Polyphosphate and pyrophosphate derivative of saccharides

The present invention provides, among other things, phosphorylated and pyrophosphate derivatives of mono-, di- and oligosaccharides, as well as structural derivatives of these compounds. These compounds have a variety of uses including for pharmaceutical applications. Also provided are methods of use in the treatment of disease, including diseases related to oxygen delivery

A New Stereocontrolled Total Synthesis of the Mast Cell inhibitory Alkaloid, (+)-Monanchorin, via the Wittig Reaction of a Stabilized Ylide with a Cyclic Guanidine Hemiaminal

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An asymmetric total synthesis of the mast cell inhibitor (+)-monanchorin is reported in which a Sharpless AD on 11 and a cyclic sulfate ring opening with an azide feature as key steps. After further manipulation, a novel guanidine-controlled ester reduction provided the guanidine-hemiaminal 25 which underwent Wittig olefination to give 27. Hydrogenation and a second guanidine-controlled reduction of the ester in 28, to obtain aldehyde 29, then set up a trifluoroacetic acid mediated cyclization to give (+)-monanchorin TFA salt.

Reactions of enantiopure cyclic diols with sulfuryl chloride

Monocyclic allylic cis-1,2-diols reacted with sulfuryl chloride at 0 °C in a regio- and stereo-selective manner to give 2-chloro-1-sulfochloridates, which were hydrolysed to yield the corresponding trans-1,2-chlorohydrins. At −78 °C, with very slow addition of sulfuryl chloride, cyclic sulfates were formed in good yields, proved to be very reactive with nucleophiles and rapidly decomposed on attempted storage. Reaction of a cyclic sulfate with sodium azide yielded a trans-azidohydrin without evidence of allylic rearrangement occurring. An enantiopure bicyclic cis-1,2-diol reacted with sulfuryl chloride to give, exclusively, a trans-1,2-dichloride enantiomer with retention of configuration at the benzylic centre and inversion at the non-benzylic centre; a mechanism is presented to rationalise the observation.

Conductivity/activation energy relationships for cement-based materials undergoing cyclic thermal excursions

The electrical conductivity of a range of concrete mixes, with and without supplementary cementitious materials (SCM), is studied through multiple cycles of heating and cooling over the extended temperature range −30/+70 °C. When presented in an Arrhenius format, the experimental results display hysteresis effects at the low-temperature end of the thermal cycle and, in those concretes containing supplementary cementitious materials at higher water/binder ratios, hysteresis effects were evident over the entire temperature range becoming more discernible with increasing number of thermal cycles. The depression in both the freezing and thawing point could be clearly identified and was used to estimate pore-neck and pore-cavity radii. A simplified approach is presented to evaluate the volumetric ratio of frozen pore water in terms of conductivity measurements. The results also show that the conductivity and activation energy of the concrete specimens were related to the water/binder ratio, type of SCM, physical state of the pore water and the thermal cycling regime.

Cyclic nanoindentation and nano-impact fatigue characterisation of functionally graded TiN/TiNi shape memory film

This paper investigates the mechanism of nanoscale fatigue of functionally graded TiN/TiNi films using nano-impact and multiple-loading-cycle nanoindentation tests. The functionally graded films were deposited on silicon substrate, in which TiNi films maintain shape memory and pseudo elastic behavior, while a modified TiN surface layer provides tribological and anti-corrosion properties. Nanomechanical tests were performed to comprehend the localized film performance and failure modes of the functionally graded film using NanoTestTM equipped with Berkovich and conical indenter between 100 μN to 500 mN loads. The loading mechanism and load history are critical to define film failure modes (i.e. backward depth deviation) including the shape memory effect of the functionally graded layer. The results are sensitive to the applied load, loading type (e.g. semi-static, dynamic) and probe geometry. Based on indentation force-depth profiles, depth-time data and post-test surface observations of films, it is concluded that the shape of the nanoindenter is critical in inducing the localized indentation stress and film failure, including shape recovery at the lower load range. Elastic-plastic finite element (FE) simulation during nanoindentation loading indicated that the location of subsurface maximum stress near the interface influences the backward depth deviation type of film failure. A standalone, molecular dynamics simulation was performed with the help of a long range potential energy function to simulate the tensile test of TiN nanowire with two different aspect ratios to investigate the theory of its failure mechanism.

3-Methylpiperidinium ionic liquids

A wide range of room temperature ionic liquids based on the 3-methylpiperdinium cation core were produced from 3-methylpiperidine, which is a derivative of DYTEK® A amine. First, reaction with 1-bromoalkanes or 1-bromoalkoxyalkanes generated the corresponding tertiary amines (Rmβpip, R = alkyl or alkoxyalkyl); further quaternisation reactions with the appropriate methylating agents yielded the quaternary [Rmmβpip]X salts (X(-) = I(-), [CF3CO2](-) or [OTf](-); Tf = -SO2CF3), and [Rmmβpip][NTf2] were prepared by anion metathesis from the corresponding iodides. All [NTf2](-) salts are liquids at room temperature. [Rmmβpip]X (X(-) = I(-), [CF3CO2](-) or [OTf](-)) are low-melting solids when R = alkyl, but room temperature liquids upon introduction of ether functionalities on R. Neither of the 3-methylpiperdinium ionic liquids showed any signs of crystallisation, even well below 0 °C. Some related non-C-substituted piperidinium and pyrrolidinium analogues were prepared and studied for comparison. Crystal structures of 1-hexyl-1,3-dimethylpiperidinium tetraphenylborate, 1-butyl-3-methylpiperidinium bromide, 1-(2-methoxyethyl)-1-methylpiperidinium chloride and 1-(2-methoxyethyl)-1-methylpyrrolidinium bromide are reported. Extensive structural and physical data are collected and compared to literature data, with special emphasis on the systematic study of the cation ring size and/or asymmetry effects on density, viscosity and ionic conductivity, allowing general trends to be outlined. Cyclic voltammetry shows that 3-methylpiperidinium ionic liquids, similarly to azepanium, piperidinium or pyrrolidinium counterparts, are extremely electrochemically stable; the portfolio of useful alternatives for safe and high-performing electrolytes is thus greatly extended.

Discrete cyclic di-GMP-dependent control of bacterial predation versus axenic growth in Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus is a Delta-proteobacterium that oscillates between free-living growth and predation on Gram-negative bacteria including important pathogens of man, animals and plants. After entering the prey periplasm, killing the prey and replicating inside the prey bdelloplast, several motile B. bacteriovorus progeny cells emerge. The B. bacteriovorus HD100 genome encodes numerous proteins predicted to be involved in signalling via the secondary messenger cyclic di-GMP (c-di-GMP), which is known to affect bacterial lifestyle choices. We investigated the role of c-di-GMP signalling in B. bacteriovorus, focussing on the five GGDEF domain proteins that are predicted to function as diguanylyl cyclases initiating c-di-GMP signalling cascades. Inactivation of individual GGDEF domain genes resulted in remarkably distinct phenotypes. Deletion of dgcB (Bd0742) resulted in a predation impaired, obligately axenic mutant, while deletion of dgcC (Bd1434) resulted in the opposite, obligately predatory mutant. Deletion of dgcA (Bd0367) abolished gliding motility, producing bacteria capable of predatory invasion but unable to leave the exhausted prey. Complementation was achieved with wild type dgc genes, but not with GGAAF versions. Deletion of cdgA (Bd3125) substantially slowed predation; this was restored by wild type complementation. Deletion of dgcD (Bd3766) had no observable phenotype. In vitro assays showed that DgcA, DgcB, and DgcC were diguanylyl cyclases. CdgA lacks enzymatic activity but functions as a c-di-GMP receptor apparently in the DgcB pathway. Activity of DgcD was not detected. Deletion of DgcA strongly decreased the extractable c-di-GMP content of axenic Bdellovibrio cells. We show that c-di-GMP signalling pathways are essential for both the free-living and predatory lifestyles of B. bacteriovorus and that obligately predatory dgcC- can be made lacking a propensity to survive without predation of bacterial pathogens and thus possibly useful in anti-pathogen applications. In contrast to many studies in other bacteria, Bdellovibrio shows specificity and lack of overlap in c-di-GMP signalling pathways.

The structure of an unconventional HD-GYP protein from Bdellovibrio reveals the roles of conserved residues in this class of cyclic-di-GMP phosphodiesterases

UNLABELLED: Cyclic-di-GMP is a near-ubiquitous bacterial second messenger that is important in localized signal transmission during the control of various processes, including virulence and switching between planktonic and biofilm-based lifestyles. Cyclic-di-GMP is synthesized by GGDEF diguanylate cyclases and hydrolyzed by EAL or HD-GYP phosphodiesterases, with each functional domain often appended to distinct sensory modules. HD-GYP domain proteins have resisted structural analysis, but here we present the first structural representative of this family (1.28 Å), obtained using the unusual Bd1817 HD-GYP protein from the predatory bacterium Bdellovibrio bacteriovorus. Bd1817 lacks the active-site tyrosine present in most HD-GYP family members yet remains an excellent model of their features, sharing 48% sequence similarity with the archetype RpfG. The protein structure is highly modular and thus provides a basis for delineating domain boundaries in other stimulus-dependent homologues. Conserved residues in the HD-GYP family cluster around a binuclear metal center, which is observed complexed to a molecule of phosphate, providing information on the mode of hydroxide ion attack on substrate. The fold and active site of the HD-GYP domain are different from those of EAL proteins, and restricted access to the active-site cleft is indicative of a different mode of activity regulation. The region encompassing the GYP motif has a novel conformation and is surface exposed and available for complexation with binding partners, including GGDEF proteins.

IMPORTANCE: It is becoming apparent that many bacteria use the signaling molecule cyclic-di-GMP to regulate a variety of processes, most notably, transitions between motility and sessility. Importantly, this regulation is central to several traits implicated in chronic disease (adhesion, biofilm formation, and virulence gene expression). The mechanisms of cyclic-di-GMP synthesis via GGDEF enzymes and hydrolysis via EAL enzymes have been suggested by the analysis of several crystal structures, but no information has been available to date for the unrelated HD-GYP class of hydrolases. Here we present the multidomain structure of an unusual member of the HD-GYP family from the predatory bacterium Bdellovibrio bacteriovorus and detail the features that distinguish it from the wider structural family of general HD fold hydrolases. The structure reveals how a binuclear iron center is formed from several conserved residues and provides a basis for understanding HD-GYP family sequence requirements for c-di-GMP hydrolysis.

Capturing Goodwillie's Derivative

Recent work of Biedermann and Roendigs has translated Goodwillie's calculus of functors into the language of model categories. Their work focuses on symmetric multilinear functors and the derivative appears only briefly. In this paper we focus on understanding the derivative as a right Quillen functor to a new model category. This is directly analogous to the behaviour of Weiss's derivative in orthogonal calculus. The immediate advantage of this new category is that we obtain a streamlined and more informative proof that the n-homogeneous functors are classified by spectra with an action of the symmetric group on n objects. In a later paper we will use this new model category to give a formal comparison between the orthogonal calculus and Goodwillie's calculus of functors.