I09-Surface and Interface Structural Analysis
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Galo J.
Paez
,
Christopher N.
Singh
,
Matthew J.
Wahila
,
Keith E.
Tirpak
,
Nicholas F.
Quackenbush
,
Shawn
Sallis
,
Hanjong
Paik
,
Yufeng
Liang
,
Darrell G.
Schlom
,
Tien-lin
Lee
,
Christoph
Schlueter
,
Wei-cheng
Lee
,
Louis F. J.
Piper
Diamond Proposal Number(s):
[13812, 25355]
Abstract: Recent reports have identified new metaphases of
VO
2
with strain and/or doping, suggesting the structural phase transition and the metal-to-insulator transition might be decoupled. Using epitaxially strained
VO
2
/
Ti
O
2
(001) thin films, which display a bulklike abrupt metal-to-insulator transition and rutile to monoclinic transition structural phase transition, we employ x-ray standing waves combined with hard x-ray photoelectron spectroscopy to simultaneously measure the structural and electronic transitions. This x-ray standing waves study elegantly demonstrates the structural and electronic transitions occur concurrently within experimental limits (±1K).
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May 2020
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Krios III-Titan Krios III at Diamond
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Diamond Proposal Number(s):
[19832]
Open Access
Abstract: Neisseria meningitidis is carried by nearly a billion humans, causing developmental impairment and over 100 000 deaths a year. A quinol-dependent nitric oxide reductase (qNOR) plays a critical role in the survival of the bacterium in the human host. X-ray crystallographic analyses of qNOR, including that from N. meningitidis (NmqNOR) reported here at 3.15 Å resolution, show monomeric assemblies, despite the more active dimeric sample being used for crystallization. Cryo-electron microscopic analysis of the same chromatographic fraction of NmqNOR, however, revealed a dimeric assembly at 3.06 Å resolution. It is shown that zinc (which is used in crystallization) binding near the dimer-stabilizing TMII region contributes to the disruption of the dimer. A similar destabilization is observed in the monomeric (∼85 kDa) cryo-EM structure of a mutant (Glu494Ala) qNOR from the opportunistic pathogen Alcaligenes (Achromobacter) xylosoxidans, which primarily migrates as a monomer. The monomer–dimer transition of qNORs seen in the cryo-EM and crystallographic structures has wider implications for structural studies of multimeric membrane proteins. X-ray crystallographic and cryo-EM structural analyses have been performed on the same chromatographic fraction of NmqNOR to high resolution. This represents one of the first examples in which the two approaches have been used to reveal a monomeric assembly in crystallo and a dimeric assembly in vitrified cryo-EM grids. A number of factors have been identified that may trigger the destabilization of helices that are necessary to preserve the integrity of the dimer. These include zinc binding near the entry of the putative proton-transfer channel and the preservation of the conformational integrity of the active site. The mutation near the active site results in disruption of the active site, causing an additional destabilization of helices (TMIX and TMX) that flank the proton-transfer channel helices, creating an inert monomeric enzyme.
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May 2020
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[16036, 19288]
Abstract: The efficient transport of electrons from the sunlight-harvesting dye molecules into the electrical circuit of a dye-sensitized solar cell (DSSC) is imperative to its effective operation. A dye···semiconductor interface comprises the working electrode of a DSSC. Dye molecules adsorb onto the semiconductor surface, whereupon they transfer electronic charge into the conduction band of the semiconductor; this process initiates the electrical circuit. It is therefore important to characterize this interfacial structure in order to understand how efficiently the dye binds, or anchors, onto the semiconductor surface and imparts charge transfer to it. Armed with such knowledge, the performance of DSSCs may then be improved systematically. The structural determination of a thin-film interface is nonetheless a challenging task. We herein report the results of a glancing-angle pair distribution function (gaPDF) experiment that generated synchrotron x-ray diffraction patterns of N3- and N749-sensitized DSSC working electrodes. This gaPDF experimental approach represents the first diffraction-based strategy for the characterization of intact DSSC working electrodes. The gaPDF structural signatures were compared with PDFs simulated from two possible interfacial structures that were computed using density functional theory (DFT); these simulated structures showed the dyes anchoring in two distinct modes: a bridging bidentate and a monodentate ester configuration. The differences between the experimental observation and these simulated structures revealed a preference for each dye, N3 and N749, to adopt a bidentate bridging dye anchoring mode when sensitized onto TiO2. This work not only demonstrates the successful application of a gaPDF method to DSSC research, it also advocates the applicability of gaPDF to many types of thin-film samples.
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May 2020
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Mohamed
Ibrahim
,
Thomas
Fransson
,
Ruchira
Chatterjee
,
Mun Hon
Cheah
,
Rana
Hussein
,
Louise
Lassalle
,
Kyle D.
Sutherlin
,
Iris D.
Young
,
Franklin D.
Fuller
,
Sheraz
Gul
,
In-sik
Kim
,
Philipp S.
Simon
,
Casper
De Lichtenberg
,
Petko
Chernev
,
Isabel
Bogacz
,
Cindy C.
Pham
,
Allen M.
Orville
,
Nicholas
Saichek
,
Trent
Northen
,
Alexander
Batyuk
,
Sergio
Carbajo
,
Roberto
Alonso-mori
,
Kensuke
Tono
,
Shigeki
Owada
,
Asmit
Bhowmick
,
Robert
Bolotovsky
,
Derek
Mendez
,
Nigel W.
Moriarty
,
James M.
Holton
,
Holger
Dobbek
,
Aaron S.
Brewster
,
Paul D.
Adams
,
Nicholas K.
Sauter
,
Uwe
Bergmann
,
Athina
Zouni
,
Johannes
Messinger
,
Jan
Kern
,
Vittal K.
Yachandra
,
Junko
Yano
Open Access
Abstract: In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a “water wheel”-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.
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May 2020
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B22-Multimode InfraRed imaging And Microspectroscopy
Optics
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Abstract: Vibrational microspectroscopy via Fourier transform infrared (FTIR) faces an experimental trade-off among the signal to noise ratio (SNR), acquisition time, spatial resolution, and sample coverage. This is mainly associated with broadband source type: e.g. low brightness thermal sources with high flux for large field of view imaging at low resolution, or low ´etendue of synchrotron radiation infrared (SRIR) for diffraction-limited scanning mi- croanalysis at high magnification.1 Adaptive optics (AO), in this case deformable mirror (DM), is a potent tool in tackling the problem by modulating the intensity of high brightness structured SRIR beam toward a homo- geneous field illumination for IR imaging at high magnification. The latter is required for an efficient coupling of SRIR source to a multi-pixel detector such as focal plane array (FPA).2 Additionally, DM enables to achieve different shapes, optimized for different Cassegrain IR objective. Regardless, the quality of the generated beam relies upon the performance of the adaptive elements, i.e. actuators and their linear and reproducible response to the applied voltage. Moreover, the beam shaping capability of a single DM in controlling light beam position and angle is limited by its actuators influence function. In this work, we implemented two DMs for intensity shaping for the complex SRIR beam. A variation of multi-conjugate AO is implemented to characterize the performance of DMs and their actuators transfer function at multiple locations. An IR sensitive microbolometer array has been optically conjugated to the focal plane of individual actuators and the far-field of DM, in order to probe the corresponding actuating response. By analysing each actuator’s response individually, a measure of linear independence, uniformity in response, and cross-coupling can be obtained in a spectral range, from visible to near and mid IR. Additionally, by assembling the vectorized version of each actuator response, the transfer matrix can be formed. This matrix describes the relationship between the actuation effect on the beam and the response of the IR microbolometer, at the given conjugate planes. Based on such discussion, we assess the stability of the deformable mirror for open-loop (i.e. without feedback) operation.
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May 2020
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B18-Core EXAFS
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Diamond Proposal Number(s):
[16478]
Abstract: The methodology for experimentally verifying the point-defect chemistry (site of substitution, valence, and charge compensation mechanisms) in manganese-doped SrTiO3 ceramics is presented for dilute and non-dilute dopant concentrations. Experimental and theoretical techniques have strengths and weaknesses depending upon defect types and concentrations, so a combinatorial characterization approach is required. Using electron-paramagnetic-resonance and X-ray-absorption-fine-structure measurements combined with density functional theory calculations, the charge compensation mechanisms and local structural relaxations for five unique manganese defect centers are identified. Mn4+, as an isovalent dopant, occupies the octahedrally coordinated Ti sites without the need for charge compensation; its smaller ionic radius relative to Ti is accommodated by isotropic contraction of the [MnO6] octahedra. Mn3+ is an aliovalent dopant that also favors the Ti sites with the [MnO6] octahedra exhibiting Jahn-Teller distortions. The charge difference associated with the Mn3+Ti4+ substitution is compensated by formation of oxygen vacancies. A more complex behavior is observed for the Mn2+ species which can occupy either the Sr or Ti sites depending on the Sr/Ti ratio. The effects of Mn concentration or high-temperature annealing on the site preference (i.e., Sr vs Ti) are negligible. The Mn2+ species on the Sr sites are strongly off-centered in the relatively large cuboctahedral cages within the oxygen framework. The dynamic nature of the Mn displacements in these configurations is confirmed using ab initio molecular dynamics simulations.
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May 2020
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I15-Extreme Conditions
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Abstract: By combining hydrogen and sulfur within diamond-anvil cells we synthesize
(H2S)2H2 at 5 GPa and 373 K. Through a series of Raman spectroscopy, infrared spectroscopy, and synchrotron x-ray diffraction experiments we have constrained the phase diagram of
(H2S)2H2
within a wide
P
−
T
range. On compression we observe the phase transition sequence of
I-II-II
′
-III
, where
II
′
is a previously unreported phase; at room temperature this sequence spans from 5 to 47 GPa, while the application of low temperatures stabilizes this sequence to 127 GPa
(
<
80
K
)
. Above these pressures we propose that phase III of
(H2S)2H2
transforms to a nonmolecular
H3S
network. Our Raman and infrared measurements indicate that the transition from
(
H
2
S
)
2
H
2
to
H
3
S
is reversible at room temperature. X-ray diffraction reveals that the symmetry of the underlying S lattice of
(
H
2
S
)
2
H
2
and
H
3
S
is retained along this compression path up to at least 135 GPa.
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May 2020
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B22-Multimode InfraRed imaging And Microspectroscopy
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Diamond Proposal Number(s):
[21061]
Abstract: Synchrotron resonance-enhanced infrared-atomic force microscopy (RE-AFM-IR) is a near-field photothermal vibrational nanoprobe developed at the Diamond Light Source (DLS), capable of measuring mid-infrared absorption spectra with spatial resolution around 100 nm. The present study reports a first application of synchrotron RE-AFM-IR to interrogate biological soft matter at subcellular level, in this case on a cellular model of drug-induced phospholipidosis (DIPL). J774A-1 macrophages were exposed to amiodarone (10 µM) or medium for 24 hours and chemically fixed. AFM topography maps revealed amiodarone-treated cells with enlarged cytoplasm and very thin regions corresponding to collapsed vesicles. IR maps of the whole cell were analysed by exploiting the RE-AFM-IR overall signal, i.e. the integrated RE-AFM-IR signal amplitude versus AFM-derived cell thickness, also on lateral resolution around 100 nm. Results shown that vibrational band assignment was possible and all characteristic peaks for lipids, proteins and DNA/RNA were identified. Both peak ratio and unsupervised chemometric analysis of RE-AFM-IR nanospectra generated from the nuclear and perinuclear regions of untreated and amiodarone-treated cells showed that the perinuclear region (i.e. cytoplasm) of amiodarone-treated cells had significantly elevated band intensities in the regions corresponding to phosphate and carbonyl groups, indicating detection of phospholipid-rich inclusion bodies typical for cells with DIPL. The results of this study are of importance to demonstrate not only the applicability of Synchrotron RE-AFM-IR to soft biological matters with subcellular spatial resolution, but also that the spectral information gathered from an individual sub-micron sample volume enables chemometric identification of treatment and biochemical differences between mammalian cells.
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May 2020
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[17102]
Abstract: Understanding peptide self-assembly mechanisms and stability of the formed assemblies is crucial for development of functional nanomaterials. Herein, we have adopted rational design approach to demonstrate how minimal structural modification to a non-assembling ultra-short ionic self-complementary tetrapeptide FEFK (Phe4) remarkably enhanced stability of self-assembly into β-sheet nanofibres and induced hydrogelation. This was achieved by replacing flexible phenylalanine residue (F) by the rigid phenylglycine (Phg) resulting in constrained analogue PhgEPhgK (Phg4), which positioned aromatic rings in an orientation favourable for aromatic stacking. Phg4 self-assembly into stable β-sheet ladders was facilitated by π-staking of aromatic sidechains alongside hydrogen bonding between backbone amides along the nanofibre axis. The contribution of these non-covalent interactions in stabilising self-assembly was predicted by in silico modelling using molecular dynamics simulations and semi-empirical quantum mechanics calculations. In aqueous medium, Phg4 β-sheet nanofibres entangled at a critical gelation concentration > 20 mg/mL forming a network of nanofibrous hydrogel. Phg4 also demonstrated unique surface activity in presence of immiscible oils and was superior to commercial emulsifiers in stabilising oil-in-water emulsions. This was attributed to interfacial adsorption of amphiphilic nanofibrilles forming nanofibrillised microspheres. To our knowledge, Phg4 is the shortest ionic self-complementary peptide rationally designed to self-assemble into stable β-sheet nanofibres capable of gelation and emulsification. Our results suggest that Ultra-short Ionic-complementary Constrained Peptides or UICPs have significant potential for the development of cost-effective, sustainable and multifunctional soft bionanomaterials.
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May 2020
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[20038]
Open Access
Abstract: Recently, there has been growing interest in the amorphous states of metal–organic frameworks (MOFs). Particular focus has been given to melt-quenched MOF glasses. In this work, to improve our understanding of the factors influencing melting, the thermal response of four closely related zeolitic imidazolate frameworks (ZIFs) was studied. Electron withdrawing ligands were found to lower both the melting and glass transition temperatures, providing a promising strategy for improving the processability of MOFs in the liquid state. Crucially, dense frameworks appear to be essential for melting, with their presence also initiating the melting of open pore frameworks. This opens up the rich polymorphic landscape of ZIFs to the preparation of novel MOF liquids and glasses.
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May 2020
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