The Influence of Copper Binding on the Stability of the SCO Protein from Bacillus subtilis

Every aerobic organism expresses cytochrome c oxidase to catalyze reduction of molecular oxygen to water, and takes advantage of this energy releasing reaction to produce an electrochemical gradient used in cellular energy production. The protein SCO (Synthesis of cytochrome c oxidase) is a required assembly factor for the oxidase, conserved across many species. SCO is implicated in the assembly of one of two copper centres (ie., CuA) of cytochrome oxidase. The exact mechanism of SCO’s participation in CuA assembly is not known. SCO has been proposed to bind and deliver copper, or alternatively to act in reductive preparation of the CuA site within the oxidase. In this body of work, the strength and stability of Cu(II) binding to Bacillus subtilis SCO is explored via electronic absorption and fluorescence spectroscopies and by calorimetric methods. An equilibrium dissociation constant (Kd) of 3.5x10-12 M was determined as an upper limit for the BsSCO-Cu(II) interaction, via differential scanning calorimetry. In the first reported case for a SCO homolog, dissociation kinetics of Cu(II) from BsSCO were characterized, and found to be dependent on both ionic strength and the presence of free Cu(II) in solution. Further differential scanning calorimetry experiments performed at high ionic strength support a two-step model of BsSCO and Cu(II) binding. The implications of this model for the BsSCO-Cu(II) interaction are presented in relation to the mechanism of interaction between SCO and the CuA site of cytochrome c oxidase.

Bismuth embrittlement of copper is an atomic size effect

Embrittlement by the segregation of impurity elements to grain boundaries is one of a small number of phenomena that can lead to metallurgical failure by fast fracture(1). Here we settle a question that has been debated for over a hundred years(2): how can minute traces of bismuth in copper cause this ductile metal to fail in a brittle manner? Three hypotheses for Bi embrittlement of Cu exist: two assign an electronic effect to either a strengthening(3) or weakening(4) of bonds, the third postulates a simple atomic size effect(5). Here we report first principles quantum mechanical calculations that allow us to reject the electronic hypotheses, while supporting a size effect. We show that upon segregation to the grain boundary, the large Bi atoms weaken the interatomic bonding by pushing apart the Cu atoms at the interface. The resolution of the mechanism underlying grain boundary weakening should be relevant for all cases of embrittlement by oversize impurities.

Observational Evidence for Mode Coupling in the Chromospheric Network

Oscillations in network bright points (NBPs) are studied at a variety of chromospheric heights. In particular, the three-dimensional variation of NBP oscillations is studied using image segmentation and cross-correlation analysis between images taken in light of Ca II K3, Ha core, Mg I b2, and Mg I b1-0.4 Å. Wavelet analysis is used to isolate wave packets in time and to search for height-dependent time delays that result from upward- or downward-directed traveling waves. In each NBP studied, we find evidence for kink-mode waves (1.3, 1.9 mHz), traveling up through the chromosphere and coupling with sausage-mode waves (2.6, 3.8 mHz). This provides a means for depositing energy in the upper chromosphere. We also find evidence for other upward- and downward-propagating waves in the 1.3-4.6 mHz range. Some oscillations do not correspond to traveling waves, and we attribute these to waves generated in neighboring regions.

Propagating waves and magnetohydrodynamic mode coupling in the quiet-sun network

High-cadence multiwavelength optical observations were taken with the Dunn Solar Telescope at the National Solar Observatory, Sacramento Peak, accompanied by Advanced Stokes Polarimeter vector magnetograms. A total of 11 network bright points (NBPs) have been studied at different atmospheric heights using images taken in wave bands centered on Mg I b(1) - 0.4 Angstrom, Halpha, and Ca II K-3. Wavelet analysis was used to study wave packets and identify traveling magnetohydrodynamic waves. Wave speeds were estimated through the temporal cross-correlation of signals, in selected frequency bands of wavelet power, in each wavelength. Four mode-coupling cases were identified, one in each of four of the NBPs, and the variation of the associated Fourier power with height was studied. Three of the detected mode-coupling, transverse-mode frequencies were observed in the 1.2-1.6 mHz range (mean NBP apparent flux density magnitudes over 99-111 Mx cm(-2)), with the final case showing 2.0-2.2 mHz (with 142 Mx cm(-2)). Following this, longitudinal-mode frequencies were detected in the range 2.6-3.2 mHz for three of our cases, with 3.9-4.1 mHz for the remaining case. After mode coupling, two cases displayed a decrease in longitudinal-mode Fourier power in the higher chromosphere.

Cross-Kerr-based information transfer processes

The realization of nonclassical states is an important task for many applications of quantum information processing. Usually, properly tailored interactions, different from goal to goal, are considered in order to accomplish specific tasks within the general framework of quantum state engineering. In this paper, we remark on the flexibility of a cross-Kerr nonlinear coupling in hybrid systems as an important ingredient in the engineering of nonclassical states. The general scenario we consider is the implementation of high cross-Kerr nonlinearity in cavity-quantum electrodynamics. In this context, we discuss the possibility of performing entanglement transfer and swapping between matter qubits and light fields initially prepared in separable coherent states. The recently introduced concept of entanglement reciprocation is also considered and shown to be possible with our scheme. We reinterpret some of our results in terms of applications of a generalized Ising interaction to systems of different nature.

Direct observation of strong coupling in a dense plasma

We present differential x-ray scattering cross sections for a radiatively heated plasma showing overall consistency, in both form and absolute value, with theoretical simulations. In particular, the evolution of the plasma from a strongly coupled high density phase to a lower density weakly coupled phase is quite clearly shown in both experiment and simulation. The success of this experiment shows that x-ray scattering has the potential to become an extremely useful diagnostic technique for dense plasma physics.

Electromigration of vacancies in copper

The total current-induced force on atoms in a Cu wire containing a vacancy are calculated using the self consistent one-electron density matrix in the presence of an electric current, without separation into electron-wind and direct forces. By integrating the total current-induced force, the change in vacancy migration energy due to the current is calculated. We use the change in migration energy with current to infer an effective electromigration driving force F-e. Finally, we calculate the proportionality constant rho* between F-e and the current density in the wire.

Structural and chemical embrittlement of grain boundaries by impurities: A general theory and first-principles calculations for copper

First-principles calculations of the Sigma 5(310)[001] symmetric tilt grain boundary in Cu with Bi, Na, and Ag substitutional impurities provide evidence that in the phenomenon of Bi embrittlement of Cu grain boundaries electronic effects do not play a major role; on the contrary, the embrittlement is mostly a structural or "size" effect. Na is predicted to be nearly as good an embrittler as Bi, whereas Ag does not embrittle the boundary in agreement with experiment. While we reject the prevailing view that "electronic" effects (i.e., charge transfer) are responsible for embrittlement, we do not exclude the role of chemistry. However, numerical results show a striking equivalence between the alkali metal Na and the semimetal Bi, small differences being accounted for by their contrasting "size" and "softness" (defined here). In order to separate structural and chemical effects unambiguously if not uniquely, we model the embrittlement process by taking the system of grain boundary and free surfaces through a sequence of precisely defined gedanken processes; each of these representing a putative mechanism. We thereby identify three mechanisms of embrittlement by substitutional impurities, two of which survive in the case of embrittlement or cohesion enhancement by interstitials. Two of the three are purely structural and the third contains both structural and chemical elements that by their very nature cannot be further unraveled. We are able to take the systems we study through each of these stages by explicit computer simulations and assess the contribution of each to the net reduction in intergranular cohesion. The conclusion we reach is that embrittlement by both Bi and Na is almost exclusively structural in origin; that is, the embrittlement is a size effect.

Synthesis of Piano Stool Complexes Employing the Pentafluorophenyl Substituted Diphosphine (C6F5)2PCH2P(C6F5)2 and the Effect of Phosphine Modifiers on Hydrogen Transfer Catalysis.

Ruthenium, rhodium, and iridium piano stool complexes of the pentafluorophenyl-substituted diphosphine (C6F5)2PCH2P(C6F5)2 (2) have been prepared and structurally characterized by single-crystal X-ray diffraction. The Cp-P tethered complex [{(C5Me4CH2C6F4(C6F5)CH2P(C6F5)2}RhCl2] (9), in which only one phosphorus is coordinated to the rhodium, was prepared by thermolysis of a slurry of [Cp*RhCl(-Cl)]2 and 2 and was structurally characterized by single-crystal X-ray diffraction. The tethering occurs by intramolecular dehydrofluorinative coupling of the pentamethylcyclopentadienyl ligand and P,P-coordinated 2. The geometric changes that occur on tethering force dissociation of one of the phosphorus atoms. The effects of introducing phosphine ligands to the coordination sphere of piano stool hydrogen transfer catalysts have been studied. The complexes of fluorinated phosphine complexes are found to transfer hydrogen at rates that compare favorably with leading catalysts, particularly when the phosphine and cyclopentadienyl functionalities are tethered. The highly chelating Cp-PP complex [(C5Me4CH2-2-C5F3N-4-PPhCH2CH2PPh2)RhCl]BF4 (1) was found to outperform all other complexes tested. The mechanism of hydrogen transfer catalyzed by piano stool phosphine complexes is discussed with reference to the trends in activity observed.

Absolute Absorption Cross-Section Measurement of a Submonolayer film on a silica microresonator

Conventional absorption spectroscopy is not nearly sensitive enough for quantitative overtone measurements on submonolayer coatings. While cavity-enhanced absorption detection methods using microresonators have the potential to provide quantitative absorption cross sections of even weakly absorbing submonolayer films, this potential has not yet been fully realized. To determine the absorption cross section of a submonolayer film of ethylene diamine (EDA) on a silica microsphere resonator, we use phase-shift cavity ringdown spectroscopy simultaneously on near-IR radiation that is Rayleigh backscattered from the microsphere and transmitted through the coupling fiber taper. We then independently determine both the coupling coefficient and the optical loss within the resonator. Together with a coincident measurement of the wavelength frequency shift, an absolute overtone absorption cross section of adsorbed EDA, at submonolayer coverage, was obtained and was compared to the bulk value. The smallest quantifiable absorption cross section is σmin 2.7 × 10−12 cm2. This absorption cross section is comparable to the extinction coefficients of, e.g., single gold nanoparticles or aerosol particles. We therefore propose that the present method is also a viable route to absolute extinction measurements of single particles.

Boron in copper: A perfect misfit in the bulk and cohesion enhancer at a grain boundary

Using first principles electronic structure methods, we calculate the effects of boron impurities in bulk copper and at surfaces and grain boundaries. We find that boron segregation to the Sigma5(310)[001] grain boundary should strengthen the boundary up to 1.5 ML coverage (15.24 at./nm2). The maximal effect is observed at 0.5 ML and corresponds to boron atoms filling exclusively grain boundary interstices. In copper bulk, B causes significant distortion both in interstitial and regular lattice sites, for which boron atoms are either too big or too small. The distortion is compensated to a large extent when the interstitial and substitutional boron combine together to form a strongly bound dumbbell. Our prediction is that bound boron impurities should appear in a sizable proportion if not dominate in most experimental conditions. A large discrepancy between calculated heats of solution and experimental terminal solubility of B in Cu is found, indicating either a significant failure of the density functional approach or, more likely, strongly overestimated solubility limits in the existing B-Cu phase diagram.

Recyclable copper catalysts based on imidazolium-tagged bis(oxazolines): A marked enhancement in rate and enantioselectivity for Diels-Alder reactions in ionic liquid

Imidazolium-tagged bis(oxazolines) have been prepared and used as chiral ligands in the copper(II)-catalysed Diels-Alder reaction of N-acryloyl- and N-crotonoyloxazolidinones with cyclopentadiene and 1,3-cyclohexadiene in the ionic liquid 1-ethyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, [emim][NTf2]. A significant and substantial enhancement in the rate and enantioselectivity was achieved in [emim][NTf2] compared with dichloromethane. For example, complete conversion and enantioselectivities up to 95 % were obtained for the reaction between N-acryloyloxazolidinone and cyclopentadiene within 2 min in [emim][NTf2] whereas the corresponding reaction in dichloromethane required 60 min to reach completion and gave an ee of only 16 %. The enhanced rates obtained in the ionic liquid enabled a catalyst loading as low as 0.5 mol % to give complete conversion within 2 min while retaining the same level of enantioselectivity. The imidazolium-tagged catalysts can be recycled ten times without any loss in activity or enantioselectivity and showed much higher affinity for the ionic liquid phase during the recycle procedure than the analogous uncharged ligand.

Enzymatic and chemoenzymatic synthesis of arene trans-dihydrodiols

Several potential approaches to the enzyme-catalysed synthesis of arene trans-diols have been examined including epoxidation/hydrolysis, bis-benzylic hydroxylation, cis-dihydroxylation/alcohol dehydrogenation/ketone reduction, cisdihydroxylation/cis-trans isomerisation. and multi-enzyme synthesis of trans-dihydrodiol secondary metabolites from primary metabolites. The lack of general applicability of these enzymatic methods has led to the development of several chemoenzymatic routes for the synthesis of a series of trans-dihydrodiols from the readily available cis-dihydrodiol precursors. Partial hydrogenation of cis-dihydrodiol metabolites to yield the corresponding cis-tetrahydrodiols followed by a regioselective Mitsunobu inversion process gave trans-tetrahydrodiols that were in turn converted to trans-dihydrodiols. The formation of anti-benzene dioxides or iron tricarbonyl complexes from the corresponding cis-dihydrodiol precursors provided shorter and more convenient chemoenzymatic routes to trans-dihydrodiols. The application of cis-dihydrodiol metabolites of polycyclic azaarenes in the synthesis of the corresponding arene oxides followed by chemical hydrolysis provides a convenient route to trans-dihydrodiols. (C) 2002 Elsevier Science B.V. All rights reserved.

Adsorption characteristics of Cu and Ni on Irish peat moss

Peat has been widely used as a low cost adsorbent to remove a variety of materials including organic compounds and heavy metals from water. Various functional groups in lignin allow such compounds to bind on active sites of peat. The adsorption of Cu²⁺ and Ni²⁺ from aqueous solutions on Irish peat moss was studied both as a pure ion and from their binary mixtures under both equilibrium and dynamic conditions in the concentration range of 5–100 mg/L. The pH of the solutions containing either Cu²⁺ or Ni²⁺ was varied over a range of 2–8. The adsorption of Cu²⁺ and Ni⁺² on peat was found to be pH dependent. The adsorption data could be fitted to a two-site Langmuir adsorption isotherm and the maximum adsorption capacity of peat was determined to be 17.6 mg/g for Cu²⁺ and 14.5 mg/g for Ni²⁺ at 298 K when the initial concentration for both Cu²⁺ and Ni²⁺ was 100 mg/L, and the pH of the solution was 4.0 and 4.5, respectively. Column studies were conducted to generate breakthrough data for both pure component and binary mixtures of copper and nickel. Desorption experiments showed that 2 mM EDTA solution could be used to remove all of the adsorbed copper and nickel from the bed.

Ionic Liquid Effect on the Reversal of Configuration for the Magnesium(II) and Copper(II) Bis(oxazoline)-Catalysed Enantioselective Diels-Alder Reaction

Ionic liquids have been used to support a range of magnesium-and copper-based bis(oxazoline) complexes for the enantioselective Diels-Alder reaction between N-acryloyloxazolidinone and cyclopentadiene. Compared with reaction performed in dichloromethane or diethyl ether, an enhancement in ee is observed with a large increase in reaction rate. In addition, for non-sterically hindered bis(oxazoline) ligands, that is, phenyl functionalised ligands, a reversal in configuration is found in the ionic liquid, 1-ethyl-3-methylimidazolium bis[(trifluoromethanesulfonyl)imide], compared with molecular solvents. Supported ionic liquid phase catalysts have also been developed using surface-modified silica which show good reactivity and enantioselectivity for the case of the magnesium-based bis(oxazoline) complexes. Poor ees and conversion were observed for the analogous copper-based systems. Some drop in ee was found on supporting the catalyst due a drop in the rate of reaction and, therefore, an increase in the contribution from the uncatalysed a chiral reaction.