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Open Access
Abstract: Pyridine and related heterocyclic sulfinates have recently emerged as effective nucleophilic coupling partners in palladium-catalyzed cross-coupling reactions with (hetero)aryl halides. These sulfinate reagents are straightforward to prepare, stable to storage and coupling reaction conditions, and deliver efficient reactions, thus offering many advantages, compared to the corresponding boron-derived reagents. Despite the success of these reactions, there are only scant details of the reaction mechanism. In this study, we use structural and kinetic analysis to investigate the mechanism of these important coupling reactions in detail. We compare a pyridine-2-sulfinate with a carbocyclic sulfinate and establish different catalyst resting states, and turnover limiting steps, for the two classes of reagent. For the carbocyclic sulfinate, the aryl bromide oxidative addition complex is the resting state intermediate, and transmetalation is turnover-limiting. In contrast, for the pyridine sulfinate, a chelated Pd(II) sulfinate complex formed post-transmetalation is the resting-state intermediate, and loss of SO2 from this complex is turnover-limiting. We also investigated the role of the basic additive potassium carbonate, the use of which is crucial for efficient reactions, and deduced a dual function in which carbonate is responsible for the removal of free sulfur dioxide from the reaction medium, and the potassium cation plays a role in accelerating transmetalation. In addition, we show that sulfinate homocoupling is responsible for converting Pd(OAc)2 to a catalytically active Pd(0) complex. Together, these studies shed light on the challenges that must be overcome to deliver improved, lower temperature versions of these synthetically important processes.
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Feb 2020
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I22-Small angle scattering & Diffraction
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Abstract: Novel bolapolyphiles, built of a p-terphenyl or bistolane core with polar glycerol end-groups and two laterally attached n-alkyl or semiperfluoroalkyl chains, form the first “single plumber’s nightmare network”, the simplest soft-matter cubic phase (Pm3̅m). Its cage-like grid comprises bundles of aromatic rods lying along the cubic unit cell edges, connected by six-way hydrogen-bonded junctions. Side-chains fill the remaining volume of this unique noninterpenetrating liquid-crystalline organic framework.
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Feb 2020
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I04-Macromolecular Crystallography
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Nicholas G. S.
Mcgregor
,
Marta
Artola
,
Alba
Nin-hill
,
Daniel
Linzel
,
Mireille
Haon
,
Jos
Reijngoud
,
Arthur F. J.
Ram
,
Marie-noelle
Rosso
,
Gijsbert A.
Van Der Marel
,
Jeroen D. C.
Codée
,
Gilles P.
Van Wezel
,
Jean-guy
Berrin
,
Carme
Rovira
,
Herman S.
Overkleeft
,
Gideon J.
Davies
Diamond Proposal Number(s):
[18598]
Abstract: Identifying and characterizing the enzymes responsible for an observed activity within a complex eukaryotic catabolic system remains one of the most significant challenges in the study of biomass-degrading systems. The debranching of both complex hemicellulosic and pectinaceous polysaccharides requires the production of α-L-arabinofuranosidases among a wide variety of co-expressed carbohydrate-active enzymes. To selectively detect and identify α-L-arabinofuranosidases produced by fungi grown on complex biomass, potential covalent inhibitors and probes which mimic α-L-arabinofuranosides were sought. The conformational free energy landscapes of free α-L-arabinofuranose and several rationally designed covalent α-L-arabinofuranosidase inhibitors were analyzed. A synthetic route to these inhibitors was subsequently developed based on a key Wittig-Still rearrangement. Through a combination of kinetic measurements, intact mass spectrometry, and structural experiments, the designed inhibitors were shown to efficiently label the catalytic nucleophiles of retaining GH51 and GH54 α-L-arabinofuranosidases. Activity-based probes elaborated from an inhibitor with an aziridine warhead were applied to the identification and characterization of α-L-arabinofuranosidases within the secretome of A. niger grown on arabinan. This method was extended to the detection and identification of α-L-arabinofuranosidases produced by eight biomass-degrading basidiomycete fungi grown on complex biomass. The broad applicability of the cyclophellitol-derived activity-based probes and inhibitors presented here make them a valuable new tool in the characterization of complex eukaryotic carbohydrate-degrading systems and in the high-throughput discovery of α-L-arabinofuranosidases.
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Feb 2020
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[23087]
Open Access
Abstract: Carbon dioxide/epoxide copolymerization is an efficient way to add value to waste CO2 and to reduce pollution in polymer manufacturing. Using this process to make low molar mass polycarbonate polyols is a commercially relevant route to new thermosets and polyurethanes. In contrast, high molar mass polycarbonates, produced from CO2, generally under-deliver in terms of properties, and one of the most widely investigated, poly(cyclohexene carbonate), is limited by its low elongation at break and high brittleness. Here, a new catalytic polymerization process is reported that selectively and efficiently yields degradable ABA-block polymers, incorporating 6–23 wt % CO2. The polymers are synthesized using a new, highly active organometallic heterodinuclear Zn(II)/Mg(II) catalyst applied in a one-pot procedure together with biobased ε-decalactone, cyclohexene oxide, and carbon dioxide to make a series of poly(cyclohexene carbonate-b-decalactone-b-cyclohexene carbonate) [PCHC-PDL-PCHC]. The process is highly selective (CO2 selectivity >99% of theoretical value), allows for high monomer conversions (>90%), and yields polymers with predictable compositions, molar mass (from 38–71 kg mol–1), and forms dihydroxyl telechelic chains. These new materials improve upon the properties of poly(cyclohexene carbonate) and, specifically, they show good thermal stability (Td,5 ∼ 280 °C), high toughness (112 MJ m–3), and very high elongation at break (>900%). Materials properties are improved by precisely controlling both the quantity and location of carbon dioxide in the polymer chain. Preliminary studies show that polymers are stable in aqueous environments at room temperature over months, but they are rapidly degraded upon gentle heating in an acidic environment (60 °C, toluene, p-toluene sulfonic acid). The process is likely generally applicable to many other lactones, lactides, anhydrides, epoxides, and heterocumulenes and sets the scene for a host of new applications for CO2-derived polymers.
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Feb 2020
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Aleksandr
Baklanov
,
Manuela
Garnica
,
Anton
Robert
,
Marie-laure
Bocquet
,
Knud
Seufert
,
Johannes T.
Kuchle
,
Paul T. P.
Ryan
,
Felix
Haag
,
Reza
Kakavandi
,
Francesco
Allegretti
,
Willi
Auwärter
Abstract: We report the on-surface synthesis of a nonmetal porphyrin, namely, silicon tetraphenylporphyrin (Si-TPP), by the deposition of atomic silicon onto a free-base TPP layer on a Ag(100) surface under ultrahigh vacuum (UHV) conditions. Scanning tunneling microscopy provides insights into the self-assembly of the TPP molecules before and after Si insertion. Silicon coordinates with all four nitrogen atoms of the TPP macrocycle and interacts with a silver atom of the substrate as confirmed by scanning tunneling spectroscopy, X-ray photoelectron spectroscopy, and complementary density functional theory calculations. The Si-TPP complex presents a saddle-shaped conformation that is stable under STM manipulation. Our study shows how protocols established for the on-surface metalation of tetrapyrroles can be adopted to achieve nonmetal porphyrins. Complementary experiments yielding Si-TPP and Ge-TPP on Ag(111) highlight the applicability to different main group elements and supports. The success of our nonmetal porphyrin synthesis procedure is further corroborated by a temperature-programmed desorption experiment, revealing the desorption of Ge-TPP. This extension of interfacial complex formation beyond metal elements opens promising prospects for new tetrapyrrole architectures with distinct properties and functionalities.
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Jan 2020
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I15-1-X-ray Pair Distribution Function (XPDF)
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Jingwei
Hou
,
María Laura
Ríos Gómez
,
Andraž
Krajnc
,
Aoife
Mccaul
,
Shichun
Li
,
Alice M.
Bumstead
,
Adam F.
Sapnik
,
Zeyu
Deng
,
Rijia
Lin
,
Philip A.
Chater
,
Dean S.
Keeble
,
David A.
Keen
,
Dominique
Appadoo
,
Bun
Chan
,
Vicki
Chen
,
Gregor
Mali
,
Thomas D.
Bennett
Diamond Proposal Number(s):
[20038]
Abstract: The synthesis of four novel crystalline zeolitic imidazolate framework (ZIF) structures using a mixed-ligand approach is reported. The inclusion of both imidazolate and halogenated benzimidazolate-derived linkers leads to glass-forming behavior by all four structures. Melting temperatures are observed to depend on both electronic and steric effects. Solid-state NMR and terahertz (THz)/Far-IR demonstrate the presence of a Zn-F bond for fluorinated ZIF glasses. In situ THz/Far-IR spectroscopic techniques reveal the dynamic structural properties of crystal, glass and liquid phases of the halogenated ZIFs, linking the melting behavior of ZIFs to the propensity of the ZnN4 tetrahedra to undergo thermally-induced deformation. The inclusion of halogenated ligands within MOF-glasses improves their gas uptake properties.
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Jan 2020
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Open Access
Abstract: An atom-economical methodology to access substituted acyl-cyclohexenes from pentamethylacetophenone and 1,5-diols is described. This process is catalyzed by an iridium(I) catalyst in conjunction with a bulky electron rich phosphine ligand (CataCXium A) which favors acceptorless dehydrogenation over conjugate reduction to the corresponding cyclohexane. The reaction produces water and hydrogen gas as the sole byproducts and a wide range of functionalized acyl-cyclohexene products can be synthesized using this method in very high yields. A series of control experiments were carried out, which revealed that the process is initiated by acceptorless dehydrogenation of the diol followed by a redox-neutral cascade process, which is independent of the iridium catalyst. Deuterium labeling studies established that the key step of this cascade involves a novel base-mediated [1,5]-hydride shift. The cyclohexenyl ketone products could readily be cleaved under mildly acidic conditions to access a range of valuable substituted cyclohexene derivatives.
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Jan 2020
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B18-Core EXAFS
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Diamond Proposal Number(s):
[24909]
Abstract: Polyoxometalates (POMs) provide rigid and highly symmetric coordination sites and can be used as a strategy for the stabilization of magnetic ions. Herein, we report a new member of the Keggin archetype – the Cr-centered Keggin anion [α-CrW12O40]5- (CrW12) – with the unusual tetrahedral coordination of CrIII reported for the first time in POMs conferring unattended magnetic properties. POM chemistry has recently presented excellent examples of single molecule and single-ion magnets (SMMs and SIMs) as well as molecular spin qubits; however, the majority of POM-based SIMs reported to date contain lanthanoid ions. CrW12, as the first example of chromium (III) SIM, exhibits slow relaxation of magnetization and quantum tunneling with a single-ion magnetic behavior even above 10 K with an energy barrier for the reversal of the magnetization of 3.0 K. The first 3d-metal SIM based on a non-lacunary Keggin anion is the foundation for a new research area in POM chemistry.
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Jan 2020
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[9948]
Abstract: The Pictet–Spengler reaction is a valuable route to 1,2,3,4-tetrahydro-β-carboline (THBC) and isoquinoline scaffolds found in many important pharmaceuticals. Strictosidine synthase (STR) catalyzes the Pictet–Spengler condensation of tryptamine and the aldehyde secologanin to give (S)-strictosidine as a key intermediate in indole alkaloid biosynthesis. STRs also accept short-chain aliphatic aldehydes to give enantioenriched alkaloid products with up to 99% ee STRs are thus valuable asymmetric organocatalysts for applications in organic synthesis. The STR catalysis of reactions of small aldehydes gives an unexpected switch in stereopreference, leading to formation of the (R)-products. Here we report a rationale for the formation of the (R)-configured products by the STR enzyme from Ophiorrhiza pumila (OpSTR) using a combination of X-ray crystallography, mutational, and molecular dynamics (MD) studies. We discovered that short-chain aldehydes bind in an inverted fashion compared to secologanin leading to the inverted stereopreference for the observed (R)-product in those cases. The study demonstrates that the same catalyst can have two different productive binding modes for one substrate but give different absolute configuration of the products by binding the aldehyde substrate differently. These results will guide future engineering of STRs and related enzymes for biocatalytic applications.
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Jan 2020
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B07-C-Versatile Soft X-ray beamline: Ambient Pressure XPS and NEXAFS
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Abstract: Solar fuels production is a cornerstone in the development of emerging sustainable energy conversion and storage technologies. Light-induced H2 production from water represents one of the most crucial challenges to produce renewable fuel. Metal-organic frameworks (MOFs) are being investigated, due to the ability to assemble new structures with the use of suitable photoactive building blocks. However, the identification of the reaction intermediates remains elusive, which negatively impacts in the design of more efficient materials. Here, we report the synthesis and characterization of a new MOF prepared with the use of bismuth and dithieno[3,2-b:2',3'-d]thiophene-2,6-dicarboxylic acid (DTTDC), an electron-rich linker with hole transport ability. By combining theoretical studies and time-resolved spectroscopies, such as core hole clock and laser flash photolysis measurements, we have completed a comprehensive study at different time scales (fs to-ms) to determine the effect of competitive reactions on the overall H2 production. We found that an intermediate radical anion is formed upon reaction of photogenerated holes with an electron donor, which play a key role in the photoelectrocatalytic processes. These results shed new light on the use of MOFs for solar fuel production.
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Dec 2019
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