EWE: Toward electro-mechanical cardiac simulations with MOOSE

We present the software framework EWE, which is designed for coupled electromechanical simulations in computational cardiology. EWE is build on the multi-physics framework MOOSE. Numerical simulations of coupled problems on an idealized geometry for a left ventricle are shown. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Tyrosine 263 in Cyanobacterial Phytochrome Cph1 Optimizes Photochemistry at the prelumi‐R→lumi‐R Step

We report a low‐temperature fluorescence spectroscopy study of the PAS‐GAF‐PHY sensory module of Cph1 phytochrome, its Y263F mutant (both with known 3D structures) as well as Y263H and Y263S to connect their photochemical parameters with intramolecular interactions. None of the holoproteins showed photochemical activity at low temperature, and the activation barriers for the Pr→lumi‐R photoreaction (2.5–3.1 kJ mol^?1) and fluorescence quantum yields (0.29–0.42) were similar. The effect of the mutations on Pr→Pfr photoconversion efficiency (Φ_Pr→Pfr) was observed primarily at the prelumi‐R S₀ bifurcation point corresponding to the conical intersection of the energy surfaces at which the molecule relaxes to form lumi‐R or Pr, lowering Φ_Pr→Pfr from 0.13 in the wild type to 0.05–0.07 in the mutants. We suggest that the E_a activation barrier in the Pr* S₁ excited state might correspond to the D‐ring (C19) carbonyl – H290 hydrogen bond or possibly to the hindrance caused by the C13¹/C17¹ methyl groups of the C and D rings. The critical role of the tyrosine hydroxyl group can be at the prelumi‐R bifurcation point to optimize the yield of the photoprocess and energy storage in the form of lumi‐R for subsequent rearrangement processes culminating in Pfr formation.     

An Operando FTIR Spectroscopic and Kinetic Study of Carbon Monoxide Pressure Influence on Rhodium‐Catalyzed Olefin Hydroformylation

The influence of carbon monoxide concentration on the kinetics of the hydroformylation of 3,3‐dimethyl‐1‐butene with a phosphite‐modified rhodium catalyst has been studied for the pressure range p(CO)=0.20–3.83 MPa. Highly resolved time‐dependent concentration profiles of the organometallic intermediates were derived from IR spectroscopic data collected in situ for the entire olefin‐conversion range. The dynamics of the catalyst and organic components are described by enzyme‐type kinetics with competitive and uncompetitive inhibition reactions involving carbon monoxide taken into account. Saturation of the alkyl–rhodium intermediates with carbon monoxide as a cosubstrate occurs between 1.5 and 2 MPa of carbon monoxide pressure, which brings about a convergence of aldehyde regioselectivity. Hydrogenolysis of the acyl intermediate is fast at 30 °C and low pressure of p(CO)=0.2 MPa, but is of minus first order with respect to the solution concentration of carbon monoxide. Resting 18‐electron hydrido and acyl complexes that correspond to early and late rate‐determining states, respectively, coexist as long as the conversion of the substrate is not complete.     

Ferromagnetic Ordering in the Layer‐Structured Pd(HS2O7)2

The reaction of (NO₂)(CF₃SO₃) and elemental palladium in oleum (65 % SO₃) leads to violet single crystals of Pd(HS₂O₇)₂ (monoclinic, P2₁/c, Z=2, a=927.80(9), b=682.58(7), c=920.84(9) pm, β=117.756(2)°, wR₂=0.0439). In the crystal structure, the Pd²⁺ ions show an uncommon octahedral coordination of six oxygen atoms belonging to six HS₂O₇^? ions. The linkage of [PdO₆] octahedra and the hydrogendisulfate anions leads to a layer structure, and the layers are held together by hydrogen bonds. The unusual coordination of the Pd²⁺ ions results in an electronic d⁸ high‐spin configuration, which leads to the paramagnetic behavior of the compound. Moreover, at low temperature, a ferromagnetic ordering was observed with a Curie temperature of 8 K.     

On the Oxidation of the Three‐Dimensional Aromatics [B12X12]2− (X=F,Cl, Br,I)

The perhalogenated closo‐dodecaborate dianions [B₁₂X₁₂]^2? (X=H, F, Cl, Br, I) are three‐dimensional counterparts to the two‐dimensional aromatics C₆X₆ (X=H, F, Cl, Br, I). Whereas oxidation of the parent compounds [B₁₂H₁₂]^2? and benzene does not lead to isolable radicals, the perhalogenated analogues can be oxidized by chemical or electrochemical methods to give stable radicals. The chemical oxidation of the closo‐dodecaborate dianions [B₁₂X₁₂]^2? with the strong oxidizer AsF₅ in liquid sulfur dioxide (lSO₂) yielded the corresponding radical anions [B₁₂X₁₂] ^{? ?} (X=F, Cl, Br). The presence of radical ions was proven by EPR and UV/Vis spectroscopy and supported by quantum chemical calculations. Use of an excess amount of the oxidizing agent allowed the synthesis of the neutral perhalogenated hypercloso‐boranes B₁₂X₁₂ (X=Cl, Br). These compounds were characterized by single‐crystal X‐ray diffraction of dark blue B₁₂Cl₁₂ and [Na(SO₂)₆][B₁₂Br₁₂] ? B₁₂Br₁₂. Sublimation of the crude reaction products that contained B₁₂X₁₂ (X=Cl, Br) resulted in pure dark blue B₁₂Cl₁₂ or decomposition to red B₉Br₉, respectively. The energetics of the oxidation processes in the gas phase were calculated by DFT methods at the PBE0/def2‐TZVPP level of theory. They revealed the trend of increasing ionization potentials of the [B₁₂X₁₂]^2? dianions by going from fluorine to bromine as halogen substituent. The oxidation of all [B₁₂X₁₂]^2? dianions was also studied in the gas phase by mass spectrometry in an ion trap. The electrochemical oxidation of the closo‐dodecaborate dianions [B₁₂X₁₂]^2? (X=F, Cl, Br, I) by cyclic and Osteryoung square‐wave voltammetry in liquid sulfur dioxide or acetonitrile showed very good agreement with quantum chemical calculations in the gas phase. For [B₁₂X₁₂]^2? (X=F, Cl, Br) the first and second oxidation processes are detected. Whereas the first process is quasi‐reversible (with oxidation potentials in the range between +1.68 and +2.29 V (lSO₂, versus ferrocene/ferrocenium (Fc^0/+))), the second process is irreversible (with oxidation potentials ranging from +2.63 to +2.71 V (lSO₂, versus Fc^0/+)). [B₁₂I₁₂]^2? showed a complex oxidation behavior in cyclic voltammetry experiments, presumably owing to decomposition of the cluster anion under release of iodide, which also explains the failure to isolate the respective radical by chemical oxidation.     

Estimating the quadratic covariation of an asynchronously observed semimartingale with jumps

We consider estimation of the quadratic (co)variation of a semimartingale from discrete observations which are irregularly spaced under high-frequency asymptotics. In the univariate setting, results by Jacod for regularly spaced observations are generalized to the case of irregular observations. In the two-dimensional setup under non-synchronous observations, we derive a stable central limit theorem for the Hayashi–Yoshida estimator in the presence of jumps. We reveal how idiosyncratic and simultaneous jumps affect the asymptotic distribution. Observation times generated by Poisson processes are explicitly discussed.     

Electrophysiological Characterization of Transport Across Outer‐Membrane Channels from Gram‐Negative Bacteria in Presence of Lipopolysaccharides

Multi‐drug resistance in Gram‐negative bacteria is often associated with low permeability of the outer membrane. To investigate the role of membrane channels in the uptake of antibiotics, we present an approach using fusion of native outer membrane vesicles (OMVs) into a planar lipid bilayer, allowing characterization of membrane protein channels in their native environment. Two major membrane channels from E. coli, OmpF and OmpC, were overexpressed from the host and the corresponding OMVs were collected. Each OMV fusion surprisingly revealed only single or few channel activities. The asymmetry of the OMVs translates after fusion into the lipid membrane with the lipopolysaccharides (LPS) dominantly present at the side of OMV addition. Compared to the conventional reconstitution method, the channels fused from OMVs containing LPS have similar conductance but a much broader distribution and significantly lower permeation. We suggest using outer membrane vesicles for functional and structural studies of membrane channels in the native membrane.     

Bridging and Conformational Control of Porphyrin Units through Non-Traditional Rigid Scaffolds

Connecting two porphyrin units in a rigid linear fashion, without any undesired electron delocalization or communication between the chromophores, remains a synthetic challenge. Herein, a broad library of functionally diverse multi-porphyrin arrays that incorporate the non-traditional rigid linker groups cubane and bicyclo[1.1.1]pentane (BCP) is described. A robust, reliable, and versatile synthetic procedure was employed to access porphyrin-cubane/BCP-porphyrin arrays, representing the largest non-polymeric structures available for cubane/BCP derivatives. These reactions demonstrate considerable substrate scope, from utilization of small phenyl moieties to large porphyrin rings, with varying lengths and different angles. To control conformational flexibility, amide bonds were introduced between the bridgehead carbon of BCP/cubane and the porphyrin rings. Through varying the orientation of the substituents around the amide bond of cubane/BCP, different intermolecular interactions were identified through single crystal X-ray analysis. These studies revealed non-covalent interactions that are the first-of-their-kind including a unique iodine-oxygen interaction between cubane units. These supramolecular architectures indicate the possibility to mimic a protein structure due to the sp³ rigid scaffolds (BCP or cubane) that exhibit the essential conformational space for protein function while simultaneously providing amide bonds for molecular recognition.     

Enhancing the CO2 Electroreduction of Fe/Ni-Pentlandite Catalysts by S/Se Exchange

The electrochemical reduction of CO₂ is an attractive strategy towards the mitigation of environmental pollution and production of bulk chemicals as well as fuels by renewables. The bimetallic sulfide Fe_4.5Ni_4.5S₈ (pentlandite) was recently reported as a cheap and robust catalyst for electrochemical water splitting, as well as for CO₂ reduction with a solvent-dependent product selectivity. Inspired by numerous reports on monometallic sulfoselenides and selenides revealing higher catalytic activity for the CO₂ reduction reaction (CO₂RR) than their sulfide counterparts, the authors investigated the influence of stepwise S/Se exchange in seleno-pentlandites Fe_4.5Ni_4.5S_8-YSe_Y (Y=1–5) and their ability to act as CO₂ reducing catalysts. It is demonstrated that the incorporation of higher equivalents of selenium favors the CO₂RR with Fe_4.5Ni_4.5S₄Se₄ revealing the highest activity for CO formation. Under galvanostatic conditions in acetonitrile, Fe_4.5Ni_4.5S₄Se₄ generates CO with a Faradaic Efficiency close to 100 % at applied current densities of −50 mA cm⁻² and −100 mA cm⁻². This work offers insight into the tunability of the pentlandite based electrocatalysts for the CO₂ reduction reaction.