Synthesis of 2,2-difluoro-1,3-diketone and 2,2-difluoro-1,3-ketoester derivatives using fluorine gas.

Solutions of 1,3-diketones and 1,3-ketoester derivatives react with fluorine to give the corresponding 2,2-difluoro-1,3-dicarbonyl derivatives in the presence of quinuclidine. Quinuclidine reacts with fluorine in situ to generate a fluoride ion that facilitates limiting enolization processes, and an electrophilic N-F fluorinating agent that is reactive towards neutral enol species.

Going Full Circle with Organocatalysis and Biocatalysis: The Latent Potential of Cofactor Mimics in Asymmetric Synthesis.

Many enzymes work in tandem with small molecule cofactors, which have inspired organocatalyst designs. Chemical modification of cofactor scaffolds has increased organocatalytic reactivity and reaction scope. This synopsis presents a selection of recent advances in the use of cofactors (native and mimics) in organocatalysis and biocatalysis. We aim to highlight the benefits of combining fundamental knowledge gained in both bio- and organo-catalysis for asymmetric biocatalysis.

Allophycocyanin A is a carbon dioxide receptor in the cyanobacterial phycobilisome.

Light harvesting is fundamental for production of ATP and reducing equivalents for CO2 fixation during photosynthesis. However, electronic energy transfer (EET) through a photosystem can harm the photosynthetic apparatus when not balanced with CO2. Here, we show that CO2 binding to the light-harvesting complex modulates EET in photosynthetic cyanobacteria. More specifically, CO2 binding to the allophycocyanin alpha subunit of the light-harvesting complex regulates EET and its fluorescence quantum yield in the cyanobacterium Synechocystis sp. PCC 6803. CO2 binding decreases the inter-chromophore distance in the allophycocyanin trimer. The result is enhanced EET in vitro and in live cells. Our work identifies a direct target for CO2 in the cyanobacterial light-harvesting apparatus and provides insights into photosynthesis regulation.

Ubiquitin is a carbon dioxide-binding protein.

The identification of CO2-binding proteins is crucial to understanding CO2-regulated molecular processes. CO2 can form a reversible posttranslational modification through carbamylation of neutral N-terminal α-amino or lysine ε-amino groups. We have previously developed triethyloxonium (TEO) ion as a chemical proteomics tool for covalent trapping of carbamates, and here, we deploy TEO to identify ubiquitin as a mammalian CO2-binding protein. We use 13C-NMR spectroscopy to demonstrate that CO2 forms carbamates on the ubiquitin N terminus and ε-amino groups of lysines 6, 33, 48, and 63. We demonstrate that biologically relevant pCO2 levels reduce ubiquitin conjugation at lysine-48 and down-regulate ubiquitin-dependent NF-κB pathway activation. Our results show that ubiquitin is a CO2-binding protein and demonstrates carbamylation as a viable mechanism by which mammalian cells can respond to fluctuating pCO2.

Reactivities of electrophilic N-F fluorinating reagents.

Electrophilic fluorination represents one of the most direct and useful methods available for the selective introduction of fluorine into organic compounds. Electrophilic fluorinating reagents of the N-F class have revolutionised the incorporation of fluorine atoms into both pharmaceutically- and agrochemically-important substrates. Since the earliest N-F reagents were commercialised in the 1990s, their reactivities have been investigated using qualitative and, more recently, quantitative methods. This review discusses the different experimental approaches employed to determine reactivities of N-F reagents, focussing on the kinetics studies reported in recent years. We make critical evaluations of the experimental approaches against each other, theoretical approaches, and their applicability towards practical problems. The opportunities for achieving more efficient synthetic electrophilic fluorination processes through kinetic understanding are highlighted.

Kinetics of Electrophilic Fluorination of Steroids and Epimerisation of Fluorosteroids.

Fluorinated steroids, which are synthesised by electrophilic fluorination, form a significant proportion of marketed pharmaceuticals. To gain quantitative information on fluorination at the 6-position of steroids, kinetics studies were conducted on enol ester derivatives of progesterone, testosterone, cholestenone and hydrocortisone with a series of electrophilic N-F reagents. The stereoselectivities of fluorination reactions of progesterone enol acetate and the kinetic effects of additives, including methanol and water, were investigated. The kinetics of epimerisation of 6ß-fluoroprogesterone to the more pharmacologically active 6α-fluoroprogesterone isomer in HCl/acetic acid solutions are detailed.

Stereoselective Syntheses of 3'-Hydroxyamino- and 3'-Methoxyamino-2',3'-Dideoxynucleosides.

Aminonucleosides are used as key motifs in medicinal and bioconjugate chemistry; however, existing strategies toward 3'-hypernucleophilic amine systems do not readily deliver deoxyribo-configured products. We report diastereoselective syntheses of deoxyribo- and deoxyxylo-configured 3'-hydroxyamino- and 3'-methoxyamino-nucelosides from 3'-imine intermediates. The presence or absence of the 5'-hydroxyl-group protection dictates facial selectivity via inter- or intramolecular delivery of hydride from BH3 (borane). Protecting group screening gave one access to previously unknown 3'-methoxyamino-deoxyguanosine derivatives.

Enolization rates control mono- versus di-fluorination of 1,3-dicarbonyl derivatives.

Fluorine-containing 1,3-dicarbonyl derivatives are essential building blocks for drug discovery and manufacture. To understand the factors that determine selectivity between mono- and di-fluorination of 1,3-dicarbonyl systems, we have performed kinetic studies of keto-enol tautomerism and fluorination processes. Photoketonization of 1,3-diaryl-1,3-dicarbonyl derivatives and their 2-fluoro analogues is coupled with relaxation kinetics to determine enolization rates. Reaction additives such as water accelerate enolization processes, especially of 2-fluoro-1,3-dicarbonyl systems. Kinetic studies of enol fluorination with Selectfluor™ and NFSI reveal the quantitative effects of 2-fluorination upon enol nucleophilicity towards reagents of markedly different electrophilicity. Our findings have important implications for the synthesis of α,α-difluoroketonic compounds, providing valuable quantitative information to aid in the design of fluorination and difluorination reactions.

Author Correction: The identification of carbon dioxide mediated protein post-translational modifications.

The original version of this Article omitted the following from the Acknowledgements: 'This work was support by EPSRC grant EP/K504336/1 and Leverhulme Trust grant RPG-2016-017.' This has been corrected in both the PDF and HTML versions of the Article.

The identification of carbon dioxide mediated protein post-translational modifications.

Carbon dioxide is vital to the chemistry of life processes including metabolism, cellular homoeostasis, and pathogenesis. CO2 is generally unreactive but can combine with neutral amines to form carbamates on proteins under physiological conditions. The most widely known examples of this are CO2 regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase and haemoglobin. However, the systematic identification of CO2-binding sites on proteins formed through carbamylation has not been possible due to the ready reversibility of carbamate formation. Here we demonstrate a methodology to identify protein carbamates using triethyloxonium tetrafluoroborate to covalently trap CO2, allowing for downstream proteomic analysis. This report describes the systematic identification of carbamates in a physiologically relevant environment. We demonstrate the identification of carbamylated proteins and the general principle that CO2 can impact protein biochemistry through carbamate formation. The ability to identify protein carbamates will significantly advance our understanding of cellular CO2 interactions.

A quantitative reactivity scale for electrophilic fluorinating reagents.

Electrophilic N-F fluorination agents underpin the introduction of fluorine in aliphatic systems across drug and academic research. The choice of N-F reagent is currently determined through empirical experimentation in the absence of quantitative values for electrophilicities. Here we report an experimentally-determined kinetic reactivity scale for ten N-F fluorinating reagents, including Selectfluor™, NFSI, Synfluor™ and several N-fluoropyridinium salts, in CH3CN. The reactivity scale, which covers eight orders of magnitude, employs para-substituted 1,3-diaryl-1,3-dicarbonyl derivatives to measure relative and absolute rate constants. The para-substituted 1,3-diaryl-1,3-dicarbonyl scaffold delivers a convenient, sensitive spectrophotometric reporter of reactivity that also led to the discovery of a unique form of tautomeric polymorphism.

Nucleophilic displacement reactions of 5'-derivatised nucleosides in a vibration ball mill.

Vibration ball-milling in a zirconia-lined vessel afforded clean and quantitative nucleophilic displacement reactions between 4-methoxybenzylthiolate salts and nucleoside 5'-halides or 5'-tosylates in five to 60 minutes. Under these conditions, commonly-encountered nucleoside cyclisation byproducts (especially of purine nucleosides) were not observed. Liquid-assisted grinding of the same 5'-iodide and 5'-tosylate substrates with potassium selenocyanate in the presence of DMF produced the corresponding 5'-selenocyanates in variable yields over the course of between one and eleven hours thereby avoiding the preparation and use of hygroscopic tetrabutylammonium salts.

The synthesis, conformation and hydrolytic stability of an N,S-bridging thiophosphoramidate analogue of thymidylyl-3',5'-thymidine.

A 3'-N,5'-S-bridging thiophosphoramidate analogue of thymidylyl-3',5'-thymidine was synthesised under aqueous conditions. (1)H NMR conformational measurements show that the 3'-N-substituted deoxyribose ring is biased towards the 'north', RNA-like conformation. Rate constants for hydrolysis of the analogue were measured at 90 °C in the pH range 1.3-10.9. The pH-log kobs profile displays a pH-independent region between approximately pH 7 and 10 (t1/2 ∼13 days). Under acidic conditions, kobs displays a first order dependence on [H3O(+)].

Synthesis of novel pyrophosphorothiolate-linked dinucleoside cap analogues in a ball mill.

Michaelis-Arbuzov reactions of S-aryl disulfide derivatives of 3'-thiothymidine or 5'-thioadenosine with tris(trimethylsilyl) phosphite proceeded in high yields to the corresponding phosphorothiolate monoesters. Subsequent hydrolytic desilylation and phosphate coupling were effected in one-pot using liquid-assisted grinding in a vibration ball mill. Novel 3',5'- and 5',5'-pyrophosphorothiolate-linked dinucleoside cap analogues were thereby prepared.

Preparation of an Antibacterial Poly(ionic liquid) Graft Copolymer of Hydroxyethyl Cellulose.

Poly(ionic liquid)s (P(IL)s) of different degrees of polymerization (10, 50, and 100) were prepared via RAFT polymerization using an alkyne-terminated xanthate as transfer agent, with a monomer conversion of up to ∼80% and a DM of 1.5 for P(IL)100. Subsequently, P(IL) chains were coupled to (15)N-labeled azido-functionalized hydroxyethyl cellulose (HEC), forming graft copolymers of HEC with different chain length and graft densities, which were characterized using ((13)C and (15)N) CP-MAS NMR and FT-IR spectroscopies. The antibacterial activities of HEC-g-P(IL)s were tested against Escherichia coli and Staphylococcus aureus and were comparable to ampicillin, a well-known antibiotic, demonstrating efficient activity of the graft copolymers against bacteria. Moreover, HEC-g-P(IL)s were slightly more effective against E. coli than S. aureus. A decrease in graft density of P(IL)10 on the HEC backbone decreased the activity of the graft copolymers against both bacteria. These findings suggest that HEC-g-P(IL) could find applications as an antiseptic compound, for example, in paint formulation.

Metal ion-promoted cleavage of nucleoside diphosphosugars: a model for reactions of phosphodiester bonds in carbohydrates.

Cleavage of five different nucleoside diphosphosugars has been studied in the presence of Cu(2+) and Zn(2+) complexes. The results show that metal ion catalysts promote the cleavage via intramolecular transesterification whenever a neighbouring HO group can adopt a cis-orientation with respect to the phosphate. The HO group attacks the phosphate and two monophosphate products are formed. If such a nucleophile is not available, Cu(2+) complexes are able to promote a nucleophilic attack of an external nucleophile, e.g. a water molecule or metal ion coordinated HO ligand, on phosphate. With the Zn(2+) complex, this was not observed.

The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein.

Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. Both experimental and theoretical evidence demonstrate that allostery can be communicated through altered slow relaxation protein dynamics without conformational change. The catabolite activator protein (CAP) of Escherichia coli is an exemplar for the analysis of such entropically driven allostery. Negative allostery in CAP occurs between identical cAMP binding sites. Changes to the cAMP-binding pocket can therefore impact the allosteric properties of CAP. Here we demonstrate, through a combination of coarse-grained modeling, isothermal calorimetry, and structural analysis, that decreasing the affinity of CAP for cAMP enhances negative cooperativity through an entropic penalty for ligand binding. The use of variant cAMP ligands indicates the data are not explained by structural heterogeneity between protein mutants. We observe computationally that altered interaction strength between CAP and cAMP variously modifies the change in allosteric cooperativity due to second site CAP mutations. As the degree of correlated motion between the cAMP-contacting site and a second site on CAP increases, there is a tendency for computed double mutations at these sites to drive CAP toward noncooperativity. Naturally occurring pairs of covarying residues in CAP do not display this tendency, suggesting a selection pressure to fine tune allostery on changes to the CAP ligand-binding pocket without a drive to a noncooperative state. In general, we hypothesize an evolutionary selection pressure to retain slow relaxation dynamics-induced allostery in proteins in which evolution of the ligand-binding site is occurring.

A procedure for the preparation and isolation of nucleoside-5'-diphosphates.

Tris[bis(triphenylphosphoranylidene)ammonium] pyrophosphate (PPN pyrophosphate) was used in the SN2 displacements of the tosylate ion from 5'-tosylnucleosides to afford nucleoside-5'-diphosphates. Selective precipitation permitted the direct isolation of nucleoside-5'-diphosphates from crude reaction mixtures.

Understanding thio-effects in simple phosphoryl systems: role of solvent effects and nucleophile charge.

Recent experimental work (J. Org. Chem., 2012, 77, 5829) demonstrated pronounced differences in measured thio-effects for the hydrolysis of (thio)phosphodichloridates by water and hydroxide nucleophiles. In the present work, we have performed detailed quantum chemical calculations of these reactions, with the aim of rationalizing the molecular bases for this discrimination. The calculations highlight the interplay between nucleophile charge and transition state solvation in SN2(P) mechanisms as the basis of these differences, rather than a change in mechanism.

The preparation of graft copolymers of cellulose and cellulose derivatives using ATRP under homogeneous reaction conditions.

In this comprehensive review, we report on the preparation of graft-copolymers of cellulose and cellulose derivatives using atom transfer radical polymerization (ATRP) under homogeneous conditions. The review is divided into four sections according to the cellulosic material that is graft-copolymerised; (i) cellulose, (ii) ethyl cellulose, (iii) hydroxypropyl cellulose and (iv) other cellulose derivatives. In each section, the grafted synthetic polymers are described as well as the methods used for ATRP macro-initiator formation and graft-copolymerisation. The physical properties of the graft-copolymers including their self-assembly in solution into nanostructures and their stimuli responsive behaviour are described. Potential applications of the self-assembled graft copolymers in areas such as nanocontainers for drug delivery are outlined.