Diamond Light Source Research Articles

Validating 3D two-parameter fracture mechanics models for structural integrity assessments

In-situ fracture tests were carried out on the I12 beamline at the Diamond Light Source. Four Al-Ti metal-matrix composites, with two crack lengths, were studied to assess for the impact of in-plane constraint. Synchrotron X-ray computed tomography and synchrotron X-ray diffraction were used to measure total strain and elastic strain respectively. In this work, the measured elastic strains in the samples are detailed as a function of applied load and compared against those predicted from a 3D elastic-plastic finite element model. The modelled strains increased asymptotically towards the tip of the electro discharge machined notch. The experimental results do not highlight the same response, which is due to a combination of blunting and low experimental spatial resolution. Far field experimental and measured strain fields converged, notably in the test piece containing a long notch (a/W = 0.5) and higher levels of constraint.

1 m long multilayer-coated deformable piezoelectric bimorph mirror for adjustable focusing of high-energy X-rays.

The Diamond Light Source (DLS) beamline I15-1 measures atomic pair distribution functions (PDF) using scattering of 40-80 keV X-rays. A unique focusing element was needed to condense these X-rays from an initial large cross section (11.0 mm H × 4.2 mm V) into a required spot size of FWHM ≈680 μm (H) × 20 μm (V) at a variable position between the sample and the detector. The large numerical aperture is achieved by coating a silicon substrate over 1 m long with three multilayer stripes of Bragg angle 4.2 mrad. One stripe selects X-rays of each energy 40.0, 65.4, and 76.6 keV. Sixteen piezoelectric bimorph actuators attached to the sides of the mirror substrate adjusted the reflecting surface's shape. Focal spots of vertical width < 15 µm were obtained at three positions over a 0.92 m range, with fast, easy switching from one focal position to another. Minimized root mean square slope errors were close to 0.5 µrad after subtraction of a uniform curvature. Reflectivity curves taken along each stripe showed consistent high peaks with generally small angular variation of peak positions. This is the first application of a 1 m long multilayer-coated bimorph mirror at a synchrotron beamline. Data collected with its help on a slice of a lithium ion battery's cathode are presented.

Highly stable fullerene-based porous molecular crystals with open metal sites.

The synthesis of conventional porous crystals involves building a framework using reversible chemical bond formation, which can result in hydrolytic instability. In contrast, porous molecular crystals assemble using only weak intermolecular interactions, which generally do not provide the same environmental stability. Here, we report that the simple co-crystallization of a phthalocyanine derivative and a fullerene (C60 or C70) forms porous molecular crystals with environmental stability towards high temperature and hot aqueous base or acid. Moreover, by using diamond anvil cells and synchrotron single-crystal measurements, stability towards extreme pressure (>4 GPa) is demonstrated, with the stabilizing fullerene held between two phthalocyanines and the hold tightening at high pressure. Access to open metal centres within the porous molecular co-crystal is demonstrated by in situ crystallographic analysis of the chemisorption of pyridine, oxygen and carbon monoxide. This suggests strategies for the formation of highly stable and potentially functional porous materials using only weak van der Waals intermolecular interactions.

Investigation of Structural Changes during Long-Term Cycling of NCM-811 Used As Cathode Active Material in Li-Ion Batteries

Layered lithium transition metal oxides, typically containing nickel, cobalt and manganese (NCM, Li1+δ[NixCoyMnz]1-δO2 with x+y+z=1), are the most widely used cathode active material (CAM) in Li-ion batteries for portable devices and battery electric vehicles.1 The class of NCM materials has several advantageous properties such as high energy and power densities and good cycling stability. However, depending on the Ni:Co:Mn ratio, the electrochemical performance characteristics of the materials can differ significantly. Increasing the Ni content is a current research focus, as it typically allows for a higher reversible lithium usage at a given cell potential, thereby improving the specific capacity.2 At the same time, highly Ni-rich NCM materials undergo severe structural and mechanical changes, which adversely affect their cycling stability. In this respect, NCM-811 (Li1+δ[Ni0.8Co0.1Mn0.1]1-δO2) is currently one of the most Ni-rich NCM materials with proven cycling stability.3 In this work, we study the structural processes in NCM-811 over the course of 1000 cycles, cycled at a C-rate of C/2 until 4.5 V vs. Li+/Li in a pouch-cell setup at the Diamond Light Source (see Figure 1a). By means of in-situ synchrotron X-ray powder diffraction, the structural evolution of NCM-811 was monitored in regular intervals both in the completely charged and discharged state (under open circuit voltage conditions). As the lattice parameter ratio, c/a, directly correlates with the lithium amount, xLi, in the bulk material,4,5 the application of a calibration curve, xLi = f(c/a), allows for monitoring the effective capacity window of the NCM-811 CAM during cycling, and thus for clarifying the observed electrochemical capacity loss (ΔCEC, see Figure 2b). Due to an increasing cathode overpotential, the accessible capacity determined by XRD analysis becomes smaller within the fixed potential cut-offs both in the charged (ΔCcharge) and discharged state (ΔCdischarge). As the sum of these two loss terms, ΔCXRD, does not reach the actual capacity loss, ΔCEC, some fraction of the NCM-811 material has to be entirely lost during cycling (see Figure 1c). By using additional techniques such as electrochemical impedance spectroscopy and X-ray photoelectron spectroscopy, this material loss can be assigned to a nm-thick, resistive surface layer around the primary particles. This resistive layer is in turn responsible for the observed overpotential losses. In contrast to the surface layer, the bulk material turned out to be stable, with a constant Ni disorder of ≈3% on the Li layer over 1000 cycles. For this reason, we think that future research on Ni-rich materials has to make substantial progress in controlling and stabilizing their surface properties. Figure 1: NCM-811/pre-lithiated graphite pouch-cells cycled at the Diamond Light Source over 1000 cycles at C/2 and ≈22°C in the potential window of 3.0-4.5 V vs. Li+/Li (cathode potential controlled vs. Li reference-electrode). (a) Discharge capacity of two cells. (b) Comparison of the observed electrochemical capacity loss and the losses determined by XRD analysis relative to the 18th cycle, illustrated for cell 1. (c) Absolute material loss under these cycling conditions relative to the pristine state for both cells (accounting to ≈2 mAh/g already in the 18th cycle). Acknowledgements: We want to acknowledge BASF SE for the support within the frame of its scientific network on electrochemistry and batteries. We also thank the Diamond Light Source for access to beamline I11 (Beamtime Award EE16866).

Solid solution formation in the metatorbernite-metazeunerite system (Cu(UO2)2(PO4)2- x(AsO4) x. nH2O) and their stability under conditions of variable temperature.

Mineral phases which can be thought of as members of a metatorbernite-metazeunerite solid solution (Cu(UO2)2(PO4)2- x(AsO4) x.8H2O have been identified in radioactive samples from spoil heaps at the uranium mine site in South Terras, Cornwall (grid reference SW935523). A complete solid solution (0 < x < 2) was synthesized by precipitation from solution using uranium (VI) nitrate and copper (II) chloride and phosphoric acid/arsenic acid in the appropriate molar proportions. Refined unit cell parameters determined by Pawley fitting of powder X-ray diffraction data showed a linear variation in the a unit cell parameter according to Vegard's Law, allowing the composition of the natural mineral phases found at South Terras to be determined from measurement of their unit cell parameters. High-resolution variable-temperature synchrotron powder X-ray diffraction studies were carried out at the Diamond Light Source on three members of this solid solution ( x = 0, 1, 2) and showed different structural behaviour as a function of composition and temperature. Metatorbenite ( x = 0) retains its tetragonal symmetry at low temperatures and dehydrates to an amorphous phase at 473 K, whereas metazeunrite ( x = 2) transforms to an orthorhombic phase at low temperatures, regains its tetragonal symmetry on heating to 323 K and undergoes a further transition to an, as yet, unidentified phase at 473 K. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.

The development and exploitation of synchrotron single-crystal diffraction for chemistry and materials.

A historical account is given of the 25-year development of dedicated synchrotron beamlines for single-crystal diffraction as applied to the so-called small-molecule fields of chemistry and materials science. Designs have drawn on previous successful models in macromolecular crystallography, with appropriate modifications in view of the different properties and behaviour of the respective sample types. Key factors in making these facilities attractive and productive for users include familiarity of operational procedures and the availability of experimental techniques and features normally found in local chemical crystallography laboratories, especially for the handling of samples and processing of diffraction data. Beamlines dedicated to single-crystal diffraction rather than shared with other techniques can be optimized for effective and efficient use. The experience gained from the original design, development and exploitation of stations 9.8 and 16.2SMX at the Daresbury Laboratory Synchrotron Radiation Source and beamline 11.3.1 at the Advanced Light Source have led to highly productive current facilities at ALS beamline 12.2.1 and Diamond Light Source beamline I19, including the recent introduction of remote-access operation. Such facilities have generated and continue to provide major impact in academic and commercial research that could otherwise not be achieved, including patents and applications in pharmaceuticals, energy and gas storage systems, and government policy. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.

Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping.

Structure-guided drug discovery emerged in the 1970s and 1980s, stimulated by the three-dimensional structures of protein targets that became available, mainly through X-ray crystal structure analysis, assisted by the development of synchrotron radiation sources. Structures of known drugs or inhibitors were used to guide the development of leads. The growth of high-throughput screening during the late 1980s and the early 1990s in the pharmaceutical industry of chemical libraries of hundreds of thousands of compounds of molecular weight of approximately 500 Da was impressive but still explored only a tiny fraction of the chemical space of the predicted 1040 drug-like compounds. The use of fragments with molecular weights less than 300 Da in drug discovery not only decreased the chemical space needing exploration but also increased promiscuity in binding targets. Here we discuss advances in X-ray fragment screening and the challenge of identifying sites where fragments not only bind but can be chemically elaborated while retaining their positions and binding modes. We first describe the analysis of fragment binding using conventional X-ray difference Fourier techniques, with Mycobacterium abscessus SAICAR synthetase (PurC) as an example. We observe that all fragments occupy positions predicted by computational hotspot mapping. We compare this with fragment screening at Diamond Synchrotron Light Source XChem facility using PanDDA software, which identifies many more fragment hits, only some of which bind to the predicted hotspots. Many low occupancy sites identified may not support elaboration to give adequate ligand affinity, although they will likely be useful in drug discovery as ‘warm spots’ for guiding elaboration of fragments bound at hotspots. We discuss implications of these observations for fragment screening at the synchrotron sources.This article is part of the theme issue ‘Fifty years of synchrotron science: achievements and opportunities’.

Zinc binding to Muscle LIM Protein regulates its structure and interaction with binding partners

Muscle LIM protein (MLP) is a member of the cysteine‐rich protein family, localising predominantly to the Z‐disk of the myofilaments in cardiac myocytes. MLP is a mechanosensor and functions through its translocation to the nucleus from the myofilaments and through protein‐protein interactions in the cytoplasm. Mechanosensing enables the heart to adapt appropriately to alterations in hemodynamic load, whilst mutations in the MLP gene lead to cardiomyopathy and heart failure. MLP contains two LIM domains each consisting of a double zinc‐finger motif. Rather than interacting with DNA, LIM domains mediate protein‐protein interactions associated with cellular signalling.The aim of this investigation is to determine how zinc binding regulates the structure of MLP and determine the impact on its interaction with binding partners. The analysis was performed using a combination of circular dichroism (CD), bioinformatics tools and online servers. CD is the difference in absorption between left‐handed and right‐handed circularly polarised light, occurring when a molecule contains light‐absorbing groups. It can be used to study the secondary, tertiary and quaternary structure of proteins, as well as studying its conformational stability under different conditions.In this study, we used CD to determine structural changes to MLP in the presence and absence of zinc. MLP is predominantly helical (~36%) with a small percentage of beta‐strands of ~8%, 34% of unordered and 21% of turns. In the presence of excess zinc, the helical content was reduced to ~19% with a gain of beta‐strand component to 30%. The presence of EDTA caused MLP to lose some helical conformation to 22% with an increased in the beta‐strand content to 16%. These data suggest that zinc increases the structural folding and organization of MLP.The full length wildtype MLP sequence was submitted to a variety of servers along with the C58G mutation known to reduce zinc binding in the first LIM domain. This mutation in humans leads to heart failure. Heart failure is defined as a progressive condition in which the heart is unable to pump enough blood to meet the body's needs for oxygen and nutrients. Bioinformatic protein‐protein analysis indicated that the C58G mutation inhibits interaction with NRAP, TCAP, alpha‐actinin and cofilin 2 which would interfere with MLP binding to the z‐disk and the myofilaments within cardiac myocytes. This would have a significant negative impact on mechanosensing in the heart and explains why the C58G mutation in MLP leads to heart failure.Support or Funding InformationUniversity of Reading and Diamond Light SourceThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Mapping the depleted area of silicon diodes using a micro-focused X-ray beam

For the Phase-II Upgrade of the ATLAS detector at CERN, the current ATLAS Inner Detector will be replaced with the ATLAS Inner Tracker (ITk). The ITk will be an all-silicon detector, consisting of a pixel tracker and a strip tracker. Sensors for the ITk strip tracker are required to have a low leakage current up to bias voltages of −500 V to maintain a low noise and power dissipation. In order to minimise sensor leakage currents, particularly in the high-radiation environment inside the ATLAS detector, sensors are foreseen to be operated at low temperatures and to be manufactured from wafers with a high bulk resistivity of several kΩ·cm. Simulations showed the electric field inside sensors with high bulk resistivity to extend towards the sensor edge, which could lead to increased surface currents for narrow dicing edges. In order to map the electric field inside biased silicon sensors with high bulk resistivity, three diodes from ATLAS silicon strip sensor prototype wafers were studied with a monochromatic, micro-focused X-ray beam at the Diamond Light Source (Didcot, U.K.). For all devices under investigation, the electric field inside the diode was mapped and its dependence on the applied bias voltage was studied.

Zone plates for angle-resolved photoelectron spectroscopy providing sub-micrometre resolution in the extreme ultraviolet regime.

This article reports on the fabrication and testing of dedicated Fresnel zone plates for use at the nano-ARPES branch of the I05-ARPES beamline of Diamond Light Source to perform angle-resolved photoelectron spectroscopy with sub-micrometre resolution in real space. The aim of the design was to provide high photon flux combined with sub-micrometre spot sizes. The focusing lenses were tested with respect to efficiency and spatial resolution in the extreme ultraviolet between 50 eV and 90 eV. The experimentally determined diffraction efficiencies of the zone plates are as high as 8.6% at 80 eV, and a real-space resolution of 0.4 µm was demonstrated. Using the zone-plate-based setup, monolayer flakes of the two-dimensional semiconductor WS2 were investigated. This work demonstrates that the local electronic structure can be obtained from an area of a few micrometres across a two-dimensional heterostructure.

Diamond B23 Beamline for Synchrotron Radiation Circular Dichroism (SRCD): High Throughput CD (HTCD) and CD Imaging (CDi) Applications

High throughput (HTCD) using 96 and 384 multiplate for the optimisation of protein crystallization conditions, protein-ligand binding screening, and CD Imaging (CDi) of thin films of materials (proteins, nucleic acids, carbohydrates, polymers with embedded drugs, organic LED, and in general any chiral material with or without achiral substrates) are the results of the unique highly collimated microbeam light generated at B23 beamline at Diamond Light Source in the vacuum UV to visible wavelength range (130-650nm). B23 is the only bespoke beamline worldwide to characterise the structural and conformational properties of biologically important molecules using micro-devices unattainable with bespoke bench-top CD instruments. Recent applications and latest beamline upgrades will be discussed.

Room temperature ultrafast InGaAs Schottky diode based detectors for terahertz spectroscopy

The design and characterisation of rectifying terahertz detectors, based on InGaAs zero-bias Schottky diodes, is reported. These uncooled devices offer a spectral detection range from tens of GHz to above 3 THz, high response speed, and the prospect of low cost for mass production and arrayed implementation. We describe the airbridged semiconductor devices, their incorporation into waveguide mounts and quasi-optical substrate lens/planar antenna structures. Noise equivalent powers of 5 pW/Hz1/2 at 100 GHz, increasing to 50 pW/Hz1/2 at 300 GHz been achieved, along with rise and fall times of tens of picoseconds. We shall discuss examples of the use of the detectors: characterising a picosecond transistor-based source, spectrally narrow and broad band sources in the laboratory and coherent THz synchrotron radiation in the range 0.15–1.4 THz at the MIRIAM beamline B22 on the Diamond Light Source. The latter radiation was emitted from bunches of electrons circulating in the Diamond storage ring operating in THz-dedicated low-alpha mode. Spectral information on coherent synchrotron radiation originating from a single bunch of electrons is obtained, as well as the usefulness of this for spectroscopy, is evaluated.

Ptychographic X-ray computed tomography at a high-brilliance X-ray source

Ptychographic X-ray computed tomography is a phase-contrast imaging technique capable of retrieving three-dimensional maps of the index of refraction of the imaged volumes with nanometric resolution. Despite its unmatched reach, its application remains prerogative of a limited number of laboratories at synchrotron sources. We present a detailed description of an experimental procedure and a data analysis pipeline which can be both exploited for ptychographic X-ray computed tomography experiments at any high-brilliance X-ray source. These have been validated at the I13-1 Coherence Branchline within the first experiment of its kind to be successfully carried out on a biological sample at Diamond Light Source.

A water-cooled monochromator for the B16 Test beamline at the Diamond Light Source: capabilities and performance characterization.

Systematic studies of the performance of a water-cooled X-ray monochromator, designed and built for the B16 Test beamline at the Diamond Light Source, UK, are presented. A technical description of the monochromator is given and the results of commissioning measurements are discussed. Overall, the monochromator satisfies the original specifications well and meets all the major requirements of the versatile beamline. Following its successful implementation on B16, the basic monochromator design has been reproduced and adapted on other Diamond Light Source beamlines, including B18 and B21.

VMXi: a fully automated, fully remote, high-flux insitu macromolecular crystallography beamline.

VMXi is a new high-flux microfocus macromolecular crystallography beamline at Diamond Light Source. The beamline, dedicated to fully automated and fully remote data collection of macromolecular crystals in situ, allows rapid screening of hundreds of crystallization plates from multiple user groups. Its main purpose is to give fast feedback at the complex stages of crystallization and crystal optimization, but it also enables data collection of small and delicate samples that are particularly difficult to harvest using conventional cryo-methods, crystals grown in the lipidic cubic phase, and allows for multi-crystal data collections in drug discovery programs. The beamline is equipped with two monochromators: one with a narrow band-pass and fine energy resolution (optimal for regular oscillation experiments), and one with a wide band-pass and a high photon flux (optimal for fast screening). The beamline has a state-of-the-art detector and custom goniometry that allows fast data collection. This paper describes the beamline design, current status and future plans.

The Percival 2-Megapixel monolithic active pixel imager

The peak brilliance reached by today's Free-Electron Laser and Synchrotron light sources requires photon detectors matching their output intensity and other characteristics in order to fully realize the sources' potential. The Pixellated Energy Resolving CMOS Imager, Versatile And Large (Percival) is a dedicated soft X-ray imager (0.25–1 keV) developed for this purpose by a collaboration of DESY, Rutherford Appleton Laboratory/STFC, Elettra Sincrotrone Trieste, Diamond Light Source, and Pohang Accelerator Laboratory. Following several generations of prototypes, the Percival “P2M” 2-Megapixel imager—a 4.5×5 cm monolithic, stitched sensor with an uninterrupted imaging area of 4×4 cm2 (1408×1484 pixels of 27×27 μm—was produced and has demonstrated basic functionality with a first-light image using visible light. It is currently being brought to full operation in a front-illuminated configuration. The readout system being commissioned in parallel has been developed specifically for this imager which will produce—at full 300 Hz frame rate—data at 20 Gbit/s. A first wafer with eight Percival P2M chips has undergone backthinning to enable soft X-ray detection. It has been diced and chips are currently being wirebonded. We summarize here the P2M system, the project status, and show the P2M sensor's first response to visible light.

The Long-wavelength Macromolecular Crystallography I23 at Diamond Light Source

The Long-wavelength Macromolecular Crystallography I23 at Diamond Light Source

Characterisation of sensor kinase by CD spectroscopy: golden rules and tips.

This is a review that describes the golden rules and tips on how to characterise the molecular interactions of membrane sensor kinase proteins with ligands using mainly circular dichroism (CD) spectroscopy. CD spectroscopy is essential for this task as any conformational change observed in the far-UV (secondary structures (α-helix, β-strands, poly-proline of type II, β-turns, irregular and folding) and near-UV regions [local environment of the aromatic side-chains of amino acid residues (Phe, Tyr and Trp) and ligands (drugs) and prosthetic groups (porphyrins, cofactors and coenzymes (FMN, FAD, NAD))] upon ligand addition to the protein can be used to determine qualitatively and quantitatively ligand-binding interactions. Advantages of using CD versus other techniques will be discussed. The difference CD spectra of the protein–ligand mixtures calculated subtracting the spectra of the ligand at various molar ratios can be used to determine the type of conformational changes induced by the ligand in terms of the estimated content of the various elements of protein secondary structure. The highly collimated microbeam and high photon flux of Diamond Light Source B23 beamline for synchrotron radiation circular dichroism (SRCD) enable the use of minimal amount of membrane proteins (7.5 µg for a 0.5 mg/ml solution) for high-throughput screening. Several examples of CD titrations of membrane proteins with a variety of ligands are described herein including the protocol tips that would guide the choice of the appropriate parameters to conduct these titrations by CD/SRCD in the best possible way.

Bragg coherent diffraction imaging of iron diffusion into gold nanocrystals

Understanding how diffusion takes place within nanocrystals is of great importance for their stability and for controlling their synthesis. In this study, we used the strain sensitivity of Bragg coherent diffraction imaging (BCDI) to study the diffusion of iron into individual gold nanocrystals in situ at elevated temperatures. The BCDI experiments were performed at the I-07 beamline at Diamond Light Source, UK. The diffraction pattern of individual gold nanocrystals was measured around the (11-1) Bragg peak of gold before and after iron deposition as a function of temperature and time. Phase retrieval algorithms were used to obtain real space reconstructions of the nanocrystals from their measured diffraction patterns. Alloying of iron with gold at sample temperatures of 300 °C–500 °C and dealloying of iron from gold at 600 °C were observed. The volume of the alloyed region in the nanocrystals was found to increase with the dose of iron. However, no significant time dependence was observed for the structure following each iron deposition, suggesting that the samples reached equilibrium relatively quickly. The resulting phase distribution within the gold nanocrystals after the iron depositions suggests a contraction due to diffusion of iron. Our results show that BCDI is a useful technique for studying diffusion in three dimensions and alloying behaviour in individual crystalline grains.

Quantitative measurement of olivine composition in three dimensions using helical-scan X-ray micro-tomography

Olivine is a key constituent in the silicate Earth; its composition and texture informs petrogenetic understanding of numerous rock types. Here we develop a quantitative and reproducible method to measure olivine composition in three dimensions without destructive analysis, meaning full textural context is maintained. The olivine solid solution between forsterite and fayalite was measured using a combination of three-dimensional (3D) X-ray imaging techniques, 2D backscattered electron imaging, and spot-analyses using wavelength-dispersive electron probe microanalysis. The linear attenuation coefficient of natural crystals across a range of forsterite content from ∼73–91 mol% were confirmed to scale linearly with composition using 53, 60, and 70 kV monochromatic beams at I12-JEEP beamline, Diamond Light Source utilizing the helical fly-scan acquisition. A polychromatic X-ray source was used to scan the same crystals, which yielded image contrast equivalent to measuring the mol% of forsterite with an accuracy of 3 mm domains within a large crystal of San Carlos forsterite that varies by ∼2 Fo mol%. This offers a solution to an outstanding question of inter-laboratory standardization, and also demonstrates the utility of 3D, non-destructive, chemical measurement. To our knowledge, this study is the first to describe the application of XMT to quantitative chemical measurement across a mineral solid solution. Our approach may be expanded to calculate the chemistry of other mineral systems in 3D, depending upon the number, chemistry, and density of end-members.