Structural basis of head to head polyketide fusion by CorB

Corallopyronin A is a polyketide derived from the myxobacterium Corallococcus coralloides with potent antibiotic features. The gene cluster responsible for the biosynthesis of corallopyronin A has been described recently, and it was proposed that CorB acts as a ketosynthase to interconnect two polyketide chains in a rare head-to-head condensation reaction. We determined the structure of CorB, the interconnecting polyketide synthase, to high resolution and found that CorB displays a thiolase fold. Site-directed mutagenesis showed that the catalytic triad consisting of a cysteine, a histidine and an asparagine is crucial for catalysis, and that this triad shares similarities with the triad found in HMG-CoA synthases. We synthesized a substrate mimic to derivatize purified CorB and confirmed substrate attachment by ESI-MS. Structural analysis of the complex yielded an electron density-based model for the polyketide chain and showed that the unusually wide, T-shaped active site is able to accommodate two polyketides simultaneously. Our structural analysis provides a platform for understanding the unusual head-to-head polyketide-interconnecting reaction catalyzed by CorB.     

Fluorine teams up with water to restore inhibitor activity to mutant BPTI

Introducing fluorine into molecules has a wide range of effects on their physicochemical properties, often desirable but in most cases unpredictable. The fluorine atom imparts the C–F bond with low polarizability and high polarity, and significantly affects the behavior of neighboring functional groups, in a covalent or noncovalent manner. Here, we report that fluorine, present in the form of a single fluoroalkyl amino acid side chain in the P1 position of the well-characterized serine-protease inhibitor BPTI, can fully restore inhibitor activity to a mutant that contains the corresponding hydrocarbon side chain at the same site. High resolution crystal structures were obtained for four BPTI variants in complex with bovine β-trypsin, revealing changes in the stoichiometry and dynamics of water molecules in the S1 subsite. These results demonstrate that the introduction of fluorine into a protein environment can result in “chemical complementation” that has a significantly favorable impact on protein–protein interactions.     

Accurate molecular weight determination of small molecules via DOSY-NMR by using external calibration curves with normalized diffusion coefficients

Determination of the aggregation and solvation numbers of organometallic complexes in solution is an important task to increase insight in reaction mechanisms. Thus knowing which aggregates are formed during a reaction is of high interest to develop better selectivity and higher yields. Diffusion-ordered spectroscopy (DOSY), which separates NMR signals according to the diffusion coefficient, finds increasing use to identify species in solution. However, there still is no simple relationship between diffusion coefficient and molecular weight (MW). Some methods have been developed to estimate the MW but still with a significant error of ±30%. Here we describe a novel development of MW-determination by using an external calibration curve (ECC) approach with normalized diffusion coefficients. Taking the shape of the molecules into account enables accurate MW-predictions with a maximum error of smaller than ±9%. Moreover we show that the addition of multiple internal references is dispensable. One internal reference (that also can be the solvent) is sufficient. If the solvent signal is not accessible, 16 other internal standards (aliphatics and aromatics) are available to avoid signal overlapping problems and provide flexible choice of analytes. This method is independent of NMR-device properties and diversities in temperature or viscosity and offers an easy and robust method to determine accurate MWs in solution.     

Conducting polyfurans by electropolymerization of oligofurans

Polyfurans have never been established as useful conjugated polymers, as previously they were considered to be inherently unstable and poorly conductive. Here, we show the preparation of stable and conducting polyfuran films by electropolymerization of a series of oligofurans of different chain lengths substituted with alkyl groups. The polyfuran films show good conductivity in the order of 1 S cm^–1, good environmental and electrochemical stabilities, very smooth morphologies (roughness 1–5 nm), long effective conjugation lengths, well-defined spectroelectrochemistry and electro-optical switching (in the Vis-NIR region), and have optical band-gaps in the range of 2.2–2.3 eV. A low oxidation potential needed for polymerization of oligofurans (compared to furan) is a key factor in achievement of improved properties of polyfurans reported in this work. DFT calculations and experiments show that polyfurans are much more rigid than polythiophenes, and alkyl substitution does not disturb backbone planarity and conjugation. The obtained properties of polyfuran films are similar or superior to the properties of electrochemically prepared poly(oligothiophene)s under similar conditions.     

Structural diversity of small molecule libraries

A novel method for assessing structural diversity is presented. Maximum common subgraph identity is used as the measure of similarity between two chemical structures. A conditional probability treatment of similarity distributions for libraries of chemical structures is used to define diversity. This evaluation method together with the evaluation of traditional physicochemical properties is used to assess a large number of chemical libraries and to understand structural differences between these.     

N-Heterocyclic carbene catalysed redox isomerisation of esters to functionalised benzaldehydes

N-Heterocyclic carbene catalysed redox isomerisation with reduction about the carbonyl has been developed in the transformation of trienyl esters to tetrasubstituted benzaldehydes. The reaction proceeds in good to excellent yield, and in cases that provide 2,2′-biaryls, enantioselectivity is observed. Mechanistic studies demonstrate the intermediacy of a cyclohexenyl β-lactone, while implicating formation of the homoenolate as turnover limiting.     

Experiences with a researcher-centric ELN

Electronic Laboratory Notebooks (ELNs) are progressively replacing traditional paper books in both commercial research establishments and academic institutions. University researchers require specific features from ELNs, given the need to promote cross-institutional collaborative working, to enable the sharing of procedures and results, and to facilitate publication. The LabTrove ELN, which we use as our exemplar, was designed to be researcher-centric (i.e., not only aimed at the individual researcher''s basic needs rather than to a specific institutional or subject or disciplinary agenda, but also able to be tailored because it is open source). LabTrove is being used in a heterogeneous set of academic laboratories, for a range of purposes, including analytical chemistry, X-ray studies, drug discovery and a biomaterials project. Researchers use the ELN for recording experiments, preserving data collected, and for project coordination. This perspective article describes the experiences of those researchers from several viewpoints, demonstrating how a web-based open source electronic notebook can meet the diverse needs of academic researchers.     

Reaction of a diaryldigermyne with ethylene

Reaction of the stable digermyne BbtGeGeBbt (Bbt = 2,6-[CH(SiMe₃)₂]₂-4-[C(SiMe₃)₃]-C₆H₂) with ethylene initially afforded the corresponding 1,2-digermacyclobutene. Depending on the reaction conditions applied, further reaction of this 1,2-digermacyclobutene with ethylene furnished two different reaction products: a 1,4-digermabicyclo[2.2.0]hexane or a bis(germiranyl)ethane. Combined experimental and theoretical results suggested that the 1,4-digermabicyclo[2.2.0]hexane and the bis(germiranyl)ethane are the thermodynamic and kinetic reaction products, respectively. A reaction mechanism in agreement with these results was proposed.     

Oxygen diffusion pathways in a cofactor-independent dioxygenase

Molecular oxygen plays an important role in a wide variety of enzymatic reactions. Through recent research efforts combining computational and experimental methods a new view of O₂ diffusion is emerging, where specific channels guide O₂ to the active site. The focus of this work is DpgC, a cofactor-independent oxygenase. Molecular dynamics simulations, together with mutagenesis experiments and xenon-binding data, reveal that O₂ reaches the active site of this enzyme using three main pathways and four different access points. These pathways connect a series of dynamic hydrophobic pockets, concentrating O₂ at a specific face of the enzyme substrate. Extensive molecular dynamics simulations provide information about which pathways are more frequently used. This data is consistent with the results of kinetic measurements on mutants and is difficult to obtain using computational cavity-location methods. Taken together, our results reveal that although DpgC is rare in its ability of activating O₂ in the absence of cofactors or metals, the way O₂ reaches the active site is similar to that reported for other O₂-using proteins: multiple access channels are available, and the architecture of the pathway network can provide regio- and stereoselectivity. Our results point to the existence of common themes in O₂ access that are conserved among very different types of proteins.     

Synthesis and structural analysis of nonstoichiometric ternary fulleride K 1.5 Ba 0.25 CsC 60

The existence of cation-vacancy sites in fullerides might lead to long-range ordering and generate a new vacancy-ordered superstructure. The purpose of this work is to search whether or not long-range ordering of vacant tetrahedral sites, namely superstructure emerges in nonstoichiometric K _1.5 Ba _0.25 CsC ₆₀ fulleride. Therefore, K _1.5 Ba _0.25 CsC ₆₀ with cation-vacancy sites is synthesized using a precursor method to avoid inadequate stoichiometry control and formation of impurity phases within the target composition. For this purpose, first, phase-pure K ₆ C ₆₀ , Ba ₆ C ₆₀ and Cs ₆ C ₆₀ precursors are synthesized. Stoichiometric quantities of these precursors are used for further reaction with C ₆₀ to afford K _1.5 Ba _0.25 CsC ₆₀ . Rietveld analysis of the high-resolution synchrotron X-ray powder diffraction data of the precursors and K _1.5 Ba _0.25 CsC ₆₀ confirms that K ₆ C ₆₀ , Ba ₆ C ₆₀ and Cs ₆ C ₆₀ are single-phase and they crystallize in a body-centered-cubic structure ( Im 3) as reported in the literature. The analysis also shows that K _1.5 Ba _0.25 CsC ₆₀ phase can be perfectly modeled using a face-centered cubic structure. No new peaks appear which could have implied the appearance of a superstructure. This suggests that there is no long-range ordered arrangement of vacant tetrahedral sites in K _1.5 Ba _0.25 CsC ₆₀ .     

Extending N-heterocyclic carbene ligands into the third dimension: a new type of hybrid phosphazane/NHC system

A simple, “click” synthetic approach to a new type of hybrid phosph(III)azane/NHC system is described. The presence of the phosphazane P₂N₂ ring unit, with P atoms flanking the NCN fragment and with this ring perpendicular to the binding site of the NHC, provides unique opportunities for modifying the electronic and steric character of these carbenes.     

Exploiting parameter space in MOFs: a 20-fold enhancement of phosphate-ester hydrolysis with UiO-66-NH2

The hydrolysis of nerve agents is of primary concern due to the severe toxicity of these agents. Using a MOF-based catalyst (UiO-66), we have previously demonstrated that the hydrolysis can occur with relatively fast half-lives of 50 minutes. However, these rates are still prohibitively slow to be efficiently utilized for some practical applications (e.g., decontamination wipes used to clean exposed clothing/skin/vehicles). We thus turned our attention to derivatives of UiO-66 in order to probe the importance of functional groups on the hydrolysis rate. Three UiO-66 derivatives were explored; UiO-66-NO₂ and UiO-66-(OH)₂ showed little to no change in hydrolysis rate. However, UiO-66-NH₂ showed a 20 fold increase in hydrolysis rate over the parent UiO-66 MOF. Half-lives of 1 minute were observed with this MOF. In order to probe the role of the amino moiety, we turned our attention to UiO-67, UiO-67-NMe₂ and UiO-67-NH₂. In these MOFs, the amino moiety is in close proximity to the zirconium node. We observed that UiO-67-NH₂ is a faster catalyst than UiO-67 and UiO-67-NMe₂. We conclude that the role of the amino moiety is to act as a proton-transfer agent during the catalytic cycle and not to hydrogen bond or to form a phosphorane intermediate.     

Emptying and filling a tunnel bronze

The classical orthorhombic layered phase of V₂O₅ has long been regarded as the thermodynamic sink for binary vanadium oxides and has found great practical utility as a result of its open framework and easily accessible redox states. Herein, we exploit a cation-exchange mechanism to synthesize a new stable tunnel-structured polymorph of V₂O₅ (ζ-V₂O₅) and demonstrate the subsequent ability of this framework to accommodate Li and Mg ions. The facile extraction and insertion of cations and stabilization of the novel tunnel framework is facilitated by the nanometer-sized dimensions of the materials, which leads to accommodation of strain without amorphization. The topotactic approach demonstrated here indicates not just novel intercalation chemistry accessible at nanoscale dimensions but also suggests a facile synthetic route to ternary vanadium oxide bronzes (M_xV₂O₅) exhibiting intriguing physical properties that range from electronic phase transitions to charge ordering and superconductivity.     

Biosynthesis of fosfazinomycin is a convergent process

Fosfazinomycin A is a phosphonate natural product in which the C-terminal carboxylate of a Val–Arg dipeptide is connected to methyl 2-hydroxy-2-phosphono-acetate (Me-HPnA) via a unique hydrazide linkage. We report here that Me-HPnA is generated from phosphonoacetaldehyde (PnAA) in three biosynthetic steps through the combined action of an O-methyltransferase (FzmB) and an α-ketoglutarate (α-KG) dependent non-heme iron dioxygenase (FzmG). Unexpectedly, the latter enzyme is involved in two different steps, oxidation of the PnAA to phosphonoacetic acid as well as hydroxylation of methyl 2-phosphonoacetate. The N-methyltransferase (FzmH) was able to methylate Arg-NHNH₂ (3) to give Arg-NHNHMe (4), constituting the second segment of the fosfazinomycin molecule. Methylation of other putative intermediates such as desmethyl fosfazinomycin B was not observed. Collectively, our current data support a convergent biosynthetic pathway to fosfazinomycin.     

Direct in vivo imaging of ferrous iron dyshomeostasis in ageing Caenorhabditis elegans

Iron is essential for eukaryotic biochemistry. Systematic trafficking and storage is required to maintain supply of iron while preventing it from catalysing unwanted reactions, particularly the generation of oxidising reactive species. Iron dyshomeostasis has been implicated in major age-associated diseases including cancers, neurodegeneration and heart disease. Here, we employ population-level X-ray fluorescence imaging and native-metalloproteomic analysis to determine that altered iron coordination and distribution is a pathological imperative of ageing in the nematode, Caenorhabditis elegans. Our approach provides a method to simultaneously study iron metabolism across different scales of biological organisation, from populations to cells. Here we report how and where iron homeostasis is lost during C. elegans ageing, and its relationship to the age-related elevation of damaging reactive oxygen species. We find that wild types utilise ferritin to sustain longevity, buffering against exogenous iron and showing rapid ageing if ferritin is ablated. After reproduction, escape of iron from safe-storage in ferritin raised cellular Fe²⁺ load in the ageing C. elegans, and increased generation of reactive species. These findings support the hypothesis that iron-mediated processes drive senescence. We propose that loss of iron homeostasis may be a fundamental and inescapable consequence of ageing that could represent a critical target for therapeutic strategies to improve health outcomes in ageing.     

Operando X-ray absorption and EPR evidence for a single electron redox process in copper catalysis

An unprecedented single electron redox process in copper catalysis is confirmed using operando X-ray absorption and EPR spectroscopies. The oxidation state of the copper species in the interaction between Cu(ii) and a sulfinic acid at room temperature, and the accurate characterization of the formed Cu(i) are clearly shown using operando X-ray absorption and EPR evidence. Further investigation of anion effects on Cu(ii) discloses that bromine ions can dramatically increase the rate of the redox process. Moreover, it is proven that the sulfinic acids are converted into sulfonyl radicals, which can be trapped by 2-arylacrylic acids and various valuable β-keto sulfones are synthesized with good to excellent yields under mild conditions.     

Rational design of small indolic squaraine dyes with large two-photon absorption cross section

Small organic dyes with large two-photon absorption (TPA) cross sections (δ) are more desirable in many applications compared with large molecules. Herein, we proposed a facile theoretical method for the fast screening of small organic molecules as potential TPA dyes. This method is based on a theoretical analysis to the natural transition orbitals (NTOs) directly associated with the TPA transition. Experimental results on the small indolic squaraine dyes (ISD) confirmed that their TPA cross sections is strongly correlated to the delocalization degree of the NTOs of the S₂ excited states. Aided by this simple and intuitive method, we have successfully designed and synthesized a small indolic squaraine dye (ISD) with a remarkable δ value above 8000 GM at 780 nm. The ISD dye also exhibits a high singlet oxygen generation quantum yield about 0.90. The rationally designed TPA dye was successfully applied in both two-photon excited fluorescence cell imaging and in vivo cerebrovascular blood fluid tracing.     

Addition of aluminium,zinc and magnesium hydrides to rhodium(iii)

We report the addition of M–H bonds (M = Al, Zn, Mg) to a Rh(iii) intermediate generated from the reductive elimination of triethylsilane from [Cp*Rh(H)₂(SiEt₃)₂]. A series of new heterobimetallic complexes possessing Rh–M bonds have been isolated and characterised by a number of spectroscopic (¹H, ²⁹Si, ¹³C, ¹⁰³Rh NMR, infrared, and X-ray diffraction) and computational techniques (NBO and QTAIM analysis). Experimental and computational data are consistent with cleavage of the M–H bond upon addition to rhodium with formation of new Rh–M and Rh–H bonds. Upon photolysis the Al analogue of this series undergoes a further elimination reaction producing triethylsilane and a highly unusual Rh₂Al₂H₄ containing cluster proposed to contain an Al(i) bridging ligand.     

Rapid access to phospholipid analogs using thiol-yne chemistry

Phospholipids and glycolipids constitute an essential part of biological membranes, and are of tremendous fundamental and practical interest. Unfortunately, the preparation of functional phospholipids, or synthetic analogs, is often synthetically challenging. Here we utilize thiol-yne click chemistry methodology to gain access to phospho- and glycolipid analogs. Alkynyl hydrophilic head groups readily photoreact with numerous thiol modified lipid tails to yield the appropriate dithioether phospho- or glycolipids. The resulting structures closely resemble the structure and function of native diacylglycerolipids. Dithioether phosphatidylcholines (PCs) are suitable for forming giant unilamellar vesicles (GUV), which can be used as vessels for cell-free expression systems. The unnatural thioether linkages render the lipids resistant to phospholipase A2 hydrolysis. We utilize the improved stability of these lipids to control the shrinkage of GUVs composed of a mixture of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and dioleyl-dithioether PC, concentrating encapsulated nanoparticles. We imagine that these readily accessible lipids could find a number of applications as natural lipid substitutes.