Numerical simulation of fluid-structure interaction problems on hybrid meshes with algebraic multigrid methods

Fluid-structure interaction problems arise in many fields of application such as flows around elastic structures and blood flow in arteries. The method presented in this paper for solving such a problem is based on a reduction to an equation at the interface, involving the so-called Steklov-Poincaré operators. This interface equation is solved by a Newton iteration, for which directional derivatives involving shape derivatives with respect to the interface perturbation have to be evaluated appropriately. One step of the Newton iteration requires the solution of several decoupled linear sub-problems in the structure and the fluid domains. These sub-problems are spatially discretized by a finite element method on hybrid meshes. For the time discretization, implicit first-order methods are used for both sub-problems. The discretized equations are solved by algebraic multigrid methods.     

Selective homogeneous hydrogenation of biogenic carboxylic acids with [Ru(TriPhos)H]+: a mechanistic study

Selective hydrogenation of biogenic carboxylic acids is an important transformation for biorefinery concepts based on platform chemicals. We herein report a mechanistic study on the homogeneously ruthenium/phosphine catalyzed transformations of levulinic acid (LA) and itaconic acid (IA) to the corresponding lactones, diols, and cyclic ethers. A density functional theory (DFT) study was performed and corroborated with experimental data from catalytic processes and NMR investigations. For [Ru(TriPhos)H](+) as the catalytically active unit, a common mechanistic pathway for the reduction of the C═O functionality in aldehydes, ketones, lactones, and even free carboxylic acids could be identified. Hydride transfer from the Ru-H group to the carbonyl or carboxyl carbon is followed by protonation of the resulting Ru-O unit via σ-bond metathesis from a coordinated dihydrogen molecule. The energetic spans for the reduction of the different functional groups increase in the order aldehyde < ketone < lactone ≈ carboxylic acid. This reactivity pattern as well as the absolute values are in full agreement with experimentally observed activities and selectivities, forming a rational basis for further catalyst development.     

Determination of polycyclic aromatic hydrocarbons with molecular weight 302 in water samples by solid-phase nano-extraction and laser excited time-resolved Shpol'skii spectroscopy

Monitoring of high-molecular weight polycyclic aromatic hydrocarbons (HMW-PAH) via simple and cost effective methods still remains a challenge. In this article, we combine solid-phase nano-extraction (SPNE) and 4.2 K laser-excited time resolved Shpol'skii spectroscopy (LETRSS) into a valuable alternative for the water analysis of dibenzo[a,l]pyrene, dibenzo[a,h]pyrene, dibenzo[a,i]pyrene and naphtho[2,3-a]pyrene. In comparison to the original SPNE procedure, the present method improves PAH recoveries and reduces extraction time from 30 to 20 min per sample. Quantitative release of HMW-PAH into the Shpol'skii matrix (n-octane) is best accomplished with a mixture of 48 μL of methanol and 2 μL of 1-pentanethiol. Their migration into the 50 μL layer of n-octane provides highly resolved spectra with distinct fluorescence lifetimes for unambiguous isomer determination. Complete analysis takes less than 30 min per sample and consumes only 100 micro-liters of organic solvents. 500 μL of water are sufficient to obtain limits of detection ranging from 16 ng L(-1) (dibenzo[a,l]pyrene) to 55 ng L(-1) (dibenzo[a,i]pyrene), relative standard deviations better than 3% and analytical recoveries above 90%. Although a straightforward comparison to chromatographic methods is not possible because of the lack of analytical figures of merit on HMW-PAH, the excellent precision of measurements, limits of detection and overall recoveries makes SPNE-LETRSS an attractive approach to water analysis of HMW-PAH.     

The design of a new concept chromatography column

Active Flow Management is a new separation technique whereby the flow of mobile phase and the injection of sample are introduced to the column in a manner that allows migration according to the principles of the infinite diameter column. A segmented flow outlet fitting allows for the separation of solvent or solute that elutes along the central radial section of the column from that of the sample or solvent that elutes along the wall region of the column. Separation efficiency on the analytical scale is increased by 25% with an increase in sensitivity by as much as 52% compared to conventional separations.     

Redox cycling amplified electrochemical detection of DNA hybridization: application to pathogen E. coli bacterial RNA

An electrochemical genosensor in which signal amplification is achieved using p-aminophenol (p-AP) redox cycling by nicotinamide adenine dinucleotide (NADH) is presented. An immobilized thiolated capture probe is combined with a sandwich-type hybridization assay, using biotin as a tracer in the detection probe, and streptavidin-alkaline phosphatase as reporter enzyme. The phosphatase liberates the electrochemical mediator p-AP from its electrically inactive phosphate derivative. This generated p-AP is electrooxidized at an Au electrode modified self-assembled monolayer to p-quinone imine (p-QI). In the presence of NADH, p-QI is reduced back to p-AP, which can be re-oxidized on the electrode and produce amplified signal. A detection limit of 1 pM DNA target is offered by this simple one-electrode, one-enzyme format redox cycling strategy. The redox cycling design is applied successfully to the monitoring of the 16S rRNA of E. coli pathogenic bacteria, and provides a detection limit of 250 CFU μL⁻¹.     

Trialkylphosphine-stabilized copper(I) phenylchalcogenolate complexes--crystal structures and copper-chalcogenolate bonding

A series of trialkylphosphine-stabilized copper(I) phenylchalcogenolate complexes [(R(3)P)(m)(CuEPh)(n)] (R = Me, Et, (i)Pr, (t)Bu; E = S, Se, Te) has been prepared and structurally characterized by X-ray diffraction. Structures were found to be mono-, di-, tri-, tetra-, hexa-, hepta-, or decanuclear, depending mainly on size and amount of phosphine ligand. Several structural details were observed, including unusually long Cu-E bonds or secondary Cu-E connections, μ(4)-bridging, and planar bridging chalcogenolate ligands. Relatively rigid Cu-E-C angles were found to be of significant influence on the flexible molecular structures, especially for bridging chalcogenolate ligands, since in these cases a correlation results between the Cu-E-Cu angles and the inclination of the E-C bonds to their Cu-E-Cu planes. We further address some of these phenomena by means of density functional computations.     

Efficient organic monoliths prepared by γ-radiation induced polymerization in the evaluation of histone deacetylase inhibitors by capillary(nano)-high performance liquid chromatography and ion trap mass spectrometry

New monolithic HPLC columns were prepared by γ-radiation-triggered polymerization of hexyl methacrylate and ethylene glycol dimethacrylate monomers in the presence of porogenic solvents. Polymerization was carried out directly within capillary (250-200 μm I.D.) and nano (100-75 μm I.D.) fused-silica tubes yielding highly efficient columns for cap(nano)-LC applications. The columns were applied in the complete separation of core (H2A, H2B, H3, and H4) and linker (H1) histones under gradient elution with UV and/or electrospray ionization (ESI) ion trap mass spectrometry (MS) detections. Large selectivity towards H1, H2A-1, H2A-2, H2B, H3-1, H3-2 and H4 histones and complete separation were obtained within 8 min time windows, using fast gradients and very high linear flow velocities, up to 11 mm/s for high throughput applications. The method developed was the basis of a simple and efficient protocol for the evaluation of post-translational modifications (PTMs) of histones from NCI-H460 human non-small-cell lung cancer (NSCLC) and HCT-116 human colorectal carcinoma cells. The study was extended to monitoring the level of histone acetylation after inhibition of Histone DeACetylase (HDAC) enzymes with suberoylanilide hydroxamic acid (SAHA), the first HDAC inhibitor approved by the FDA for cancer therapy. Attractive features of our cap(nano)-LC/MS approach are the short analysis time, the minute amount of sample required to complete the whole procedure and the stability of the polymethacrylate-based columns. A lab-made software package ClustMass was ad hoc developed and used to elaborate deconvoluted mass spectral data (aligning, averaging, clustering) and calculate the potency of HDAC inhibitors, expressed through a Relative half maximal Inhibitory Concentration parameter, namely R_IC(50) and an averaged acetylation degree.     

Atomic interactions in the p-type clathrate I Ba8Au5.3Ge40.7

Single crystals of Ba(8)Au(5.3)Ge(40.7) [space group Pm(3)n (No. 223), a = 10.79891(8) ?] were prepared by a Bridgman technique. The crystal structure refinement based on single-crystal X-ray diffraction data does not reveal any vacancies in the Au/Ge framework or in the cages. In addition to the ionic bonding between Ba and the anionic framework, a direct interaction between Ba and Au atoms was identified in Ba(8)Au(5.3)Ge(40.7) by applying the electron localizability indicator. As expected by the chemical-bonding picture, Ba(8)Au(5.3)Ge(40.7) is a diamagnet and shows p-type electrical conductivity with a hole carrier concentration of 7.14 × 10(19) cm(-3) at 300 K and very low lattice thermal conductivity of ≈0.6 W m(-1) K(-1) at 500 K. The thermoelectric figure of merit ZT of single crystals of Ba(8)Au(5.3)Ge(40.7) attains 0.3 at 511 K and reaches 0.9 at 680 K in a polycrystalline sample of closely similar composition. This opens up an opportunity for tuning of the thermoelectric properties of materials in the Ba-Au-Ge clathrate system by changing the chemical composition.     

A new "spectroscopic" potential energy surface for formaldehyde in its ground electronic state

We report a new "spectroscopic" potential energy surface (PES) of formaldehyde (H(2)(12)C(16)O) in its ground electronic state, obtained by refining an ab initio PES in a least-squares fitting to the experimental spectroscopic data for formaldehyde currently available in the literature. The ab initio PES was computed using the CCSD(T)/aug-cc-pVQZ method at 30 840 geometries that cover the energy range up to 44 000 cm(-1) above equilibrium. Ro-vibrational energies of formaldehyde were determined variationally for this ab initio PES by means of the program TROVE [Theoretical ROtation-Vibration Energies; S. N. Yurchenko, W. Thiel, and P. Jensen, J. Mol. Spectrosc. 245, 126 (2007)]. The parameter values in the analytical representation of the PES were optimized in fittings to 319 ro-vibrational energies with J = 0, 1, 2, and 5. The initial parameter values in the fittings were those of the ab initio PES, the ro-vibrational eigenfunctions obtained from this PES served as a basis set during the fitting process, and constraints were imposed to ensure that the refined PES does not deviate unphysically from the ab initio one in regions of configuration space not sampled by the experimental data. The resulting refined PES, referred to as H(2)CO-2011, reproduces the available experimental J ≤ 5 data with a root-mean-square error of 0.04 cm(-1).