Homogenous synthesis of 3-allyloxy-2-hydroxypropyl-cellulose in NaOH/urea aqueous system

3-Allyloxy-2-hydroxypropylcelluloses (AHP-celluloses), reactive unsaturated cellulose derivatives, were homogeneously synthesized by the reaction of cellulose with allyl glycidyl ether (AGE) in NaOH/urea aqueous solution. Water-soluble AHP-celluloses with DS_NMR = 0.32–0.67 were prepared from microcrystalline cellulose. The degree of substitution (DS) of AHP-celluloses could be controlled by varying the molar ratio of AGE and NaOH to AGU and the reaction conditions. The structure of AHP-cellulose samples were characterized by means of FT-IR, NMR spectroscopy and size exclusion chromatography. The cellulose ether shows thermoreversible flocculation. Bromination reactions were carried out as subsequent functionalization both to illustrate the reactivity of the allyl function and to determine the DS values.     

Highly functionalized bridged silsesquioxanes

The objective of this work was to synthesize functionalized mesoporous silsesquioxanes with high concentrations of amine groups. During typical sol–gel syntheses, these materials are obtained by co-condensation of organic precursors with suitable linkers, such as tetraethoxysilane, necessary to prevent the mesoporous structure from collapsing. Thus, concentrations of amine groups in organosilicas usually do not exceed 2.7–3.4 mmol g⁻¹. The use of bridged bis-trimethoxysilanes, however, allowed formation of mesoporous materials with no linker. Polycondensation of bis-trimethoxysilanes containing amine groups was conducted in acidic, neutral and basic media, resulting in high yields of solid bridged silsesquioxanes. Gelation occurred quickly if no acid or base was added to the reaction mixture. The hybrid organic/inorganic nature of obtained materials was confirmed by FT-IR and MAS CP NMR spectroscopy. Elemental analysis showed that amino group concentration in the products was 3.3–4.1 mmol g⁻¹. Measurement of particle size distribution confirmed that choice of reaction media significantly affects particle sizes and agglomeration degrees, with the largest agglomerates (up to 50 μm) formed in basic media. A morphology study, using small-angle X-Ray scattering, displayed two-level fractal structures composed of aggregated 6.5–10.5 nm particles. Reactions in the presence of a surfactant resulted in formation of mesoporous structures. Furthermore, the obtained bridged silsesquioxanes were thermally stable down to 260 °C, but could reversibly absorb water and CO₂ at temperatures below 120 °C. Thus, condensation of the bridged precursor without a linker resulted in formation of a highly functionalized mesoporous material.     

On the applicability of elastic network normal modes in small-molecule docking

Incorporating backbone flexibility into protein-ligand docking is still a challenging problem. In protein-protein docking, normal mode analysis (NMA) has become increasingly popular as it can be used to describe the collective motions of a biological system, but the question of whether NMA can also be useful in predicting the conformational changes observed upon small-molecule binding has only been addressed in a few case studies. Here, we describe a large-scale study on the applicability of NMA for protein-ligand docking using 433 apo/holo pairs of the Astex data sets. On the basis of sets of the first normal modes from the apo structure, we first generated for each paired holo structure a set of conformations that optimally reproduce its C(α) trace with respect to the underlying normal mode subspace. Using AutoDock, GOLD, and FlexX we then docked the original ligands into these conformations to assess how the docking performance depends on the number of modes used to reproduce the holo structure. The results of our study indicate that, even for such a best-case scenario, the use of normal mode analysis in small-molecule docking is restricted and that a general rule on how many modes to use does not seem to exist or at least is not easy to find.     

Co4(OH)2(C10H16O4)3 metal-organic framework: slow magnetic relaxation in the ordered phase of magnetic chains

Reported here are the synthesis and structural and topological analysis as well as a magnetic investigation of the new Co(4)(OH)(2)(C(10)H(16)O(4))(3) metal-organic framework. The structural analysis reveals a one-dimensional inorganic subnetwork based on complex chains of cobalt(II) ions in two different oxygen environments. Long alkane dioic acid molecules bridge these inorganic chains together to afford large distances and poor magnetic media between dense spin chains. The thermal dependence of the χT product provides evidence for uncompensated antiferromagnetic interactions within the cobaltous chains. In zero-field, dynamic magnetic susceptibility measurements show slow magnetic relaxation below 5.4 K while both neutron diffraction and heat capacity measurements give evidence of long-range order (LRO) below this temperature. The slow dynamics may originate from the motion of broad domain walls and is characterized by an Arrhenius law with a single energy barrier Δ(τ)/k(B) = 67(1) K for the [10-5000 Hz] frequency range. Moreover, in nonzero dc fields the ac susceptibility signal splits into a low-temperature frequency-dependent peak and a high-temperature frequency-independent peak which strongly shifts to higher temperature upon increasing the bias dc field. Heat capacity measurements have been carried out for various applied field values, and the recorded C(P)(T) data are used for the calculation of the thermal variations of both the adiabatic temperature change ΔT(ad) and magnetic entropy change ΔS(m). The deduced data show a modest magnetocaloric effect at low temperature. Its maximum moves up to higher temperature upon increasing the field variation, in relation with the field-sensibility of the intrachain magnetic correlation length.     

Interfacial free energy driven nanophase separation in poly(3-hexylthiophene)/[6,6]-phenyl-C61-butyric acid methyl ester thin films

The nanostructure of thermally annealed thin films of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) blends on hydrophobic and hydrophilic substrates was studied to unravel the relationship between the substrate properties and the phase structure of polymer blends in confined geometry. Indeed, the nature of the employed substrates was found to affect the extent of phase separation, the PCBM aggregation state and the texture of the whole system. In particular, annealing below the melting temperature of the polymer yielded the formation of PCBM nanometric crystallites on the hydrophobic substrates, while mostly amorphous microscopic aggregates were formed on the hydrophilic ones. Moreover, while an enhanced in-plane orientation of P3HT lamellae was promoted on hydrophobic substrates, a markedly tilted geometry was produced on the hydrophilic ones. The observed effects were interpreted in terms of a simple model connecting the interface free energy for the blend films to the different polymer chain mobility and diffusion velocity of PCBM molecules on the different substrates.     

Molecular modeling on pyrimidine-urea inhibitors of TNF-α production: an integrated approach using a combination of molecular docking, classification techniques, and 3D-QSAR CoMSIA

Molecular docking, classification techniques, and 3D-QSAR CoMSIA were combined in a multistep framework with the ultimate goal of identifying potent pyrimidine-urea inhibitors of TNF-α production. Using the crystal structure of p38α, all the compounds were docked into the enzyme active site. The docking pose of each compound was subsequently used in a receptor-based alignment for the generation of the CoMSIA fields. "Active" and "inactive" compounds were used to build a Random Tree classification model using the docking score and the CoMSIA fields as input parameters. Domain of applicability indicated the compounds for which activity estimations can be accepted with confidence. For the active compounds, a 3D-QSAR CoMSIA model was subsequently built to accurately estimate the IC(50) values. This novel multistep framework gives insight into the structural characteristics that affect the binding and the inhibitory activity of these analogues on p38α MAP kinase, and it can be extended to other classes of small-molecule inhibitors. In addition, the simplicity of the proposed approach provides expansion to its applicability such as in virtual screening procedures.     

Chiral uranium phosphonates constructed from achiral units with three-dimensional frameworks

Two chiral, porous uranium methylenediphosphonates, [C(2)H(10)N(2)]{UO(2)[CH(2)(PO(3))(2)]}·H(2)O (UC1P2N-1) and [N(C(2)H(5))(4)]K{(UO(2))(3)[CH(2)(PO(3))(2)](2)(H(2)O)(2)}·1.5H(2)O (KUC1P2-1), have been synthesized without chiral starting materials. Both compounds display channels ~1 × 1 nm that are large enough for these materials to conduct ion-exchange with coordination complexes such as [Co(en)(3)](3+).     

Stable-isotope dilution GC-MS method for ethanol in vapour ethanol and microdialysis systems based on carbonate-catalyzed extractive pentafluorobenzoylation

Common ethanol detection methods are not applicable to cell culture media and microdialysates due to interference with medium constituents including amino acids and pH indicators. We present a novel GC-MS method for the accurate and precise analysis of ethanol in cell cultures and microdialysates. The method is based on the carbonate-catalyzed extractive pentafluorobenzoylation of ethanol and deuterium-labelled ethanol serving as the internal standard and on their GC-MS analysis in the electron-capture negative-ion chemical ionization mode. The method was used to optimize experimental conditions in a custom-made ethanol vapour system utilized for studies examining ethanol influences on neuronal cell lines and in microdialysis.     

Highly sensitive and selective analysis of urinary steroids by comprehensive two-dimensional gas chromatography combined with positive chemical ionization quadrupole mass spectrometry

Comprehensive two dimensional gas chromatography (GC × GC) provides greater separation space than conventional GC. Because of fast peak elution, a time of flight mass spectrometer (TOFMS) is the usual structure-specific detector of choice. The quantitative capabilities of a novel GC × GC fast quadrupole MS were investigated with electron ionization (EI), and CH(4) or NH(3) positive chemical ionization (PCI) for analysis of endogenous urinary steroids targeted in anti-doping tests. Average precisions for steroid quantitative analysis from replicate urine extractions were 6% (RSD) for EI and 8% for PCI-NH(3). The average limits of detection (LODs) calculated by quantification ions for 12 target steroids spiked into steroid-free urine matrix (SFUM) were 2.6 ng mL(-1) for EI, 1.3 ng mL(-1) for PCI-CH(4), and 0.3 ng mL(-1) for PCI-NH(3), all in mass scanning mode. The measured limits of quantification (LOQs) with full mass scan GC × GC-qMS were comparable with the LOQ values measured by one-dimensional GC-MS in selected ion monitoring (SIM) mode. PCI-NH(3) yields fewer fragments and greater (pseudo)molecular ion abundances than EI or PCI-CH(4). These data show that a benchtop GC × GC-qMS system has the sensitivity, specificity, and resolution to analyze urinary steroids at normal urine concentrations, and that PCI-NH(3), not currently available on most GC × GC-TOFMS instruments, is of particular value for generation of structure-specific ions.