Krios I-Titan Krios I at Diamond
Krios II-Titan Krios II at Diamond
Krios III-Titan Krios III at Diamond
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Luiza
Mendonca
,
Dapeng
Sun
,
Jiying
Ning
,
Jiwei
Liu
,
Abhay
Kotecha
,
Mateusz
Olek
,
Thomas
Frosio
,
Xiaofeng
Fu
,
Benjamin A.
Himes
,
Alex B.
Kleinpeter
,
Eric O.
Freed
,
Jing
Zhou
,
Christopher
Aiken
,
Peijun
Zhang
Diamond Proposal Number(s):
[18477, 21005, 21004]
Open Access
Abstract: Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), SP2 and p6 domains. SP1, together with the last eight residues of CA, have been hypothesized to form a six-helix bundle responsible for the higher-order multimerization of Gag necessary for HIV particle assembly. However, the structure of the complete six-helix bundle has been elusive. Here, we determined the structures of both Gag in vitro assemblies and Gag viral-like particles (VLPs) to 4.2 Å and 4.5 Å resolutions using cryo-electron tomography and subtomogram averaging by emClarity. A single amino acid mutation (T8I) in SP1 stabilizes the six-helix bundle, allowing to discern the entire CA-SP1 helix connecting to the NC domain. These structures provide a blueprint for future development of small molecule inhibitors that can lock SP1 in a stable helical conformation, interfere with virus maturation, and thus block HIV-1 infection.
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Apr 2021
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E02-JEM ARM 300CF
I15-1-X-ray Pair Distribution Function (XPDF)
I22-Small angle scattering & Diffraction
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Adam F.
Sapnik
,
Irene
Bechis
,
Sean M.
Collins
,
Duncan N.
Johnstone
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Giorgio
Divitini
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Andrew J.
Smith
,
Philip A.
Chater
,
Matthew A.
Addicoat
,
Timothy
Johnson
,
David A.
Keen
,
Kim E.
Jelfs
,
Thomas D.
Bennett
Diamond Proposal Number(s):
[20038, 24563]
Open Access
Abstract: Amorphous metal–organic frameworks (MOFs) are an emerging class of materials. However, their structural characterisation represents a significant challenge. Fe-BTC, and the commercial equivalent Basolite® F300, are MOFs with incredibly diverse catalytic ability, yet their disordered structures remain poorly understood. Here, we use advanced electron microscopy to identify a nanocomposite structure of Fe-BTC where nanocrystalline domains are embedded within an amorphous matrix, whilst synchrotron total scattering measurements reveal the extent of local atomic order within Fe-BTC. We use a polymerisation-based algorithm to generate an atomistic structure for Fe-BTC, the first example of this methodology applied to the amorphous MOF field outside the well-studied zeolitic imidazolate framework family. This demonstrates the applicability of this computational approach towards the modelling of other amorphous MOF systems with potential generality towards all MOF chemistries and connectivities. We find that the structures of Fe-BTC and Basolite® F300 can be represented by models containing a mixture of short- and medium-range order with a greater proportion of medium-range order in Basolite® F300 than in Fe-BTC. We conclude by discussing how our approach may allow for high-throughput computational discovery of functional, amorphous MOFs.
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Apr 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[18069]
Open Access
Abstract: Human prolyl‐hydroxylases (PHDs) are hypoxia‐sensing 2‐oxoglutarate (2OG) oxygenases, catalysis by which suppresses the transcription of hypoxia‐inducible factor target genes. PHD inhibition enables the treatment of anaemia/ischaemia‐related disease. The PHD inhibitor Molidustat is approved for the treatment of renal anaemia; it differs from other approved/late‐stage PHD inhibitors in lacking a glycinamide side chain. The first reported crystal structures of Molidustat and IOX4 (a brain‐penetrating derivative) complexed with PHD2 reveal how their contiguous triazole, pyrazolone and pyrimidine/pyridine rings bind at the active site. The inhibitors bind to the active‐site metal in a bidentate manner through their pyrazolone and pyrimidine nitrogens, with the triazole π‐π‐stacking with Tyr303 in the 2OG binding pocket. Comparison of the new structures with other PHD inhibitor complexes reveals differences in the conformations of Tyr303, Tyr310, and a mobile loop linking β2–β3, which are involved in dynamic substrate binding/product release.
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Apr 2021
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Open Access
Abstract: Multiply‐bonded lanthanide oxo groups are rare in coordination compounds and have not previously been reported for a surface termination of a lanthanide oxide. Here we report the observation of a Ce=O terminated ceria surface in a CeO 2 (111)‐( [[EQUATION]] x [[EQUATION]] )R30° reconstruction of ~3 nm thick ceria islands prepared on Pt(111). This is evidenced by scanning tunnelling microscopy, low energy electron diffraction and high‐resolution electron energy loss spectroscopy (HREELS) measurements in conjunction with density functional theory (DFT) calculations. A Ce=O stretching frequency of 775 cm ‐1 is observed in HREELS, compared with 766 cm ‐1 calculated by DFT. The calculations also predict that the Ce=O bond is weak, with an oxygen vacancy formation energy of 0.85 eV. This could play an important role in the facile removal of lattice oxygen from CeO 2 , accompanied by the reduction of Ce IV to Ce III , which is a key attribute of ceria‐based systems in connection with their unique catalytic properties.
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Apr 2021
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Abstract: Sulfinylamines (R‐N=S=O), monoaza analogues of sulfur dioxide, have been known for well over a century, and their reactivity as sulfur electrophiles and in Diels‐Alder reactions is well‐established. However, they have only rarely been used in organic synthesis in recent decades despite the increasing prominence of compounds containing N=S=O functionality, such as sulfoximines and sulfonimidamides. This Minireview aims to bring wider visibility to the unique chemistry enabled by this class of compounds. We focus on advances from the last 10 years, including the first examples of their use in the one‐pot syntheses of sulfoximines and sulfonimidamides. Also covered are the reactions of sulfinylamines with carbon‐centred radicals, their use for formation of heterocycles through cycloadditions, and catalytic enantioselective allylic oxidation of alkenes via a hetero‐ene reaction. These examples highlight the different reactivity modes of sulfinylamines and their underappreciated potential for forming molecules which contain high‐ or low‐valent sulfur, or even no sulfur at all.
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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):
[21780]
Abstract: Weld residual stress and fracture behavior of 316L electron beam weldments, which are of particular interest in power generation industry, were investigated in this work. Two butt‐weld joints were manufactured in stainless steel 316L plates of 6 mm and 25.4 mm thicknesses. Three complementary methods were used to measure the three orthogonal components of the residual stress in the weld coupons, and fracture tests were conducted on single edge notched bending specimens extracted from different regions of the welds and parent metals.
The residual stress measurements showed a maximum value of 450 MPa in longitudinal direction, while it was less than 150 MPa in the other two orthogonal directions, revealing that in our material, and with the chosen weld parameters, the residual stresses were biaxial. The fracture resistance of the weldment and parent material was similar, with material microstructure differences being more significant than the measured residual stresses.
The study suggests that 316L electron beam weldments are not susceptible to fracture failure due to their high ductility and ability to relieve residual stresses through gross plasticity. Electron beam welding may therefore be suggested as a reliable manufacturing technology for safety critical 316L components.
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Apr 2021
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[26447]
Open Access
Abstract: Circular Dichroism imaging in the 190–650 nm spectral region pionered at Diamond Light Source B23 beamline, has been made possible by the highly collimated microbeam generated at the beamline and has been used to study the homogeneity of the supramolecular structures of thin films of chiral materials deposited on fused quartz substrates. This facility has been expanded with the installation of a Mueller Matrix Polarimeter, MMP, coupled to the beamlight, of which a preliminary data will be discussed. In the solid state, the measurement of CD related to the supramolecular structure is hampered by the presence of circular birefringence, linear dichroism, and linear birefringence that can only be evaluated using the MMP technique. The ability to characterize the chiroptical property of thin chiral films prepared under a variety of conditions and protocols such as drop cast, spin coating, spray at different temperatures and concentrations will enable the determination of the critical parameters for reproducible, uniform and homogeneous specimen preparation, which is the sine qua non for any commercial application. This is of particular importance for optoelectronic materials, but it can also be extended to a broad variety of materials with applications from biosensors to biological tissues.
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Apr 2021
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I07-Surface & interface diffraction
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Kejun
Liu
,
Jiang
Li
,
Haoyuan
Qi
,
Mike
Hambsch
,
Jonathan
Rawle
,
Adrián Romaní
Vázquez
,
Ali Shaygan
Nia
,
Alexej
Pashkin
,
Harald
Schneider
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Mirosllav
Polozij
,
Thomas
Heine
,
Manfred
Helm
,
Stefan C. B.
Mannsfeld
,
Ute
Kaiser
,
Renhao
Dong
,
Xinliang
Feng
Diamond Proposal Number(s):
[25070]
Abstract: Two‐dimensional polymers (2DPs) are a class of atomically/molecularly thin crystalline organic 2D materials. They are intriguing candidates for the development of unprecedented organic‐inorganic 2D van der Waals heterostructures (vdWHs) with exotic physicochemical properties. In this work, we demonstrate the on‐water surface synthesis of large‐area (cm 2 ), monolayer 2D polyimide (2DPI) with 3.1‐nm lattice. Such 2DPI comprises metal‐free porphyrin and perylene units linked by imide bonds. We further achieve a scalable synthesis of 2DPI‐graphene (2DPI‐G) vdWHs via a face‐to‐face co‐assembly of graphene and 2DPI on the water surface. Remarkably, femtosecond transient absorption spectroscopy reveals an ultra‐fast interlayer charge transfer (~60 fs) in the resultant 2DPI‐G vdWH upon protonation by acid, which is equivalent to that of the fastest reports among inorganic 2D vdWHs. Such large interlayer electronic coupling is ascribed to the interlayer cation‐π interaction between 2DP and graphene. Our work opens opportunities to develop 2DP‐based vdWHs via the on‐water surface synthesis strategy and highlights the unique interface‐induced optoelectronic properties.
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Apr 2021
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Open Access
Abstract: Structural biology methods have delivered over 150 000 high-resolution structures of macromolecules, which have fundamentally altered our understanding of biology and our approach to developing new medicines. However, the description of molecular flexibility is instrinsically flawed and in almost all cases, regardless of the experimental method used for structure determination, there remains a strong overfitting bias during molecular model building and refinement. In the worst case this can lead to wholly incorrect structures and thus incorrect biological interpretations. Here, by reparametrizing the description of these complex structures in terms of bonds rather than atomic positions, and by modelling flexibility using a deterministic ensemble of structures, it is demonstrated that structures can be described using fewer parameters than in conventional refinement. The current implementation, applied to X-ray diffraction data, significantly reduces the extent of overfitting, allowing the experimental data to reveal more biological information in electron-density maps.
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Apr 2021
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I15-1-X-ray Pair Distribution Function (XPDF)
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Abstract: A method for generating the atomic pair distribution function (PDF) from powder diffraction data by the removal of instrument contributions, such as Kα2 from laboratory instruments or peak asymmetry from neutron time-of-flight data, has been implemented in the computer programs TOPAS and TOPAS-Academic. The resulting PDF is sharper, making it easier to identify structural parameters. The method fits peaks to the reciprocal-space diffraction pattern data whilst maximizing the intensity of a background function. The fit to the raw data is made `perfect' by including a peak at each data point of the diffraction pattern. Peak shapes are not changed during refinement and the process is a slight modification of the deconvolution procedure of Coelho [J. Appl. Cryst. (2018[Coelho, A. A. (2018a). J. Appl. Cryst. 51, 112-123.]), 51, 112–123]. Fitting to the raw data and subsequently using the calculated pattern as an estimation of the underlying signal reduces the effects of division by small numbers during atomic scattering factor and polarization corrections. If the peak shape is sufficiently accurate then the fitting process should also be able to determine the background if the background intensity is maximized; the resulting calculated pattern minus background should then comprise coherent scattering from the sample. Importantly, the background is not allowed complete freedom; instead, it comprises a scan of an empty capillary sample holder with a maximum of two additional parameters to vary its shape. Since this coherent scattering is a calculated pattern, it can be easily recalculated without instrumental aberrations such as capillary sample aberration or Kα2 from laboratory emission profiles. Additionally, data reduction anomalies such as incorrect integration of data from two-dimensional detectors, resulting in peak position errors, can be easily corrected. Multiplicative corrections such as polarization and atomic scattering factors are also performed. Once corrected, the pattern can be scaled to produce the total scattering structure factor F(Q) and from there the sine transform is applied to obtain the pair distribution function G(r).
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Apr 2021
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