I19-Small Molecule Single Crystal Diffraction
|
Diamond Proposal Number(s):
[17379]
Abstract: We report on the stereoselective synthesis of trefoil knots of single topological handedness in up to 90 % yield (over two steps), through the formation of trimeric circular helicates from ligand strands containing either imine or, unexpectedly, amide chelating units and metal ion templates of the appropriate coordination character (zinc(II) for imines; cobalt(III) for amides). The coordination stereochemistry of the octahedral metal complexes is determined by asymmetric carbon centers in the strands, ulti-mately translating into trefoil knots that are a single enantiomer, both physically and in terms of their fundamental topology. Both the imine-zinc and amide-cobalt systems display self-sorting behavior, with racemic ligands forming knots that individually contain only building blocks of the same chirality. The knots and the corresponding trimeric circular helicate intermediates (Zn(II)3 com-plex for the imine ligands; Co(III)3 complex for the amide ligands) were characterized by NMR spectroscopy, mass spectrometry and X-ray crystallography. The latter confirms the trefoil knots as 84-membered macrocycles with each of the metal ions sited at crossing points for three parts of the strand. The stereochemistry of the octahedral coordination centers impart alternating crossings of the same handedness. The expression of chirality of the knotted molecules was probed by circular dichroism: the topological handedness of the demetallated knots was found to have a greater effect on the CD response than the Euclidean chirality of individual chiral centers.
|
Aug 2019
|
|
I22-Small angle scattering & Diffraction
|
Diamond Proposal Number(s):
[16256]
Open Access
Abstract: The controlled crystallisation of struvite (MgNH4PO4∙6H2O) is a viable means for the recovery and recycling of phosphorus (P) from municipal and industrial wastewaters. However, an efficient implementation of this recovery method in water treatment systems requires a fundamental understanding of struvite crystallisation mechanisms, including the behavior and effect of metal contaminants during struvite precipitation. Here, we studied the crystallisation pathways of struvite from aqueous solutions using a combination of ex situ and in situ time-resolved synthesis and characterization techniques, including synchrotron-based small- and wide-angle X-ray scattering (SAXS/WAXS) and cryogenic transmission electron microscopy (cryo-TEM). Struvite syntheses were performed both in the pure Mg-NH4-PO4 system as well as in the presence of cobalt (Co), which, among other metals, is typically present in waste streams targeted for P-recovery. Our results show that in the pure system and at Co concentrations < 0.5 mM, struvite crystals nucleate and grow directly from solution, much in accordance with the classical notion of crystal formation. In contrast, at Co concentrations ≥ 1 mM, crystallisation was preceded by the transient formation of an amorphous nanoparticulate phosphate phase. Depending on the aqueous Co/P ratio, this amorphous precursor was found to transform into either (i) Co-bearing struvite (at Co/P < 0.3) or (ii) cobalt phosphate octahydrate (at Co/P > 0.3). These amorphous-to-crystalline transformations were accompanied by a marked colour change from blue to pink, indicating a change in Co2+ coordination in the formed solid from tetrahedral to octahedral. Our findings have implications for the recovery of nutrients and metals during struvite crystallisation and contribute to the ongoing general discussion about the mechanisms of crystal formation.
|
Aug 2019
|
|
I11-High Resolution Powder Diffraction
|
Abstract: Metal–organic framework nanosheets (MONs) are attracting increasing attention as a diverse class of two-dimensional materials derived from metal–organic frameworks (MOFs). The principles behind the design of layered MOFs that can readily be exfoliated to form nanosheets, however, remain poorly understood. Here we systematically investigate an isoreticular series of layered MOFs functionalized with alkoxy substituents in order to understand the effect of substituent alkyl chain length on the structure and properties of the resulting nanosheets. A series of 2,5-alkoxybenzene-1,4-dicarboxylate ligands (O2CC6H2(OR)2CO2, R = methyl–pentyl, 1–5, respectively) was used to synthesize copper paddle-wheel MOFs. Rietveld and Pawley fitting of powder diffraction patterns for compounds Cu(3–5)(DMF) showed they adopt an isoreticular series with two-dimensional connectivity in which the interlayer distance increases from 8.68 Å (R = propyl) to 10.03 Å (R = pentyl). Adsorption of CO2 by the MOFs was found to increase from 27.2 to 40.2 cm3 g–1 with increasing chain length, which we attribute to the increasing accessible volume associated with increasing unit-cell volume. Ultrasound was used to exfoliate the layered MOFs to form MONs, with shorter alkyl chains resulting in higher concentrations of exfoliated material in suspension. The average height of MONs was investigated by AFM and found to decrease from 35 ± 26 to 20 ± 12 nm with increasing chain length, with the thinnest MONs observed being only 5 nm, corresponding to five framework layers. These results indicate that careful choice of ligand functionalities can be used to tune nanosheet structure and properties, enabling optimization for a variety of applications.
|
Aug 2019
|
|
I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
|
Diamond Proposal Number(s):
[14744, 10627]
Open Access
Abstract: Semaphorin ligands and their plexin receptors are one of the major cell guidance factors that trigger localised changes in the cytoskeleton. Binding of semaphorin homodimer to plexin brings two plexins in close proximity which is a prerequisite for plexin signalling. This model appears to be too simplistic to explain the complexity and functional versatility of these molecules. Here, we determine crystal structures for all members of Drosophila class 1 and 2 semaphorins. Unlike previously reported semaphorin structures, Sema1a, Sema2a and Sema2b show stabilisation of sema domain dimer formation via a disulfide bond. Unexpectedly, our structural and biophysical data show Sema1b is a monomer suggesting that semaphorin function may not be restricted to dimers. We demonstrate that semaphorins can form heterodimers with members of the same semaphorin class. This heterodimerization provides a potential mechanism for cross-talk between different plexins and co-receptors to allow fine-tuning of cell signalling.
|
Aug 2019
|
|
B21-High Throughput SAXS
|
Diamond Proposal Number(s):
[8311]
Abstract: IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the rate-limiting step in the de novo guanine nucleotide biosynthetic pathway. Because of its involvement in the control of cell division and proliferation, IMPDH represents a therapeutic for managing several diseases, including microbial infections and cancer. IMPDH must be tightly regulated, but the molecular mechanisms responsible for its physiological regulation remain unknown. To this end, we recently reported an important role of adenine and guanine mononucleotides that bind to the regulatory Bateman domain to allosterically modulate the catalytic activity of eukaryotic IMPDHs. Here, we have used enzyme kinetics, X-ray crystallography, and small angle Xray scattering (SAXS) methodologies to demonstrate that adenine/guanine dinucleoside polyphosphates bind to the Bateman domain of IMPDH from the fungus Ashbya gossypii with submicromolar affinities. We found that these dinucleoside polyphosphates modulate the catalytic activity of IMPDHs in vitro by efficiently competing with the adenine/guanine mononucleotides for the allosteric sites. These results suggest that dinucleoside polyphosphates play important physiological roles in the allosteric regulation of IMPDHs by adding an additional mechanism for fine-tuning the activities of these enzymes. We propose that these findings may have important implications for the design of therapeutic strategies to inhibit IMPDHs.
|
Aug 2019
|
|
I10-Beamline for Advanced Dichroism
|
Diamond Proposal Number(s):
[22532]
Abstract: Interlayer interactions in layered transition metal dichalcogenides are known to be important for describing their electronic properties. Here, we demonstrate that the absence of interlayer coupling in monolayer VTe2 also causes their structural modification from a distorted 1T′ structure in bulk and multilayer samples to a hexagonal 1T structure in the monolayer. X-ray photoemission spectroscopy indicates that this structural transition is associated with electron transfer from the vanadium d bands to the tellurium atoms for the monolayer. This charge transfer may reduce the in-plane d orbital hybridization and thus favor the undistorted 1T structure. Phonon-dispersion calculations show that, in contrast to the 1T′ structure, the 1T structure exhibits imaginary phonon modes that lead to a charge density wave (CDW) instability, which is also observed by low-temperature scanning tunneling microscopy as a 4 × 4 periodic lattice distortion. Thus, this work demonstrates a novel CDW material, whose properties are tuned by interlayer interactions.
|
Aug 2019
|
|
E02-JEM ARM 300CF
|
Abstract: It is shown that tilt grain boundaries (GBs) in bilayer 2D crystals of the transition metal dichalcogenide WS2 can be atomically sharp, where top and bottom layer GBs are located within sub‐nanometer distances of each other. This expands the current knowledge of GBs in 2D bilayer crystals, beyond the established large overlapping GB types typically formed in chemical vapor deposition growth, to now include atomically sharp dual bilayer GBs. By using atomic‐resolution annular dark‐field scanning transmission electron microscopy (ADF‐STEM) imaging, different atomic structures in the dual GBs are distinguished considering bilayers with a 3R (AB stacking)/2H (AA′ stacking) interface as well as bilayers with 2H/2H boundaries. An in situ heating holder is used in ADF‐STEM and the GBs are stable to at least 800 °C, with negligible thermally induced reconstructions observed. Normal dislocation cores are seen in one WS2 layer, but the second WS2 layer has different dislocation structures not seen in freestanding monolayers, which have metal‐rich clusters to accommodate the stacking mismatch of the 2H:3R interface. These results reveal the competition between maintaining van der Waals bilayer stacking uniformity and dislocation cores required to stitch tilted bilayer GBs together.
|
Aug 2019
|
|
I19-Small Molecule Single Crystal Diffraction
|
Diamond Proposal Number(s):
[17379]
Abstract: We report a family of hybrid [2]rotaxanes based on inorganic [Cr7NiF8(O2CtBu)16]- (“{Cr7Ni}”) rings templated about organic threads that are terminated at one end with pyridyl groups. These rotaxanes can be coordinated to [Cu(hfac)2] (where hfac = 1,1,1,5,5,5-hexafluoroacetylacetone), to give 1:1 or 1:2 Cu:{Cr7Ni} adducts: {[Cu(hfac)2](py-CH2NH2CH2CH2Ph)[Cr7NiF8(O2CtBu)16]}, {[Cu(hfac)2][py-CH2NH2CH2CH3][Cr7NiF8(O2CtBu)16]}, {[Cu(hfac)2]([py-CH2CH2NH2CH2C6H4SCH3][Cr7NiF8(O2CtBu)16])2}, {[Cu(hfac)2]([py-C6H4-CH2NH2(CH2)4Ph][Cr7NiF8(O2CtBu)16])2}, and {[Cu(hfac)2]([3-py-CH2CH2NH2(CH2)3SCH3][Cr7NiF8(O2CtBu)16])2}, the structures of which have been determined by X-ray diffraction. The {Cr7Ni} rings and CuII ions both have electronic spin S = ½, but with very different g-values. Continuous-wave EPR spectroscopy reveals the exchange interactions between these dissimilar spins, and hence the communication between the different molecular components that comprise these supramolecular systems. The interactions are weak such that we observe AX or AX2 type spectra. The connectivity between the {Cr7Ni} ring and thread terminus is varied such that the magnitude of the exchange interaction J can be tuned. The coupling is shown to be dominated by through-bond rather than through-space mechanisms.
|
Aug 2019
|
|
I03-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[10515]
Abstract: Hydrogenases are metalloenzymes that catalyze the redox conversion between H2 and protons. The so-called [NiFeSe] hydrogenases are highly active for both H2 production and oxidation, but like all hydrogenases, they are inhibited by O2. In the [NiFeSe] enzyme from Desulfovibrio vulgaris Hildenborough this results from the oxidation of an active site cysteine ligand. We designed mutations that constrict a hydrophilic channel that connects the protein surface to this active site cysteine. Two of the variants show markedly increased tolerance to O2 inactivation, while retaining high catalytic activities in both directions of the reaction, and structural studies confirm that these mutations prevent the oxidation of the cysteine. Our results indicate that the diffusion of O2 or ROS to the active site can occur through a hydrophilic water channel, in contrast to the widely held assumption that only hydrophobic channels are involved in active site inactivation. This provides an original strategy for optimizing the enzyme by protein engineering.
|
Aug 2019
|
|
I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[12342, 17212]
Abstract: Clostridioides difficile is the primary cause of antibiotic-associated diarrhoea and colitis, a healthcare-associated intestinal disease resulting in a significant fatality rate. Colonization of the gut is critical for C. difficile pathogenesis, and the bacterial molecules essential for efficient colonization therefore offer great potential as vaccine candidates. Here we present findings demonstrating that the C. difficile immunogenic lipoprotein CD0873 plays a critical role in pathogen success in vivo. We found that in a dixenic colonization model, a CD0873-positive strain of C. difficile significantly outcompeted a CD0873-negative strain. Immunization of mice with recombinant CD0873 prevented long-term gut colonization and was correlated with a strong secretory IgA immune response. We further present high-resolution crystal structures of CD0873, at 1.80-2.50 Å resolutions, offering a first view of the ligand-binding pocket of CD0873 and provide evidence that this lipoprotein adhesin is part of a tyrosine import system, an amino acid key in C. difficile infection. These findings suggest that CD0873 could serve as a effective component in a vaccine against C. difficile.
|
Aug 2019
|
|
