I14-Hard X-ray Nanoprobe
I18-Microfocus Spectroscopy
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Diamond Proposal Number(s):
[39618, 39938, 302085, 31588, 5116, 36811]
Open Access
Abstract: Correlative microscopy linking synchrotron X-ray fluorescence (SXRF) with optical imaging is valuable for contextualizing chemical element distributions in biology. The spatial correlation necessary to achieve this presents fundamental challenges and can be a significant constraint on accuracy and data interpretation. We present a technical solution based on a finder grid concept, optimized for SXRF correlative studies of metals in biological tissues, with scope for wider adaptation and application. A hierarchically patterned fiducial system was directly etched onto spectroscopically clean quartz substrates via femtosecond laser ablation. This design enables improved correlation among SXRF, optical imaging, and histological staining over a greater range of length scales than conventional registration methods such as the use of tissue architecture from serial sections and the use of electron-microscopy-resolution finder grids and applied fiduciary markers that can introduce XRF-signal-dominating levels of elements such as copper, nickel, gold, and titanium. We present two quartz finder grid formats: a microgrid and a nanogrid design. We demonstrate their utility for rapid ROI relocalization and same-section correlative workflows using human brain tissue. The etched quartz finder grid approach facilitates rapid and reproducible ROI relocalization and alignment across instruments, particularly where integral fiducial markers are sparse or ambiguous.
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Mar 2026
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Open Access
Abstract: We present serial electron diffraction with tilt (t-SerialED), a method for fast autonomous phase and structural analysis of beam-sensitive, nano-sized polycrystalline materials. Unlike traditional workflows collecting datasets crystal by crystal, t-SerialED acquires datasets using a batch-by-batch approach, which speeds up the data acquisition. t-SerialED combines robust indexing from 3D reciprocal space with still-shot integration and merging methods from serial crystallography. t-SerialED enables high-throughput analysis of beam-sensitive, multi-phase mixtures across a wide range of materials, from nanoporous frameworks to pharmaceutical compounds. By resolving key challenges in serial crystallography such as indexing and preferred orientation, this method enables precise structure determination, including the visualization of guest molecules and non-covalent interactions like hydrogen bonding and proton charge transfer. Demonstrated on a range of samples from nanoporous materials to pharmaceuticals, t-SerialED expands the capabilities of serial chemical crystallography from single-phase to complex multi-phase systems. It can become a complementary method to traditional crystallography methods, offering a robust solution for routine quantitative phase analysis and structure determination.
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Oct 2025
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I15-1-X-ray Pair Distribution Function (XPDF)
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Janis
Timoshenko
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David
Kordus
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Jette K.
Mathiesen
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Uta
Hejral
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Patrik
Zeller
,
Gereon
Behrendt
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Eylül
Öztuna
,
Jihao
Wang
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Zahra
Gheisari
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Rene
Eckert
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Stephan
Reitmeier
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Andreas
Reitzmann
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Holger
Ruland
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Jan
Folke
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Thomas
Lunkenbein
,
Beatriz
Roldan Cuenya
Diamond Proposal Number(s):
[28439]
Open Access
Abstract: Sample homogeneity on the microscopic scale is critical for the reliable interpretation of x-ray absorption spectra collected in transmission mode. Unfortunately, it is not always easy to ensure it in practice. Especially in operando studies of catalysts and functional materials, the microstructure of the sample can evolve during its operation and even become the key descriptor for understanding structure-property relationships of the material, as exemplified by the transformations taking place in technical iron-based catalysts for ammonia synthesis under operating conditions. Here we present a simple approach for the identification and quantification of the material's microgranular structure effect on its x-ray absorption spectrum. We demonstrate that the quantitative information on the sizes of microscopic sample particles can be extracted from the observed distortions in the x-ray absorption near-edge structure spectra. The obtained insight can also be used to correct for the artifacts in extended x-ray absorption fine structure fitting, associated with the presence of microscopic inhomogeneities in the sample.
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Jul 2025
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[33014, 35357]
Open Access
Abstract: The increasing availability of ultrabright Light Sources is facilitating the study of smaller crystals at faster timescales but with an increased risk of severe X-ray damage, leading to developments in multi-crystal methods such as serial crystallography (SX). SX studies on crystals with small unit cells are challenging as very few reflections are recorded in a single data image, making it difficult to determine the orientation matrix for each crystal and thus preventing the combination of the data from all crystals for structure solution. We herein present a Small-Rotative Fixed-Target Serial Synchrotron Crystallography (SR-FT-SSX) methodology, in which rotation of the serial target through a small diffraction angle at each crystal delivers high-quality data, facilitating ab initio unit cell determination and atomic-scale structure solution. The method is benchmarked using microcrystals of the small-molecule photoswitch sodium nitroprusside dihydrate, obtaining complete data to dmin = 0.6 Å by combining just 66 partial datasets selected against rigorous quality criteria.
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Nov 2024
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I18-Microfocus Spectroscopy
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Diamond Proposal Number(s):
[31385]
Open Access
Abstract: A free-standing and compact reaction cell for combined in situ/operando x-ray spectroscopy, scattering, and imaging measurements at high pressures and high temperatures is described. The cell permits measurements under realistic operating conditions (up to 50 bar and 1000 °C), under static and flow conditions (up to 100 ml/min), over a wide range of hard x-ray energies, variable detection modes (transmission, fluorescence, and scattering), and at all angles of rotation. An operando XAS, x-ray fluorescence, x-ray computed tomography, and x-ray diffraction computed tomography case study on the reduction of a heterogeneous catalyst is presented to illustrate the performance of the reaction cell.
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Oct 2024
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I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[28859, 30113]
Open Access
Abstract: Here, the novel technique of extended-range high-energy-resolution fluorescence detection (XR-HERFD) has successfully observed the n = 2 satellite in manganese to a high accuracy. The significance of the satellite signature presented is many hundreds of standard errors and well beyond typical discovery levels of three to six standard errors. This satellite is a sensitive indicator for all manganese-containing materials in condensed matter. The uncertainty in the measurements has been defined, which clearly observes multiple peaks and structure indicative of complex physical quantum-mechanical processes. Theoretical calculations of energy eigenvalues, shake-off probability and Auger rates are also presented, which explain the origin of the satellite from physical n = 2 shake-off processes. The evolution in the intensity of this satellite is measured relative to the full Kα spectrum of manganese to investigate satellite structure, and therefore many-body processes, as a function of incident energy. Results demonstrate that the many-body reduction factor S02 should not be modelled with a constant value as is currently done. This work makes a significant contribution to the challenge of understanding many-body processes and interpreting HERFD or resonant inelastic X-ray scattering spectra in a quantitative manner.
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Jul 2024
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I23-Long wavelength MX
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Yishun
Lu
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Ramona
Duman
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James
Beilsten-Edmands
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Graeme
Winter
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Mark
Basham
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Gwyndaf
Evans
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Jos J. A. G.
Kamps
,
Allen M.
Orville
,
Hok-Sau
Kwong
,
Konstantinos
Beis
,
Wesley
Armour
,
Armin
Wagner
Open Access
Abstract: rocessing of single-crystal X-ray diffraction data from area detectors can be separated into two steps. First, raw intensities are obtained by integration of the diffraction images, and then data correction and reduction are performed to determine structure-factor amplitudes and their uncertainties. The second step considers the diffraction geometry, sample illumination, decay, absorption and other effects. While absorption is only a minor effect in standard macromolecular crystallography (MX), it can become the largest source of uncertainty for experiments performed at long wavelengths. Current software packages for MX typically employ empirical models to correct for the effects of absorption, with the corrections determined through the procedure of minimizing the differences in intensities between symmetry-equivalent reflections; these models are well suited to capturing smoothly varying experimental effects. However, for very long wavelengths, empirical methods become an unreliable approach to model strong absorption effects with high fidelity. This problem is particularly acute when data multiplicity is low. This paper presents an analytical absorption correction strategy (implemented in new software AnACor) based on a volumetric model of the sample derived from X-ray tomography. Individual path lengths through the different sample materials for all reflections are determined by a ray-tracing method. Several approaches for absorption corrections (spherical harmonics correction, analytical absorption correction and a combination of the two) are compared for two samples, the membrane protein OmpK36 GD, measured at a wavelength of λ = 3.54 Å, and chlorite dismutase, measured at λ = 4.13 Å. Data set statistics, the peak heights in the anomalous difference Fourier maps and the success of experimental phasing are used to compare the results from the different absorption correction approaches. The strategies using the new analytical absorption correction are shown to be superior to the standard spherical harmonics corrections. While the improvements are modest in the 3.54 Å data, the analytical absorption correction outperforms spherical harmonics in the longer-wavelength data (λ = 4.13 Å), which is also reflected in the reduced amount of data being required for successful experimental phasing.
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Jun 2024
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B18-Core EXAFS
I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[25824]
Open Access
Abstract: The application of X-ray spectro-microscopy to image changes in the chemical state in application areas such as catalysis, environmental science, or biological samples can be limited by factors such as the speed of measurement, the presence of dilute concentrations, radiation damage, and thermal drift during the measurement. We have adapted a reduced-order model approach, known as the discrete empirical interpolation method, which identifies how to optimally subsample the spectroscopic information, accounting for background variations in the signal, to provide an accurate approximation of an equivalent full spectroscopic measurement from the sampled material. This approach uses readily available prior information to guide and significantly reduce the sampling requirements impacting both the total X-ray dose and the acquisition time. The reduced-order model approach can be adapted more broadly to any spectral or spectro-microscopy measurement where a low-rank approximation can be made from prior information on the possible states of a system, and examples of the approach are presented.
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Mar 2024
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I08-Scanning X-ray Microscopy beamline (SXM)
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James
Everett
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Jake
Brooks
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Vindy Tjendana
Tjhin
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Frederik
Lermyte
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Ian
Hands-Portman
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Germán
Plascencia-Villa
,
George
Perry
,
Peter J.
Sadler
,
Peter B.
O’connor
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Joanna F.
Collingwood
,
Neil D.
Telling
Open Access
Abstract: The accumulation of amyloid plaques and increased brain redox burdens are neuropathological hallmarks of Alzheimer’s disease. Altered metabolism of essential biometals is another feature of Alzheimer’s, with amyloid plaques representing sites of disturbed metal homeostasis. Despite these observations, metal-targeting disease treatments have not been therapeutically effective to date. A better understanding of amyloid plaque composition and the role of the metals associated with them is critical. To establish this knowledge, the ability to resolve chemical variations at nanometer length scales relevant to biology is essential. Here, we present a methodology for the label-free, nanoscale chemical characterization of amyloid plaques within human Alzheimer’s disease tissue using synchrotron X-ray spectromicroscopy. Our approach exploits a C–H carbon absorption feature, consistent with the presence of lipids, to visualize amyloid plaques selectively against the tissue background, allowing chemical analysis to be performed without the addition of amyloid dyes that alter the native sample chemistry. Using this approach, we show that amyloid plaques contain elevated levels of calcium, carbonates, and iron compared to the surrounding brain tissue. Chemical analysis of iron within plaques revealed the presence of chemically reduced, low-oxidation-state phases, including ferromagnetic metallic iron. The zero-oxidation state of ferromagnetic iron determines its high chemical reactivity and so may contribute to the redox burden in the Alzheimer’s brain and thus drive neurodegeneration. Ferromagnetic metallic iron has no established physiological function in the brain and may represent a target for therapies designed to lower redox burdens in Alzheimer’s disease. Additionally, ferromagnetic metallic iron has magnetic properties that are distinct from the iron oxide forms predominant in tissue, which might be exploitable for the in vivo detection of amyloid pathologies using magnetically sensitive imaging. We anticipate that this label-free X-ray imaging approach will provide further insights into the chemical composition of amyloid plaques, facilitating better understanding of how plaques influence the course of Alzheimer’s disease.
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Mar 2024
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[22240]
Open Access
Abstract: Single-crystal X-ray diffraction analysis of small molecule active pharmaceutical ingredients is a key technique in the confirmation of molecular connectivity, including absolute stereochemistry, as well as the solid-state form. However, accessing single crystals suitable for X-ray diffraction analysis of an active pharmaceutical ingredient can be experimentally laborious, especially considering the potential for multiple solid-state forms (solvates, hydrates and polymorphs). In recent years, methods for the exploration of experimental crystallization space of small molecules have undergone a `step-change', resulting in new high-throughput techniques becoming available. Here, the application of high-throughput encapsulated nanodroplet crystallization to a series of six dihydropyridines, calcium channel blockers used in the treatment of hypertension related diseases, is described. This approach allowed 288 individual crystallization experiments to be performed in parallel on each molecule, resulting in rapid access to crystals and subsequent crystal structures for all six dihydropyridines, as well as revealing a new solvate polymorph of nifedipine (1,4-dioxane solvate) and the first known solvate of nimodipine (DMSO solvate). This work further demonstrates the power of modern high-throughput crystallization methods in the exploration of the solid-state landscape of active pharmaceutical ingredients to facilitate crystal form discovery and structural analysis by single-crystal X-ray diffraction.
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Dec 2023
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