I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[20552]
Open Access
Abstract: Most metallodrugs are prodrugs that can undergo ligand exchange and redox reactions in biological media. Here we have investigated the cellular stability of the anticancer complex [OsII[(η6‐p‐cymene)(RR/SS‐MePh‐DPEN)] [1] (MePh‐DPEN=tosyl‐diphenylethylenediamine) which catalyses the enantioselective reduction of pyruvate to lactate in cells. The introduction of a bromide tag at an unreactive site on a phenyl substituent of Ph‐DPEN allowed us to probe the fate of this ligand and Os in human cancer cells by a combination of X‐ray fluorescence (XRF) elemental mapping and inductively coupled plasma‐mass spectrometry (ICP‐MS). The BrPh‐DPEN ligand is readily displaced by reaction with endogenous thiols and translocated to the nucleus, whereas the Os fragment is exported from the cells. These data explain why the efficiency of catalysis is low, and suggests that it could be optimised by developing thiol resistant analogues. Moreover, this work also provides a new way for the delivery of ligands which are inactive when administered on their own.
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Feb 2021
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[13284]
Open Access
Abstract: Yb6(BDC)7(OH)4(H2O)4 contains both bridging hydroxyls and metal-coordinated waters, possessing Brønsted and Lewis acid sites. The material crystallises from water at 200 °C. Using the solid as a heterogenous catalyst, glucose is converted into 5-hydroxymethylfurfural, via fructose, with a total selectivity of ∼70% after 24 hours at 140 °C in water alone: the material is recyclable with no loss of crystallinity.
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Sep 2019
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B18-Core EXAFS
I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[14239, 13284]
Abstract: The rhodium(III) hydrogarnets Ca3Rh2(OH)12 and Sr3Rh2(OH)12 crystallize as polycrystalline powders under hydrothermal conditions at 200 °C from RhCl3·3H2O and either Ca(OH)2 or Sr(OH)2 in either 12 M NaOH or KOH. Rietveld refinements against synchrotron powder X-ray diffraction (XRD) data allow the first crystal structures of the two materials to be determined. If BaO2 is used as a reagent and the concentration of hydroxide increased to hydroflux conditions (excess NaOH), then single crystals of a new complex rhodium hydroxide, BaNaRh(OH)6, are formed in a phase-pure sample, with sodium included from the flux. Structure solution from single-crystal XRD data reveals isolated octahedral Rh centers that share hydroxides with 10-coordinate Ba and two independent 8-coordinate Na sites. 23Na magic-angle spinning NMR confirms the presence of the two crystallographically distinct Na sites and also verifies the diamagnetic nature of the sample, expected for Rh(III). The thermal behavior of the hydroxides on heating in air was investigated using X-ray thermodiffractometry, showing different decomposition pathways for each material. Ca3Rh2(OH)12 yields CaRh2O4 and CaO above 650 °C, from which phase-pure CaRh2O4 is isolated by washing with dilute nitric acid, a material previously only reported by high-pressure or high-temperature synthesis. Sr3Rh2(OH)12 decomposes to give a less crystalline material with a powder XRD pattern that is matched to the 2H-layered hexagonal perovskite Sr6Rh5O15, which contains mixed-valent Rh3+/4+, confirmed by Rh K-edge XANES spectroscopy. On heating BaNaRh(OH)6, a complex set of decomposition events takes place via transient phases.
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Aug 2018
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[11070]
Abstract: The templated zeolite-analogue GaPO-34 (CHA structure type) crystallises from a gel precursor Ga2O3:2H3PO4:1HF:1.7SDA:70H2O (where SDA = structure directing agent), treated hydrothermally for 24 hours at 170 °C using either pyridine or 1-methylimizadole as SDA and one of either poorly crystalline ε-Ga2O3 or γ-Ga2O3 as gallium precursor. If the same gels are stirred for periods shorter than 2 hours but treated under identical hydrothermal conditions, then a second phase crystallises, free of GaPO-34. If β-Ga2O3 is used as a reagent only the second phase is found to crystallise, irrespective of gel aging time. The competing phase, which we denote GaPO-34A, has been structurally characterised using synchrotron powder X-ray diffraction for the pyridine material, GaPO-34A(pyr), and using single-crystal X-ray diffraction for the 1-methylimiazole material, GaPO-34A(mim). The structure of GaPO-34A(pyr), P1 , a = 10.22682(6) Å, b = 12.09585(7) Å, c = 13.86713(8) Å, α = 104.6531(4) °, β = 100.8111(6) °, γ = 102.5228(6) °, contains 7 unique gallium sites and 6 phosphorus sites, with empirical formula [Ga7P6O24(OH)2F3(H2O)2].2(C5NH6). GaPO-34A(mim) is isostructural but is modelled as a half volume unit cell, P1 , a = 5.0991(2) Å, b = 12.0631(6) Å, c = 13.8405(9) Å, α = 104.626(5) °, β = 100.346(5) °, γ = 101.936(4) °, with a gallium and a bridging fluoride partially occupied and two partially occupied SDA sites. Solid-state 31P and 71Ga NMR spectroscopy confirms the structural complexity of GaPO-34A with signals resulting from overlapping lineshapes from multiple Ga and P sites, while 1H and 13C solid-state NMR spectra confirm the presence of the protonated SDA and provide evidence for disorder in the SDA. The protonated SDA is located in 14-ring one-dimensional channels with hydrogen bonding deduced from the SDA nitrogens to framework oxygen distances. Upon thermal treatment to investigate SDA removal, structure collapse occurs, which may be due the large number of bridging hydroxides and fluorides in the as-made material, and the unequal amounts of gallium and phosphorus present.
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Nov 2017
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I11-High Resolution Powder Diffraction
I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[7303, 7645]
Abstract: The ytterbium 1,4-benzenedicarboxylate (BDC) framework [Yb2(BDC)3(DMF)2]·H2O (1) crystallises from a N,N-dimethylformamide (DMF)-rich solution at 80–120 °C. (1) is constructed from infinite chains of dicarboxylate-bridged seven-coordinate Yb atoms, cross-linked in two directions by BDC to yield diamond-shaped channels (sra topology) lined by coordinated DMF molecules and occluded water. Increasing the water content in the synthesis solution yields a material with more crystal water Yb2(BDC)3(DMF)2(H2O)2 (2), in which the Yb centres are eight-coordinate and form dimers bridged by BDC to give two interpenetrating networks of pcu (α-Po) topology. Upon extended reaction in this water-rich solvent mixture, an alternative phase is formed: an anhydrous mixed BDC-formate, Yb(BDC)(HCO2), (3), which has a pillared, layered structure, with formate produced by hydrolysis of the DMF. An isoreticular version of (2) can also be formed under similar conditions using 2,6-naphthalene-dicarboxylate (NDC) as linker: [Yb2(NDC)3(H2O)4]·2DMF (4). Despite their different structures, (1) and (2) are calcined to a common porous, desolvated phase Yb2(BDC)3 at 300 °C. Using high energy X-rays at Diamond Light Source we are able to penetrate the solvothermal reaction vessels and to follow the formation of (1) and (2) in real time. This allows accurate crystallisation curves to be obtained from which qualitative kinetic information is extracted. Importantly, the high angular resolution of the in situ powder XRD patterns allows refinement of crystal structure: this permits the temporal evolution of unit cell parameters to be followed, which are ascribed to changes in coordinated solvent composition within the materials during their formation, while analysis of phase fraction allows kinetic parameters to be quantified using the nucleation-growth model of Gualtieri.
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Apr 2017
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I12-JEEP: Joint Engineering, Environmental and Processing
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Open Access
Abstract: Using time-resolved monochromatic high energy X-ray diffraction, we present an in situ study of the solvothermal crystallisation of a new MOF [Yb2(BDC)3(DMF)2]⋅H2O (BDC=benzene-1,4-dicarboxylate and DMF=N,N-dimethylformamide) under solvothermal conditions, from mixed water/DMF solvent. Analysis of high resolution powder patterns obtained reveals an evolution of lattice parameters and electron density during the crystallisation process and Rietveld analysis shows that this is due to a gradual topochemical replacement of coordinated solvent molecules. The water initially coordinated to Yb3+ is replaced by DMF as the reaction progresses.
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Apr 2016
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[7303]
Open Access
Abstract: Using time-resolved monochromatic high energy X-ray diffraction, we present an in situ study of the solvothermal crystallisation of a new MOF [Yb2(BDC)3(DMF)2]⋅H2O (BDC=benzene-1,4-dicarboxylate and DMF=N,N-dimethylformamide) under solvothermal conditions, from mixed water/DMF solvent. Analysis of high resolution powder patterns obtained reveals an evolution of lattice parameters and electron density during the crystallisation process and Rietveld analysis shows that this is due to a gradual topochemical replacement of coordinated solvent molecules. The water initially coordinated to Yb3+ is replaced by DMF as the reaction progresses
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Mar 2016
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B18-Core EXAFS
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Abstract: The synthesis and structures of metal-organic framework materials with three-dimensional structures related to the well-known MIL-53 framework are described. These have general chemical formula M(BDC)(PNO), where BDC = 1,4-benzenedicarboxylate, PNO = pyridine-N-oxide, and M =Mn, Co or Ni.
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Aug 2013
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I24-Microfocus Macromolecular Crystallography
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Open Access
Abstract: Background
Many critical cellular functions are performed by multisubunit circular protein oligomers whose internal geometry has evolved to meet functional requirements. The subunit number is arguably the most critical parameter of a circular protein assembly, affecting the internal and external diameters of the assembly and often impacting on the protein's function. Although accurate structural information has been obtained for several circular proteins, a lack of accurate information on alternative oligomeric states has prevented engineering such transitions. In this study we used the bacterial transcription regulator TRAP as a model system to investigate the features that define the oligomeric state of a circular protein and to question how the subunit number could be manipulated.
Methodology/Principal Findings
We find that while Bacillus subtilis and Bacillus stearothermophilus TRAP form 11-subunit oligomers, the Bacillus halodurans TRAP exclusively forms 12-subunit assemblies. Significantly, the two states of TRAP are related by a simple rigid body rotation of individual subunits around inter-subunit axes. We tested if such a rotation could be induced by insertion or deletion mutations at the subunit interface. Using wild type 11-subunit TRAP, we demonstrate that removal of five C-terminal residues at the outer side of the inter-subunit axis or extension of an amino acid side chain at the opposite, inner side, increased the subunit number from 11 to 12. Our findings are supported by crystal structures of TRAP oligomers and by native mass spectrometry data.
Conclusions/Significance
The subunit number of the TRAP oligomer can be manipulated by introducing deletion or addition mutations at the subunit interface. An analysis of available and emerging structural data on alternative oligomeric states indicates that the same principles may also apply to the subunit number of other circular assemblies suggesting that the deletion/addition approach could be used generally to engineer transitions between different oligomeric states.
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Oct 2011
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B18-Core EXAFS
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Diamond Proposal Number(s):
[2451]
Abstract: We report the results of an exploratory synthetic study of iridium-containing materials using hydrothermal methods from simple metal salts. Three alkali-earth iridium hydroxides are isolated as phase-pure samples and their structures examined by single-crystal or powder diffraction methods: each contains Ir(IV)-centred octahedra, isolated from each other and sharing bridging hydroxides or fluoride with alkali-earth (Ca, Sr or Ba) centres. One of these hydroxides, Ca(2)IrF(OH)(6)center dot OH, possesses a unique open structure, consisting of a positively-charged framework that has one-dimensional channels in which infinite chains of hydrogen-bonded hydroxide anions are encapsulated. The addition of hydrogen peroxide or sodium peroxide to otherwise identical hydrothermal reactions yields dense oxide materials in which iridium is found in an oxidation state between +4 and +5: the novel oxide Na(0.8)Sr(2.2)Ir(3)O(10.1) has a KSbO(3)-type structure with an iridium oxidation state of +5, while the new pyrochlore (Na(0.27)Ca(0.59))(2)Ir(2)O(6)center dot 0.66H(2)O contains iridium with an average oxidation state close to +4.5. Our results illustrate the utility for hydrothermal synthesis in the discovery of novel complex structures that may be inaccessible using conventional high-temperature synthesis, with control of the metal oxidation state possible with judicious choice of reagents.
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May 2011
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