E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[24610]
Abstract: Each 2D material has a distinct structure for its grain boundary and dislocation cores, which is dictated by both the crystal lattice geometry and the elements that participate in bonding. For the class of noble metal dichalcogenides, this has yet to be thoroughly investigated at the atomic scale. Here, we examine the atomic structure of the dislocations and grain boundaries (GBs) in two-dimensional PtSe2, using atomic-resolution annular dark field scanning transmission electron microscopy, combined with density functional theory and empirical force field calculations. The PtSe2 we study adopts the 1T phase in large-area polycrystalline films with numerous planar tilt GB distinct dislocations, including 5|7+Se and 4|4|8+Se polygons, in tilt-angle monolayer GBs, with features sharply distinguished from those in 2H-phase TMDs. On the basis of dislocation cores, the GB structures are investigated in terms of pathways of dislocation chain arrangement, dislocation core distributions in different misorientation angles, and 2D strain fields induced. Based on the Frank–Bilby equation, the deduced Burgers vector magnitude is close to the lattice constant of 1T-PtSe2, building the quantitative relationship of dislocation spacings and small GB angles. The 30° GBs are most frequently formed as a stitched interface between the armchair and zigzag lattices, constructed by a string of 5|7+Se dislocations asymmetrically with a small deviation angle. Another special angle GB, mirror twin 60° GB, is also mapped linearly by metal-condensed asymmetric or Se-rich symmetric dislocations. This report gives atomic-level insights into the GBs and dislocations in 1T-phase noble metal TMD PtSe2, which is a promising material to underpin extending properties of 2D materials by local structure engineering.
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Oct 2021
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E02-JEM ARM 300CF
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Jingjing
Liu
,
Zhichao
Gong
,
Christopher
Allen
,
Wen
Ge
,
Haisheng
Gong
,
Jiangwen
Liao
,
Jianbin
Liu
,
Kang
Huang
,
Minmin
Yan
,
Rui
Liu
,
Guanchao
He
,
Juncai
Dong
,
Gonglan
Ye
,
Huilong
Fei
Diamond Proposal Number(s):
[27260]
Abstract: Metal- and nitrogen-coordinated nanocarbons (M-N/Cs) represent the most promising nonprecious catalysts for the oxygen reduction reaction (ORR), but it remains challenging to simultaneously achieve high intrinsic activity, fast mass transport, and efficient utilization of active sites in a single catalyst. Herein, we design an Fe-N/C catalyst consisting of edge-hosted Fe-N3 sites dispersed on multiscale porous carbon frameworks (eFe-N3/PCF). The low coordination and edge effect of the Fe-N3 moieties endow eFe-N3/PCF with high intrinsic activity, while the enriched nanopores enable improved mass transport and atom utilization efficiency. When evaluated by a rotating disk electrode in the base, eFe-N3/PCF presents early-onset and half-wave potentials of 1.090 and 0.934 V versus the reversible hydrogen electrode, respectively. Furthermore, when employed as gas diffusion electrodes, eFe-N3/PCF displays excellent mass-transport efficiency that enables high-rate/power capabilities at practically high current densities. This work opens up opportunities for designing high-performance ORR electrocatalysts toward applications in diverse energy conversion and storage technologies.
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Oct 2021
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B18-Core EXAFS
E01-JEM ARM 200CF
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George F.
Tierney
,
Shahram
Alijani
,
Monik
Panchal
,
Donato
Decarolis
,
Martha
Briceno De Gutierrez
,
Khaled
Mohammed
,
June
Callison
,
Emma
Gibson
,
Paul
Thompson
,
Paul
Collier
,
Nikolaos
Dimitratos
,
E. Crina
Corbos
,
Frederic
Pelletier
,
Alberto
Villa
,
Peter
Wells
Abstract: We demonstrate a modified sol-immobilization procedure using (MeOH) x /(H 2 O) 1-x solvent mixtures to prepare Pd/TiO 2 catalysts that are able to reduce the formation of acid catalyzed products, e.g. ethers, for the hydrogenation of furfural. Transmission electron microscopy found a significant increase in polyvinyl alcohol (PVA) deposition at the metal-support interface and temperature programmed reduction found a reduced uptake of hydrogen, compared to an established Pd/TiO 2 preparation. We propose that the additional PVA hinders hydrogen spillover onto the TiO 2 support and limits the formation of Brønsted acid sites, required to produce ethers. Elsewhere, the new preparation route was able to successfully anchor colloidal Pd to the TiO 2 surface, without the need for acidification. This work demonstrates the potential for minimizing process steps as well as optimizing catalyst selectivity – both important objectives for sustainable chemistry.
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Oct 2021
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Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[18659]
Open Access
Abstract: Unregulated complement activation causes inflammatory and immunological pathologies with consequences for human disease. To prevent bystander damage during an immune response, extracellular chaperones (clusterin and vitronectin) capture and clear soluble precursors to the membrane attack complex (sMAC). However, how these chaperones block further polymerization of MAC and prevent the complex from binding target membranes remains unclear. Here, we address that question by combining cryo electron microscopy (cryoEM) and cross-linking mass spectrometry (XL-MS) to solve the structure of sMAC. Together our data reveal how clusterin recognizes and inhibits polymerizing complement proteins by binding a negatively charged surface of sMAC. Furthermore, we show that the pore-forming C9 protein is trapped in an intermediate conformation whereby only one of its two transmembrane β-hairpins has unfurled. This structure provides molecular details for immune pore formation and helps explain a complement control mechanism that has potential implications for how cell clearance pathways mediate immune homeostasis.
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Oct 2021
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Krios III-Titan Krios III at Diamond
Krios IV-Titan Krios IV at Diamond
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Diamond Proposal Number(s):
[20287]
Open Access
Abstract: RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.
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Sep 2021
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Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[14704]
Open Access
Abstract: Hexameric helicases are motor proteins that unwind double-stranded DNA (dsDNA) during DNA replication but how they are optimised for strand separation is unclear. Here we present the cryo-EM structure of the full-length E1 helicase from papillomavirus, revealing all arms of a bound DNA replication fork and their interactions with the helicase. The replication fork junction is located at the entrance to the helicase collar ring, that sits above the AAA + motor assembly. dsDNA is escorted to and the 5´ single-stranded DNA (ssDNA) away from the unwinding point by the E1 dsDNA origin binding domains. The 3´ ssDNA interacts with six spirally-arranged β-hairpins and their cyclical top-to-bottom movement pulls the ssDNA through the helicase. Pulling of the RF against the collar ring separates the base-pairs, while modelling of the conformational cycle suggest an accompanying movement of the collar ring has an auxiliary role, helping to make efficient use of ATP in duplex unwinding.
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Sep 2021
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I14-Hard X-ray Nanoprobe
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Sofiia
Kosar
,
Andrew J.
Winchester
,
Tiarnan A. S.
Doherty
,
Stuart
Macpherson
,
Christopher E.
Petoukhoff
,
Kyle
Frohna
,
Miguel
Anaya
,
Nicholas S.
Chan
,
Julien
Madéo
,
Michael K. L.
Man
,
Samuel D.
Stranks
,
Keshav M.
Dani
Diamond Proposal Number(s):
[19023]
Open Access
Abstract: With rapidly growing photoconversion efficiencies, hybrid perovskite solar cells have emerged as promising contenders for next generation, low-cost photovoltaic technologies. Yet, the presence of nanoscale defect clusters, that form during the fabrication process, remains critical to overall device operation, including efficiency and long-term stability. To successfully deploy hybrid perovskites, we must understand the nature of the different types of defects, assess their potentially varied roles in device performance, and understand how they respond to passivation strategies. Here, by correlating photoemission and synchrotron-based scanning probe X-ray microscopies, we unveil three different types of defect clusters in state-of-the-art triple cation mixed halide perovskite thin films. Incorporating ultrafast time-resolution into our photoemission measurements, we show that defect clusters originating at grain boundaries are the most detrimental for photocarrier trapping, while lead iodide defect clusters are relatively benign. Hexagonal polytype defect clusters are only mildly detrimental individually, but can have a significant impact overall if abundant in occurrence. We also show that passivating defects with oxygen in the presence of light, a previously used approach to improve efficiency, has a varied impact on the different types of defects. Even with just mild oxygen treatment, the grain boundary defects are completely healed, while the lead iodide defects begin to show signs of chemical alteration. Our findings highlight the need for multi-pronged strategies tailored to selectively address the detrimental impact of the different defect types in hybrid perovskite solar cells.
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Sep 2021
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Krios I-Titan Krios I at Diamond
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Dmitry
Ghilarov
,
Satomi
Inaba-Inoue
,
Piotr
Stepien
,
Feng
Qu
,
Elizabeth
Michalczyk
,
Zuzanna
Pakosz
,
Norimichi
Nomura
,
Satoshi
Ogasawara
,
Graham Charles
Walker
,
Sylvie
Rebuffat
,
So
Iwata
,
Jonathan
Gardiner Heddle
,
Konstantinos
Beis
Diamond Proposal Number(s):
[18659]
Open Access
Abstract: Antibiotic metabolites and antimicrobial peptides mediate competition between bacterial species. Many of them hijack inner and outer membrane proteins to enter cells. Sensitivity of enteric bacteria to multiple peptide antibiotics is controlled by the single inner membrane protein SbmA. To establish the molecular mechanism of peptide transport by SbmA and related BacA, we determined their cryo–electron microscopy structures at 3.2 and 6 Å local resolution, respectively. The structures show a previously unknown fold, defining a new class of secondary transporters named SbmA-like peptide transporters. The core domain includes conserved glutamates, which provide a pathway for proton translocation, powering transport. The structures show an outward-open conformation with a large cavity that can accommodate diverse substrates. We propose a molecular mechanism for antibacterial peptide uptake paving the way for creation of narrow-targeted therapeutics.
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Sep 2021
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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[16967]
Open Access
Abstract: Single-atom catalysts with maximum metal utilization efficiency show great potential for sustainable catalytic applications and fundamental mechanistic studies. We here provide a convenient molecular tailoring strategy based on graphitic carbon nitride as support for the rational design of single-site and dual-site single-atom catalysts. Catalysts with single Fe sites exhibit impressive oxygen reduction reaction activity with a half-wave potential of 0.89 V vs. RHE. We find that the single Ni sites are favorable to promote the key structural reconstruction into bridging Ni-O-Fe bonds in dual-site NiFe SAC. Meanwhile, the newly formed Ni-O-Fe bonds create spin channels for electron transfer, resulting in a significant improvement of the oxygen evolution reaction activity with an overpotential of 270 mV at 10 mA cm−2. We further reveal that the water oxidation reaction follows a dual-site pathway through the deprotonation of *OH at both Ni and Fe sites, leading to the formation of bridging O2 atop the Ni-O-Fe sites.
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Sep 2021
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Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[14393]
Open Access
Abstract: Dynamin belongs to the large GTPase superfamily, and mediates the fission of vesicles during endocytosis. Dynamin molecules are recruited to the neck of budding vesicles to assemble into a helical collar and to constrict the underlying membrane. Two helical forms were observed: the one-start helix in the constricted state and the two-start helix in the super-constricted state. Here we report the cryoEM structure of a super-constricted two-start dynamin 1 filament at 3.74 Å resolution. The two strands are joined by the conserved GTPase dimeric interface. In comparison with the one-start structure, a rotation around Hinge 1 is observed, essential for communicating the chemical power of the GTPase domain and the mechanical force of the Stalk and PH domain onto the underlying membrane. The Stalk interfaces are well conserved and serve as fulcrums for adapting to changing curvatures. Relative to one-start, small rotations per interface accumulate to bring a drastic change in the helical pitch. Elasticity theory rationalizes the diversity of dynamin helical symmetries and suggests corresponding functional significance.
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Sep 2021
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