Characterization of the patina formed on a low tin bronze exposed to aqueous hydrogen sulfide

The dark gray corrosion layer (patina) formed on the surface of a polished low tin bronze alloy following exposure to a deoxygenated and saturated aqueous solutions of H₂S has been characterized by X‐ray photoelectron spectroscopy, scanning electron microscopy‐energy dispersive spectroscopy and X‐ray diffraction. The system represents a model for bronze corrosion in reducing conditions where sulfate‐reducing bacteria in soils or deoxygenated seawater may generate H₂S during respiration. The initial surface was dominated by metallic copper together with Sn, Pb and Zn oxides and hydroxides. Surface enrichment of Pb and Zn was noted because of a smearing effect during polishing. At least some of the lead was crystalline. In contrast, the corrosion layer formed by H₂S(aq) exposure was dominated by polycrystalline Cu₂S (low and high chalcocite) and smaller concentrations of CuSO₄ · nH₂O. This surface was enriched with Zn as Zn(OH)₂. Lead was present as redeposited PbS (galena) crystallites in at least two different morphologies. Unlike bronzes exposed to oxidizing conditions, which develop protective SnO₂ layers, the H₂S(aq)‐exposed surface was considerably depleted in Sn. Copyright © 2014 John Wiley & Sons, Ltd.     

Three-dimensional subwavelength imaging by a photonic-crystal flat lens using negative refraction at microwave frequencies

We experimentally demonstrate subwavelength resolution imaging at microwave frequencies by a three-dimensional (3D) photonic-crystal flat lens using full 3D negative refraction. The photonic crystal was fabricated in a layer-by-layer process. A subwavelength pinhole source and a dipole detector were employed for the measurement. By point-by-point scanning, we obtained the image of the pinhole source shown in both amplitude and phase, which demonstrated the imaging mechanism and subwavelength feature size in all three dimensions. An image of two pinhole sources with subwavelength spacing showed two resolved spots, which further verified subwavelength resolution.     

Detailed large-signal dynamic modelling of DFB laser structures and comparison with experiment

This paper describes the first general large-signal dynamic multiple-mode laser model that incorporates all the main mechanisms known to influence the dynamic behaviour of DFB laser structures with the exception of thermal effects: longitudinal mode spatial hole burning, carrier transport effects, nonlinear gain, and laser and submount parasitics. The time evolution of the output power and wavelength of all modes is predicted, and full spectra can be plotted as a function of time. The model has been extended to include an approximation to the effects of propagation down dispersive fibre, thereby allowing the simulation of filtered received eye diagrams. Detailed comparison of the model with the experimental performance of 2×/8 DFB lasers has shown good agreement, allowing the performance to be optimized, particularly with respect to longitudinal hole burning and carrier transport. The model is also applied to gain-switched operation of 2×/8 DFB structures, fast pulsing of three-section /4 DFB lasers, and the dynamic behaviour of complex coupling coefficient DFB laser structures.     

Nature of the pygmy resonance in continuous <Emphasis Type="Italic">γ</Emphasis> spectra

Two-step-cascade spectra of the ¹⁷¹Yb(n, γγ)¹⁷²Yb reaction have been measured using thermal neutrons. They are compared to calculations based on experimental values of the level density and radiative strength function obtained from the ¹⁷³Yb(³He, aγ)¹⁷²Yb reaction. The multipolarity of a 6.5(15) μ _N ² resonance at 3.3(1) MeV in the strength function is determined to be M1 by this comparison.     

Efficient terahertz coupling lens based on planar photonic crystals on silicon on insulator

We present a promising coupling device, namely, a terahertz (THz) planar photonic crystal (PhC) lens based on the effective refractive-index contrast between the PhC and the surrounding unpatterned area. Three-dimensional finite-difference time-domain calculations show a 90% power transfer from a 100-microm silicon waveguide to a 10-microm waveguide, and 45% coupling efficiency is confirmed experimentally. These results demonstrate the utility of the PhC lens as an effective approach to coupling into PhC THz circuits.     

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

Summary AutoDock 2.4 predicts the bound conformations of a small, flexible ligand to a nonflexible macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation based on the AMBER force field. AutoDock has been optimized in performance without sacrificing accuracy; it incorporates many enhancements and additions, including an intuitive interface. We have developed a set of tools for launching and analyzing many independent docking jobs in parallel on a heterogeneous network of UNIX-based workstations. This paper describes the current release, and the results of a suite of diverse test systems. We also present the results of a systematic investigation into the effects of varying simulated-annealing parameters on molecular docking. We show that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 Å from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallographic conformation when there are more degrees of freedom.The AutoDock 2.4 suite is written in ANSI C, and is supplied with Makefiles for the following platforms: Convex, DEC Alpha OSF/1, Hewlett-Packard Precision Architecture, Silicon Graphics, and Sun. The AutoDock suite of programs is freely available to the noncommercial scientific community and to educational establishments. Further information, including additional figures and MPEG animations showing all docked conformations for each test system, can be found at the following URL: http://www.scripps.edu/pub/olson-web/doc/autodock.     

Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments

The major rate-limiting step in high-throughput NMR protein structure determination involves the calculation of a reliable initial fold, the elimination of incorrect nuclear Overhauser enhancement (NOE) assignments, and the resolution of NOE assignment ambiguities. We present a robust approach to automatically calculate structures with a backbone coordinate accuracy of 1.0-1.5 A from datasets in which as much as 80% of the long-range NOE information (i.e., between residues separated by more than five positions in the sequence) is incorrect. The current algorithm differs from previously published methods in that it has been expressly designed to ensure that the results from successive cycles are not biased by the global fold of structures generated in preceding cycles. Consequently, the method is highly error tolerant and is not easily funnelled down an incorrect path in either three-dimensional structure or NOE assignment space. The algorithm incorporates three main features: a linear energy function representation of the NOE restraints to allow maximization of the number of simultaneously satisfied restraints during the course of simulated annealing; a method for handling the presence of multiple possible assignments for each NOE cross-peak which avoids local minima by treating each possible assignment as if it were an independent restraint; and a probabilistic method to permit both inactivation and reactivation of all NOE restraints on the fly during the course of simulated annealing. NOE restraints are never removed permanently, thereby significantly reducing the likelihood of becoming trapped in a false minimum of NOE assignment space. The effectiveness of the algorithm is demonstrated using completely automatically peak-picked experimental NOE data from two proteins: interleukin-4 (136 residues) and cyanovirin-N (101 residues). The limits of the method are explored using simulated data on the 56-residue B1 domain of Streptococcal protein G.     

Modeling oil droplets in plateau borders

It is widely known that oil droplets can decrease the stability of aqueous films and foams. While less widely recognized, it has also been observed that oil droplets can, under certain circumstances, increase the stability of foams, especially if they are caught in the Plateau borders. In this paper, how the oil droplet deforms and is, in turn, deformed by the Plateau border is modeled using Surface Evolver. The two dimensionless parameters that affect these shapes are the size of the oil droplet relative to the Plateau border and the ratio of the oil-water interfacial tension to the air-water interfacial tension. The calculated pressures in all the phases were used to obtain the pressure exerted on the oil-water-air pseudoemulsion film, which allows the factors that influence the stability of these droplets in the Plateau border to be investigated. The final section of the paper demonstrates that the presence of an oil droplet in a Plateau border can have a major influence on the drainage of the aqueous phase along the Plateau border. This retardation of the flow would result in the oil droplets in the Plateau borders increasing the stability of foams in which they are found.     

Characterization and dynamics of substituted ruthenacyclobutanes relevant to the olefin cross-metathesis reaction

The reaction of the phosphonium alkylidene [(H(2)IMes)RuCl(2)=CHP(Cy)(3))](+) BF(4)(-) with propene, 1-butene, and 1-hexene at -45 °C affords various substituted, metathesis-active ruthenacycles. These metallacycles were found to equilibrate over extended reaction times in response to decreases in ethylene concentrations, which favored increased populations of α-monosubstituted and α,α'-disubstituted (both cis and trans) ruthenacycles. On an NMR time scale, rapid chemical exchange was found to preferentially occur between the β-hydrogens of the cis and trans stereoisomers prior to olefin exchange. Exchange on an NMR time scale was also observed between the α- and β-methylene groups of the monosubstituted ruthenacycle (H(2)IMes)Cl(2)Ru(CHRCH(2)CH(2)) (R = CH(3), CH(2)CH(3), (CH(2))(3)CH(3)). EXSY NMR experiments at -87 °C were used to determine the activation energies for both of these exchange processes. In addition, new methods have been developed for the direct preparation of metathesis-active ruthenacyclobutanes via the protonolysis of dichloro(1,3-bis(2,4,6-trimethylphenyl)-2-imidazolidinylidene)(benzylidene) bis(pyridine)ruthenium(II) and its 3-bromopyridine analogue. Using either trifluoroacetic acid or silica-bound toluenesulfonic acid as the proton source, the ethylene-derived ruthenacyclobutane (H(2)IMes)Cl(2)Ru(CH(2)CH(2)CH(2)) was observed in up to 98% yield via NMR at -40 °C. On the basis of these studies, mechanisms accounting for the positional and stereochemical exchange within ruthenacyclobutanes are proposed, as well as the implications of these dynamics toward olefin metathesis catalyst and reaction design are described.     

Oxidation of cyclopentane-1,2-dione: a study with O labeled reagents

The asymmetric oxidation of 3-alkyl-cyclopentane-1,2-diones with the Ti(OⁱPr)₄/tartaric ester/t-BuOOH complex, which gives, in a cascade process, highly enantiomerically enriched γ-lactone acids, was studied by ¹⁸O isotopic labeling in the substrate and in the oxidant. The path of the labeled atoms was followed by ¹³C NMR spectroscopy. It was found that the oxidative ring cleavage of 1,2-dione proceeds via a Baeyer-Villiger-type oxidation mechanism.