I03-Macromolecular Crystallography
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Takashi
Miura
,
Tika R.
Malla
,
C. David
Owen
,
Anthony
Tumber
,
Lennart
Brewitz
,
Michael A.
Mcdonough
,
Eidarus
Salah
,
Naohiro
Terasaka
,
Takayuki
Katoh
,
Petra
Lukacik
,
Claire
Strain-Damerell
,
Halina
Mikolajek
,
Martin A.
Walsh
,
Akane
Kawamura
,
Christopher J.
Schofield
,
Hiroaki
Suga
Diamond Proposal Number(s):
[27088]
Open Access
Abstract: γ-Amino acids can play important roles in the biological activities of natural products; however, the ribosomal incorporation of γ-amino acids into peptides is challenging. Here we report how a selection campaign employing a non-canonical peptide library containing cyclic γ2,4-amino acids resulted in the discovery of very potent inhibitors of the SARS-CoV-2 main protease (Mpro). Two kinds of cyclic γ2,4-amino acids, cis-3-aminocyclobutane carboxylic acid (γ1) and (1R,3S)-3-aminocyclopentane carboxylic acid (γ2), were ribosomally introduced into a library of thioether-macrocyclic peptides. One resultant potent Mpro inhibitor (half-maximal inhibitory concentration = 50 nM), GM4, comprising 13 residues with γ1 at the fourth position, manifests a 5.2 nM dissociation constant. An Mpro:GM4 complex crystal structure reveals the intact inhibitor spans the substrate binding cleft. The γ1 interacts with the S1′ catalytic subsite and contributes to a 12-fold increase in proteolytic stability compared to its alanine-substituted variant. Knowledge of interactions between GM4 and Mpro enabled production of a variant with a 5-fold increase in potency.
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May 2023
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B18-Core EXAFS
I11-High Resolution Powder Diffraction
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Shunsuke
Sasaki
,
Souvik
Giri
,
Simon J.
Cassidy
,
Sunita
Dey
,
Maria
Batuk
,
Daphne
Vandemeulebroucke
,
Giannantonio
Cibin
,
Ronald I.
Smith
,
Philip
Holdship
,
Clare P.
Grey
,
Joke
Hadermann
,
Simon J.
Clarke
Diamond Proposal Number(s):
[25166, 14239]
Open Access
Abstract: Topochemistry enables step-by-step conversions of solid-state materials often leading to metastable structures that retain initial structural motifs. Recent advances in this field revealed many examples where relatively bulky anionic constituents were actively involved in redox reactions during (de)intercalation processes. Such reactions are often accompanied by anion-anion bond formation, which heralds possibilities to design novel structure types disparate from known precursors, in a controlled manner. Here we present the multistep conversion of layered oxychalcogenides Sr2MnO2Cu1.5Ch2 (Ch = S, Se) into Cu-deintercalated phases where antifluorite type [Cu1.5Ch2]2.5- slabs collapsed into two-dimensional arrays of chalcogen dimers. The collapse of the chalcogenide layers on deintercalation led to various stacking types of Sr2MnO2Ch2 slabs, which formed polychalcogenide structures unattainable by conventional high-temperature syntheses. Anion-redox topochemistry is demonstrated to be of interest not only for electrochemical applications but also as a means to design complex layered architectures.
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May 2023
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B18-Core EXAFS
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Nicola
Schiaroli
,
Leila
Negahdar
,
Mads
Lützen
,
Phuoc
Hoang Ho
,
Lisa J.
Allen
,
Alejandro
Natoli
,
Francesca
Ospitali
,
Francesco
Maluta
,
Enrique
Rodríguez-Castellón
,
Christian D.
Damsgaard
,
Giuseppe
Fornasari
,
Andrew M.
Beale
,
Patricia
Benito
Abstract: Pd-In2O3 catalysts are among the most promising alternatives to Cu-ZnO-Al2O3 for synthesis of CH3OH from CO2. However, the intrinsic activity and stability of In2O3 per unit mass should be increased to reduce the content of this scarcely available element and to enhance the catalyst lifetime. Herein, we propose and demonstrate a strategy for obtaining highly dispersed Pd and In2O3 nanoparticles onto an Al2O3 matrix by a one-step coprecipitation followed by calcination and activation. The activity of this catalyst is comparable with that of a Pd-In2O3 catalyst (0.52 vs. 0.55 gMeOH h-1 gcat-1 at 300°C, 30 bar, 40,800 ml h-1 gcat-1) but the In2O3 loading decreases from 98 to 12 wt.% while improving the long-term stability by three-fold at 30 bar. In the new Pd-In2O3-Al2O3 system, the intrinsic activity of In2O3 is highly increased both in terms of STY normalized to In specific surface area and In2O3 mass (4.32 vs 0.56 g gMeOH h-1 gIn2O3-1 of a Pd- In2O3 catalyst operating at 300°C, 30 bar, 40,800 ml h-1 gcat-1).The combination of ex situ and in situ catalyst characterizations during reduction provides insights into the interaction between Pd and In and with the support. The enhanced activity is likely related to the close proximity of Pd and In2O3, wherein the H2 splitting activity of Pd promotes, in combination with CO2 activation over highly dispersed In2O3 particles, facile formation of CH3OH.
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May 2023
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DL-SAXS-Offline SAXS and Sample Environment Development
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Diamond Proposal Number(s):
[2617]
Abstract: Utilizing carbon dioxide (CO2) to make polycarbonates through the ring-opening copolymerization (ROCOP) of CO2 and epoxides valorizes and recycles CO2 and reduces pollution in polymer manufacturing. Recent developments in catalysis provide access to polycarbonates with well-defined structures and allow for copolymerization with biomass-derived monomers; however, the resulting material properties are under-investigated. Here, new types of CO2-derived thermoplastic elastomers (TPEs) are described together with a generally applicable method to augment tensile mechanical strength and Young's modulus without requiring material re-design. These TPEs combine high glass transition temperature (Tg) amorphous blocks comprising CO2-derived poly(carbonates) (A-block), with low Tg poly(ε-decalactone), from castor oil, (B-block) in ABA structures. The poly(carbonate) blocks are selectively functionalized with metal-carboxylates, where the metals are Na(I), Mg(II), Ca(II), Zn(II) and Al(III). The colorless polymers, featuring <1 wt% metal, show tunable thermal (Tg), and mechanical (elongation at break, elasticity, creep-resistance) properties. The best elastomers show >50-fold higher Young's modulus and 21-times greater tensile strength, without compromise to elastic recovery, compared with the starting block polymers. They have wide operating temperatures (-20 to 200 ˚C), high creep-resistance and yet remain recyclable. In future, these materials could substitute high-volume petrochemical elastomers and be utilized in high-growth fields like medicine, robotics and electronics.
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May 2023
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I11-High Resolution Powder Diffraction
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Aizhamal
Subanbekova
,
Varvara I.
Nikolayenko
,
Andrey A.
Bezrukov
,
Debobroto
Sensharma
,
Naveen
Kumar
,
Daniel J.
O'Hearn
,
Volodymyr
Bon
,
Shi-Qiang
Wang
,
Kyriaki
Koupepidou
,
Shaza
Darwish
,
Stefan
Kaskel
,
Michael J.
Zaworotko
Diamond Proposal Number(s):
[30456]
Open Access
Abstract: In this work, we report the synthesis, structural characterisation and sorption properties of an 8-fold interpenetrated diamondoid (dia) metal–organic framework (MOF) that is sustained by a new extended linker ligand, [Cd(Imibz)2], X-dia-2-Cd, HImibz or 2 = 4-((4-(1H-imidazol-1-yl)phenylimino)methyl)benzoic acid. X-dia-2-Cd was found to exhibit reversible single-crystal-to-single-crystal (SC–SC) transformations between four distinct phases: an as-synthesised (from N,N-dimethylformamide) wide-pore phase, X-dia-2-Cd-α; a narrow-pore phase, X-dia-2-Cd-β, formed upon exposure to water; a narrow-pore phase obtained by activation, X-dia-2-Cd-γ; a medium-pore CO2-loaded phase X-dia-2-Cd-δ. While the space group remained constant in the four phases, the cell volumes and calculated void space ranged from 4988.7 Å3 and 47% (X-dia-2-Cd-α), respectively, to 3200.8 Å3 and 9.1% (X-dia-2-Cd-γ), respectively. X-dia-2-Cd-γ also exhibited a water vapour-induced structural transformation to the water-loaded X-dia-2-Cd-β phase, resulting in an S-shaped sorption isotherm. The inflection point occurred at 18% RH with negligible hysteresis on the desorption profile. Water vapour temperature-humidity swing cycling (60% RH, 300 K to 0% RH, 333 K) indicated hydrolytic stability of X-dia-2-Cd and working capacity was retained after 128 cycles of sorbent regeneration. CO2 (at 195 K) was also observed to induce a structural transformation in X-dia-2-Cd-γ and in situ PXRD studies at 1 bar of CO2, 195 K revealed the formation of X-dia-2-Cd-δ, which exhibited 31% larger unit cell volume than X-dia-2-Cd-γ.
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May 2023
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[19951]
Open Access
Abstract: Facultative anaerobic bacteria such as Escherichia coli have two α2β2 heterotetrameric trifunctional enzymes (TFE), catalyzing the last three steps of the β-oxidation cycle: soluble aerobic TFE (EcTFE) and membrane-associated anaerobic TFE (anEcTFE), closely related to the human mitochondrial TFE (HsTFE). The cryo-EM structure of anEcTFE and crystal structures of anEcTFE-α show that the overall assembly of anEcTFE and HsTFE is similar. However, their membrane-binding properties differ considerably. The shorter A5-H7 and H8 regions of anEcTFE-α result in weaker α-β as well as α-membrane interactions, respectively. The protruding H-H region of anEcTFE-β is therefore more critical for membrane-association. Mutational studies also show that this region is important for the stability of the anEcTFE-β dimer and anEcTFE heterotetramer. The fatty acyl tail binding tunnel of the anEcTFE-α hydratase domain, as in HsTFE-α, is wider than in EcTFE-α, accommodating longer fatty acyl tails, in good agreement with their respective substrate specificities.
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May 2023
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I13-1-Coherence
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Valerio
Bellucci
,
Marie-Christine
Zdora
,
Ladislav
Mikes
,
Šarlota
Birnšteinová
,
Peter
Oberta
,
Marco
Romagnoni
,
Andrea
Mazzolari
,
Pablo
Villanueva-Perez
,
Rajmund
Mokso
,
Christian
David
,
Mikako
Makita
,
Silvia
Cipiccia
,
Jozef
Ulicny
,
Alke
Meents
,
Adrian P.
Mancuso
,
Henry N.
Chapman
,
Patrik
Vagovic
Diamond Proposal Number(s):
[17739]
Open Access
Abstract: The characterisation of fast phenomena at the microscopic scale is required for the understanding of catastrophic responses of materials to loads and shocks, the processing of materials by optical or mechanical means, the processes involved in many key technologies such as additive manufacturing and microfluidics, and the mixing of fuels in combustion. Such processes are usually stochastic in nature and occur within the opaque interior volumes of materials or samples, with complex dynamics that evolve in all three dimensions at speeds exceeding many meters per second. There is therefore a need for the ability to record three-dimensional X-ray movies of irreversible processes with resolutions of micrometers and frame rates of microseconds. Here we demonstrate a method to achieve this by recording a stereo phase-contrast image pair in a single exposure. The two images are combined computationally to reconstruct a 3D model of the object. The method is extendable to more than two simultaneous views. When combined with megahertz pulse trains of X-ray free-electron lasers (XFELs) it will be possible to create movies able to resolve 3D trajectories with velocities of kilometers per second.
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May 2023
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[24948]
Open Access
Abstract: We report a chemo-biocatalytic cascade for the synthesis of substituted pyrroles, driven by the action of an irreversible, thermostable, pyridoxal 5′-phosphate (PLP)-dependent, C–C bond-forming biocatalyst (ThAOS). The ThAOS catalyzes the Claisen-like condensation between various amino acids and acyl-CoA substrates to generate a range of α-aminoketones. These products are reacted with β-keto esters in an irreversible Knorr pyrrole reaction. The determination of the 1.6 Å resolution crystal structure of the PLP-bound form of ThAOS lays the foundation for future engineering and directed evolution. This report establishes the AOS family as useful and versatile C–C bond-forming biocatalysts.
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May 2023
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B21-High Throughput SAXS
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Biswanath
Hansda
,
Jhilam
Majumder
,
Biplab
Mondal
,
Akash
Chatterjee
,
Subhadeep
Das
,
Sourav
Kumar
,
Ratan
Gachhui
,
Valeria
Castelletto
,
Ian W.
Hamley
,
Prosenjit
Sen
,
Arindam
Banerjee
Diamond Proposal Number(s):
[29895]
Abstract: A histidine-based amphiphilic peptide (P) has been found to form an injectable transparent hydrogel in phosphate buffer solution over a pH range from 7.0 to 8.5 with an inherent antibacterial property. It also formed a hydrogel in water at pH = 6.7. The peptide self-assembles into a nanofibrillar network structure which is characterized by high-resolution transmission electron microscopy, field-emission scanning electron microscopy, atomic force microscopy, small-angle X-ray scattering, Fourier-transform infrared spectroscopy, and wide-angle powder X-ray diffraction. The hydrogel exhibits efficient antibacterial activity against both Gram-positive bacteria Staphylococcus aureus (S. aureus) and Gram-negative bacteria Escherichia coli (E. coli). The minimum inhibitory concentration of the hydrogel ranges from 20 to 100 μg/mL. The hydrogel is capable of encapsulation of the drugs naproxen (a non-steroidal anti-inflammatory drug), amoxicillin (an antibiotic), and doxorubicin, (an anticancer drug), but, selectively and sustainably, the gel releases naproxen, 84% being released in 84 h and amoxicillin was released more or less in same manner with that of the naproxen. The hydrogel is biocompatible with HEK 293T cells as well as NIH (mouse fibroblast cell line) cells and thus has potential as a potent antibacterial and drug releasing agent. Another remarkable feature of this hydrogel is its magnification property like a convex lens.
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May 2023
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Y.
Liu
,
D. M.
Sanchez
,
M. R.
Ware
,
E. G.
Champenois
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J.
Yang
,
J. P. F.
Nunes
,
A.
Attar
,
M.
Centurion
,
J. P.
Cryan
,
R.
Forbes
,
K.
Hegazy
,
M. C.
Hoffmann
,
F.
Ji
,
M.-F.
Lin
,
D.
Luo
,
S. K.
Saha
,
X.
Shen
,
X. J.
Wang
,
T. J.
Martínez
,
T. J. A.
Wolf
Open Access
Abstract: Electrocyclic reactions are characterized by the concerted formation and cleavage of both σ and π bonds through a cyclic structure. This structure is known as a pericyclic transition state for thermal reactions and a pericyclic minimum in the excited state for photochemical reactions. However, the structure of the pericyclic geometry has yet to be observed experimentally. We use a combination of ultrafast electron diffraction and excited state wavepacket simulations to image structural dynamics through the pericyclic minimum of a photochemical electrocyclic ring-opening reaction in the molecule α-terpinene. The structural motion into the pericyclic minimum is dominated by rehybridization of two carbon atoms, which is required for the transformation from two to three conjugated π bonds. The σ bond dissociation largely happens after internal conversion from the pericyclic minimum to the electronic ground state. These findings may be transferrable to electrocyclic reactions in general.
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May 2023
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