E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[20431, 22317]
Abstract: Electron ptychography is a 4-D STEM phase-contrast imaging technique with applications to light-element and beam-sensitive materials. Although the electron dose (electrons incident per unit area on the sample) is the primary figure of merit for imaging beam-sensitive materials, it is also necessary to consider the contrast transfer properties of the imaging technique. Here, we explore the contrast transfer properties of electron ptychography. The contrast transfer of focused-probe, non-iterative electron ptychography using the single-side-band (SSB) method is demonstrated experimentally. The band-pass nature of the phase-contrast transfer function (PCTF) for SSB ptychography places strict limitations on the probe convergence semi-angles required to resolve specific sample features with high contrast. The PCTF of the extended ptychographic iterative engine (ePIE) is broader than that for SSB ptychography, although when both high and low spatial frequencies are transferred, band-pass filtering is required to remove image artefacts. Normalisation of the transfer function with respect to the noise level shows that the transfer window is increased while avoiding noise amplification. Avoiding algorithms containing deconvolution steps may also increase the dose-efficiency of ptychographic phase reconstructions.
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Feb 2021
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I04-Macromolecular Crystallography
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Kyriacos C.
Nicolaou
,
Saiyong
Pan
,
Kiran K.
Pulukuri
,
Qiuji
Ye
,
Stephan
Rigol
,
Rohan D.
Erande
,
Dionisios
Vourloumis
,
Bogusław P.
Nocek
,
Stefan
Munneke
,
Joseph
Lyssikatos
,
Amanda
Valdiosera
,
Christine
Gu
,
Baiwei
Lin
,
Hetal
Sarvaiaya
,
Jose
Trinidad
,
Joseph
Sandoval
,
Christina
Lee
,
Mikhail
Hammond
,
Monette
Aujay
,
Nicole
Taylor
,
Marybeth
Pysz
,
James W.
Purcell
,
Julia
Gavrilyuk
Abstract: Molecular design, synthesis, and biological evaluation of tubulysin analogues, linker-drugs, and antibody–drug conjugates are described. Among the new discoveries reported is the identification of new potent analogues within the tubulysin family that carry a C11 alkyl ether substituent, rather than the usual ester structural motif at that position, a fact that endows the former with higher plasma stability than that of the latter. Also described herein are X-ray crystallographic analysis studies of two tubulin–tubulysin complexes formed within the α/β interface between two tubulin heterodimers and two highly potent tubulysin analogues, one of which exhibited a different binding mode to the one previously reported for tubulysin M. The X-ray crystallographic analysis-derived new insights into the binding modes of these tubulysin analogues explain their potencies and provide inspiration for further design, synthesis, and biological investigations within this class of antitumor agents. A number of these analogues were conjugated as payloads with appropriate linkers at different sites allowing their attachment onto targeting antibodies for cancer therapies. A number of such antibody–drug conjugates were constructed and tested, both in vivo and in vitro, leading to the identification of at least one promising ADC (Herceptin–LD3), warranting further investigations.
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Feb 2021
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I04-Macromolecular Crystallography
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Abstract: The anaerobic bacterium Chrysiogenes arsenatis respires using the oxyanion arsenate (AsO43–) as the terminal electron acceptor, where it is reduced to arsenite (AsO33–) while concomitantly oxidizing various organic (e.g., acetate) electron donors. This respiratory activity is catalyzed in the periplasm of the bacterium by the enzyme arsenate reductase (Arr), with expression of the enzyme controlled by a sensor histidine kinase (ArrS) and a periplasmic-binding protein (PBP), ArrX. Here, we report for the first time, the molecular structure of ArrX in the absence and presence of bound ligand arsenate. Comparison of the ligand-bound structure of ArrX with other PBPs shows a high level of conservation of critical residues for ligand binding by these proteins; however, this suite of PBPs shows different structural alterations upon ligand binding. For ArrX and its homologue AioX (from Rhizobium sp. str. NT-26), which specifically binds arsenite, the structures of the substrate-binding sites in the vicinity of a conserved and critical cysteine residue contribute to the discrimination of binding for these chemically similar ligands.
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Feb 2021
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I07-Surface & interface diffraction
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Alberto
Privitera
,
Ross
Warren
,
Giacomo
Londi
,
Pascal
Kaienburg
,
Junjie
Liu
,
Andreas
Sperlich
,
Andreas E.
Lauritzen
,
Oliver
Thimm
,
Arzhang
Ardavan
,
David
Beljonne
,
Moritz
Riede
Diamond Proposal Number(s):
[20426]
Open Access
Abstract: We use the electron spin as a probe to gain insight into the mechanism of molecular doping in a p-doped zinc phthalocyanine host across a broad range of temperatures (80–280 K) and doping concentrations (0–5 wt% of F6-TCNNQ). Electron paramagnetic resonance (EPR) spectroscopy discloses the presence of two main paramagnetic species distinguished by two different g-tensors, which are assigned based on density functional theory calculations to the formation of a positive polaron on the host and a radical anion on the dopant. Close inspection of the EPR spectra shows that radical anions on the dopants couple in an antiferromagnetic manner at device-relevant doping concentrations, thereby suggesting the presence of dopant clustering, and that positive polarons on the molecular host move by polaron hopping with an activation energy of 5 meV. This activation energy is substantially smaller than that inferred from electrical conductivity measurements (∼233 meV), as the latter also includes a (major) contribution from charge-transfer state dissociation. It emerges from this study that probing the electron spin can provide rich information on the nature and dynamics of charge carriers generated upon doping molecular semiconductors, which could serve as a basis for the design of the next generation of dopant and host materials.
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Feb 2021
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I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[22264]
Abstract: The high-voltage (4.7 V vs Li+/Li) spinel lithium nickel manganese oxide (LiNi0.5Mn1.5O4, LNMO) is a promising candidate for the next generation of lithium-ion batteries due to its high energy density, low cost, and low environmental impact. However, poor cycling performance at high cutoff potentials limits its commercialization. Herein, hollow-structured LNMO is synergistically paired with an ionic liquid electrolyte, 1 M lithium bis(fluorosulfonyl)imide (LiFSI) in N-propyl-N-methylpyrrolidinium bis(fluorosulfonyl)imide (Pyr1,3FSI), to achieve stable cycling performance and improve the rate capability. The optimized cathode–electrolyte system exhibits extended cycling performance (>85% capacity retention after 300 cycles) and high rate performance (106.2 mAh g–1 at 5C) even at an elevated temperature of 65 °C. X-ray photoelectron spectroscopy and spatially resolved X-ray fluorescence analyses confirm the formation of a robust, LiF-rich cathode–electrolyte interphase. This study presents a comprehensive design strategy to improve the electrochemical performance of high-voltage cathode materials.
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Feb 2021
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Open Access
Abstract: The utilization of operando spectroscopy has allowed us to watch the dynamic nature of supported metal nanoparticles. However, the realization that subtle changes to environmental conditions affect the form of the catalyst necessitates that we assess the structure of the catalyst across the reactant/product gradient that exists across a fixed bed reactor. In this study, we have performed spatial profiling of a Pd/Al2O3 catalyst during NH3 oxidation, simultaneously collecting mass spectrometry and X-ray absorption spectroscopy data at discrete axial positions along the length of the catalyst bed. The spatial analysis has provided unique insights into the structure–activity relationships that govern selective NH3 oxidation—(i) our data is consistent with the presence of PdNx after the spectroscopic signatures for bulk PdNx disappear and that there is a direct correlation to the presence of this structure and the selectivity toward N2; (ii) at high temperatures, ≥400 °C, we propose that there are two simultaneous reaction pathways—the oxidation of NH3 to NOx by PdO and the subsequent catalytic reduction of NOx by NH3 to produce N2. The results in this study confirm the structural and catalytic diversity that exists during catalysis and the need for such an understanding if improvements to important emission control technologies, such as the selective catalytic oxidation of NH3, are to be made.
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Feb 2021
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[20161]
Open Access
Abstract: Iron is a fundamental element for virtually all forms of life. Despite its abundance, its bioavailability is limited, and thus, microbes developed siderophores, small molecules, which are synthesized inside the cell and then released outside for iron scavenging. Once inside the cell, iron removal does not occur spontaneously, instead this process is mediated by siderophore-interacting proteins (SIP) and/or by ferric-siderophore reductases (FSR). In the past two decades, representatives of the SIP subfamily have been structurally and biochemically characterized; however, the same was not achieved for the FSR subfamily. Here, we initiate the structural and functional characterization of FhuF, the first and only FSR ever isolated. FhuF is a globular monomeric protein mainly composed by α-helices sheltering internal cavities in a fold resembling the “palm” domain found in siderophore biosynthetic enzymes. Paramagnetic NMR spectroscopy revealed that the core of the cluster has electronic properties in line with those of previously characterized 2Fe–2S ferredoxins and differences appear to be confined to the coordination of Fe(III) in the reduced protein. In particular, the two cysteines coordinating this iron appear to have substantially different bond strengths. In similarity with the proteins from the SIP subfamily, FhuF binds both the iron-loaded and the apo forms of ferrichrome in the micromolar range and cyclic voltammetry reveals the presence of redox-Bohr effect, which broadens the range of ferric-siderophore substrates that can be thermodynamically accessible for reduction. This study suggests that despite the structural differences between FSR and SIP proteins, mechanistic similarities exist between the two classes of proteins.
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Feb 2021
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[20757]
Open Access
Abstract: Understanding the kinetics of the crystallization process for organometal halide perovskite formation is critical in determining the crystalline, nanoscale morphology and therefore the electronic properties of the films produced during thin film formation from solution. In this work, in situ grazing incidence small-angle X-ray scattering (GISAXS) and optical microscopy measurements are used to investigate the processes of nucleation and growth of pristine mixed halide perovskite (MAPbI3–xClx) crystalline films deposited by bar coating at 60 °C, with and without additives in the solution. A small amount of 1,8-diiodooctane (DIO) and hydriodic acid (HI) added to MAPbI3–xClx is shown to increase the numbers of nucleation centers promoting heterogeneous nucleation and accelerate and modify the size of nuclei during nucleation and growth. A generalized formation mechanism is derived from the overlapping parameters obtained from real-time GISAXS and optical microscopy, which revealed that during nucleation, perovskite precursors cluster before becoming the nuclei that function as elemental units for subsequent formation of perovskite crystals. Additive-free MAPbI3–xClx follows reaction-controlled growth, in contrast with when DIO and HI are present, and it is highly possible that the growth then follows a hindered diffusion-controlled mechanism. These results provide important details of the crystallization mechanisms occurring and will help to develop greater control over perovskite films produced.
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Feb 2021
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B22-Multimode InfraRed imaging And Microspectroscopy
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Diamond Proposal Number(s):
[16420]
Abstract: Simple n-alcohols, such as 1-dodecanol, show anomalous film-forming and friction behaviors under elastohydrodynamic lubrication (EHL) conditions, as found inside bearings and gears. Using tribometer, diamond anvil cell (DAC), and differential scanning calorimetry (DSC) experiments, we show that liquid 1-dodecanol undergoes a pressure-induced solidification when entrained into EHL contacts. Different solid polymorphs are formed inside the contact depending on the temperature and pressure conditions. Surprisingly, at a moderate temperature and pressure, 1-dodecanol forms a polymorph that exhibits robust macroscale superlubricity. The DAC and DSC experiments show that superlubricity is facilitated by the formation of lamellar, hydrogen-bonded structures of hexagonally close-packed molecules, which promote interlayer sliding. This novel superlubricity mechanism is similar to that proposed for the two-dimensional materials commonly employed as solid lubricants, but it also enables the practical advantages of liquid lubricants to be maintained. When the pressure is increased, 1-dodecanol undergoes a polymorphic transformation into a phase that gives a higher friction. The DAC and DSC experiments indicate that the high-friction polymorph is an orthorhombic crystal. The polymorphic transformation pressure coincides with the onset of a dimple formation in the EHL films, revealing that the anomalous film shapes are caused by the formation of rigid orthorhombic crystals inside the contact. This is the first demonstration of a macroscale superlubricity in an EHL contact lubricated by a nonaqueous liquid that arises from bulk effects rather than tribochemical transformations at the surfaces. Since the superlubricity observed here results from phase transformations, it is continuously self-replenishing and is insensitive to surface chemistry and topology. This discovery creates the possibility of implementing superlubricity in a wide range of machine components, which would result in enormous improvements in efficiency and durability.
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Feb 2021
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I03-Macromolecular Crystallography
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Nicholas G. S.
Mcgregor
,
Joan
Coines
,
Valentina
Borlandelli
,
Satoko
Amaki
,
Marta
Artola
,
Alba
Nin‐hill
,
Daniël
Linzel
,
Chihaya
Yamada
,
Takatoshi
Arakawa
,
Akihiro
Ishiwata
,
Yukishige
Ito
,
Gijsbert A.
Marel
,
Jeroen D. C.
Codée
,
Shinya
Fushinobu
,
Herman S.
Overkleeft
,
Carme
Rovira
,
Gideon J.
Davies
Diamond Proposal Number(s):
[18598]
Abstract: The recent discovery of zinc‐dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys)3(Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on a Zn‐coordinated cysteine nucleophile and passing through a thioglycosyl enzyme intermediate, remains controversial. This is primarily due to the expected stability of the intermediate C−S bond. To facilitate the study of this atypical mechanism, we report the synthesis of a cyclophellitol‐derived β‐l‐arabinofuranosidase inhibitor, hypothesised to react with the catalytic nucleophile to form a non‐hydrolysable adduct analogous to the mechanistic covalent intermediate. This β‐l‐arabinofuranosidase inhibitor reacts exclusively with the proposed cysteine thiol catalytic nucleophiles of representatives of GH families 127 and 146. X‐ray crystal structures determined for the resulting adducts enable MD and QM/MM simulations, which provide insight into the mechanism of thioglycosyl enzyme intermediate breakdown. Leveraging the unique chemistry of cyclophellitol derivatives, the structures and simulations presented here support the assignment of a zinc‐coordinated cysteine as the catalytic nucleophile and illuminate the finely tuned energetics of this remarkable metalloenzyme clan.
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Feb 2021
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