I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[28806]
Open Access
Abstract: The influence of surfactant, cross-linker, and initiator on the final structure and thermoresponse of poly(N-isopropylmethacrylamide) (pNIPMAM) microgels was evaluated. The goals were to control particle size (into the nanorange) and transition temperature (across the physiologically accessible range). The concentration of the reactants used in the synthesis was varied, except for the monomer, which was kept constant. The thermoresponsive suspensions formed were characterized by dynamic light scattering, small-angle X-ray scattering, atomic force microscopy, and rheology. Increasing surfactant, sodium dodecyl sulfate content, produced smaller microgels, as expected, into the nanorange and with greater internal entanglement, but with no change in phase transition temperature (LCST), which is contrary to previous reports. Increasing cross-linker, N,N-methylenebis acrylamide, content had no impact on particle size but reduced particle deformability and, again contrary to previous reports of decreases, progressively increased the LCST from 39 to 46 °C. The unusual LCST trends were confirmed using different rheological techniques. Initiator, potassium persulfate, content was found to weakly influence the outcomes. An optimized content was identified that provides functional nanogels in the 100 nm (swollen) size range with controlled LCST, just above physiological temperature. The study contributes chemistry-derived design rules for thermally responsive colloidal particles with physiologically accessible LCST for a variety of biomedical and soft robotics applications.
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Aug 2024
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I07-Surface & interface diffraction
I09-Surface and Interface Structural Analysis
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Diamond Proposal Number(s):
[31429, 33153]
Open Access
Abstract: A structure determination of the commensurate phase formed by 7,7,8,8-tetracyano-2,3,5,6-tetrafluoroquinodimethane (F4TCNQ) absorbed on Ag(111) is reported. Initial characterization was performed using low-energy electron diffraction and synchrotron radiation photoelectron spectroscopy, with quantitative structural data being provided by normal incident X-ray standing waves (NIXSW) and surface X-ray diffraction (SXRD). NIXSW data show the F4TCNQ molecule to adopt a “twisted” conformation on the surface, previously found to be associated with metal adatom incorporation into a 2d-metal–organic framework for F4TCNQ on Au(111), Ag(100), and Cu(111). SXRD results provide direct evidence of the presence of Ag adatoms that are found to occupy near-bridge or fcc hollow sites with respect to the underlying surface, at an adsorption height of 2.69 ± 0.10 Å. The results show a consistent pattern of behavior for F4TCNQ adsorption on the (111) surfaces of Cu, Ag, and Au.
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Jul 2024
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I03-Macromolecular Crystallography
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Maša
Sterle
,
Martina
Durcik
,
Clare E. M.
Stevenson
,
Sara
Henderson
,
Petra Eva
Szili
,
Marton
Czikkely
,
David M.
Lawson
,
Anthony
Maxwell
,
Dominique
Cahard
,
Danijel
Kikelj
,
Nace
Zidar
,
Csaba
Pal
,
Lucija Peterlin
Mašič
,
Janez
Ilaš
,
Tihomir
Tomašič
,
Andrej Emanuel
Cotman
,
Anamarija
Zega
Diamond Proposal Number(s):
[18565]
Open Access
Abstract: We present a new series of 2-aminobenzothiazole-based DNA gyrase B inhibitors with promising activity against ESKAPE bacterial pathogens. Based on the binding information extracted from the cocrystal structure of DNA gyrase B inhibitor A, in complex with Escherichia coli GyrB24, we expanded the chemical space of the benzothiazole-based series to the C5 position of the benzothiazole ring. In particular, compound E showed low nanomolar inhibition of DNA gyrase (IC50 < 10 nM) and broad-spectrum antibacterial activity against pathogens belonging to the ESKAPE group, with the minimum inhibitory concentration < 0.03 μg/mL for most Gram-positive strains and 4–16 μg/mL against Gram-negative E. coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. To understand the binding mode of the synthesized inhibitors, a combination of docking calculations, molecular dynamics (MD) simulations, and MD-derived structure-based pharmacophore modeling was performed. The computational analysis has revealed that the substitution at position C5 can be used to modify the physicochemical properties and antibacterial spectrum and enhance the inhibitory potency of the compounds. Additionally, a discussion of challenges associated with the synthesis of 5-substituted 2-aminobenzothiazoles is presented.
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Jun 2023
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B21-High Throughput SAXS
labSAXS-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
,
Sébastien
Tardy
,
Alfonso
Zambon
,
Alexandre
Orsato
,
William H.
Bisson
,
Monica
Ceccon
,
Michela
Viltadi
,
Joseph
D’attoma
,
Sara
Pannilunghi
,
Vito
Vece
,
Jerome
Bertho
,
Peter
Goekjian
,
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
,
Balázs
Bálint
,
Zoltán B.
Szabó
,
Levente
Ondi
,
Márton
Csékei
,
Zoltán
Szlávik
,
Ágnes
Proszenyák
,
James B.
Murray
,
James
Davidson
,
Ijen
Chen
,
Pawel
Dokurno
,
Allan E.
Surgenor
,
Christopher
Pedder
,
Roderick E.
Hubbard
,
Ana-Leticia
Maragno
,
Maia
Chanrion
,
Frederic
Colland
,
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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