Structural determination of glycopeptidolipids of Mycobacterium smegmatis by high‐resolution multiple‐stage linear ion‐trap mass spectrometry with electrospray ionization

Glycopeptidolipids (GPLs) are abundant in the cell walls of different species of mycobacteria and consist of tripeptide‐amino‐alcohol core of D‐Phe‐D‐allo‐Thr‐D‐Ala‐L‐alaninol linked to 3‐hydroxy or 3‐methoxy C_26–34 fatty acyl chain at the N‐terminal of D‐Phe via amide linkage, and a 6‐deoxytalose (6‐dTal) and an O‐methyl rhamnose residues, respectively, attach to D‐allo‐Thr and the terminal L‐alaninol. They are important cell‐surface antigens that are implicated in the pathogenesis of opportunistic mycobacteria belonging to the Mycobacterium avium complex. In this contribution, we described multiple‐stage linear ion trap in conjunction with high‐resolution mass spectrometry towards structural characterization of complex GPLs as [M + Na]⁺ ions isolated from Mycobacterium smegmatis, a fast‐growing and non‐pathogenic mycobacterial species. Following resonance excitation in an ion trap, MSⁿ spectra of the [M + Na]⁺ ions of GPLs contained mainly b and y series ions that readily determine the peptide sequence. Fragment ions from MSⁿ also afford locating the 6‐dTal and O‐methyl rhamnose residues linked to the D‐allo‐Thr and terminal L‐alaninol of the peptide core, respectively, as well as recognizing the modifications of the glycosides, including their acetylation and methylation states and the presence of succinyl group. The GPL families consisting of 3‐hydroxy fatty acyl and of 3‐methoxy fatty acyl substituents are readily distinguishable. The MS profiles of the GPLs from cells are dependant on the conditions they were grown, and several isobaric isomers were identified for many of the molecular species. These multiple‐stage mass spectrometric approaches give detailed structures of GPL in complex mixtures of which the isomeric structures are difficult to define using other analytical methods. Copyright © 2012 John Wiley & Sons, Ltd.     

Self-assembly of stable monomolecular nucleic acid lipid particles with a size of 30 nm

The design of efficient nucleic acid complexes is key to progress in genetic research and therapies based on RNA interference. For optimal transport within tissue and across extracellular barriers, nucleic acid carriers need to be small and stable. In this Article, we prepare and characterize mono-nucleic acid lipid particles (mono-NALPs). The particles consist of single short double-stranded oligonucleotides or single siRNA molecules each encapsulated within a closed shell of a cationic-zwitterionic lipid bilayer, furnished with an outer polyethylene glycol (PEG) shield. The particles self-assemble by solvent exchange from a solution containing nucleic acid mixed with the four lipid components DOTAP, DOPE, DOPC, and DSPE-PEG(2000). Using fluorescence correlation spectroscopy, we monitor the formation of mono-NALPs from short double-stranded oligonucleotides or siRNA and lipids into monodisperse particles of approximately 30 nm in diameter. Small angle neutron and X-ray scattering and transmission electron microscopy experiments substantiate a micelle-like core-shell structure of the particles. The PEGylated lipid shell protects the nucleic acid core against degradation by nucleases, sterically stabilizes the mono-NALPs against disassembly in collagen networks, and prevents nonspecific binding to cells. Hence, PEG-lipid shielded mono-NALPs are the smallest stable siRNA lipid system possible and may provide a structural design to be built upon for the development of novel nucleic acid delivery systems with enhanced biodistribution in vivo.     

Hydrothermal Generation of Conjugated Polymers Using the Example of Pyrrone Polymers and Polybenzimidazoles

Various polyimides and polyamides have recently been prepared via hydrothermal synthesis in nothing but H₂O under high‐pressure and high‐temperature conditions. However, none of the prepared polymers feature a truly conjugated polymer backbone. Here, we report on an expansion of the synthetic scope of this straightforward and inherently environmentally friendly polymerization technique to the generation of conjugated polymers. Selected representatives of two different polymer classes, pyrrone polymers and polybenzimidazoles, were generated hydrothermally. We present a mechanistic discussion of the polymer formation process as well as an electrochemical characterization of the most promising product.     

Ozone oxidation of surface-adsorbed polycyclic aromatic hydrocarbons: role of PAH-surface interaction

The heterogeneous chemistry of surface-adsorbed polycyclic aromatic hydrocarbons (PAHs) plays key roles in nanoscience, environmental science, and public health. Experimental evidence shows that the substrate can influence the heterogeneous oxidation of surface-bound PAHs, however, a mechanistic understanding of the role of the surface is still lacking. We examine the effects of the PAH-substrate interaction on the oxidation of surface-adsorbed anthracene, pyrene, and benzo[a]pyrene by ozone (O(3)) using density functional theory. We find that some O(3) oxidation mechanisms for these planar PAH molecules lead to nonplanar intermediates or products, the formation of which may necessitate partial desorption or "lift-off" from a solid substrate. The energy penalty for partial desorption of each PAH from the surface is estimated for four different substrate types on the basis of literature data and accounted for in the thermodynamic analysis of the reaction pathways. We find that the attractive PAH-substrate interaction may render oxidation pathways involving nonplanar intermediates or products thermodynamically unfavorable. The influence of the PAH-substrate interaction could contribute in part to the variations in PAH oxidation kinetics and product distributions that have been observed experimentally. Our choice of test molecules enabled us to identify trends in reactivity and product formation for four types of potentially reactive site (zigzag, armchair, bridge, and internal), allowing us to infer products and mechanisms of O(3) oxidation for PAHs of larger sizes. Implications for atmospheric chemistry and the stability of graphene in the presence of O(3) are discussed.     

Convenient one-pot syntheses of 1,2-dithiole-3-thiones and 3-imino-1,2-dithioles from terminal alkynes

The reaction of acetylide anions with carbon disulfide or phenyl isothiocyanate followed by addition of sulfur in the presence of a protonating agent such as a primary amine or alcohol affords 1,2-dithiole-3-thiones or 3-imino-1,2-dithioles in good to excellent yields.     

Coordination and hydrogen‐bonding assemblies in hybrid reaction products between 5,10,15,20‐tetra‐4‐pyridylporphyrin and dysprosium trinitrate hexahydrate

Reactions of the title free‐base porphyrin compound (TPyP) with dysprosium trinitrate hexahydrate in different crystallization environments yielded two solid products, viz. [μ‐5,15‐bis(pyridin‐1‐ium‐4‐yl)‐10,20‐di‐4‐pyridylporphyrin]bis[aquatetranitratodysprosium(III)] benzene solvate, [Dy₂(NO₃)₈(C₄₀H₂₈N₈)(H₂O)₂]·C₆H₆, (I), and 5,10,15,20‐tetrakis(pyridin‐1‐ium‐4‐yl)porphyrin pentaaquadinitratodysprosate(III) pentanitrate diethanol solvate dihydrate, (C₄₀H₃₀N₈)[Dy(NO₃)₂(H₂O)₅](NO₃)₅·2C₂H₆O·2H₂O, (II). Compound (I) represents a 2:1 metal–porphyrin coordinated complex, which lies across a centre of inversion. Two trans‐related pyridyl groups are involved in Dy coordination. The two other pyridyl substituents are protonated and involved in intermolecular hydrogen bonding along with the metal‐coordinated water and nitrate ligands. Compound (II) represents an extended hydrogen‐bonded assembly between the tetrakis(pyridin‐1‐ium‐4‐yl)porphyrin tetracation, the [Dy(NO₃)₂(H₂O)₅]⁺ cation and the free nitrate ions, as well as the ethanol and water solvent molecules. This report provides the first structural characterization of the exocyclic dysprosium complex with tetrapyridylporphyrin. It also demonstrates that charge balance can be readily achieved by protonation of the peripheral pyridyl functions, which then enhances their capacity in hydrogen bonding as H‐atom donors rather than H‐atom acceptors.     

Unsolvated 5,10,15,20‐tetra‐4‐pyridylporphyrin,its sesquihydrate and its 2‐chlorophenol disolvate: conformational versatility of the ligand

Unsolvated 5,10,15,20‐tetra‐4‐pyridylporphyrin, C₄₀H₂₆N₈, (I), its sesquihydrate, C₄₀H₂₆N₈·1.514H₂O, (II), and its 2‐chlorophenol disolvate, C₄₀H₂₆N₈·2C₆H₅ClO, (III), reveal different conformational features of the porphyrin core. In (I), the latter is severely deformed from planarity, apparently in order to optimize the intermolecular interactions and efficient crystal packing of the molecular entities. The molecular framework has a C₁ symmetry. In (II), the porphyrin molecules are located on symmetry axes, preserving the marked deformation from planarity of the porphyrin core. The molecular units are interlinked into a single‐framework supramolecular architecture by hydrogen bonding to one another via molecules of water, which lie on twofold rotation axes. In (III), the porphyrin molecules are located across centres of inversion and are characterized by a planar conformation of the 24‐membered macrocyclic porphyrin ring. Two trans‐related pyridyl substituents are hydrogen bonded to the 2‐chlorophenol solvent molecules. The interporphyrin organization in (III) is similar to that observed for many other tetraarylporphyrin compounds. However, the organization observed in (I) and (II) is different and of a type rarely observed before. This study reports for the first time the crystal structure of the unsolvated tetrapyridylporphyrin.     

Comparison and correlation of in vitro, in vivo and in silico evaluations of alpha, beta and gamma cyclodextrin complexes of curcumin

In the present study investigated the effect of curcumin (CUR) alpha (α), beta (β) and gamma (γ) cyclodextrin (CD) complexes on its solubility and bioavailability. CUR the active principle of turmeric is a natural antioxidant agent with potent anti-inflammatory activity along with chemotherapeutic and chemopreventive properties. Poor solubility and poor oral bioavailability are the main reasons which preclude CUR use in therapy. Extent of complexation was β-CD complex (82 %) > γ-CD (71 %) > α-CD (65 %). Pulverization method resulted in significant enhancement of CUR (0.002 mg/ml) solubility with CUR α-CD complex (0.364 mg/ml) > CUR β-CD complex (0.186 mg/ml) > CUR γ-CD complex (0.068 mg/ml). Gibbs-free energy and in silico molecular docking studies favour formation of α-CD complex > β-CD complex > γ-CD complex. With reference to CUR, relative bioavailability of CUR α-CD, CUR β-CD and CUR γ-CD complexes were 460, 365 and 99 % respectively. CUR–CD complexes exhibited increased bioavailability with an increase in t_½, tmax, Cmax, AUC, Ka, and MRT; and a decrease in Ke, clearance and Vd values. AUC increase was CUR α-CD complex > CUR β-CD complex > CUR γ-CD complex. Significant difference (p < 0.05) was observed between CUR α-CD complex and CUR γ-CD complex by one-way ANOVA and Dunnett’s post hoc test for multiple comparison analysis. Correlation observed between in vitro, in vivo and in silico methods indicates potential of in silico and in vitro methods in CD selection.     

NMR Crystallography: Evaluation of Hydrogen Positions in Hydromagnesite by 13C{1H} REDOR Solid‐State NMR and Density Functional Theory Calculation of Chemical Shielding Tensors

Solid‐state NMR measurements coupled with density functional theory (DFT) calculations demonstrate how hydrogen positions can be refined in a crystalline system. The precision afforded by rotational‐echo double‐resonance (REDOR) NMR to interrogate ¹³C–¹H distances is exploited along with DFT determinations of the ¹³C tensor of carbonates (CO₃^2?). Nearby ¹H nuclei perturb the axial symmetry of the carbonate sites in the hydrated carbonate mineral, hydromagnesite [4 MgCO₃?Mg(OH)₂?4 H₂O]. A match between the calculated structure and solid‐state NMR was found by testing multiple semi‐local and dispersion‐corrected DFT functionals and applying them to optimize atom positions, starting from X‐ray diffraction (XRD)‐determined atomic coordinates. This was validated by comparing calculated to experimental ¹³C{¹H} REDOR and ¹³C chemical shift anisotropy (CSA) tensor values. The results show that the combination of solid‐state NMR, XRD, and DFT can improve structure refinement for hydrated materials.