Synthesis, structure and stereodynamics of atropisomeric N-chloroamides.

Atropisomeric N-chloroamides were efficiently accessed by electrophilic halogenation of ortho-substituted secondary anilides. The stereodynamics of atropisomerism in these novel scaffolds was interrogated by detailed experimental and computational studies, revealing that racemization is correlated with amide isomerization. The stereoelectronic nature of the amide was shown to significantly influence racemization rates, with potentially important implications for other C-N atropisomeric scaffolds.

Amine-modified polyionic liquid supports enhance the efficacy of PdNPs for the catalytic hydrogenation of CO2 to formate.

Palladium nanoparticles stabilised by aniline modified polymer immobilised ionic liquid is a remarkably active catalyst for the hydrogenation of CO2 to formate; the initial TOF of 500 h-1 is markedly higher than either unmodified catalyst or its benzylamine and N,N-dimethylaniline modified counterparts and is among the highest to be reported for a PdNP-based catalyst.

Exploring the effect of utilising organic acid solutions in ultrasound-assisted extraction of pectin from apple pomace, and its potential for biomedical purposes.

Biomass resulting from food production represents valuable material to recover different biomolecules. In our study, we used apple pomace to obtain pectin, which is traditionally extracted using mineral acids. Our hypothesis consisted of carrying out extractions with organic acids, assisted by ultrasound, by varying processing parameters including time, temperature, and type of acid. The analytical determinations of galacturonic acid content, methoxylation and esterification degree, ζ-potential and extraction yield were used as pectin quality indicators. Pectins extracted using treatment conditions with better performance were assessed biologically in vitro for their potential to be used in biomedical applications. Overall, the extracted pectin presented a galacturonic acid content, methoxylation and esterification degree ranged from 19.7 to 67%, 26.8-41.4% and 58-65.2% respectively, and were negatively charged (-24.1 to -13.2 mV). It was found that factors of time and temperature greatly influenced the response variables excepting the esterification degree, while the acid type influenced the ζ-potential, methoxylation and esterification degrees. Additionally, it was seen that the longer extraction time (50 min) and higher temperature (50 °C) exhibited the better extraction yield (∼10.9%). Finally, the selected pectin showed high cytocompatibility up to 500 µg/mL of concentration when seeded with Neonatal Normal Human Dermal Fibroblasts.

Conformational study into N-alkyl-N'-aryl ureas to inform drug discovery.

Ureas are an important functional group in small molecule drugs as well as having wider applications in organic chemistry. Understanding of their conformation is of critical importance for rational design of urea-containing bioactive compounds. Whilst the conformational preferences of biaryl ureas have been extensively studied, very little attention has been paid to alkylated analogues. We carried out a systematic study of N-aryl (phenyl and pyridyl)-N'-cyclopentyl ureas with differing N-methylation patterns using Well Tempered Metadynamics at a semi-empirical level in implicit water (GBSA) using Well-Tempered Metadynamics to generate their conformational free-energy landscapes. Geometries and energetics of the most relevant configurations are further refined using DFT level of theory. Validation for the computation was obtained by synthesis of all 8 analogues followed by conformational studies by X-ray crystallography and NMR. These findings reveal that the methylation pattern significantly affects the conformational preference of the system. Most notably, N-phenyl-N'-cyclopentyl urea is shown to adopt both the trans-trans, and cis-trans conformations with equal energy and that the cis-trans conformation can be significantly stabilised by the presence of an internal hydrogen bond to the N'-hydrogen. This study will be of utility for the design of N-alkyl-N'-aryl ureas as drug candidates.

A thirty-year old mystery solved: identification of a new heptatungstate from non-aqueous solutions.

A new isopolyoxotungstate has been characterised, thirty years since the first spectroscopic evidence of its existence. The heptatungstate [W7O24H]5-, containing a {W5} lacunary Lindqvist unit fused to a ditungstate fragment, has significant stability and is only the third isopolytungstate structure to be obtained from non-aqueous systems.

Li vs Na: Divergent Reaction Patterns between Organolithium and Organosodium Complexes and Ligand-Catalyzed Ketone/Aldehyde Methylenation.

Organosodium chemistry is underdeveloped compared with organolithium chemistry, and all the reported organosodium complexes exhibit similar, if not identical, reactivity patterns to their lithium counterparts. Herein, we report a rare organosodium monomeric complex, namely, [Na(CH2SiMe3)(Me6Tren)] (1-Na) (Me6Tren: tris[2-(dimethylamino)ethyl]amine) stabilized by a tetra-dentate neutral amine ligand Me6Tren. Employing organo-carbonyl substrates (ketones, aldehydes, amides, ester), we demonstrated that 1-Na features distinct reactivity patterns compared with its lithium counterpart, [Li(CH2SiMe3)(Me6Tren)] (1-Li). Based on this knowledge, we further developed a ligand-catalysis strategy to conduct ketone/aldehyde methylenations, using [NaCH2SiMe3]∞ as the CH2 feedstock, replacing the widely used but hazardous/expensive C═O methylenation methods, such as Wittig, Tebbe, Julia/Julia-Kocienski, Peterson, and so on.

Stereochemical Control of Secondary Benzamide-based BODIPY Emitters.

Aromatic amides can be used to construct light-harvesting materials with valuable optical properties. The amide bond is formed using well-known coupling agents in near quantitative yield, as illustrated here through the synthesis of two boron dipyrromethene derivatives bearing an amide linkage. The primary concern with acyl amides is rotation around the C-N bond, leading to cis and trans isomers. Using NMR spectroscopy, quantum chemical calculations and critical comparison to simpler benzamides, the stereochemistry of the target compounds has been addressed. The N-cyclohexyl derivative gave diffraction quality crystals that established a trans geometry for the amide bond. Quantum chemical calculations support the trans geometry as being the lowest-energy structure in solution but indicate that inversion of the aryl ring is an important structural feature. Indeed, rotation around the C(sp2 )-C(aryl) bond has a strong influence on the solution-phase NMR spectra. The amide connection has minimal effect on the photophysical properties.

Mirubactin C rescues the lethal effect of cell wall biosynthesis mutations in Bacillus subtilis.

Growth of most rod-shaped bacteria is accompanied by the insertion of new peptidoglycan into the cylindrical cell wall. This insertion, which helps maintain and determine the shape of the cell, is guided by a protein machine called the rod complex or elongasome. Although most of the proteins in this complex are essential under normal growth conditions, cell viability can be rescued, for reasons that are not understood, by the presence of a high (mM) Mg2+ concentration. We screened for natural product compounds that could rescue the growth of mutants affected in rod-complex function. By screening > 2,000 extracts from a diverse collection of actinobacteria, we identified a compound, mirubactin C, related to the known iron siderophore mirubactin A, which rescued growth in the low micromolar range, and this activity was confirmed using synthetic mirubactin C. The compound also displayed toxicity at higher concentrations, and this effect appears related to iron homeostasis. However, several lines of evidence suggest that the mirubactin C rescuing activity is not due simply to iron sequestration. The results support an emerging view that the functions of bacterial siderophores extend well beyond simply iron binding and uptake.

Elucidating Solution-State Coordination Modes of Multidentate Neutral Amine Ligands with Group-1 Metal Cations: Variable-Temperature NMR Studies.

Multidentate neutral amine ligands play vital roles in coordination chemistry and catalysis. In particular, these ligands are used to tune the reactivity of Group-1 metal reagents, such as organolithium reagents. Most, if not all, of these Group-1 metal reagent-mediated reactions occur in solution. However, the solution-state coordination behaviors of these ligands with Group-1 metal cations are poorly understood, compared to the plethora of solid-state structural studies based on single-crystal X-ray diffraction (SCXRD) studies. In this work, we comprehensively mapped out the coordination modes with Group-1 metal cations for three multidentate neutral amine ligands: tridentate 1,4,7-trimethyl-1,4,7-triazacyclononane (Me3TACN), tetradentate tris[2-(dimethylamino)ethyl]amine (Me6Tren), and hexadentate N,N',N″-tris-(2-N-diethylaminoethyl)-1,4,7-triaza-cyclononane (DETAN). The macrocycles in the Me3TACN and DETAN are identified as the rigid structural directing motif, with the sidearms of DETAN providing flexible "on-demand" coordination sites. In comparison, the Me6Tren ligand features more robust coordination, with the sidearms less likely to undergo the decoordinating-coordinating equilibrium. This work will provide a guidance for coordination chemists in applying these three ligands, in particular, the new DETAN ligand to design metal complexes which suit their purposes.

Discovery, isolation, heterologous expression and mode-of-action studies of the antibiotic polyketide tatiomicin from Amycolatopsis sp. DEM30355.

A genomic and bioactivity informed analysis of the metabolome of the extremophile Amycolatopsis sp. DEM30355 has allowed for the discovery and isolation of the polyketide antibiotic tatiomicin. Identification of the biosynthetic gene cluster was confirmed by heterologous expression in Streptomyces coelicolor M1152. Structural elucidation, including absolute stereochemical assignment, was performed using complementary crystallographic, spectroscopic and computational methods. Tatiomicin shows antibiotic activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Cytological profiling experiments suggest a putative antibiotic mode-of-action, involving membrane depolarisation and chromosomal decondensation of the target bacteria.

Spontaneous Decomposition of an Extraordinarily Twisted and Trans-Bent Fully-Phosphanyl-Substituted Digermene to an Unusual GeI Cluster.

Ditetrelenes R2 E=ER2 (E=Si, Ge, Sn, Pb) substituted by multiple N/P/O/S-donor groups are extremely rare due to their propensity to disaggregate into their tetrylene monomers R2 E. We report the synthesis of the first fully phosphanyl-substituted digermene {(Mes)2 P}2 Ge=Ge{P(Mes)2 }2 (3, Mes=2,4,6-Me3 C6 H2 ), which adopts a highly unusual structure in the solid state, that is both strongly trans-bent and highly twisted. Variable-temperature 31 P{1 H} NMR spectroscopy suggests that 3 persists in solution, but is subject to a dynamic equilibrium between two conformations, which have different geometries about the Ge=Ge bond (twisted/non-twisted) due to a difference in the nature of their π-stacking interactions. Compound 3 undergoes unprecedented, spontaneous decomposition in solution to give a unique GeI cluster {(Mes)2 P}4 Ge4 ⋅5 CyMe (7).

Versatile Coordination Modes of Multidentate Neutral Amine Ligands with Group 1 Metal Cations.

This work comprehensively investigated the coordination chemistry of a hexa-dentate neutral amine ligand, namely, N,N',N"-tris-(2-N-diethylaminoethyl)-1,4,7-triaza-cyclononane (DETAN), with group-1 metal cations (Li+, Na+, K+, Rb+, Cs+). Versatile coordination modes were observed, from four-coordinate trigonal pyramidal to six-coordinate trigonal prismatic, depending on the metal ionic radii and metal's substituent. For comparison, the coordination chemistry of a tetra-dentate tris-[2-(dimethylamino)ethyl]amine (Me6Tren) ligand was also studied. This work defines the available coordination modes of two multidentate amine ligands (DETAN and Me6Tren), guiding future applications of these ligands for pursuing highly reactive and elusive s-block and rare-earth metal complexes.

A monomeric (trimethylsilyl)methyl lithium complex: synthesis, structure, decomposition and preliminary reactivity studies.

Monomeric organolithium (LiR) complexes could provide enhanced Li-C bond reactivity and suggest mechanisms for a plethora of LiR-mediated reactions. They are highly sought-after but remain a synthetic challenge for organometallic chemists. In this work, we report the synthesis and characterisation of a monomeric (trimethylsilyl)methyl lithium complex, namely [Li(CH2SiMe3)(κ3-N,N',N''-Me6Tren)] (1), where Me6Tren is a tetradentate neutral amine ligand. The structure of 1 was comprehensively examined by single-crystal X-ray diffraction, variable temperature NMR spectroscopy and electron absorption spectroscopy. Complex 1 decomposes via ligand C-H and C-N activations to produce a Li amide complex 2. Preliminary reactivity studies of 1 reveal CO insertion and C-H activation reaction patterns.

Optical spectroscopic properties recorded for simple BOPHY dyes in condensed media: The mirror-symmetry factor.

The BOPHY structural scaffold provides opportunities for the synthesis of innumerable derivatives with linear geometries and well-controlled π-conjugation pathways. The simpler BOPHY chromophores are highly fluorescent but exhibit poor mirror symmetry between absorption and fluorescence spectra at ambient temperature. In particular, the absorption (and excitation) spectra are broad and appear as two overlapping bands of comparable intensity. In constrained media, such as low-temperature rigid glasses or stretched poly(ethylene) films, mirror symmetry is restored. Analysis of the temperature dependence recorded for simple BOPHY derivatives indicates that the vibronic envelope accompanying the electronic transitions can be well described in terms of low- and medium-frequency modes. Whereas the fluorescence spectral profile is only weakly dependent on temperature, the excitation spectrum is far more affected. The magnitude of the low-frequency mode, and the associated electron-phonon coupling, increase substantially with increasing temperature and is responsible for temperature broadening and distortion of the excitation spectrum in solution. This critical low-frequency vibronic mode is associated with out-of-plane torsional bending of the BOPHY unit. Variable temperature NMR studies failed to provide unequivocal evidence for conformational changes of one of the derivatives over the temperature range 193-353 K.

The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29.

Glycosaminoglycans (GAGs) and GAG-degrading enzymes have wide-ranging applications in the medical and biotechnological industries. The former are also an important nutrient source for select species of the human gut microbiota (HGM), a key player in host-microbial interactions. How GAGs are metabolized by the HGM is therefore of interest and has been extensively investigated in the model human gut microbe Bacteroides thetaiotaomicron. The presence of as-yet uncharacterized GAG-inducible genes in its genome and of related species, however, is testament to our incomplete understanding of this process. Nevertheless, it presents a potential opportunity for the discovery of additional GAG-degrading enzymes. Here, we investigated a gene of unknown function (BT_3328) from the chondroitin sulfate (CS) utilization locus of B. thetaiotaomicron NMR and UV spectroscopic assays revealed that it encodes a novel polysaccharide lyase (PL), hereafter referred to as BtCDH, reflecting its source (B. thetaiotaomicron (Bt)) and its ability to degrade the GAGs CS, dermatan sulfate (DS), and hyaluronic acid (HA). When incubated with HA, BtCDH generated a series of unsaturated HA sugars, including Δ4,5UA-GlcNAc, Δ4,5UA-GlcNAc-GlcA-GlcNac, Δ4,5UA-[GlcNAc-GlcA]2-GlcNac, and Δ4,5UA-[GlcNAc-GlcA]3-GlcNac, as end products and hence was classed as endo-acting. A combination of genetic and biochemical assays revealed that BtCDH localizes to the cell surface of B. thetaiotaomicron where it enables extracellular GAG degradation. BtCDH homologs were also detected in several other HGM species, and we therefore propose that it represents the founding member of a new polysaccharide lyase family (PL29). The current discovery also contributes new insights into CS metabolism by the HGM.

Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis.

Antibiotic-resistant bacterial pathogens pose an urgent healthcare threat, prompting a demand for new medicines. We report the mode of action of the natural ansamycin antibiotic kanglemycin A (KglA). KglA binds bacterial RNA polymerase at the rifampicin-binding pocket but maintains potency against RNA polymerases containing rifampicin-resistant mutations. KglA has antibiotic activity against rifampicin-resistant Gram-positive bacteria and multidrug-resistant Mycobacterium tuberculosis (MDR-M. tuberculosis). The X-ray crystal structures of KglA with the Escherichia coli RNA polymerase holoenzyme and Thermus thermophilus RNA polymerase-promoter complex reveal an altered-compared with rifampicin-conformation of KglA within the rifampicin-binding pocket. Unique deoxysugar and succinate ansa bridge substituents make additional contacts with a separate, hydrophobic pocket of RNA polymerase and preclude the formation of initial dinucleotides, respectively. Previous ansa-chain modifications in the rifamycin series have proven unsuccessful. Thus, KglA represents a key starting point for the development of a new class of ansa-chain derivatized ansamycins to tackle rifampicin resistance.

Identification of a xenobiotic as a potential environmental trigger in primary biliary cholangitis.

BACKGROUND & AIMS: Primary biliary cholangitis (PBC) is an autoimmune-associated chronic liver disease triggered by environmental factors, such as exposure to xenobiotics, which leads to a loss of tolerance to the lipoic acid-conjugated regions of the mitochondrial pyruvate dehydrogenase complex, typically to the E2 component. We aimed to identify xenobiotics that might be involved in the environmental triggering of PBC. METHODS: Urban landfill and control soil samples from a region with high PBC incidence were screened for xenobiotic activities using analytical, cell-based xenobiotic receptor activation assays and toxicity screens. RESULTS: A variety of potential xenobiotic classes were ubiquitously present, as identified by their interaction with xenobiotic receptors - aryl hydrocarbon receptor, androgen receptor and peroxisome proliferator activated receptor alpha - in cell-based screens. In contrast, xenoestrogens were present at higher levels in soil extracts from around an urban landfill. Furthermore, two landfill sampling sites contained a chemical(s) that inhibited mitochondrial oxidative phosphorylation and induced the apoptosis of a hepatic progenitor cell. The mitochondrial effect was also demonstrated in human liver cholangiocytes from three separate donors. The chemical was identified as the ionic liquid [3-methyl-1-octyl-1H-imidazol-3-ium]+ (M8OI) and the toxic effects were recapitulated using authentic pure chemical. A carboxylate-containing human hepatocyte metabolite of M8OI, bearing structural similarity to lipoic acid, was also enzymatically incorporated into the E2 component of the pyruvate dehydrogenase complex via the exogenous lipoylation pathway in vitro. CONCLUSIONS: These results identify, for the first time, a xenobiotic in the environment that may be related to and/or be a component of an environmental trigger for PBC. Therefore, further study in experimental animal models is warranted, to determine the risk of exposure to these ionic liquids. LAY SUMMARY: Primary biliary cholangitis is a liver disease in which most patients have antibodies to mitochondrial proteins containing lipoic acid binding site(s). This paper identified a man-made chemical present in soils around a waste site. It was then shown that this chemical was metabolized into a product with structural similarity to lipoic acid, which was capable of replacing lipoic acid in mitochondrial proteins.

Structural Reassignment and Absolute Stereochemistry of Madurastatin C1 (MBJ-0034) and the Related Aziridine Siderophores: Madurastatins A1, B1, and MBJ-0035.

The madurastatins are pentapeptide siderophores originally described as containing an unusual salicylate-capped N-terminal aziridine ring. Isolation of madurastatin C1 (1) (also designated MBJ-0034), from Actinomadura sp. DEM31376 (itself isolated from a deep sea sediment), prompted structural reevaluation of the madurastatin siderophores, in line with the recent work of Thorson and Shaaban. NMR spectroscopy in combination with partial synthesis allowed confirmation of the structure of madurastatin C1 (1) as containing an N-terminal 2-(2-hydroxyphenyl)oxazoline in place of the originally postulated aziridine, while absolute stereochemistry was determined via Harada's advanced Marfey's method. Therefore, this work further supports Thorson and Shaaban's proposed structural revision of the madurastatin class of siderophores (madurastatins A1 (2), B1 (3), C1 (1), and MBJ-0036 (4)) as N-terminal 2-(2-hydroxyphenyl)oxazolines.

Production of 17-O-demethyl-geldanamycin, a cytotoxic ansamycin polyketide, by Streptomyces hygroscopicus DEM20745.

The actinomycete DEM20745, collected from non-rhizosphere soil adjacent to Paraserianthes falactaria trees (Cangkringan, Indonesia), is an efficient producer of the anticancer ansamycin polyketide 17-O-demethyl-geldanamycin (17-O-DMG), a biosynthetic precursor of the Hsp90 inhibitor geldanamycin (GDM). In DEM20745, 17-O-DMG is the major ansamycin product observed reaching a maximum titre of 17 mg/L in the fermentation broth. 17-O-DMG has the potential to be a key starting material for the semi-synthesis of GDM analogues for use in anticancer therapy. Thus, this preferential biosynthesis of 17-O-DMG facilitates easy access to this important molecule and provides further insight in the biosynthesis of the geldanamycins.

A comparison of MOP-phosphonite ligands and their applications in Rh(i)- and Pd(ii)-catalysed asymmetric transformations.

Six chiral MOP-phosphonites have been synthesised and compared via experimental and computational methods in an effort to quantify their differing structural and electronic profiles. They were found to be electron-poor ligands in comparison to their arylphosphine analogues and have a larger trans influence in square planar Pt(ii) complexes. Four [Rh(LP)(η2:η2-cod)Cl] complexes were synthesised and characterised by NMR, HRMS and X-ray crystallography. Two [Rh(LP)2]BF4 complexes were prepared where one ligand acts as a chelating P,C-π-donor; detailed NMR studies demonstrated a hemilabile η6-coordination mode, which in one case was confirmed by X-ray crystallography. Rh(i) complexes were used as catalysts in asymmetric hydrogenation and hydroformylation reactions and in the addition of phenyl boronic acid to an isatin. Pd(ii) complexes were successfully employed in asymmetric Suzuki-Miyaura cross-coupling reactions yielding binaphthyl products. Two [Pd(LP)2Cl2] complexes were synthesised and characterised by X-ray crystallography, both adopting cis orientations, with one of the complexes crystallising as two pseudo-polymorphs.