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Small-ring cage hydrocarbons are popular bioisosteres (molecular replacements) for commonly-foundpara-substituted benzene rings in drug design1. The utility of these cage structures derives from their superior pharmacokinetic properties compared to the parent aromatics, including improved solubility and reduced susceptibility to metabolism2,3. A prime example is the bicyclo[1.1.1]pentane motif, which is mainly synthesised by ring-opening of the inter-bridgehead bond of the strained hydrocarbon [1.1.1]propellane with radicals or anions4. In contrast, scaffolds mimickingmeta-substituted arenes are lacking due to the challenge of synthesising saturated isosteres that accurately reproduce substituent vectors5. Here we show that bicyclo[3.1.1]heptanes (BCHeps), hydrocarbons whose bridgehead substituents map precisely onto the geometry ofmeta-substituted benzenes, can be conveniently accessed from [3.1.1]propellane. We found that [3.1.1]propellane can be synthesized on multigram scale, and readily undergoes a range of radical-based transformations to generate medicinally-relevant carbon- and heteroatom-substituted BCHeps, including pharmaceutical analogues. Comparison of ADME properties of these analogues revealed enhanced metabolic stability relative to their parent arene-containing drugs, validating the potential of thismeta-arene analogue as an sp3-rich motif in drug design. Collectively, our results show that BCHeps can be prepared on useful scales using a variety of methods, offering a novel surrogate formeta-substituted benzene rings for implementation in drug discovery programmes.

Cyclic porphyrin oligomers have been studied as models for photosynthetic light-harvesting antenna complexes and as potential receptors for supramolecular chemistry. Here, we report the synthesis of unprecedented β,β-directly linked cyclic zinc porphyrin oligomers, the trimer (CP3) and tetramer (CP4), by Yamamoto coupling of a 2,3-dibromoporphyrin precursor. Their three-dimensional structures were confirmed by nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and single-crystal X-ray diffraction analyses. The minimum-energy geometries of CP3 and CP4 have propeller and saddle shapes, respectively, as calculated using density functional theory. Their different geometries result in distinct photophysical and electrochemical properties. The smaller dihedral angles between the porphyrin units in CP3, compared with CP4, result in stronger π-conjugation, splitting the ultraviolet–vis absorption bands and shifting them to longer wavelengths. Analysis of the crystallographic bond lengths indicates that the central benzene ring of the CP3 is partially aromatic [harmonic oscillator model of aromaticity (HOMA) 0.52], whereas the central cyclooctatetraene ring of the CP4 is non-aromatic (HOMA –0.02). The saddle-shaped structure of CP4 makes it a ditopic receptor for fullerenes, with affinity constants of (1.1 ± 0.4) × 105 M–1 for C70 and (2.2 ± 0.1) × 104 M–1 for C60, respectively, in toluene solution at 298 K. The formation of a 1:2 complex with C60 is confirmed by NMR titration and single-crystal X-ray diffraction.

The first examples of halogen bonding (XB) heteroditopic homo[2]catenanes were prepared by discrete Na+ template-directed assembly of oligo(ethylene glycol) units derived from XB donor-containing macrocycles and acyclic bis-azide precursors, followed by a Cu(I) mediated azide-alkyne cycloaddition macrocyclisation reaction. Extensive 1H NMR spectroscopic studies show that the [2]catenane hosts exhibit positive cooperative ion-pair recognition behaviour, wherein XB-mediated halide recognition is enhanced by alkali metal cation pre-complexation. Notably, subtle changes in the catenanes' oligo(ethylene glycol) chain length dramatically alters ion binding affinity, stoichiometry, complexation mode and conformational dynamics. Solution phase and single crystal X-ray diffraction studies provide evidence for competing host-separated and direct contact ion-pair binding modes. We further demonstrate the [2]catenanes are capable of extracting solid alkali metal halide salts into organic media.

X-ray characterisation methods have undoubtedly enabled cutting-edge advances in all aspects of materials research. Despite the enormous breadth of information that can be extracted from these techniques, the challenge of radiation-induced sample change and damage remains prevalent. This is largely due to the emergence of modern, high-intensity X-ray source technologies and the growing potential to carry out more complex, longer duration

X-ray characterisation methods have undoubtedly enabled cutting-edge advances in all aspects of materials research. Despite the enormous breadth of information that can be extracted from these techniques, the challenge of radiation-induced sample change and damage remains prevalent. This is largely due to the emergence of modern, high-intensity X-ray source technologies and growing potential to carry out more complex, longer duration in-situ or in-operando studies. The tunability of synchrotron beamlines enables the routine application of photon energy-dependent experiments. This work explores the structural stability of [Rh(COD)Cl]2, a widely used catalyst and precursor in the chemical industry, across a range of beamline parameters that target X-ray energies of 8 keV, 15 keV, 18 keV and 25 keV, on a powder X-ray diffraction synchrotron beamline at room temperature. Structural changes are discussed with respect to absorbed X-ray dose at each experimental setting associated with the respective photon energy. In addition, the X-ray radiation hardness of the catalyst is discussed, by utilising the diffraction data at the different energies to determine a dose limit, which is often considered in protein crystallography and typically overlooked in small molecule crystallography. This work not only gives fundamental insight into how damage manifests in this organometallic catalyst, but will encourage careful consideration of experimental X-ray parameters before conducting diffraction on similar radiation-sensitive organometallic materials., 20 pages, 7 figures

Laurefurenynes C–F are four natural products isolated from Laurencia species whose structures were originally determined on the basis of extensive nuclear magnetic resonance experiments. On the basis of a proposed biogenesis, involving a tricyclic oxonium ion as a key intermediate, we have reassigned the structures of these four natural products and synthesized the four reassigned structures using a biomimetic approach demonstrating that they are the actual structures of the natural products. In addition, we have developed a synthesis of the enantiomers of the natural products laurencin and deacetyllaurencin from the enantiomer of (E)-laurefucin using an unusual retrobiomimetic strategy. All of these syntheses have been enabled by the use of tricyclic oxonium ions as pivotal synthetic intermediates.

New strategies for synthesizing polyyne polyrotaxanes are being developed as an approach to stable carbyne “insulated molecular wires”. Here we report an active metal template route to polyyne [3]rotaxanes, using dicobalt carbonyl masked alkyne equivalents. We synthesized two [3]rotaxanes, both with the same C28 polyyne dumbbell component, one with a phenanthroline-based macrocycle and one using a 2,6-pyridyl cycloparaphenylene nanohoop. The thermal stabilities of the two rotaxanes were compared with that of the naked polyyne dumbbell in decalin at 80 °C, and the nanohoop rotaxane was found to be 4.5 times more stable.

X-ray characterization techniques are invaluable for probing material characteristics and properties, and have been instrumental in discoveries across materials research. However, there is a current lack of understanding of how X-ray-induced effects manifest in small molecular crystals. This is of particular concern as new X-ray sources with ever-increasing brilliance are developed. In this paper, systematic studies of X-ray-matter interactions are reported on two industrially important catalysts, [Ir(COD)Cl]

X-ray characterization techniques are invaluable for probing material characteristics and properties, and have been instrumental in discoveries across materials research. However, there is a current lack of understanding of how X-ray-induced effects manifest in small molecular crystals. This is of particular concern as new X-ray sources with ever-increasing brilliance are developed. In this paper, systematic studies of X-ray-matter interactions are reported on two industrially important catalysts, [Ir(COD)Cl]2 and [Rh(COD)Cl]2, exposed to radiation in X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) experiments. From these complementary techniques, changes to structure, chemical environments, and electronic structure are observed as a function of X-ray exposure, allowing comparisons of stability to be made between the two catalysts. Radiation dose is estimated using recent developments to the RADDOSE-3D software for small molecules and applied to powder XRD and XPS experiments. Further insights into the electronic structure of the catalysts and changes occurring as a result of the irradiation are drawn from density functional theory (DFT). The techniques combined here offer much needed insight into the X-ray-induced effects in transition-metal catalysts and, consequently, their intrinsic stabilities. There is enormous potential to extend the application of these methods to other small molecular systems of scientific or industrial relevance.

Laurefurenynes C–F are four natural products isolated from Laurencia species whose structures were originally determined on the basis of extensive nuclear magnetic resonance experiments. On the basis of a proposed biogenesis, involving a tricyclic oxonium ion as a key intermediate, we have reassigned the structures of these four natural products and synthesized the four reassigned structures using a biomimetic approach demonstrating that they are the actual structures of the natural products. In addition, we have developed a synthesis of the enantiomers of the natural products laurencin and deacetyllaurencin from the enantiomer of (E)-laurefucin using an unusual retrobiomimetic strategy. All of these syntheses have been enabled by the use of tricyclic oxonium ions as pivotal synthetic intermediates., The synthesis and structural reassignment of laurefurenynes C–F has been achieved, with the new structures fitting with a proposed biosynthesis. Also reported is the synthesis of ent-laurencin and ent-deacetyllaurencin via a retrobiomimetic approach.

The root microbiota is critical for agricultural yield, with growth-promoting bacteria able to solubilise phosphate, produce plant growth hormones, antagonise pathogens and fix N2. Plants control the microorganisms in their immediate environment and this is at least in part through direct selection, the immune system, and interactions with other microorganisms. Considering the importance of the root microbiota for crop yields it is attractive to artificially regulate this environment to optimise agricultural productivity. Towards this aim we express a synthetic pathway for the production of the rhizopine scyllo-inosamine in plants. We demonstrate the production of this bacterial derived signal in both Medicago truncatula and barley and show its perception by rhizosphere bacteria, containing bioluminescent and fluorescent biosensors. This study lays the groundwork for synthetic signalling networks between plants and bacteria, allowing the targeted regulation of bacterial gene expression in the rhizosphere for delivery of useful functions to plants., The root microbiota is critical for promoting crop yield. Here, the authors create a synthetic pathway for the production of the rhizopine scyllo-inosamine in Medicago truncatula and barley, and show its perception by rhizosphere bacteria for targeted regulation of bacterial gene expression.

There is an increasing trend to reduce diffraction data collection to a set of numbers and the crystallography to a set of criteria. Many of these criteria have been passed on through gener...

Synthetic phosphatidylinositol phosphate (PtdInsPn) derivatives play a pivotal role in broadening our understanding of PtdInsPn metabolism. However, the development of such tools is reliant on efficient enantioselective and regioselective synthetic strategies. Here we report the development of a divergent synthetic route applicable to the synthesis of deuterated PtdIns4P and PtdIns5P derivatives. The synthetic strategy developed involves a key enzymatic desymmetrisation step using Lipozyme TL-IM®. In addition, we optimised the large-scale synthesis of deuterated myo-inositol, allowing for the preparation of a series of saturated and unsaturated deuterated PtdIns4P and PtdIns5P derivatives. Experiments in MCF7 cells demonstrated that these deuterated probes enable quantification of the corresponding endogenous phospholipids in a cellular setting. Overall, these deuterated probes will be powerful tools to help improve our understanding of the role played by PtdInsPn in physiology and disease.

Bulky photolabile 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 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 toward the synthesis of encapsulated carbon allotropes.

Formaldehyde (HCHO) is a simple and highly reactive human metabolite but its biochemistry is poorly defined. A limiting factor in HCHO research is lack of validated quantification methods for HCHO relevant to biological samples. We describe spectroscopic studies on a reported fluorescence-based HCHO detection method involving its reaction with ampicillin. The results validate the structure and fluorescence properties of the HCHO-ampicillin reaction product. However, the same adduct is observed after reaction of ampicillin with glyoxylate. Related fluorophores were formed with other biologically relevant carbonyl compounds. Overall, our studies suggest the ampicillin method is not reliable for selective detection and quantification of HCHO in biological samples.

A new bis‐triazacyclononane tris‐pyridyl N9‐azacryptand ligand is prepared via a convenient one‐pot [2+3] condensation reaction between triazacyclononane and 2,6‐bis(bromomethyl) pyridine in the presence of M2CO3 (M=Li, Na, K). The proton, lithium, sodium, potassium and lead(II) complexes of the ligand are characterised in the solid state. Preliminary solution‐phase competition experiments indicate that the cryptand ligand preferentially binds lead(II) in the presence of sodium, calcium, potassium and zinc cations in methanol solution.

Weinreb amide derivatives of tetramates may be effectively accessed by chemoselective Dieckmann reaction, and further react with Grignards in a fully chemoselective reaction, giving rise to unsaturated acyl derivatives not easily available by other routes. These systems are strong chelators of calcium, and some show potent activity against Gram positive bacteria, and one is a first-in-class proteasome inhibitor.

Students of single crystal X-ray diffraction are often give advice as to how best to collect their data when attempting absolute configuration determination. These ‘rules’ often have more grounding in gut-feeling than evidence. Thus, in an effort to provide advice and evidence that today’s crystallographers can pass onto to tomorrow’s young scientists, we present a systematic study of 1-deoxy- l -arabinitol, a straight chain sugar which crystalises well in the space group I 4 1 .

Electron-deficient heavy chalcogen atoms contain Lewis acidic σ-holes which are able to form attractive supramolecular interactions, known as chalcogen bonding (ChB), with Lewis bases. However, their potential in solution-phase anion binding applications is only just beginning to be realized in simple acyclic systems. Herein, we explore the 5-(methylchalcogeno)-1,2,3-triazole (chalcogen = Se, Te) motif as a novel ChB donor for anion binding. Other than being chemically robust enough to be incorporated into macrocyclic structures, thereby significantly expanding the scope and complexity of ChB host systems, we also demonstrate, by 1H NMR and DFT calculations, that the chalcogen atoms oriented within the macrocycle cavity are able to chelate copper(I) endotopically. Exploiting this property, the first examples of mechanically interlocked [2]rotaxanes containing ChB-donor groups are prepared via an active metal template strategy. Solution-phase 1H NMR and molecular modeling studies provide compelling evidence for the dominant influence of ChB in anion binding by these interlocked host systems. In addition, unprecedented charge-assisted ChB-mediated anion binding was also studied in aqueous solvent mixtures, which revealed considerable differences in anion recognition behavior in comparison with chalcogen-free host analogues. Moreover, DFT calculations and molecular dynamics simulations in aqueous solvent mixtures indicate that the selectivity is determined by the different hydrophilic characters of the anions allied to the hydration of the binding units in the presence of the anions. Exploiting the NMR-active nuclei of the ChB-donor chalcogen atoms, heteronuclear 77Se and 125Te NMR were used to directly study how anion recognition influences the local electronic environment of the chalcogen atoms in the mechanically bonded rotaxane binding sites in organic and aqueous solvent mixtures.

Hydrothermal synthesis is described of layered lithium iron selenide hydroxides Li1-xFex(OH)Fe1-ySe (x ~ 0.2; 0.02 < y < 0.15) with a wide range of iron site vacancy concentrations in the iron selenide layers. This iron vacancy concentration is revealed as the only significant compositional variable and as the key parameter controlling the crystal structure and the electronic properties. Single crystal X-ray diffraction, neutron powder diffraction and X-ray absorption spectroscopy measurements are used to demonstrate that superconductivity at temperatures as high as 40 K is observed in the hydrothermally synthesised samples when the iron vacancy concentration is low (y < 0.05) and when the iron oxidation state is reduced slightly below +2, while samples with a higher vacancy concentration and a correspondingly higher iron oxidation state are not superconducting. The importance of combining a low iron oxidation state with a low vacancy concentration in the iron selenide layers is emphasised by the demonstration that reductive post-synthetic lithiation of the samples turns on superconductivity with critical temperatures exceeding 40 K by displacing iron atoms from the Li1-xFex(OH) reservoir layer to fill vacancies in the selenide layer, 7 pages supplementary material available from Journal, Inorganic Chemistry 2015

Highly functionalized spirocyclic tetramates were prepared via a sequential Knoevenagel reaction and [1,5]-prototropic shift (T-reaction) of bicyclic tetramates. While these compounds isomerize in solution, stable analogues can be prepared via an appropriate choice of substituents. Further modification of these compounds allows for the introduction of aromatic groups, making them suitable as skeletons for application in medicinal chemistry.

Routes to bicyclic tetramates derived from cysteine permitting ready incorporation of functionality at two different points around the periphery of a heterocyclic skeleton are reported. This has enabled the identification of systems active against Gram-positive bacteria, some of which show gyrase and RNA polymerase inhibitory activity. In particular, tetramates substituted with glycosyl side chains, chosen to impart polarity and aqueous solubility, show high antibacterial activity coupled with modest gyrase/polymerase activity in two cases. An analysis of physicochemical properties indicates that the antibacterially active tetramates generally occupy physicochemical space with MW of 300–600, clogD(7.4) of −2.5 to 4 and rel. PSA of 11–22%. This work demonstrates that biologically active 3D libraries are readily available by manipulation of a tetramate skeleton.

A new method for the stereoselective synthesis of highly functionalized oxygen heterocycles using allyl or benzyl alcohols as alkylating agents is presented. The process is efficient and atom economic, generating water as the only stoichiometric byproduct. Substoichiometric amounts of Ti(OiPr)4 in HFIP solvent are key to this reactivity, and the method tolerates a broad substitution pattern on both the alcohol initiator and homoallylic alcohol substrate. Preliminary mechanistic studies reveal in situ formation of a titanium complex with HFIP which may initiate the cyclization reaction. Further stereoselective functionalization of the products allows access to a diverse range of interesting heterocyclic structures.

We report the synthesis, crystal structure, and thermally- driven phase transformation of the dicyanometallate super- perovskite co-crystal [NBu4]Mn[Au(CN)2]3·[NBu4]ClO4. This phase is understandable in terms of the conventional ABX3 perovskite structure type, but with the NBu+4 A-site cation displaced onto the perovskite cage face and 1-dimensional AX′ chains included within framework pores opened up by these displacements. On heating to 380K, the co-crystal disproportionates into its two inorganic components: a bcs-structured ABX3 phase and [NBu4 ]ClO4 . This system illustrates a new type of structural and phase complexity accessible to dicyanometallate perovskites.

The first examples of isolable two-coordinate terphenyl-substituted germylium-ylidenes are reported. These systems, of composition [(NHC)(Ar)Ge]+, exploit a range of aryl and NHC substituents (ArMes, ArTrip; IMe4, IPrMe) and are isolated by employing weakly coordinating borate or aluminate counter-ions. The use of the smallest combination of substituents used in this study (IMe4 and ArMes) results in the formation of a dicationic dimer, [(IMe4)(ArMes)Ge=Ge(ArMes)(IMe4)]2+, which can also be viewed as an imidazolium-functionalized digermene. Increasing the steric loading (at either the NHC or terphenyl ligand) leads to the formation of the monomeric germylium-ylidene cations [(IMe4)(ArTrip)Ge]+, [(IPrMe)(ArMes)Ge]+, and [(IPrMe)(ArTrip)Ge]+, stabilized in the solid state to varying degrees by secondary interactions with the peripheral arene π systems or C–H bonds. These three systems are characterized by widening C–Ge–C angles (101.7(1), 105.0(2) and 107.2(1)°, respectively) as the steric profiles of the germanium-bound substituents increase. In the case of dication [(IMe4)(ArMes)Ge=Ge(ArMes)(IMe4)]2+, its ability to act as a functional source of the corresponding monomeric germylium-ylidene, [(IMe4)(ArMes)Ge]+, is demonstrated through its reaction with PhSiH3 in bromobenzene solution, which generates the monomeric GeIV species [(IMe4)(ArMes)Ge(H)(SiH2Ph)]+ via Si–H oxidative addition at germanium.