High-resolution 2-DE for resolving proteins, protein adducts and complexes in plasma

A 2-DE system has been devised in which proteins are first separated in their native state followed by separation according to mass under denaturing conditions (Nat/SDS-PAGE). Hydrophilic properties of the gel and the presence of dihydroxybisacrylamide in the first dimension allowed a good resolution for high-molecular-weight proteins and maintained interactions. With this method 252 plasma spots have been resolved and 140 have been characterized by MS as isoforms of 60 proteins, a relevant part of which (12) were not detected by traditional 2-D gels or by other nondenaturing 2-D techniques. The list includes complement factors (C4d, C7), coagulation factors (coagulation factor II, fibrin beta), apolipoproteins (apolipoprotein B) and cell debris (vinculin, gelsolin, tropomyosin, dystrobrevin beta, fibrinectin I). Nat/SDS PAGE also allowed separation of nicked forms of albumin, Apo B100 and alpha2-macroglobulin and showed the presence of atypical albumin adducts corresponding to post-translational and oxidation products. Our system provides therefore new tools for resolving proteins, protein aggregates and complexes and amplifies the potentiality of traditional electrophoretic analysis.     

Brownian and advective dynamics in microflow studied by coherent X‐ray scattering experiments

Combining microfluidics with coherent X‐ray illumination offers the possibility to not only measure the structure but also the dynamics of flowing samples in a single‐scattering experiment. Here, the power of this combination is demonstrated by studying the advective and Brownian dynamics of colloidal suspensions in microflow of different geometries. Using an experimental setup with a fast two‐dimensional detector and performing X‐ray correlation spectroscopy by calculating two‐dimensional maps of the intensity auto‐correlation functions, it was possible to evaluate the sample structure and furthermore to characterize the detailed flow behavior, including flow geometry, main flow directions, advective flow velocities and diffusive dynamics. By scanning a microfocused X‐ray beam over a microfluidic device, the anisotropic auto‐correlation functions of driven colloidal suspensions in straight, curved and constricted microchannels were mapped with the spatial resolution of the X‐ray beam. This method has not only a huge potential for studying flow patterns in complex fluids but also to generally characterize anisotropic dynamics in materials.     

A Mesh Adaptation Strategy to Predict Pressure Losses in LES of Swirled Flows

Large-Eddy Simulation (LES) has become a potent tool to investigate instabilities in swirl flows even for complex, industrial geometries. However, the accurate prediction of pressure losses on these complex flows remains difficult. The paper identifies localised near-wall resolution issues as an important factor to improve accuracy and proposes a solution with an adaptive mesh h-refinement strategy relying on the tetrahedral fully automatic MMG3D library of Dapogny et al. (J. Comput. Phys. 262, 358-378, 2014) using a novel sensor based on the dissipation of kinetic energy. Using a joint experimental and numerical LES study, the methodology is first validated on a simple diaphragm flow before to be applied on a swirler with two counter-rotating passages. The results demonstrate that the new sensor and adaptation approach can effectively produce the desired local mesh refinement to match the target losses, measured experimentally. Results shows that the accuracy of pressure losses prediction is mainly controlled by the mesh quality and density in the swirler passages. The refinement also improves the computed velocity and turbulence profiles at the swirler outlet, compared to PIV results. The significant improvement of results confirms that the sensor is able to identify the relevant physics of turbulent flows that is essential for the overall accuracy of LES. Finally, in the appendix, an additional comparison of the sensor fields on tetrahedral and hexahedral meshes demonstrates that the methodology is broadly applicable to all mesh types.     

Porphyrin-phthalocyanine/pyridylfullerene supramolecular assemblies

The synthesis and photophysical properties of several porphyrin (P)-phthalocyanine (Pc) conjugates (P-Pc; 1-3) are described, in which the phthalocyanines are directly linked to the β-pyrrolic position of a meso-tetraphenylporphyrin. Photoinduced energy- and electron-transfer processes were studied through the preparation of H(2)P-ZnPc, ZnP-ZnPc, and PdP-ZnPc conjugates, and their assembly through metal coordination with two different pyridylfulleropyrrolidines (4 and 5). The resulting electron-donor-acceptor hybrids, which were formed by axial coordination of compounds 4 and 5 with the corresponding phthalocyanines, mimicked the fundamental processes of photosynthesis; that is, light harvesting, the transduction of excited-state energy, and unidirectional electron transfer. In particular, photophysical studies confirmed that intramolecular energy-transfer resulted from the S(2) excited state as well as from the S(1) excited state of the porphyrins to the energetically lower-lying phthalocyanines, followed by an intramolecular charge-transfer to yield P-Pc(.+)?C(60)(.-). This unique sequence of processes opens the way for solar-energy-conversion processes.     

Photoinduced Energy and Electron Transfer in Phenylethynyl‐Bridged Zinc Porphyrin–Oligothienylenevinylene–C60 Ensembles

Donor–bridge–acceptor triad (Por‐2TV‐C₆₀) and tetrad molecules ((Por)₂‐2TV‐C₆₀), which incorporated C₆₀ and one or two porphyrin molecules that were covalently linked through a phenylethynyl‐oligothienylenevinylene bridge, were synthesized. Their photodynamics were investigated by fluorescence measurements, and by femto‐ and nanosecond laser flash photolysis. First, photoinduced energy transfer from the porphyrin to the C₆₀ moiety occurred rather than electron transfer, followed by electron transfer from the oligothienylenevinylene to the singlet excited state of the C₆₀ moiety to produce the radical cation of oligothienylenevinylene and the radical anion of C₆₀. Then, back‐electron transfer occurred to afford the triplet excited state of the oligothienylenevinylene moiety rather than the ground state. Thus, the porphyrin units in (Por)‐2TV‐C₆₀ and (Por)₂‐2TV‐C₆₀ acted as efficient photosensitizers for the charge separation between oligothienylenevinylene and C₆₀.     

A Constrained and “Inverted” [3+3] Salphen Macrocycle with an ortho-Phenylethynyl Substitution Pattern

A [3+3] Schiff-base salphen macrocycle ( 7 a ) was synthesized by imine condensation between ortho-phenylenediamine and ortho-phenylethynyl-bridged bis(5-salicylaldehyde) precursors. The triangular-shaped macrocycle 7 a has a nonclassical (or “inverted”) design in which the N₂O₂ coordination pockets are located at the sides instead of the corners. Compound 7 a could be synthesized in a reasonably good yield (64 %) considering the steric constraints imposed by the ortho substitution pattern. Subsequent zinc metalation afforded the corresponding Zn metallomacrocycle 7 b . Spectroscopic experiments evidenced weak ( 7 a ) to strong ( 7 b ) self-aggregation behavior in solution. Their ability to self-organize at the supramolecular level was further studied in the solid state by AFM and TEM, which revealed the formation of large bundles of fibers with lengths of several micrometers and widths of nanometers.     

Elucidating heteroatom influence on homonuclear 4J(H,H) coupling constants by DFT/NMR approach

We report the structural dependency of long range scalar J-coupling constant across four bonds as function of the dihedral angles Φ1 and Φ3. The calculated homonuclear coupling constants ⁴J(_H,H), obtained at a density functional theory level, were measured between C(1)─X(2) and X(2)─C(3) bonds in three-term models, where C, N, O, and S were systematically used as the second atom of the alkyl structures ( 1 - 4 ). The ⁴J_(H,H) calculated values, tabulated for variation of 30° for both Φ1 and Φ3, have disclosed an unexpected detectable coupling constant (⁴J(_H,H) ≥ 1 Hz) across heteroatoms, useful to provide valuable structural information. A 2-methyl-1,3-dithiane sulfide ( 5 ) was used as a case study to prove the applicability and reliability of the calculated values to real issues. The ⁴J(_H,H) values obtained at density functional theory for the system 4 have reproduced with good accuracy an unexpected experimental ⁴J(_H2ax-H4ax) = 1.01 Hz of sulfide molecule ( 5 ), suggesting these calculated coupling constant values as a new powerful tool for the organic synthesis and stereochemical analysis.     

Synthesis and optical properties of isomeric branched pi-conjugated systems

[structure: see text] Branched conjugated systems with a terminal alkyne function have been prepared starting from 4-(triisopropylsilylethynyl) phenylacetylene by applying the following iterative reaction sequence: (i) metal-catalyzed cross-coupling reaction of the terminal alkyne with 3,4-dibromobenzaldehyde or 2,5- dibromobenzaldehyde; (ii) Corey-Fuchs dibromoolefination and treatment with an excess of LDA. The building blocks thus prepared have been subjected to a Pd-catalyzed cross-coupling reaction with 1,4-diiodobenzene to yield isomeric branched pi-conjugated systems containing 7 (first generation) or 15 (second generation) phenyl units connected by ethynyl spacers. The different pi-conjugation patterns in those isomeric derivatives have a dramatic effect on their electronic properties, as attested by the differences observed in their absorption and emission spectra. Finally, theoretical calculations have been performed to rationalize the optical properties of these compounds.     

Decay of the transient Cu(B)-CO complex is accompanied by formation of the heme Fe-CO complex of cytochrome cbb(3)-CO at ambient temperature: evidence from time-resolved Fourier transform infrared spectroscopy

Time-resolved step-scan Fourier infrared spectroscopy has been used to study the CO-bound cbb(3)-type cytochrome c oxidase from Pseudomonas stutzeri at room temperature. We observe a single band in the FTIR spectrum at 1956 cm(-1) (beta-form). The time-resolved data indicate that upon photolysis, CO is transferred from heme b(3) (nu(CO) = 1956 cm(-1)) to CuB (nu(CO) = 2064 cm(-1)). The decay of the 2065 cm(-1) peak (t(1/2) = 120 +/- 16 ms) and the development of the 1956 cm(-1) peak (t(1/2) = 144 +/- 8 ms ) suggest that formation of the Fe-CO complex is concurrent with the decay of the CuB-CO complex. The intensity ratio of the Fe-CO/CuB-CO (2.15) remains constant for all data points, and thus we conclude that no fraction of CO escapes the binuclear center at 293 K.     

A simple and rapid method to locate fault traces by measurements of 214Bi in soils

A simple and rapid technique is presented to determine the relative counts of ²¹⁴Bi in surface soils to locate active fault traces of the El Pilar Fault in the state of Sucre, Venezuela. The method employes a portable differential gamma-ray spectrometer on site with 300 seconds of measuring time. Three transects across the El Pilar fault of very different geological aspects were studied. One of the advantages of this technique in respect to determining ²²²Rn in soil-gas is that no soil-gas probes are required to be inserted in the soil and it is not necessary to know the appropriate depth. Finally, it has been suggested that measurements of 1000 seconds would be preferred rather than 300 seconds for future studies even though this would limit the number of measurements to about 20 per day.This revised version was published online in November 2005 with corrections to the Cover Date.