A DFT and AIM analysis of the spin–spin couplings across the hydrogen bond in the 2‐fluorobenzamide and related compounds

In 1975 a large number of coupling constants were measured in 2‐fluorobenzamide labeled with ¹⁵N. Some of them were assigned to couplings through intramolecular N? H···F hydrogen bonds (HBs). These couplings change dramatically when CDCl₃ is replaced by DMSO‐d₆. In this theoretical paper we provide density functional theory (DFT) calculations that justify the existence of a weak HB in the absence of solvent, while solvents that act as HB acceptors break down the intramolecular hydrogen bond (IMHB) of 2‐fluorobenzamide. Atoms in molecules (AIM) analyses and Steiner‐Limbach plots were used to analyze the structure of the compounds. Copyright © 2009 John Wiley & Sons, Ltd.     

Bioinspired Scaffolding by Supramolecular Amines Allows the Formation of One- and Two-Dimensional Silica Superstructures

Silica materials attract an increasing amount of interest in (fundamental) research, and find applications in, for example, sensing, catalysis, and drug delivery. As the properties of these (nano)materials not only depend on their chemistry but also their size, shape, and surface area, the controllable synthesis of silica is essential for tailoring the materials to specific applications. Advantageously, bioinspired routes for silica production are environmentally friendly and straightforward since the formation process is spontaneous and proceeds under mild conditions. These strategies mostly employ amine-bearing phosphorylated (bio)polymers. In this work, we expand this principle to supramolecular polymers based on the water-soluble cationic cyanine dye Pinacyanol acetate. Upon assembly in water, these dye molecules form large, polyaminated, supramolecular fibers. The surfaces of these fibers can be used as a scaffold for the condensation of silicic acid. Control over the ionic strength, dye concentration, and silicic acid saturation yielded silica fibers with a diameter of 25 nm and a single, 4 nm pore. Unexpectedly, other unusual superstructures, namely, nummulites and spherulites, are also observed depending on the ionic strength and dye concentration. Transmission and scanning electron microscopy (TEM and SEM) showed that these superstructures are formed by aligned silica fibers. Close examination of the dye scaffold prior silicification using small-angle X-ray scattering (SAXS), and UV/Vis spectroscopy revealed minor influence of the ionic strength and dye concentration on the morphology of the supramolecular scaffold. Total internal reflection fluorescence (TIRF) during silicification unraveled that if the reaction is kept under static conditions, only silica fibers are obtained. Experiments performed on the dye scaffold and silica superstructures evidenced that the marked structural diversity originates from the arrangement of silica/dye fibers. Under these mild conditions, external force fields can profoundly influence the morphology of the produced silica.     

High-resolution micropatterned Teflon AF substrates for biocompatible nanofluidic devices

We describe a general photolithography-based process for the microfabrication of surface-supported Teflon AF structures. Teflon AF patterns primarily benefit from superior optical properties such as very low autofluorescence and a low refractive index. The process ensures that the Teflon AF patterns remain strongly hydrophobic in order to allow rapid lipid monolayer spreading and generates a characteristic edge morphology which assists directed cell growth along the structured surfaces. We provide application examples, demonstrating the well-controlled mixing of lipid films on Teflon AF structures and showing how the patterned surfaces can be used as biocompatible growth-directing substrates for cell culture. Chinese hamster ovary (CHO) cells develop in a guided fashion along the sides of the microstructures, selectively avoiding to grow over the patterned areas.     

Microscopic structure and solvation in dry and wet octanol

Octanol-water partition coefficients are extraordinarily successful for correlating and predicting numerous processes of pharmacological and environmental importance. The amphiphilic nature of the 1-octanol molecules allows the octanol phase to mimic the complexities of many different environments ranging from biomembranes to soil. However, the structural details of the octanol phase and whether its structure is altered upon water saturation are not yet fully understood. Configurational-bias Monte Carlo simulations in the Gibbs ensemble demonstrate that a diverse spectrum of hydrogen-bonded aggregates exists in dry and wet 1-octanol, and that water saturation substantially alters the 1-octanol environment from predominantly linear aggregates in dry octanol to larger cylindrical micelles with water cores in wet octanol. These simulation results are able to reconcile the conflicting views (chain-like or water-centered aggregates vs spherical micelles) of the 1-octanol structure inferred from thermodynamic arguments, spectroscopic measurements, and diffraction experiments. Calculated partition constants quantify the influence of water saturation on the solubility characteristics of the dry and wet octanol phases.     

A line integral reaction path approximation for large systems via nonlinear constrained optimization: application to alanine dipeptide and the beta hairpin of protein G

A variation of the line integral method of Elber with self-avoiding walk has been implemented using a state of the art nonlinear constrained optimization procedure. The new implementation appears to be robust in finding approximate reaction paths for small and large systems. Exact transition states and intermediates for the resulting paths can easily be pinpointed with subsequent application of the conjugate peak refinement method [S. Fischer and M. Karplus, Chem. Phys. Lett. 194, 252 (1992)] and unconstrained minimization, respectively. Unlike previous implementations utilizing a penalty function approach, the present implementation generates an exact solution of the underlying problem. Most importantly, this formulation does not require an initial guess for the path, which makes it particularly useful for studying complex molecular rearrangements. The method has been applied to conformational rearrangements of the alanine dipeptide in the gas phase and in water, and folding of the beta hairpin of protein G in water. In the latter case a procedure was developed to systematically sample the potential energy surface underlying folding and reconstruct folding pathways within the nearest-neighbor hopping approximation.     

Comparison of complex coacervate core micelles from two diblock copolymers or a single diblock copolymer with a polyelectrolyte

With light scattering titrations, we show that complex coacervate core micelles (C3Ms) form from a diblock copolymer with a polyelectrolyte block and either an oppositely charged polyelectrolyte, a diblock copolymer with an oppositely charged polyelectrolyte or a mixture of the two. The effect of added salt and pH on both types of C3Ms is investigated. The hydrodynamic radius of mixed C3Ms can be controlled by varying the percentage of oppositely charged polyelectrolyte or diblock copolymer. A simple core-shell model is used to interpret the results from light scattering, giving the same trends as the experiments for both the hydrodynamic radii and the relative scattering intensities. Temperature has only a small effect on the C3Ms. Isothermal titration calorimetry shows that the complexation is mainly driven by Coulombic attraction and by the entropy gain due to counterion release.     

Upper limits of auditory rotational motion perception

Three experiments are reported, which investigated the auditory velocity thresholds beyond which listeners are no longer able to perceptually resolve a smooth circular trajectory. These thresholds were measured for band-limited noises, white noise, and harmonic sounds (HS), and in different acoustical environments. Experiments 1 and 2 were conducted in an acoustically dry laboratory. Observed thresholds varied as a function of stimulus type and spectral content. Thresholds for band-limited noises were unaffected by center frequency and equal to that of white noise. For HS, however, thresholds decreased as the fundamental frequency of the stimulus increased. The third experiment was a replication of the second in a reverberant concert hall, which produced qualitatively similar results except that thresholds were significantly higher than in the acoustically dry laboratory.     

Tumor necrosis factor α triggers proliferation of adult neural stem cells via IKK/NF-κB signaling

Background  

Brain inflammation has been recognized as a complex phenomenon with numerous related aspects. In addition to the very well-described neurodegenerative effect of inflammation, several studies suggest that inflammatory signals exert a potentially positive influence on neural stem cell proliferation, migration and differentiation. Tumor necrosis factor alpha (TNF-α) is one of the best-characterized mediators of inflammation. To date, conclusions about the action of TNF on neural stem or progenitor cells (NSCs, NPCs) have been conflicting. TNF seems to activate NSC proliferation and to inhibit their differentiation into NPCs. The purpose of the present study was to analyze the molecular signal transduction mechanisms induced by TNF and resulting in NSC proliferation.