Show Abstract ▼

Abstract: The development and growth of heterogeneous catalysis are directly connected to the knowledge of the structure and associated changes that arise from reactions it has, under specific environmental conditions. In liquid phase catalysed reactions, which was the focus of this thesis, information associated with the reaction, e.g. the active site, is often difficult to obtain due to the solvent being present at higher quantities in comparison to the much smaller quantity of active species. Additionally, difficulties associated with the characterisation of such systems arise from the frequently short lifetime of active species, and the tendency of catalytic events to occur on the surface of the catalyst, with the bulk structure barely participating in any reactions. The purpose of this thesis was to conduct a research study, integrating modulation excitation (ME) approach with total neutron scattering (TNS) and X-ray absorption spectroscopy (XAS) techniques. The combination of periodic modulation excitation with phase-sensitive detection (PSD) analysis, and their integration within TNS and XAS, allowed us to probe surface structural changes. This approach demonstrated an enhanced signal-to-noise ratio of the experimental data and significantly improved the sensitivity of the respective instruments to weak component contributions. Periodic electrical potential switches were employed as external stimulations to perturb the investigated systems reversibly and measure the active species contributions. In contrast to XAS, where ME methodology has been extensively implemented to the study of gas-phase catalytic reactions and most recently to liquid-phase catalytic reactions; combined ME-TNS studies is a novel approach that was successfully developed and demonstrated for the first time in this thesis. Ultimately, the essential instrumentation and innovative analysis procedures to extract useful structural information from the newly acquired ME-TNS data are demonstrated in the results chapters of this thesis. Finally, the ME technique was implemented at the Energy Dispersive EXAFS (EDE) branch of the I20 X-ray absorption spectroscopy beamline at Diamond Light Source, while the NIMROD instrument at ISIS neutron and muon source was developed to enable it to obtain ME-neutron scattering data.

Open Access

Show Abstract ▼

Abstract: Archaea produce various protein filaments with specialised functions. While some archaea produce only one type of filament, the archaeal model species Sulfolobus acidocaldarius generates four. These include rotary swimming propellers analogous to bacterial flagella (archaella), pili for twitching motility (Aap), adhesive fibres (threads), and filaments facilitating homologous recombination upon UV stress (UV pili). Here, we use cryo-electron microscopy to describe the structure of the S. acidocaldarius archaellum at 2.0 Å resolution, and update the structures of the thread and the Aap pilus at 2.7 Å and 2.6 Å resolution, respectively. We define features unique to archaella of the order Sulfolobales and compare their structure to those of Aap and threads in the context of the S-layer. We define distinct N-glycan patterns in the three filaments and identify a putative O-glycosylation site in the thread. Finally, we ascertain whether N-glycan truncation leads to structural changes in archaella and Aap.

Open Access

Show Abstract ▼

Abstract: The ‘Beamline Jockey Meetings’ is a regular series of events, aimed at bringing the ­European synchrotron tomography scientist community to together, sharing ideas and challenges about the day-to-day work at their beamlines. The latest session took place at the Hamburg (Germany) outstation of the Helmholtz-Zentrum Hereon at the DESY site, June 25–26, 2024.

Open Access

Show Abstract ▼

Abstract: Protein–inhibitor crystal structures aid medicinal chemists in efficiently improving the potency and selectivity of small-molecule inhibitors. It is estimated that a quarter of lead molecules in drug discovery projects are halogenated. Protein–inhibitor crystal structures have shed light on the role of halogen atoms in ligand binding. They form halogen bonds with protein atoms and improve shape complementarity of inhibitors with protein binding sites. However, specific radiation damage (SRD) can cause cleavage of carbon–halogen (C–X) bonds during X-ray diffraction data collection. This study shows significant C–X bond cleavage in protein–ligand structures of the therapeutic cancer targets B-cell lymphoma 6 (BCL6) and heat shock protein 72 (HSP72) complexed with halogenated ligands, which is dependent on the type of halogen and chemical structure of the ligand. The study found that metrics used to evaluate the fit of the ligand to the electron density deteriorated with increasing X-ray dose, and that SRD eliminated the anomalous signal from brominated ligands. A point of diminishing returns is identified, where collecting highly redundant data reduces the anomalous signal that may be used to identify binding sites of low-affinity ligands or for experimental phasing. Straightforward steps are proposed to mitigate the effects of C–X bond cleavage on structures of proteins bound to halogenated ligands and to improve the success of anomalous scattering experiments.

Open Access

Show Abstract ▼

Abstract: We present a novel operando X-ray absorption spectroscopic (XAS) flow cell, consisting of a gas chamber for CO2 and a liquid chamber for the electrolyte, to monitor electrochemical CO2 reduction (eCO2R) over a gas diffusion electrode (GDE). The feasibility of the flow cell is demonstrated by collecting XAS data (during eCO2R over Cu-GDE) in a transmission mode at the Cu K-edge. The dynamic behaviour of copper during eCO2R is captured by XAS which is complemented by quasi in situ Raman and X-ray photoelectron spectroscopy (XPS). The linear combination analyses (LCA) of X-ray absorption near edge structure (XANES) indicate that copper oxides are the only species present during the first 20 min of eCO2R, corroborated by complementary Raman and XPS. Significantly, the complementary spectroscopic data suggests that the copper composition in the bulk and on the surface Cu-GDE evolve differently at and above 30 min of eCO2R. LCA indicates that at 60 min, 77% of copper occurs as metallic Cu and the remainder 23% in Cu (II) oxidation state, which is not evident from XPS that shows 100% of copper in < 2+ oxidation state. Thus, the Cu (II) is probably in the bulk of Cu-GDE, as also evident from Raman. The ethylene formation correlates very well with the occurrence of copper oxides and hydroxide species in Cu-GDE. The results not only demonstrate the applicability and versatility of the operando XAS GDE flow cell, but also illustrate the unique advantages of combining XAS with complementary Raman and XPS that enables the monitoring of the catalyst structural evolution from the bulk to surface and surface adsorbed species.