I05-ARPES
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Edgar
Abarca Morales
,
Gesa-R.
Siemann
,
Andela
Zivanovic
,
Philip A. E.
Murgatroyd
,
Igor
Markovic
,
Brendan
Edwards
,
Chris A.
Hooley
,
Dmitry A.
Sokolov
,
Naoki
Kikugawa
,
Cephise
Cacho
,
Matthew D.
Watson
,
Timur K.
Kim
,
Clifford W.
Hicks
,
Andrew P.
Mackenzie
,
Phil D. C.
King
Diamond Proposal Number(s):
[27471, 28412]
Abstract: We report the evolution of the electronic structure at the surface of the layered perovskite
Sr
2
RuO
4
under large in-plane uniaxial compression, leading to anisotropic
B
1
g
strains of
ϵ
x
x
−
ϵ
y
y
=
−
0.9
±
0.1
%
. From angle-resolved photoemission, we show how this drives a sequence of Lifshitz transitions, reshaping the low-energy electronic structure and the rich spectrum of van Hove singularities that the surface layer of
Sr
2
RuO
4
hosts. From comparison to tight-binding modeling, we find that the strain is accommodated predominantly by bond-length changes rather than modifications of octahedral tilt and rotation angles. Our study sheds new light on the nature of structural distortions at oxide surfaces, and how targeted control of these can be used to tune density of state singularities to the Fermi level, in turn paving the way to the possible realization of rich collective states at the
Sr
2
RuO
4
surface.
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Feb 2023
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[29165]
Open Access
Abstract: Understanding the structure–property relationship and nanoscopic behaviour of ionic liquids is of utmost importance for their potential applications. Focusing these studies on sets of homobaric ionic liquids could provide important insight into the effects of specific chemical groups on the overall interaction profile, bringing researchers one step closer to succesfully designing ionic liquids which are tailor-made for specific applications. This work focuses on ionic liquids with 12 total carbons on their side chains, studying both their bulk physical properties (such as densities and viscosities) and their nanostructuring. The results reveal that by keeping the total number of carbons constant, but arranging them differently around the imidazolium ring, either in a linear or in a branched-chain formation, can result in compounds with quite distinct properties. Some of those (such as diffusivity) appear to be more sensitive to symmetry variations, while others (such as density) are not significantly affected. X-ray scattering is used in order to get a clearer understanding of the nanostructuring of the studied compounds and to investigate to what extent the observed macroscopic properties are directly linked to the nanoscale ordering.
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Feb 2023
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B07-C-Versatile Soft X-ray beamline: Ambient Pressure XPS and NEXAFS
B18-Core EXAFS
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Huihuang
Fang
,
Simson
Wu
,
Tugce
Ayvali
,
Jianwei
Zheng
,
Joshua
Fellowes
,
Ping-Luen
Ho
,
Kwan Chee
Leung
,
Alexander
Large
,
Georg
Held
,
Ryuichi
Kato
,
Kazu
Suenaga
,
Yves Ira A.
Reyes
,
Ho Viet
Thang
,
Hsin-Yi Tiffany
Chen
,
Shik Chi Edman
Tsang
Open Access
Abstract: Ammonia is regarded as an energy vector for hydrogen storage, transport and utilization, which links to usage of renewable energies. However, efficient catalysts for ammonia decomposition and their underlying mechanism yet remain obscure. Here we report that atomically-dispersed Ru atoms on MgO support on its polar (111) facets {denoted as MgO(111)} show the highest rate of ammonia decomposition, as far as we are aware, than all catalysts reported in literature due to the strong metal-support interaction and efficient surface coupling reaction. We have carefully investigated the loading effect of Ru from atomic form to cluster/nanoparticle on MgO(111). Progressive increase of surface Ru concentration, correlated with increase in specific activity per metal site, clearly indicates synergistic metal sites in close proximity, akin to those bimetallic N2 complexes in solution are required for the stepwise dehydrogenation of ammonia to N2/H2, as also supported by DFT modelling. Whereas, beyond surface doping, the specific activity drops substantially upon the formation of Ru cluster/nanoparticle, which challenges the classical view of allegorically higher activity of coordinated Ru atoms in cluster form (B5 sites) than isolated sites.
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Feb 2023
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Open Access
Abstract: Present understanding of protein structure dynamics trails behind that of static structures. A torsion-angle based approach, called representation of protein entities (RoPE), derives an interpretable conformational space which correlates with data collection temperature, resolution and reaction coordinate. For more complex systems, atomic coordinates fail to separate functional conformational states, which are still preserved by torsion angle-derived space. This indicates that torsion angles are often a more sensitive and biologically relevant descriptor for protein conformational dynamics than atomic coordinates.
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Feb 2023
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Krios IV-Titan Krios IV at Diamond
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Yang
Yang
,
Holly J.
Garringer
,
Yang
Shi
,
Sofia
Lovestam
,
Sew
Peak-Chew
,
Xianjun
Zhang
,
Abhay
Kotecha
,
Mehtap
Bacioglu
,
Atsuo
Koto
,
Masaki
Takao
,
Maria Grazia
Spillantini
,
Bernardino
Ghetti
,
Ruben
Vidal
,
Alexey G.
Murzin
,
Sjors H. W.
Scheres
,
Michel
Goedert
Diamond Proposal Number(s):
[23268]
Open Access
Abstract: A 21-nucleotide duplication in one allele of SNCA was identified in a previously described disease with abundant α-synuclein inclusions that we now call juvenile-onset synucleinopathy (JOS). This mutation translates into the insertion of MAAAEKT after residue 22 of α-synuclein, resulting in a protein of 147 amino acids. Both wild-type and mutant proteins were present in sarkosyl-insoluble material that was extracted from frontal cortex of the individual with JOS and examined by electron cryo-microscopy. The structures of JOS filaments, comprising either a single protofilament, or a pair of protofilaments, revealed a new α-synuclein fold that differs from the folds of Lewy body diseases and multiple system atrophy (MSA). The JOS fold consists of a compact core, the sequence of which (residues 36–100 of wild-type α-synuclein) is unaffected by the mutation, and two disconnected density islands (A and B) of mixed sequences. There is a non-proteinaceous cofactor bound between the core and island A. The JOS fold resembles the common substructure of MSA Type I and Type II dimeric filaments, with its core segment approximating the C-terminal body of MSA protofilaments B and its islands mimicking the N-terminal arm of MSA protofilaments A. The partial similarity of JOS and MSA folds extends to the locations of their cofactor-binding sites. In vitro assembly of recombinant wild-type α-synuclein, its insertion mutant and their mixture yielded structures that were distinct from those of JOS filaments. Our findings provide insight into a possible mechanism of JOS fibrillation in which mutant α-synuclein of 147 amino acids forms a nucleus with the JOS fold, around which wild-type and mutant proteins assemble during elongation.
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Feb 2023
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E01-JEM ARM 200CF
E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[31082]
Abstract: Despite extensive efforts to develop high-performance H2 evolution catalysts, this remains a major challenge. Here, we demonstrate the use of Cd/Pt precursor solutions for significant photocatalytic H2 production (154.7 mmol g-1 h-1), removing the need for a pre-synthesized photocatalyst. In addition, we also report simultaneous in-situ synthesis of Pt single-atoms anchored CdS nanoparticles (PtSA-CdSIS) during photoirradiation. The highly dispersed in-situ incorporation of extensive Pt single atoms on CdSIS enables the enhancement of active sites and suppresses charge recombination, which results in exceptionally high solar-to-hydrogen conversion efficiency of ~1% and an apparent quantum yield of over 91% (365 nm) for H2 production. Our work not only provides a promising strategy for maximising H2 production efficiency but also provides a green process for H2 production and the synthesis of highly photoactive PtSA-CdSIS nanoparticles.
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Feb 2023
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Abstract: Over the past few years, numerous advances have been made in X-ray imaging technology. X-ray imaging plays an important role in the non-destructive exploration of the internal structures of objects for research, medical and industrial applications. When X-rays are used in computed tomography (CT), the differences in density of various components of a specimen result in different degrees of absorption of the X-rays and are ultimately responsible for image formation and image contrast. However, in some situations, this contrast is not sufficient for the sample, e.g. in the case of fossils embedded in rock, there are often situations where the fossil and rock have similar grey values. Poor contrast causes the loss of valuable detail and makes further image processing steps such as segmentation challenging. There is a continuous need to improve and develop new image acquisition techniques with the goal to improve the quality of the obtained CT data. Computed tomography techniques have been extended to phase contrast imaging in recent years using the principle of Talbot-Lau interferometers. Initially performed in synchrotron facilities the method was extended to work with incoherent polychromatic X-ray sources by introducing a source grating into the setup and therefore reducing the requirements on the spatial coherence of the source significantly. In this work, we report on the experimental characterization of gold absorption gratings used in such a laboratory-based cone-beam phase contrast setup. The gold gratings are characterized by Angular X-ray Transmission using different laboratory X-ray sources, providing insights not only into the grating feature sizes but also validating the suitability of the available laboratory source for phase contrast imaging. This work is the first step in a project implementing phase contrast X-ray imaging in laboratory setups in South Africa.
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Feb 2023
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[29710]
Open Access
Abstract: The origin of jaws and teeth remains contentious in vertebrate evolution. ‘Placoderms’ (Silurian-Devonian armoured jawed fishes) are central to debates on the origins of these anatomical structures. ‘Acanthothoracids’ are generally considered the most primitive ‘placoderms’. However, they are so far known mainly from disarticulated skeletal elements that are typically incomplete. The structure of the jaws—particularly the jaw hinge—is poorly known, leaving open questions about their jaw function and comparison with other placoderms and modern gnathostomes. Here we describe a near-complete ‘acanthothoracid’ upper jaw, allowing us to reconstruct the likely orientation and angle of the bite and compare its morphology with that of other known ‘placoderm’ groups. We clarify that the bite position is located on the upper jaw cartilage rather than on the dermal cheek and thus show that there is a highly conserved bite morphology among most groups of ‘placoderms’, regardless of their overall cranial geometry. Incorporation of the dermal skeleton appears to provide a sound biomechanical basis for jaw origins. It appears that ‘acanthothoracid’ dentitions were fundamentally similar in location to that of arthrodire ‘placoderms’, rather than resembling bony fishes. Irrespective of current phylogenetic uncertainty, the new data here resolve the likely general condition for ‘placoderms’ as a whole, and as such, ancestral morphology of known jawed vertebrates.
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Feb 2023
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VMXm-Versatile Macromolecular Crystallography microfocus
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Lennart
Brewitz
,
Leo
Dumjahn
,
Yilin
Zhao
,
C. David
Owen
,
Stephen M.
Laidlaw
,
Tika R.
Malla
,
Dung
Nguyen
,
Petra
Lukacik
,
Eidarus
Salah
,
Adam D.
Crawshaw
,
Anna J.
Warren
,
Jose
Trincao
,
Claire
Strain-Damerell
,
Miles W.
Carroll
,
Martin A.
Walsh
,
Christopher J.
Schofield
Diamond Proposal Number(s):
[27088]
Open Access
Abstract: Nirmatrelvir (PF-07321332) is a nitrile-bearing small-molecule inhibitor that, in combination with ritonavir, is used to treat infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Nirmatrelvir interrupts the viral life cycle by inhibiting the SARS-CoV-2 main protease (Mpro), which is essential for processing viral polyproteins into functional nonstructural proteins. We report studies which reveal that derivatives of nirmatrelvir and other Mpro inhibitors with a nonactivated terminal alkyne group positioned similarly to the electrophilic nitrile of nirmatrelvir can efficiently inhibit isolated Mpro and SARS-CoV-2 replication in cells. Mass spectrometric and crystallographic evidence shows that the alkyne derivatives inhibit Mpro by apparent irreversible covalent reactions with the active site cysteine (Cys145), while the analogous nitriles react reversibly. The results highlight the potential for irreversible covalent inhibition of Mpro and other nucleophilic cysteine proteases by alkynes, which, in contrast to nitriles, can be functionalized at their terminal position to optimize inhibition and selectivity, as well as pharmacodynamic and pharmacokinetic properties.
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Feb 2023
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E01-JEM ARM 200CF
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Open Access
Abstract: An understanding the organic matter (OM) in primitive interplanetary materials can provide us with important constraints on both the early solar system carbon cycle and incipient prebiotic synthesis before the origin of life. As a window to the past, primitive chondrites preserve the most pristine record of parent body, nebular and interstellar components and the occurrence of OM in them has been shown in both soluble (SOM) (1) and insoluble (IOM) (2) form. Total organic carbon (TOC) abundance reaches ~3-4 wt% in the most primitive carbonaceous chondrite (CCs) (3), such as Ivuna-type chondrites (CIs) – thus making them highly desirable for the OM studies, and relevant to the study of Asteroid 162173 Ryugu samples from the Hayabusa-2 mission.
A combination of both SOM and IOM analysis of organic bulk meteorite separates together with in-situ analysis of OM have provided a comprehensive account of chondritic OM (4). In the case of in-situ analysis, the combination of both scanning (SEM) and transmission electron microscopy (TEM) together with soft X-Ray scanning transmission microscopy (STXM) have shown the presence of micron to submicron distinctive organic particles (OPs) (5). Carbon K-edge X-ray absorption near edge structure (XANES) has shown the aromatic-carbonyl-carboxyl chemical nature of these organic particles (5). In addition, aromatic-poorer and carboxylic-richer diffuse OM (6) within both amorphous and phyllosilicate occurs as well.
As observation techniques are getting better, aberration corrected TEM coupled with electron energy loss spectroscopy (EELS) might provide the same results as carbon XANES, but with higher image magnification, rapid data acquisition and better accessibility. In this context, we present the results of a comparative carbon K-edge XANES and EELS study of CI meteorite Ivuna. An approximately 100 nm lamella of the Ivuna meteorite was prepared using focused ion beam (FIB)-SEM with the Helios 5 Hydra DualBeam (CEITEC, Masaryk University, Czechia) and analysed by TEM-EELS with the JEOL ARM200CF (ePSIC, Diamond Light Source, UK) and STXM-XANES at Beamline BL19A of the KEK Photon Factory, Japan. We observed that (I) XANES on samples that did not experience TEM-EELS are in agreement with the previous studies of aromatic-carbonyl-carboxylic macromolecular OPs and IOM, while (II) the TEM-EELS of OPs show aromatic-carbonyl functional chemistry but with amorphous carbon convoluting the carboxylic peak, and aromatic-poor spectra with a sharp carbonate peak in diffuse OM. The difference between XANES and EELS particularly in the diffuse OM can be interpreted by electron-beam damage. Thickness and e-beam damage leads to amorphous C formation in the OPs. In the case of more labile OM in the phyllosilicate, its change by heating and oxidation is expected.
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Feb 2023
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