratories. Here, the Shifter, a motorized, interactive microscope stage that transforms the entire crystal-mounting workflow from a rate-limiting manual activity to a controllable, high-throughput semi-automated process, is described. By combining the visual acuity and fine motor skills of humans with targeted hardware and software automation, it was possible to transform the speed and robustness of crystal mounting. Control software, triggered by the operator, manoeuvres crystallization plates beneath a clear protective cover, allowing the complete removal of film seals and thereby eliminating the tedium of repetitive seal cutting. The software, either upon request or working from an imported list, controls motors to position crystal drops under a hole in the cover for human mounting at a microscope. The software automatically captures experimental annotations for uploading to the user's data repository, removing the need for manual documentation. The Shifter facilitates mounting rates of 100–240 crystals per hour in a more controlled process than manual mounting, which greatly extends the lifetime of the drops and thus allows a dramatic increase in the number of crystals retrievable from any given drop without loss of X-ray diffraction quality. In 2015, the first in a series of three Shifter devices was deployed as part of the XChem fragment-screening facility at Diamond Light Source, where they have since facilitated the mounting of over 120 000 crystals. The Shifter was engineered to have a simple design, providing a device that could be readily commercialized and widely adopted owing to its low cost. The versatile hardware design allows use beyond fragment screening and protein crystallography.
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Jan 2021
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B18-Core EXAFS
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Diamond Proposal Number(s):
[17243]
Abstract: Understanding the speciation and fate of radium during operational discharge from the offshore oil and gas industry into the marine environment is important in assessing its long term environmental impact. In the current work, 226Ra concentrations in marine sediments contaminated by produced water discharge from a site in the UK were analysed using gamma spectroscopy. Radium was present in field samples (0.1 - 0.3 Bq g-1) within International Atomic Energy Agency activity thresholds and was found to be primarily associated with micron sized radiobarite particles (≤2 μm). Experimental studies of synthetic/field produced water and seawater mixing under laboratory conditions showed that a significant proportion of radium (up to 97%) co-precipitated with barite confirming the radiobarite fate pathway. The results showed that produced water discharge into the marine environment results in the formation of radiobarite particles which incorporate a significant portion of radium and can be deposited in marine sediments.
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Jan 2021
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I03-Macromolecular Crystallography
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Samuel L.
Rose
,
Svetlana V.
Antonyuk
,
Daisuke
Sasaki
,
Keitaro
Yamashita
,
Kunio
Hirata
,
Go
Ueno
,
Hideo
Ago
,
Robert R.
Eady
,
Takehiko
Tosha
,
Masaki
Yamamoto
,
S. Samar
Hasnain
Diamond Proposal Number(s):
[15991]
Open Access
Abstract: Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK. Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br2DNiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br2DNiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated.
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Jan 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Declan A.
Gray
,
Joshua B. R.
White
,
Abraham O.
Oluwole
,
Parthasarathi
Rath
,
Amy J.
Glenwright
,
Adam
Mazur
,
Michael
Zahn
,
Arnaud
Basle
,
Carl
Morland
,
Sasha L.
Evans
,
Alan
Cartmell
,
Carol V.
Robinson
,
Sebastian
Hiller
,
Neil A.
Ranson
,
David N.
Bolam
,
Bert
Van Den Berg
Diamond Proposal Number(s):
[13587, 18598]
Open Access
Abstract: In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a “pedal bin” transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the β2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to ~2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.
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Jan 2021
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