An Accurate In Vitro Model of the E. coli Envelope

Gram‐negative bacteria are an increasingly serious source of antibiotic‐resistant infections, partly owing to their characteristic protective envelope. This complex, 20 nm thick barrier includes a highly impermeable, asymmetric bilayer outer membrane (OM), which plays a pivotal role in resisting antibacterial chemotherapy. Nevertheless, the OM molecular structure and its dynamics are poorly understood because the structure is difficult to recreate or study in vitro. The successful formation and characterization of a fully asymmetric model envelope using Langmuir–Blodgett and Langmuir–Schaefer methods is now reported. Neutron reflectivity and isotopic labeling confirmed the expected structure and asymmetry and showed that experiments with antibacterial proteins reproduced published in vivo behavior. By closely recreating natural OM behavior, this model provides a much needed robust system for antibiotic development.     

Amarisolide monohydrate,a 2‐(β‐glu­cosyl)­neoclerodane

The absolute configuration of the neoclerodane glycoside amarisolide, presented here as the monohydrate, C₂₆H₃₆O₉·H₂O, has been determined by association with the known configuration of the glucose moiety. Its structure was established as 2β‐(O‐β‐d ‐gluco­pyran­osyl)­neocleroda‐3,13(16),14‐trien‐15,16‐epoxy‐18,19‐olide. Extensive hydrogen bonding among the hydroxyl groups of the sugar moiety forms layers which are interconnected by water mol­ecules.     

Free-radical pathways in the decomposition of ketones over polycrystalline TiO(2): the role of organoperoxy radicals.

The oxidative decomposition of various ketones (including acetone, 2-butanone, 4-heptanone, cyclopentanone and cyclohexanone) over dehydrated TiO(2) (P25) powder is investigated by electron paramagnetic resonance (EPR) spectroscopy. For the first time, a series of thermally unstable radical intermediates are observed both on the activated and reduced TiO(2) surface, depending on the adopted experimental conditions. These radical intermediates are identified as organoperoxy-based species of general formula ROO(.-) and RCO(3) (.-). They are formed by reaction of photogenerated charge carriers (either trapped electrons or trapped holes) with the adsorbed ketones in the presence of molecular oxygen. The organoperoxy intermediates are thermally unstable and decompose at temperatures in the region of 180-250 K. This work demonstrates that free-radical pathways involving both organoperoxy and superoxide radicals can be responsible for the thermal- and photodecomposition of ketones over polycrystalline TiO(2) (P25).     

Templating and selection in the formation of macrocycles containing [[P(micro-NtBu)(2)](micro-NH)](n) frameworks: observation of halide ion coordination

Amination of [ClP(micro-NtBu)](2) (1) using NH(3) in THF gives the cyclophospha(III)zane dimer [H(2)NP(micro-NtBu)](2) (2), in good yield. (31)P NMR spectroscopic studies of the reaction of 1 with 2 in THF/Et(3)N show that almost quantitative formation of the cyclic tetramer [[P(micro-NtBu)](2)(micro-NH)](4) (3) occurs. The remarkable selectivity of this reaction can (in part) be attributed to pre-organisation of 1 and 2, which prefer cis arrangements in the solid state and solution. The macrocycle 3 can be isolated in yields of 58-67 % using various reaction scales. The isolation of the major by-product of the reaction (ca. 0.5-1 % of samples of 3), the pentameric, host-guest complex [[P(micro-NtBu)(2)](2)(micro-NH)](5)(HCl).2 THF] (4.2 THF), gives a strong indication of the mechanism involved. In situ (31)P NMR spectroscopic studies support a stepwise condensation mechanism in which Cl(-) ions play an important role in templating and selection of 3 and 4. Amplification of the pentameric arrangement occurs in the presence of excess LiX (X=Cl, Br, I). In addition, the cyclisation reaction is solvent- and anion-dependent. The X-ray structures of 2 and 4.2 THF are reported.     

Correlation between Solution and the Solid State: The pH Dependent Composition in the Ternary System [Co(H2O)6]2+ or [Ni(H2O)6]2+/Piperazine/Phosphate

The protolytic equilibria of piperazine (C₄H₁₀N₂) and phosphate have been investigated in the presence of cobalt or nickel chloride or nitrate by potentiometric titrations between pH 2 and 8. Potentiometric titrations suggest the presence of [M²⁺(H₂O)₅(C₄H₁₁N₂⁺)]³⁺ and [M²⁺(H₂O)₅(C₄H₁₀N₂)]²⁺ in solution with stability constants logK of 3.1 and 3.8 for M = Co and 3.1 and 3.6 for M = Ni, respectively. Crystallization experiments were then conducted at selected pH values to isolate desired species from the known solution composition. Crystallization afforded [M(H₂O)₆]²⁺(C₄H₁₂N₂²⁺)(HPO₄^2—)₂ at pH 3.5 and 6.2 (M = Co, Ni), and Co₃(PO₄)₂·8H₂O at pH 10.5. No crystals with the dihydrogenphosphate anion or a metal‐bound piperazine ligand could be isolated under the reaction conditions. The solid‐state assembly in the isomorphous structures of [M(H₂O)₆](C₄H₁₂N₂)(HPO₄)₂ with M = Co and Ni is based on an extended hydrogen bonded network between the three ionic building blocks.     

Steric interactions mediated by multiblock polymers and biopolymers: role of block size and addition of hydrophilic side chains

To a first approximation, the primary structure of many food proteins maybe thought of as a sequence of short hydrophobic and hydrophilic blocks. The influence of this type of structure on the steric-stabilising properties of such proteins has been considered here. In line with previous studies, using Self-Consistent-Field calculations, it has been shown that the presence of such protein molecules can lead to attraction and consequently bridging flocculation of colloidal particles. In the low adsorption energy limit for the hydrophobic groups (−1k_BT), it is found that the steric potential is significantly influenced by the changes in the number of adsorbed segments, as two surfaces are brought together. This is in contrast to the well-known results in the literature for the high adsorption limiting cases, where the number of such segments remains constant. In particular, the changes in the number of adsorbed hydrophobic units are observed not to be a monotonic function of the separation distance, but increase or decrease in reasonable accord with the oscillatory nature of the steric interactions, observed for various block sizes. Effects of the addition of a moderately sized hydrophilic side chain to the above molecules have also been studied. It is found that, in principle, such a modification can lead to a purely repulsive steric potential in solutions of these hybrid biopolymers. At the hydrophilic side chain sizes considered here, the surface affinity of the molecules is observed not to be drastically different compared to those of unmodified proteins.     

Structural determination of ruthenium-porphyrin complexes relevant to catalytic epoxidation of olefins

A reproducible synthesis of a competent epoxidation catalyst, [Ru(VI)(TPP)(O)2)] (TPP = tetraphenylporphyrin dianion), starting from [Ru(II)(TPP)(CO)L] (L = none or CH3OH), is described. The molecular structure of the complex was determined by using ab initio X-ray powder diffraction (XRPD) methods, and its solution behavior was in detail investigated by NMR techniques such as PGSE (pulsed field gradient spin-echo) measurements. [Ru(IV)(TPP)(OH)]2O, a reported byproduct in the synthesis of [Ru(VI)(TPP)(O)2], was synthesized in a pure form by oxidation of [Ru(II)(TPP)(CO)L] or by a coproportionation reaction of [Ru(VI)(TPP)(O)2] and [Ru(II)(TPP)(CO)L], and its molecular structure was then determined by XRPD analysis. [Ru(VI)(TPP)(O)2] can be reduced by dimethyl sulfoxide or by carbon monoxide to yield [Ru(II)(TPP)(S-DMSO)2] or [Ru(II)(TPP)(CO)(H2O)], respectively. These two species were characterized by conventional single-crystal X-ray diffraction analysis.     

Conformational analysis of lipid molecules by self-organizing maps

The authors have studied the use of the self-organizing map (SOM) in the analysis of lipid conformations produced by atomic-scale molecular dynamics simulations. First, focusing on the methodological aspects, they have systematically studied how the SOM can be employed in the analysis of lipid conformations in a controlled and reliable fashion. For this purpose, they have used a previously reported 50 ns atomistic molecular dynamics simulation of a 1-palmitoyl-2-linoeayl-sn-glycero-3-phosphatidylcholine (PLPC) lipid bilayer and analyzed separately the conformations of the headgroup and the glycerol regions, as well as the diunsaturated fatty acid chain. They have elucidated the effect of training parameters on the quality of the results, as well as the effect of the size of the SOM. It turns out that the main conformational states of each region in the molecule are easily distinguished together with a variety of other typical structural features. As a second topic, the authors applied the SOM to the PLPC data to demonstrate how it can be used in the analysis that goes beyond the standard methods commonly used to study the structure and dynamics of lipid membranes. Overall, the results suggest that the SOM method provides a relatively simple and robust tool for quickly gaining a qualitative understanding of the most important features of the conformations of the system, without a priori knowledge. It seems plausible that the insight given by the SOM could be applied to a variety of biomolecular systems and the design of coarse-grained models for these systems.     

A structural investigation of the alkali metal site distribution within bioactive glass using neutron diffraction and multinuclear solid state NMR

The atomic-scale structure of Bioglass and the effect of substituting lithium for sodium within these glasses have been investigated using neutron diffraction and solid state magic angle spinning (MAS) NMR. Applying an effective isomorphic substitution difference function to the neutron diffraction data has enabled the Na-O and Li-O nearest-neighbour correlations to be isolated from the overlapping Ca-O, O-(P)-O and O-(Si)-O correlations. These results reveal that Na and Li behave in a similar manner within the glassy matrix and do not disrupt the short range order of the network former. Residual differences are attributed solely to the variation in ionic radius between the two species. Successful simplification of the 2 < r (?) < 3 region via the difference method has enabled all the nearest neighbour correlations to be deconvolved. The diffraction data provides the first direct experimental evidence of split Na-O nearest-neighbour correlations in these melt quench bioactive glasses, and an analogous splitting of the Li-O correlations. The observed correlations are attributed to the metal ions bonded either to bridging or to non-bridging oxygen atoms. (23)Na triple quantum MAS (3QMAS) NMR data corroborates the split Na-O correlations. The structural sites present will be intimately related to the release properties of the glass system in physiological fluids such as plasma and saliva, and hence to the bioactivity of the material. Detailed structural knowledge is therefore a prerequisite for optimizing material design.     

Identification of epigenetic DNA modifications with a protein nanopore

Two DNA bases, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (hmC), marks of epigenetic modification, are recognized in immobilized DNA strands and distinguished from G, A, T and C by nanopore current recording. Therefore, if further aspects of nanopore sequencing can be addressed, the approach will provide a means to locate epigenetic modifications in unamplified genomic DNA.