I11-High Resolution Powder Diffraction
I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[21726, 23666]
Abstract: Three-dimensional (3D) covalent organic frameworks (COFs) are rare because there is a limited choice of organic building blocks that offer multiple reactive sites in a polyhedral geometry. Here, we synthesized an organic cage molecule (cage-6-NH2), which was used as a triangular prism node to yield the first cage-based 3D COF, 3D-CageCOF-1. This COF adopts an unreported twofold interpenetrated acs topology and exhibits reversible dynamic behavior, switching between a small-pore (sp) structure and a large-pore (lp) structure. It also shows high CO2 uptake and captures water at low humidity (<40%). This demonstrates the potential for expanding the structural complexity of 3D COFs by using organic cages as the building units.
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Sep 2020
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B18-Core EXAFS
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Diamond Proposal Number(s):
[17377, 19072]
Abstract: Understanding and tuning the catalytic properties of metals atomically dispersed on oxides are major stepping-stones towards a rational development of single-atom catalysts (SACs). Beyond individual showcase studies, the design and synthesis of structurally regular series of SACs opens the door to systematic experimental investigations of performance as a function of metal identity. Herein, a series of single-atom catalysts based on various 4d (Ru, Rh, Pd) and 5d (Ir, Pt) transition metals has been synthesized on a common MgO carrier. Complementary experimental (X-ray absorption spectroscopy) and theoretical (Density Functional Theory) studies reveal that, regardless of the metal identity, metal cations occupy preferably octahedral coordination MgO lattice positions under step-edges, hence highly confined by the oxide support. Upon exposure to O2-lean CO oxidation conditions, FTIR spectroscopy indicates the partial de-confinement of the monoatomic metal centers driven by CO at pre-catalysis temperatures, followed by the development of surface carbonate species under steady-state conditions. These findings are supported by DFT calculations, which show the driving force and final structure for the surface metal protrusion to be metal-dependent, but point to an equivalent octahedral-coordinated M4+ carbonate species as the resting state in all cases. Experimentally, apparent reaction activation energies in the range of 96±19 kJ/mol are determined, with Pt leading to the lowest energy barrier. The results indicate that, for monoatomic sites in SACs, differences in CO oxidation reactivity enforceable via metal selection are of lower magnitude than those evidenced previously through the mechanistic involvement of adjacent redox centers on the oxide carrier, suggesting that tuning of the oxide surface chemistry is as relevant as the selection of the supported metal.
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Aug 2020
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[17379]
Abstract: The synthesis, structures and properties of [4]- and [3]-rotaxane complexes are reported where [2]rotaxanes, formed from het-erometallic {Cr7Ni} rings, are bound to a fluoride-centered {CrNi2} triangle. The compounds have been characterized by sin-gle crystal X-ray diffraction and have the formulae [CrNi2(F)(O2CtBu)6]{(BH)[Cr7NiF8(O2CtBu)16]}3 (3) and [CrNi2(F)(O2CtBu)6(THF)]{(BH)[Cr7NiF8(O2CtBu)16]}2 (4); where B = py-CH2CH2NHCH2C6H4SCH3. The [4]rotaxane 3 is an isosceles triangle of three [2]rotaxanes bound to the central triangle while the [3]rotaxane 4 contains only two [2]rotaxanes bound to the central triangle. Studies of the behavior of 3 and 4 in solution by small angle X-ray scattering (SAXS) and atomistic molecular dynamic simulations (AMDS) show that the structure of 3 is similar to that found in the crystal but that 4 has a different conformation to the crystal. C.w. and pulsed EPR spectroscopy were used to study the structures present and demonstrate that in frozen solutions (at 5 K) 4 forms more extended molecules than 3 and with a wider range of confor-mations.
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Aug 2020
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Vivek
Srinivas
,
Rahul
Banerjee
,
Hugo
Lebrette
,
Jason C.
Jones
,
Oskar
Aurelius
,
In-sik
Kim
,
Cindy C.
Pham
,
Sheraz
Gul
,
Kyle
Sutherlin
,
Asmit
Bhowmick
,
Juliane
John
,
Esra
Bozkurt
,
Thomas
Fransson
,
Pierre
Aller
,
Agata
Butryn
,
Isabel
Bogacz
,
Philipp Stefan
Simon
,
Stephen
Keable
,
Alexander
Britz
,
Kensuke
Tono
,
Kyung-sook
Kim
,
Sang-youn
Park
,
Sang-jae
Lee
,
Jaehyun
Park
,
Roberto
Alonso-mori
,
Franklin
Fuller
,
Alexander
Batyuk
,
Aaron S.
Brewster
,
Uwe
Bergmann
,
Nicholas
Sauter
,
Allen M.
Orville
,
Vittal K.
Yachandra
,
Junko
Yano
,
John D.
Lipscomb
,
Jan F.
Kern
,
Martin
Högbom
Abstract: Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of pure oxidation states. Here microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≦35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. This study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.
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Jul 2020
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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[20195, 21979, 20198]
Abstract: Defect engineering can enhance key properties of metal-organic frameworks (MOFs). Tailoring the distribution of de-fects, for example in correlated nanodomains, requires characterization across length scales. However, a critical na-noscale characterization gap has emerged between the bulk diffraction techniques used to detect defect nanodomains and the sub-nanometer imaging used to observe individual defects. Here, we demonstrate that the emerging technique of scanning electron diffraction (SED) can bridge this gap uniquely enabling both nanoscale crystallographic analysis and the low-dose formation of multiple diffraction contrast images for defect analysis in MOFs. We directly image defect nanodomains in the MOF UiO-66(Hf) over an area of ca. 1 000 nm and with a spatial resolution ca. 5 nm to reveal domain morphology and distribution. Based on these observations, we suggest possible crystal growth processes underpinning synthetic control of defect nanodomains. We also identify likely dislocations and small angle grain boundaries, illustrating that SED could be a key technique in developing the potential for engineering the distribution of defects, or “microstruc-ture”, in functional MOF design.
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Jul 2020
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Zachary
Armstrong
,
Chi-lin
Kuo
,
Daniël
Lahav
,
Bing
Liu
,
Rachel
Johnson
,
Thomas J. M.
Beenakker
,
Casper
De Boer
,
Chung-sing
Wong
,
Erwin R.
Van Rijssel
,
Marjoke F.
Debets
,
Bogdan I.
Florea
,
Colin
Hissink
,
Rolf G.
Boot
,
Paul P.
Geurink
,
Huib
Ovaa
,
Mario
Van Der Stelt
,
Gijsbert M.
Van Der Marel
,
Jeroen D. C.
Codée
,
Johannes M. F. G.
Aerts
,
Liang
Wu
,
Herman S.
Overkleeft
,
Gideon
Davies
Diamond Proposal Number(s):
[18598]
Abstract: Golgi mannosidase II (GMII) catalyzes the sequential hydrolysis of two mannosyl residues from GlcNAcMan5GlcNAc2 to produce GlcNAcMan3GlcNAc2, the precursor for all complex N-glycans, including the branched N-glycans associated with cancer. Inhibitors of GMII are potential cancer therapeutics, but their usefulness is limited by off-target effects, which produce α-mannosidosis-like symptoms. Despite many structural and mechanistic studies of GMII, we still lack a potent and selective inhibitor of this enzyme. Here, we synthesized manno-epi-cyclophellitol epoxide and aziridines and demonstrate their covalent modification and time-dependent inhibition of GMII. Application of fluorescent manno-epi-cyclophellitol aziridine derivatives enabled activity-based protein profiling of α-mannosidases from both human cell lysate and mouse tissue extracts. Synthesized probes also facilitated a fluorescence polarization-based screen for dGMII inhibitors. We identified seven previously unknown inhibitors of GMII from a library of over 350 iminosugars and investigated their binding modalities through X-ray crystallography. Our results reveal previously unobserved inhibitor binding modes and promising scaffolds for the generation of selective GMII inhibitors.
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Jul 2020
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I11-High Resolution Powder Diffraction
I19-Small Molecule Single Crystal Diffraction
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Yong
Yan
,
Elliot J.
Carrington
,
Rémi
Pétuya
,
George F. S.
Whitehead
,
Ajay
Verma
,
Rebecca K.
Hylton
,
Chiu C.
Tang
,
Neil G.
Berry
,
George R.
Darling
,
Matthew S.
Dyer
,
Dmytro
Antypov
,
Alexandros P.
Katsoulidis
,
Matthew J.
Rosseinsky
Open Access
Abstract: Flexible metal-organic frameworks (MOFs) undergo structural transformations in response to physical and chemical stimuli. This is hard to control because of feedback between guest uptake and host structure change. We report a family of flexible MOFs based on derivatized amino acid linkers. Their porosity consists of a one-dimensional channel connected to three peripheral pockets. This network structure amplifies small local changes in linker conformation, which are strongly coupled to the guest packing in and the shape of the peripheral pockets, to afford large changes in the global pore geometry that can, for example, segment the pore into four isolated components. The synergy between pore volume, guest packing and linker conformation that characterises this family of structures can be determined by the amino acid sidechain, because it is repositioned by linker torsion. The resulting control optimises non-covalent interactions to differentiate the uptake and structure response of host-guest pairs with similar chemistries.
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Jul 2020
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I10-Beamline for Advanced Dichroism
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Sheng-qun
Su
,
Shu-qi
Wu
,
Michael L.
Baker
,
Peter
Bencok
,
Nobuaki
Azuma
,
Yuji
Miyazaki
,
Motohiro
Nakano
,
Soonchul
Kang
,
Yoshihito
Shiota
,
Kazunari
Yoshizawa
,
Shinji
Kanegawa
,
Osamu
Sato
Diamond Proposal Number(s):
[17723]
Abstract: Orbital angular momentum plays a vital role in various applications, especially magnetic and spintronic properties. There-fore, controlling orbital angular momentum is of paramount importance to both fundamental science and new technologi-cal applications. Many attempts have been made to modulate the ligand-field induced quenching effects of orbital angular momentum to manipulate magnetic properties. However, to date, reported changes in the magnitude of orbital angular momentum are small in both molecular and solid-state magnetic materials. Moreover, no effective methods currently exist to modulate orbital angular momentum. Here, we report a dynamic bond approach to realize a large change in orbital angu-lar momentum. We have developed a Co(II) complex that exhibits coordination number switching between six and seven. This cooperative dynamic bond switching induces considerable modulation of the ligand field, thereby leading to substantial quenching and restoration of the orbital angular momentum. This switching mechanism is entirely different from those of spin-crossover and valence tautomeric compounds, which exhibit switching in spin multiplicity.
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Jun 2020
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[20876]
Abstract: Bulky photo-labile masked alkyne equivalents (MAEs) are needed for the synthesis of polyyne polyrotaxanes, as insulated molecular wires and as stabilized forms of the linear polymeric allotrope of carbon, carbyne. We have synthesized a novel MAE based on phenanthrene and compared it with an indane-based MAE. Photochemical unmasking of model compounds was studied at different wavelengths (250 nm and 350 nm), and key products were identified by NMR spectroscopy and X-ray crystallography. UV irradiation at 250 nm leads to unmasking of both MAEs. Irradiation of the phenanthrene system at 350 nm results in quantitative dimerization via [2+2] cycloaddition to form a [3]-ladderane; irradiation of this ladderane at 250 nm generates a dihydrotriphenylene, which can be oxidized easily to a triphenylene. Irradiation of the indane-based MAE at 350 nm in the presence of traces of oxygen forms an endoperoxide and a bisepoxide. Both MAEs have been incorporated into rotaxanes via copper-mediated active metal template Glaser or Cadiot-Chodkiewicz coupling. The identity of the rotaxanes was confirmed by NMR spectroscopy and mass spectrometry. The phenanthrene rotaxane decomposes during attempted photochemical unmasking, whereas photolysis of the indane rotaxane results in unmasking of the polyyne thread to form a rotaxane with a chain of 16 sp-hybridized carbon atoms. This approach opens avenues towards the synthesis of encapsulated carbon allotropes.
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Jun 2020
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[18069]
Abstract: Hydrogenase-1 (Hyd-1) from E. coli poses a conundrum regarding the properties of electrocatalytic reversibility and associated bidirectionality now established for many redox enzymes. Its excellent H2-oxidizing activity begins only once a substantial overpo-tential is applied, and it cannot produce H2. A major reason for its unidirectional behavior is that the reduction potentials of its electron-relaying FeS clusters are too positive relative to the 2H+/H2 couple at neutral pH; consequently, electrons held within the enzyme lack the energy to drive H2 production. However, Hyd-1 is O2-tolerant and even functions in air. Changing a tyrosine (Y) or threonine (T), located on the protein surface within 10 Å of the distal [4Fe-4S] and medial [3Fe-4S] clusters, to cysteine (C), allows site-selective attachment of a silver nanocluster (AgNC), the reduced or photoexcited state of which is a powerful reduct-ant. The AgNC provides a new additional redox site, capturing externally-supplied electrons with sufficiently high energy to drive H2 production. Assemblies of Y’227C (or T’225C) with AgNCs/PMAA (PMAA = polymethylacrylate templating several AgNC) are also electroactive for H2 production at a TiO2 electrode. A colloidal system for visible-light photo-H2 generation is made by building the hybrid enzyme into a heterostructure with TiO2 and graphitic carbon nitride (g-C3N4), the resulting scaffold promoting uptake of electrons excited at the AgNC. Each hydrogenase produces 40 molecules of H2 per second and sustains 20% activity in air.
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Jun 2020
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