In vitro reconstitution of α-pyrone ring formation in myxopyronin biosynthesis

Myxopyronins are α-pyrone antibiotics produced by the terrestrial bacterium Myxococcus fulvus Mx f50 and possess antibacterial activity against Gram-positive and Gram-negative pathogens. They target the bacterial RNA polymerase (RNAP) “switch region” as non-competitive inhibitors and display no cross-resistance to the established RNAP inhibitor rifampicin. Recent analysis of the myxopyronin biosynthetic pathway led to the hypothesis that this secondary metabolite is produced from two separate polyketide parts, which are condensed by the stand-alone ketosynthase MxnB. Using in vitro assays we show that MxnB catalyzes a unique condensation reaction forming the α-pyrone ring of myxopyronins from two activated acyl chains in form of their β-keto intermediates. MxnB is able to accept thioester substrates coupled to either N-acetylcysteamine (NAC) or a specific carrier protein (CP). The turnover rate of MxnB for substrates bound to CP was 12-fold higher than for NAC substrates, demonstrating the importance of protein–protein interactions in polyketide synthase (PKS) systems. The crystal structure of MxnB reveals the enzyme to be an unusual member of the ketosynthase group capable of binding and condensing two long alkyl chains bound to carrier proteins. The geometry of the two binding tunnels supports the biochemical data and allows us to propose an order of reaction, which is supported by the identification of novel myxopyronin congeners in the extract of the producer strain. Insights into the mechanism of this unique condensation reaction do not only expand our knowledge regarding the thiolase enzyme family but also opens up opportunities for PKS bioengineering to achieve directed structural modifications.     

Unveiling the nature of supramolecular crown ether–C60 interactions

A series of exTTF-(crown ether)₂ receptors, designed to host C₆₀, has been prepared. The size of the crown ether and the nature of the heteroatoms have been systematically changed to fine tune the association constants. Electrochemical measurements and transient absorption spectroscopy assisted in corroborating charge transfer in the ground state and in the excited state, leading to the formation of radical ion pairs featuring lifetimes in the range from 12 to 21 ps. To rationalize the nature of the exTTF-(crown ether)₂·C₆₀ stabilizing interactions, theoretical calculations have been carried out, suggesting a synergetic interplay of donor–acceptor, π–π, n–π and CH···π interactions, which is the basis for the affinity of our novel receptors towards C₆₀.     

A carbon–carbon hybrid – immobilizing carbon nanodots onto carbon nanotubes

The thrust of this work is to integrate small and uniformly sized carbon nanodots (CNDs) with single-walled carbon nanotubes (SWCNT) of different diameters as electron donors and electron acceptors, respectively, and to test their synergetic interactions in terms of optoelectronic devices. CNDs (denoted pCNDs, where p indicates pressure) were prepared by pressure-controlled microwave decomposition of citric acid and urea. pCNDs were immobilized on single-walled carbon nanotubes by wrapping the latter with poly(4-vinylbenzyl trimethylamine) (PVBTA), which features positively charged ammonium groups in the backbone. Negatively charged surface groups on the CNDs lead to attractive electrostatic interactions. Ground state interactions between the CNDs and SWCNTs were confirmed by a full-fledged photophysical investigation based on steady-state and time-resolved techniques. As a complement, charge injection into the SWCNTs upon photoexcitation was investigated by ultra-short time-resolved spectroscopy.     

Designing logical codon reassignment – Expanding the chemistry in biology

Over the last decade, the ability to genetically encode unnatural amino acids (UAAs) has evolved rapidly. The programmed incorporation of UAAs into recombinant proteins relies on the reassignment or suppression of canonical codons with an amino-acyl tRNA synthetase/tRNA (aaRS/tRNA) pair, selective for the UAA of choice. In order to achieve selective incorporation, the aaRS should be selective for the designed tRNA and UAA over the endogenous amino acids and tRNAs. Enhanced selectivity has been achieved by transferring an aaRS/tRNA pair from another kingdom to the organism of interest, and subsequent aaRS evolution to acquire enhanced selectivity for the desired UAA. Today, over 150 non-canonical amino acids have been incorporated using such methods. This enables the introduction of a large variety of structures into proteins, in organisms ranging from prokaryote, yeast and mammalian cells lines to whole animals, enabling the study of protein function at a level that could not previously be achieved. While most research to date has focused on the suppression of ‘non-sense’ codons, recent developments are beginning to open up the possibility of quadruplet codon decoding and the more selective reassignment of sense codons, offering a potentially powerful tool for incorporating multiple amino acids. Here, we aim to provide a focused review of methods for UAA incorporation with an emphasis in particular on the different tRNA synthetase/tRNA pairs exploited or developed, focusing upon the different UAA structures that have been incorporated and the logic behind the design and future creation of such systems. Our hope is that this will help rationalize the design of systems for incorporation of unexplored unnatural amino acids, as well as novel applications for those already known.     

Water diffusion in atmospherically relevant α-pinene secondary organic material

Secondary organic material (SOM) constitutes a large mass fraction of atmospheric aerosol particles. Understanding its impact on climate and air quality relies on accurate models of interactions with water vapour. Recent research shows that SOM can be highly viscous and can even behave mechanically like a solid, leading to suggestions that particles exist out of equilibrium with water vapour in the atmosphere. In order to quantify any kinetic limitation we need to know water diffusion coefficients for SOM, but this quantity has, until now, only been estimated and has not yet been measured. We have directly measured water diffusion coefficients in the water soluble fraction of α-pinene SOM between 240 and 280 K. Here we show that, although this material can behave mechanically like a solid, at 280 K water diffusion is not kinetically limited on timescales of 1 s for atmospheric-sized particles. However, diffusion slows as temperature decreases. We use our measured data to constrain a Vignes-type parameterisation, which we extend to lower temperatures to show that SOM can take hours to equilibrate with water vapour under very cold conditions. Our modelling for 100 nm particles predicts that under mid- to upper-tropospheric conditions radial inhomogeneities in water content produce a low viscosity surface region and more solid interior, with implications for heterogeneous chemistry and ice nucleation.     

Copper-catalyzed intermolecular C(sp3)–H bond functionalization towards the synthesis of tertiary carbamates

We describe the development of an intermolecular unactivated C(sp³)–H bond functionalization towards the direct synthesis of tertiary carbamates. The transformation proceeded using a readily available, abundant first-row transition metal catalyst (copper), and isocyanates as the source of the amide moiety. This is a novel strategy for direct transformation of a variety of unactivated hydrocarbon feedstocks to N-alkyl-N-aryl and N,N-dialkyl carbamates without pre-functionalization or installation of a directing group. The reaction had a broad substrate scope with 3° > 2° > 1° site selectivity. The reaction proceeded even on a gram scale, and a corresponding free amine was directly obtained when the reaction was performed at high temperature. Kinetic studies suggested that radical-mediated C(sp³)–H bond cleavage was the rate-determining step.     

CO2 induced phase transitions in diamine-appended metal–organic frameworks

Using a combination of density functional theory and lattice models, we study the effect of CO₂ adsorption in an amine functionalized metal–organic framework. These materials exhibit a step in the adsorption isotherm indicative of a phase change. The pressure at which this step occurs is not only temperature dependent but is also metal center dependent. Likewise, the heats of adsorption vary depending on the metal center. Herein we demonstrate via quantum chemical calculations that the amines should not be considered firmly anchored to the framework and we explore the mechanism for CO₂ adsorption. An ammonium carbamate species is formed via the insertion of CO₂ into the M–N_amine bonds. Furthermore, we translate the quantum chemical results into isotherms using a coarse grained Monte Carlo simulation technique and show that this adsorption mechanism can explain the characteristic step observed in the experimental isotherm while a previously proposed mechanism cannot. Furthermore, metal analogues have been explored and the CO₂ binding energies show a strong metal dependence corresponding to the M–N_amine bond strength. We show that this difference can be exploited to tune the pressure at which the step in the isotherm occurs. Additionally, the mmen–Ni₂(dobpdc) framework shows Langmuir like behavior, and our simulations show how this can be explained by competitive adsorption between the new model and a previously proposed model.     

Mutual stabilisation between MII 4L6 tetrahedra and MIIX4 2– metallate guests

A complex host–guest equilibrium employing metal ions incorporated into both the host and guest is discussed. M^IIX₄ ^2– metallate guests are shown to provide a good size and shape match for encapsulation within the M₄L₆ tetrahedral capsules, facilitating the generation of previously unreported Zn₄L₆ complexes. Displacement of the initial, primary template anion (ZnBr₄ ^2–) by a secondary template anion (ClO₄ ^–) is shown to result in the formation of a pentagonal-prismatic Zn₁₀L₁₅ structure that incorporates both Br^– and ClO₄ ^–. Furthermore, the formation of heterometallic complexes provides direct evidence for metal exchange between the guest and host complex.     

Exceptional CO2 working capacity in a heterodiamine-grafted metal–organic framework

An amine-functionalized metal–organic framework (MOF), dmen-Mg₂(dobpdc) (dmen = N,N-dimethylethylenediamine), which contains a heterodiamine with both primary and tertiary amines, was prepared via a post-synthetic method. This material exhibits a significant selectivity factor for CO₂ over N₂ that is commensurate with top-performing MOFs. It is remarkable that the solid is fully regenerated under vacuum or flowing Ar at low desorption temperatures, and following this can take up CO₂ at more than 13 wt%. An exceptionally high working capacity is achieved at low regeneration temperatures and after exposure to humid conditions, which are important parameters for a real post-combustion CO₂ capture process.     

Three-phase junction for modulating electron–hole migration in anatase–rutile photocatalysts

The heterophase solid–solid junction as an important type of structure unit has wide applications for its special mechanics and electronic properties. Here we present a first three-phase atomic model for the anatase–rutile TiO₂ heterophase junction and determine its optical and electronic properties, which leads to resolution of the long-standing puzzles on the enhanced photocatalytic activity of anatase–rutile photocatalysts. By using a set of novel theoretical methods, including crystal phase transition pathway sampling, interfacial strain analysis and first principles thermodynamics evaluation of holes and electrons, we identify an unusual structurally ordered three-phase junction, a layer-by-layer “T-shaped” anatase/TiO₂-II/rutile junction, for linking anatase with rutile. The intermediate TiO₂-II phase, although predicted to be only a few atomic layers thick in contact with anatase, is critical to alleviate the interfacial strain and to modulate photoactivity. We demonstrate that the three-phase junction acts as a single-way valve allowing the photogenerated hole transfer from anatase to rutile but frustrating the photoelectron flow in the opposite direction, which otherwise cannot be achieved by an anatase–rutile direct junction. This new model clarifies the roles of anatase, rutile and the phase junction in achieving high photoactivity synergistically and provides the theoretical basis for the design of better photocatalysts by exploiting multi-phase junctions.     

What causes extended layering of ionic liquids on the mica surface?

Extended layering of ionic liquids (ILs) on the mica surface has been reported by several groups previously and it is generally accepted that the electrostatic interaction at the IL/mica interface is critical to the observed extended layering. Here we report that, indeed, water adsorption on the mica surface is the key to the extended layering of ionic liquids. The atomic force microscopy (AFM), attenuated total reflectance-fourier transform infrared spectroscopy (ATR-FTIR) and contact angle (CA) results show that ionic liquids form extended layering on a mica surface under ambient conditions when water is adsorbed on the mica surface under such conditions. However, when airborne hydrocarbon contaminants replace the water on the mica surface at the elevated temperatures, instead of layering, ionic liquids exhibit droplet structure, i.e., dewetting. Based on the experimental results, we propose that water enables ion exchange between K+ and the cations of ILs on the mica surface and thus triggers the ordered packing of cations/anions in ILs, resulting in extended layering.     

Cytocompatible in situ cross-linking of degradable LbL films based on thiol–exchange reaction

Formation of both mechanically durable and programmably degradable layer-by-layer (LbL) films in a biocompatible fashion has potential applications in cell therapy, tissue engineering, and drug-delivery systems, where the films are interfaced with living cells. In this work, we developed a simple but versatile method for generating in situ cross-linked and responsively degradable LbL films, based on the thiol–exchange reaction, under highly cytocompatible conditions (aqueous solution at pH 7.4 and room temperature). The cytocompatibility of the processes was confirmed by coating individual yeast cells with the cross-linked LbL films and breaking the films on demand, while maintaining the cell viability. In addition, the processes were applied to the controlled release of an anticancer drug in the HeLa cells.     

Insights into the structure–photoreactivity relationships in well-defined perovskite ferroelectric KNbO3 nanowires

Structure–function correlations are a central theme in heterogeneous (photo)catalysis. In this study, the geometric and electronic structure of perovskite ferroelectric KNbO₃ nanowires with respective orthorhombic and monoclinic polymorphs have been systematically addressed. By virtue of aberration-corrected scanning transmission electron microscopy, we directly visualize surface photocatalytic active sites, measure local atomic displacements at an accuracy of several picometers, and quantify ferroelectric polarization combined with first-principles calculations. The photoreactivity of the as-prepared KNbO₃ nanowires is assessed toward aqueous rhodamine B degradation under UV light. A synergy between the ferroelectric polarization and electronic structure in photoreactivity enhancement is uncovered, which accounts for the prominent reactivity order: orthorhombic > monoclinic. Additionally, by identifying new photocatalytic products, rhodamine B degradation pathways involving N-deethylation and conjugated structure cleavage are proposed. Our findings not only provide new insights into the structure–photoreactivity relationships in perovskite ferroelectric photocatalysts, but also have broad implications in perovskite-based water splitting and photovoltaics, among others.     

Linear scaling relationships and volcano plots in homogeneous catalysis – revisiting the Suzuki reaction

Linear free energy scaling relationships and volcano plots are common tools used to identify potential heterogeneous catalysts for myriad applications. Despite the striking simplicity and predictive power of volcano plots, they remain unknown in homogeneous catalysis. Here, we construct volcano plots to analyze a prototypical reaction from homogeneous catalysis, the Suzuki cross-coupling of olefins. Volcano plots succeed both in discriminating amongst different catalysts and reproducing experimentally known trends, which serves as validation of the model for this proof-of-principle example. These findings indicate that the combination of linear scaling relationships and volcano plots could serve as a valuable methodology for identifying homogeneous catalysts possessing a desired activity through a priori computational screening.     

Rh-catalyzed desymmetrization of α-quaternary centers by isomerization-hydroacylation

We describe a Rh-catalyzed desymmetrization of all-carbon quaternary centers from α,α-bis(allyl)aldehydes by a cascade featuring isomerization and hydroacylation. This desymmetrization competes with two other novel olefin functionalizations that are triggered by C–H bond activation, including carboacylation and bisacylation. A BIPHEP ligand promotes enantioselective formation of α-vinylcyclopentanones. Mechanistic studies support irreversible and enantioselective olefin-isomerization followed by olefin-hydroacylation.     

NHC-catalysed benzoin condensation – is it all down to the Breslow intermediate?

The Breslow catalytic cycle describing the benzoin condensation promoted by N-heterocyclic carbenes (NHC) as proposed in the late 1950s has since then been tried by generations of physical organic chemists. Emphasis has been laid on proofing the existence of an enaminol like structure (Breslow intermediate) that explains the observed umpolung of an otherwise electrophilic aldehyde. The present study is not focusing on spectroscopic elucidation of a thiazolydene based Breslow intermediate but rather tries to clarify if this key-intermediate is indeed directly linked with the product side of the overall reaction. The here presented EPR-spectroscopic and computational data provide a fundamentally different view on how the benzoin condensation may proceed: a radical pair could be identified as a second key-intermediate that is derived from the Breslow-intermediate via an SET process. These results highlight the close relationship to the Cannizarro reaction and oxidative transformations of aldehydes under NHC catalysis.     

Tandem trimer pyrrole–imidazole polyamide probes targeting 18 base pairs in human telomere sequences

The binding of molecules to specific DNA sequences is important for imaging genome DNA and for studying gene expression. Increasing the number of base pairs targeted by these molecules would provide greater specificity. N-Methylpyrrole–N-methylimidazole (Py–Im) polyamides are one type of such molecules and can bind to the minor groove of DNA in a sequence-specific manner without causing denaturation of DNA. Our recent work has demonstrated that tandem hairpin Py–Im polyamides conjugated with a fluorescent dye can be synthesized easily and can serve as new probes for studying human telomeres under mild conditions. Herein, to improve their selectivities to telomeres by targeting longer sequences, we designed and synthesized a fluorescent tandem trimer Py–Im polyamide probe, comprising three hairpins and two connecting regions (hinges). The new motif bound to 18 bp dsDNA in human telomeric repeats (TTAGGG)_n, the longest sequence for specific binding reported for Py–Im polyamides. We compared the binding affinities and the abilities to discriminate mismatch, the UV-visible absorption and fluorescence spectra, and telomere staining in human cells between the tandem trimer and a previously developed tandem hairpin. We found that the tandem trimer Py–Im polyamide probe has higher ability to recognize telomeric repeats and stains telomeres in chemically fixed cells with lower background signal.     

Non-equilibrium cobalt(iii) “click” capsules

Cobalt(iii) tetrahedral capsules have been prepared using an assembly-followed-by-oxidation protocol from a cobalt(ii) precursor and a readily derivatizable pyridyl-triazole ligand system. Experiments designed to probe the constitutional dynamics show that these architectures are in a non-equilibrium state. A preliminary investigation into the host–guest chemistry of a water-soluble derivative shows it can bind and differentiate a range of different neutral organic molecules. The stability of this ensemble also permits the study of guest-binding at high salt concentrations.     

Domain-swapped cytochrome cb 562 dimer and its nanocage encapsulating a Zn–SO4 cluster in the internal cavity

Protein nanostructures have been gaining in interest, along with developments in new methods for construction of novel nanostructures. We have previously shown that c-type cytochromes and myoglobin form oligomers by domain swapping. Herein, we show that a four-helix bundle protein cyt cb ₅₆₂, with the cyt b ₅₆₂ heme attached to the protein moiety by two Cys residues insertion, forms a domain-swapped dimer. Dimeric cyt cb ₅₆₂ did not dissociate to monomers at 4 °C, whereas dimeric cyt b ₅₆₂ dissociated under the same conditions, showing that heme attachment to the protein moiety stabilizes the domain-swapped structure. According to X-ray crystallographic analysis of dimeric cyt cb ₅₆₂, the two helices in the N-terminal region of one protomer interacted with the other two helices in the C-terminal region of the other protomer, where Lys51–Asp54 served as a hinge loop. The heme coordination structure of the dimer was similar to that of the monomer. In the crystal, three domain-swapped cyt cb ₅₆₂ dimers formed a unique cage structure with a Zn–SO₄ cluster inside the cavity. The Zn–SO₄ cluster consisted of fifteen Zn²⁺ and seven SO₄ ^2– ions, whereas six additional Zn²⁺ ions were detected inside the cavity. The cage structure was stabilized by coordination of the amino acid side chains of the dimers to the Zn²⁺ ions and connection of two four-helix bundle units through the conformation-adjustable hinge loop. These results show that domain swapping can be applied in the construction of unique protein nanostructures.