Properties and behaviour of tetracyclic allopsoralen derivatives inside a DPPC lipid bilayer model

Allopsoralens are angular psoralen derivatives presenting advantages over the parent compound because of monofunctional DNA-photobinding and consequent lower toxicity. Allopsoralen molecules with three different substituents and different protonation states were studied using the molecular dynamics technique. The location of these molecules when inside the lipid bilayer is of major importance because their photochemical properties can change with the environment. Also, the ability of psoralens to form photoadducts with unsaturated phospholipids depends on the preference of the molecules to locate themselves closer to the bilayer middle were the double bond functionality can be found. Herein we show that the allopsoralens tend to accumulate inside the lipid bilayer closer to the water interface when protonated or closer to the interface middle otherwise. Allopsoralens containing one amine terminated carbon chain tend to have different rotational and orientational behaviour and an orientation preference close to the ones shown by the lipids. The size and chemical nature of the substituent also affect the molecular mobility and capacity to interact with water molecules and the nitrogen or phosphorus atoms of the lipids.     

The influence of polarizability on the dielectric spectrum of the ionic liquid 1-ethyl-3-methylimidazolium triflate

This work reports for the first time the computational, frequency-dependent dielectric spectrum of the polarizable molecular ionic liquid 1-ethyl-3-methylimidazolium triflate as well as its experimental analogue. In the frequency range from 500 MHz up to 20 GHz the agreement between the computational and the experimental spectrum is quantitative. For higher frequencies up to 10 THz the agreement is still remarkably good. The experimental asymptotic limit ε(∞) is 2.3. The difference in the computational value of 1.9 comes solely from the neglect of polarizability of the hydrogen atoms. For reasons of efficiency the simulations are based on the Lagrangian algorithm for the Drude oscillator model which cannot handle polarizable hydrogens. In the computational analysis the complete spectrum of the generalized dielectric constant ∑(0)*(ν) is splitted into its translational and non-translational components, called dielectric conductivity ?(0)(ν) and dielectric permittivity ε(ν). For 1-ethyl-3-methylimidazolium triflate both components contribute with equal weight and overlap in the complete frequency range. The inclusion of polarization forces, however, is quite different for the two components: the collective non-translational dynamics is accelerated and hence the dielectric permittivity is shifted to higher frequencies. The low frequency region of the dielectric conductivity is also affected while its high frequency part remains almost unchanged. Inductive effects are not only visible at high frequencies but also contribute in the sub-GHz region. The computational peak found in this region correlates with the experimental OKE-spectrum. It may be interpreted as the correlation between the induced dipole moment of the cations and the local electric field exerted by the anionic cage.     

Concept of biogenic ferromanganese crust formation: coccoliths as bio-seeds in crusts from Central Atlantic Ocean (Senghor Seamount/Cape Verde)

At depths of 2,000 to 3,000 m, seamounts from the Cape Verde archipelago (Central Atlantic Ocean) are largely covered with ferromanganese crusts. Here we studied 60 to 150 mm thick crusts from the Senghor Seamount (depth: 2257.4 m). The crusts have a non lamellated texture and are covered with spherical nodules. The chemical composition shows a dominance of MnO2 (26.1%) and Fe2O3 (38.8%) with considerable amounts of Co (0.74%) and TiO2 (2.1%). Analysis by scanning electron probe microanalyzer (EPMA) revealed a well defined compositional zonation of micro-layers; the distribution pattern of Mn does not match that of Fe. Analysis by high resolution scanning electron microscopy (SEM) revealed that coccospheres/coccoliths exist in the crust material as microfossils; most of the coccospheres/coccoliths are not intact. The almost circular coccoliths belong to the type of heterococcoliths and are taxonomically related to species of the family Calcidiscaceae. By energy dispersive X-ray spectroscopic analysis an accumulation of the coccoliths in the Mn- and Fe rich micronodules was detected. Focused ion beam assisted SEM mapping highlighted that the coccoliths in the crust are Mn rich, suggesting that the calcareous material of the algal skeleton has been replaced by Mn-minerals. We conclude that a biologically induced mechanism has been involved in the formation of the crusts, collected from the Cape Verde archipelago from depths of 2,000 to 3,000 m in the mixing region between the oxygen-minimum surface zone and the oxygen-rich deep waters; the deposition process might have been triggered by chemical reactions during the dissolution of the Ca-carbonate skeletons of the coccoliths allowing Mn(II) to oxidize to Mn(IV) and in turn to deposit this element in the crust material.     

Cycle resolved multi-planar flow measurements in a four-valve combustion engine

The non-reacting flow in a one-cylinder four-valve combustion engine is measured via cycle resolved two-component/two-dimensional (2C/2D) particle-image velocimetry (PIV). The three-dimensional structure of the velocity field is analyzed based on the flow field measured in eight planar planes within the cylinder for several crank angles during the intake and compression phase. Using the mean and statistical values of the single planes quasi three-dimensional flow fields are reconstructed for crank angles of 80°, 160°, and 240° atdc. This enables the detailed analysis of the spatial distribution of the large and small scale flow structures, e.g., by visualizing large vortical structures and the distribution of the turbulent kinetic energy. It was found that two ring vortices evolving beneath the inlet valves are the dominant large scale structures that seem to be of major concern for the mixing process in the cylinder of a four-valve combustion engine operated at 1500 rpm. Furthermore, the temporal evolution of the flow field within the symmetry plane of the cylinder, measured for crank angles between 40° and 320° atdc in steps of 20°, is discussed. The results give new insight into the complex three-dimensional flow in the combustion chamber of a one-cylinder four-valve combustion engine. That is, the tumble vortex only seems to be of secondary importance for the flow concerning the mixing process at 1500 rpm. This is an essential result for future work considering the fluid mechanics of fuel-air-interaction processes and mixing principles in combustion engines.     

Application of particle image velocimetry and the background-oriented schlieren technique in the high-enthalpy shock tunnel G?ttingen

The applicability of the particle image velocimetry (PIV) and the background-oriented schlieren (BOS) techniques in the high-enthalpy shock tunnel G?ttingen of the German Aerospace Center, DLR is demonstrated. As a part of this feasibility study two different experiments are performed. The velocity field past a wedge in a Mach 6 flow at a total specific enthalpy of 1.5 MJ/kg is determined by means of PIV and the results are compared to numerical predictions. The BOS technique is applied to investigate the density field in the shock layer of a sphere at 12 and 22 MJ/kg total specific enthalpies. Using a ray tracer method, the BOS results are compared to the data obtained by corresponding numerical computations.     

Electronic structure of oxidized complexes derived from cis-[Ru(II)(bpy)2(H2O)2]2+ and its photoisomerization mechanism

The geometry and electronic structure of cis-[Ru(II)(bpy)(2)(H(2)O)(2)](2+) and its higher oxidation state species up formally to Ru(VI) have been studied by means of UV-vis, EPR, XAS, and DFT and CASSCF/CASPT2 calculations. DFT calculations of the molecular structures of these species show that, as the oxidation state increases, the Ru-O bond distance decreases, indicating increased degrees of Ru-O multiple bonding. In addition, the O-Ru-O valence bond angle increases as the oxidation state increases. EPR spectroscopy and quantum chemical calculations indicate that low-spin configurations are favored for all oxidation states. Thus, cis-[Ru(IV)(bpy)(2)(OH)(2)](2+) (d(4)) has a singlet ground state and is EPR-silent at low temperatures, while cis-[Ru(V)(bpy)(2)(O)(OH)](2+) (d(3)) has a doublet ground state. XAS spectroscopy of higher oxidation state species and DFT calculations further illuminate the electronic structures of these complexes, particularly with respect to the covalent character of the O-Ru-O fragment. In addition, the photochemical isomerization of cis-[Ru(II)(bpy)(2)(H(2)O)(2)](2+) to its trans-[Ru(II)(bpy)(2)(H(2)O)(2)](2+) isomer has been fully characterized through quantum chemical calculations. The excited-state process is predicted to involve decoordination of one aqua ligand, which leads to a coordinatively unsaturated complex that undergoes structural rearrangement followed by recoordination of water to yield the trans isomer.     

Pressure-energy correlations in liquids. V. Isomorphs in generalized Lennard-Jones systems

This series of papers is devoted to identifying and explaining the properties of strongly correlating liquids, i.e., liquids with more than 90% correlation between their virial W and potential energy U fluctuations in the NVT ensemble. Paper IV [N. Gnan et al., J. Chem. Phys. 131, 234504 (2009)] showed that strongly correlating liquids have "isomorphs," which are curves in the phase diagram along which structure, dynamics, and some thermodynamic properties are invariant in reduced units. In the present paper, using the fact that reduced-unit radial distribution functions are isomorph invariant, we derive an expression for the shapes of isomorphs in the WU phase diagram of generalized Lennard-Jones systems of one or more types of particles. The isomorph shape depends only on the Lennard-Jones exponents; thus all isomorphs of standard Lennard-Jones systems (with exponents 12 and 6) can be scaled onto a single curve. Two applications are given. One tests the prediction that the solid-liquid coexistence curve follows an isomorph by comparing to recent simulations by Ahmed and Sadus [J. Chem. Phys. 131, 174504 (2009)]. Excellent agreement is found on the liquid side of the coexistence curve, whereas the agreement is less convincing on the solid side. A second application is the derivation of an approximate equation of state for generalized Lennard-Jones systems by combining the isomorph theory with the Rosenfeld-Tarazona expression for the temperature dependence of the potential energy on isochores. It is shown that the new equation of state agrees well with simulations.     

Photonic chip-based all-optical XOR gate for 40 and 160 Gbit/s DPSK signals

We demonstrate a photonic chip-based all-optical exclusive-OR (XOR) gate for phase-encoded optical signals via four-wave mixing in a highly nonlinear, dispersion-engineered chalcogenide (As2S3) planar waveguide. We achieve error-free, XOR operation for 40?Gbit/s differential phase shift keying (DPSK) optical signals with no power penalty. The effectiveness and broad bandwidth operation of our approach is highlighted by implementing an XOR gate for 160?Gbit/s DPSK signals.     

Chemical approaches towards unravelling kinase-mediated signalling pathways

Protein kinases control the function of about one third of cellular proteins by catalysing the transfer of the γ-phosphate group of ATP onto their substrate proteins. Protein phosphatases counter this action and also control the activation status of many kinases. Cellular responses to environmental changes, or signalling events, temporarily tilt the balance of protein phosphorylation and dephosphorylation to one side or the other. The identification of protein-kinase-substrate pairs and substrate-phosphatase pairs is critical to understanding cell function and how cells respond to environmental changes. Identification of these substrate-enzyme pairs is non-trivial, because of the structural and mechanistic conservation of the catalytic cores of protein kinases. In this tutorial review we review recent progress towards identifying protein-kinase-substrate pairs by emphasising the use of chemical genetics and purpose-designed ATP analogues that target one particular protein kinase. In addition, we discuss activity-based chemical profiling approaches, based on ATP analogues, for the detection of active kinases.     

Modifying cage structures in metal-organic polyhedral frameworks for H2 storage

Three isostructural metal-organic polyhedral cage based frameworks (denoted NOTT-113, NOTT-114 and NOTT-115) with (3,24)-connected topology have been synthesised by combining hexacarboxylate isophthalate linkers with {Cu(2)(RCOO)(4)} paddlewheels. All three frameworks have the same cuboctahedral cage structure constructed from 24 isophthalates from the ligands and 12 {Cu(2)(RCOO)(4)} paddlewheel moieties. The frameworks differ only in the functionality of the central core of the hexacarboxylate ligands with trimethylphenyl, phenylamine and triphenylamine moieties in NOTT-113, NOTT-114 and NOTT-115, respectively. Exchange of pore solvent with acetone followed by heating affords the corresponding desolvated framework materials, which show high BET surface areas of 2970, 3424 and 3394 m(2) g(-1) for NOTT-113, NOTT-114 and NOTT-115, respectively. Desolvated NOTT-113 and NOTT-114 show high total H(2) adsorption capacities of 6.7 and 6.8 wt%, respectively, at 77 K and 60 bar. Desolvated NOTT-115 has a significantly higher total H(2) uptake of 7.5 wt% under the same conditions. Analysis of the heats of adsorption (Q(st)) for H(2) reveals that with a triphenylamine moiety in the cage wall, desolvated NOTT-115 shows the highest value of Q(st) for these three materials, indicating that functionalisation of the cage walls with more aromatic rings can enhance the H(2)/framework interactions. In contrast, measurement of Q(st) reveals that the amine-substituted trisalkynylbenzene core used in NOTT-114 gives a notably lower H(2)/framework binding energy.