B21-High Throughput SAXS
DL-SAXS-Offline SAXS and Sample Environment Development
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Diamond Proposal Number(s):
[27756, 29720]
Open Access
Abstract: Atherosclerosis is often described as a single disease entity; however, the morphology of each plaque is unique to the individual. The field currently lacks a technique that can discriminate stable from unstable plaques, to identify those at risk of a thromboembolic event. Small- and wide-angle X-ray scattering (SAXS/WAXS) holds the potential to be able to identify key materials present in a plaque, such as cholesterol species, collagen, low-density lipoproteins (LDLs), and hydroxyapatite. Protocols have been established for the preparation of excised human atherosclerotic tissue that are investigated herein. This includes the fixing, sectioning, and substrate selection of the sample. Through several sample preparation methods, vast improvements have been made to sample-to-noise ratio and background subtraction.
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Apr 2023
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[20339]
Open Access
Abstract: Industries transporting CO2 gas-saturated fluids have infrastructures made of carbon steel. This is a good material with great mechanical properties but prone to corrosion and potential failure. Corrosion in sweet environments involves the formation of FeCO3 as a corrosion film, which is recognized to play a protective role under certain conditions. This work on the dissolution of corrosion films in sweet environments, under acidic and undersaturated conditions, demonstrates that the effects on the integrity of steel are far more significant than the damage observed on the surface of the corrosion film. Our results prove that dissolution of FeCO3 involved the presence of an amorphous phase, the intermediate formation of FeCl2 or FeCl+, and the presence of a phase with short distance atom–atom correlations. The amorphous phase was identified as a mixture of retained γ-Fe and Fe3C. Partially broken α-Fe and Fe3C structures were identified to prove the damage on the material, confirming the interface zone without evident damage on the corrosion film. Dissolution affected both the α-Fe and FeCO3, with the lattice [102̅] from the FeCO3 crystalline structure being the fastest to dissolve. The damage of steel at the molecular scale was evident at the macroscale with pit depths of up to 250 μm. The impact on the integrity of steel can be, therefore, more drastic than frequently reported in industrial operations of CO2 transport industries that use cleaning procedures (e.g., acid treatment, pigging) as part of their operational activities.
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Feb 2023
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[28659]
Open Access
Abstract: Analogues of benzene-1,3,5-tricarboxamide bearing combinations of different alkyl chains (dodecyl to octadecyl) and ester-linked PEG (polyethylene glycol) chains are shown to self-assemble into either micelles or nanotapes in aqueous solution, depending on the architecture (number of alkyl vs PEG chains). The cytotoxicity to cells is selectively greater for breast cancer cells than fibroblast controls in a dose-dependent manner. The compounds show strong stability, retaining their self-assembled structures at low pH (relevant to acidic tumor conditions) and in buffer and cell culture media.
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Dec 2022
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I09-Surface and Interface Structural Analysis
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Diamond Proposal Number(s):
[23159, 26551]
Open Access
Abstract: The pursuit of new and better battery materials has given rise to numerous studies of the possibilities to use two-dimensional negative electrode materials, such as MXenes, in lithium-ion batteries. Nevertheless, both the origin of the capacity and the reasons for significant variations in the capacity seen for different MXene electrodes still remain unclear, even for the most studied MXene: Ti3C2Tx. Herein, freestanding Ti3C2Tx MXene films, composed only of Ti3C2Tx MXene flakes, are studied as additive-free negative lithium-ion battery electrodes, employing lithium metal half-cells and a combination of chronopotentiometry, cyclic voltammetry, X-ray photoelectron spectroscopy, hard X-ray photoelectron spectroscopy, and X-ray absorption spectroscopy experiments. The aim of this study is to identify the redox reactions responsible for the observed reversible and irreversible capacities of Ti3C2Tx-based lithium-ion batteries as well as the reasons for the significant capacity variation seen in the literature. The results demonstrate that the reversible capacity mainly stems from redox reactions involving the Tx–Ti–C titanium species situated on the surfaces of the MXene flakes, whereas the Ti–C titanium present in the core of the flakes remains electro-inactive. While a relatively low reversible capacity is obtained for electrodes composed of pristine Ti3C2Tx MXene flakes, significantly higher capacities are seen after having exposed the flakes to water and air prior to the manufacturing of the electrodes. This is ascribed to a change in the titanium oxidation state at the surfaces of the MXene flakes, resulting in increased concentrations of Ti(II), Ti(III), and Ti(IV) in the Tx–Ti–C surface species. The significant irreversible capacity seen in the first cycles is mainly attributed to the presence of residual water in the Ti3C2Tx electrodes. As the capacities of Ti3C2Tx MXene negative electrodes depend on the concentration of Ti(II), Ti(III), and Ti(IV) in the Tx–Ti–C surface species and the water content, different capacities can be expected when using different manufacturing, pretreatment, and drying procedures.
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Nov 2022
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Luca
Mologni
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Sébastien
Tardy
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Alfonso
Zambon
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Alexandre
Orsato
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William H.
Bisson
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Monica
Ceccon
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Michela
Viltadi
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Joseph
D’attoma
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Sara
Pannilunghi
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Vito
Vece
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Jerome
Bertho
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Peter
Goekjian
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Leonardo
Scapozza
,
Carlo
Gambacorti-Passerini
Open Access
Abstract: The anaplastic lymphoma kinase (ALK) is abnormally expressed and hyperactivated in a number of tumors and represents an ideal therapeutic target. Despite excellent clinical responses to ALK inhibition, drug resistance still represents an issue and novel compounds that overcome drug-resistant mutants are needed. We designed, synthesized, and evaluated a large series of azacarbazole inhibitors. Several lead compounds endowed with submicromolar potency were identified. Compound 149 showed selective inhibition of native and mutant drug-refractory ALK kinase in vitro as well as in a Ba/F3 model and in human ALK+ lymphoma cells. The three-dimensional (3D) structure of a 149:ALK-KD cocrystal is reported, showing extensive interaction through the hinge region and the catalytic lysine 1150.
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May 2022
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I09-Surface and Interface Structural Analysis
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Diamond Proposal Number(s):
[13947]
Open Access
Abstract: The adsorption structure of truxenone on Cu(111) was determined quantitatively using normal-incidence X-ray standing waves. The truxenone molecule was found to chemisorb on the surface, with all adsorption heights of the dominant species on the surface less than ∼2.5 Å. The phenyl backbone of the molecule adsorbs mostly parallel to the underlying surface, with an adsorption height of 2.32 ± 0.08 Å. The C atoms bound to the carbonyl groups are located closer to the surface at 2.15 ± 0.10 Å, a similar adsorption height to that of the chemisorbed O species; however, these O species were found to adsorb at two different adsorption heights, 1.96 ± 0.08 and 2.15 ± 0.06 Å, at a ratio of 1:2, suggesting that on average, one O atom per adsorbed truxenone molecule interacts more strongly with the surface. The adsorption geometry determined herein is an important benchmark for future theoretical calculations concerning both the interaction with solid surfaces and the electronic properties of a molecule with electron-accepting properties for applications in organic electronic devices.
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Dec 2021
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I02-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Szabolcs
Sipos
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Balázs
Bálint
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Zoltán B.
Szabó
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Levente
Ondi
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Márton
Csékei
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Zoltán
Szlávik
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Ágnes
Proszenyák
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James B.
Murray
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James
Davidson
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Ijen
Chen
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Pawel
Dokurno
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Allan E.
Surgenor
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Christopher
Pedder
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Roderick E.
Hubbard
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Ana-Leticia
Maragno
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Maia
Chanrion
,
Frederic
Colland
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Olivier
Geneste
,
András
Kotschy
Diamond Proposal Number(s):
[1857]
Open Access
Abstract: Following the identification of thieno[2,3-d]pyrimidine-based selective and potent inhibitors of MCL-1, we explored the effect of core swapping at different levels of advancement. During hit-to-lead optimization, X-ray-guided S-N replacement in the core provided a new vector, whose exploration led to the opening of the so-called deep-S2 pocket of MCL-1. Unfortunately, the occupation of this region led to a plateau in affinity and had to be abandoned. As the project approached selection of a clinical candidate, a series of core swap analogues were also prepared. The affinity and cellular activity of these compounds showed a significant dependence on the core structure. In certain cases, we also observed an increased and accelerated epimerization of the atropoisomers. The most potent core replacement analogues showed considerable in vivo PD response. One compound was progressed into efficacy studies and inhibited tumor growth.
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Aug 2021
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B18-Core EXAFS
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Diamond Proposal Number(s):
[9949]
Open Access
Abstract: The formation of silver and Au@Ag core@shell nanoparticles via reduction of AgNO3 by trisodium citrate was followed using in situ X-ray absorption near-edge structure (XANES) spectroscopy and time-resolved UV–visible (UV–vis) spectroscopy. The XANES data were analyzed through linear combination fitting, and the reaction kinetics were found to be consistent with first-order behavior with respect to silver cations. For the Au@Ag nanoparticles, the UV–vis data of a lab-scale reaction showed a gradual shift in dominance between the gold- and silver-localized surface plasmon absorbance bands. Notably, throughout much of the reaction, distinct gold and silver contributions to the UV–vis spectra were observed; however, in the final product, the contributions were not distinct.
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Jun 2020
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I03-Macromolecular Crystallography
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Jie
Yang
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Vladimir O.
Talibov
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Stefan
Peintner
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Claire
Rhee
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Vasanthanathan
Poongavanam
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Matthis
Geitmann
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Matteo Rossi
Sebastiano
,
Bernd
Simon
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Janosch
Hennig
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Doreen
Dobritzsch
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U. Helena
Danielson
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Jan
Kihlberg
Diamond Proposal Number(s):
[15868]
Open Access
Abstract: Lysine-specific demethylase 1 (LSD1) is an epigenetic enzyme which regulates the methylation of Lys4 of histone 3 (H3) and is overexpressed in certain cancers. We used structures of H3 substrate analogues bound to LSD1 to design macrocyclic peptide inhibitors of LSD1. A linear, Lys4 to Met-substituted, 11-mer (4) was identified as the shortest peptide distinctly interacting with LSD1. It was evolved into macrocycle 31, which was >40 fold more potent (Ki = 2.3 μM) than 4. Linear and macrocyclic peptides exhibited unexpected differences in structure–activity relationships for interactions with LSD1, indicating that they bind LSD1 differently. This was confirmed by the crystal structure of 31 in complex with LSD1-CoREST1, which revealed a novel binding mode at the outer rim of the LSD1 active site and without a direct interaction with FAD. NMR spectroscopy of 31 suggests that macrocyclization restricts its solution ensemble to conformations that include the one in the crystalline complex. Our results provide a solid basis for the design of optimized reversible LSD1 inhibitors.
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Feb 2020
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[8034, 20210]
Open Access
Abstract: The eye lens is mainly composed of the highly ordered water-soluble (WS) proteins named crystallins. The aggregation and insolubilization of these proteins lead to progressive lens opacification until cataract onset. Although this is a well-known disease, the mechanism of eye lens protein aggregation is not well understood; however, one of the recognized causes of proteins modification is related to the exposure to UV light. For this reason, the spectroscopic properties of WS lens proteins and their stability to UV irradiation have been evaluated by different biophysical methods including synchrotron radiation circular dichroism, fluorescence, and circular dichroism spectroscopies. Moreover, dynamic light scattering, gel electrophoresis, transmission electron microscopy, and protein digestion followed by tandem LC–MS/MS analysis were used to study the morphological and structural changes in protein aggregates induced by exposure to UV light. Our results clearly indicated that the exposure to UV radiation modified the protein conformation, inducing a loss of ordered structure and aggregation. Furthermore, we confirmed that these changes were attributable to the generation of reactive oxygen species due to the irradiation of the protein sample. This approach, involving the photodenaturation of proteins, provides a benchmark in high-throughput screening of small molecules suitable to prevent protein denaturation and aggregation.
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Feb 2020
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