Determining secondary structure in spider dragline silk by carbon-carbon correlation solid-state NMR spectroscopy

Two-dimensional (2D) (13)C-(13)C NMR correlation spectra were collected on (13)C-enriched dragline silk fibers produced from Nephila clavipes spiders. The 2D NMR spectra were acquired under fast magic-angle spinning (MAS) and dipolar-assisted rotational resonance (DARR) recoupling to enhance magnetization transfer between (13)C spins. Spectra obtained with short (150 ms) recoupling periods were utilized to extract distinct chemical shifts for all carbon resonances of each labeled amino acid in the silk spectra, resulting in a complete resonance assignment. The NMR results presented here permit extraction of the precise chemical shift of the carbonyl environment for each (13)C-labeled amino acid in spider silk for the first time. Spectra collected with longer recoupling periods (1 s) were implemented to detect intermolecular magnetization exchange between neighboring amino acids. This information is used to ascribe NMR resonances to the specific repetitive amino acid motifs prevalent in spider silk proteins. These results indicate that glycine and alanine are both present in two distinct structural environments: a disordered 3(1)-helical conformation and an ordered beta-sheet structure. The former can be ascribed to the Gly-Gly-Ala motif while the latter is assigned to the poly(Ala) and poly(Gly-Ala) domains.     

Preparation and characterization of superporous agarose-reticulated vitreous carbon electrodes as platforms for electrochemical bioassays

Three-dimensional flow-through electrodes were fabricated using superporous agarose (SPA) and reticulated vitreous carbon (RVC) composite materials that were suitable as a platform for sandwich assays. These SPA-RVC composite electrodes were fabricated by fitting a SPA-RVC composite cylinder inside a graphite tube and subsequently fixing the graphite tube onto a polypropylene micropipette tip. The electrode design allows for ease in reagent/washing steps involved in sandwich assay protocols and could easily be made portable. The electrode materials were characterized with respect to pore-size distribution, total free volume, ligament and bulk densities of the RVC, and physical structural characteristics. Coulometric detection of redox molecules such as K(3)Fe(CN)(6) and 4-aminophenol was possible using SPA-RVC electrodes by the trapping of these redox molecules inside the SPA-RVC electrodes. Avidin affinity molecules were covalently immobilized onto the SPA matrix inside the RVC electrodes by periodate-activation followed by reductive amination. The amount of avidin immobilized inside the SPA-RVC electrodes was (5+/-0.06)x10(-11) mol, which was determined by saturating the avidin sites with biotinylated fluorescein (b-fluo) and subsequently determining the amount of immobilized b-fluo via a standard addition method using fluorescence spectroscopy. Non-specific binding of labeled enzymes such as biotinylated alkaline phosphatase (b-ALP) onto the SPA-RVC electrodes without avidin capture sites was determined to be less than 1% compared to the specific binding of b-ALP on avidinylated SPA-RVC electrodes.     

Grafting of chain-end-functionalized perfluorocyclobutyl (PFCB) aryl ether ionomers onto mesoporous carbon supports

Water-soluble perfluorocyclobutyl (PFCB) aryl ether ionomers bearing sulfonic acid groups in the main chain and phosphonic acid end groups were prepared and used to modify the surfaces of mesoporous carbon materials containing dispersed zirconia nanoparticles. Ionomer surface grafting occurred via phosphonate bonding onto the zirconia particle surfaces.     

A Chemical Reaction to the Historiography of Biology

This article examines the often-overlooked role of chemical ideas and practices in the history of modern biology. The first section analyses how the conventional histories of the life sciences have, through the twentieth century, come to focus nearly exclusively on evolutionary theory and genetics, and why this storyline is inadequate. The second section elaborates on what the restricted neo-Darwinian history of biology misses, noting a variety of episodes in the history of biology that relied on developments in – or tools from – chemistry, including an example from the author’s own work. The diverse ways in which biologists have used chemical approaches often relate to the concrete, infrastructural side of research; a more inclusive history thus also connects to a historiography of materials and objects in science.     

Mesoporous carbon/zirconia composites: a potential route to chemically functionalized electrically-conductive mesoporous materials

Mesoporous nanocomposite materials in which nanoscale zirconia (ZrO(2)) particles are embedded in the carbon skeleton of a templated mesoporous carbon matrix were prepared, and the embedded zirconia sites were used to accomplish chemical functionalization of the interior surfaces of mesopores. These nanocomposite materials offer a unique combination of high porosity (e.g., ～84% void space), electrical conductivity, and surface tailorability. The ZrO(2)/carbon nanocomposites were characterized by thermogravimetric analysis, nitrogen-adsorption porosimetry, helium pychnometry, powder X-ray diffraction, Raman spectroscopy, scanning electron microscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy. Comparison was made with templated mesoporous carbon samples prepared without addition of ZrO(2). Treatment of the nanocomposites with phenylphosphonic acid was undertaken and shown to result in robust binding of the phosphonic acid to the surface of ZrO(2) particles. Incorporation of nanoscale ZrO(2) surfaces in the mesoporous composite skeleton offers unique promise as a means for anchoring organophosphonates inside of pores through formation of robust covalent Zr-O-P bonds.     

用蒙特卡罗方法计算光通过薄层随机分布粒子的散射

本文利用蒙特卡罗方法计算准直光束通过薄层随机分布粒子散射的透射和反射光强,并和输运理论的扩散近似结果做了比较。当散射接近各向同性时两者符合良好。当散射明显地成为各向异性时,蒙特卡罗方法的结果是合理的,而输运理论的扩散近似失效。     

Competitive self-assembly and electrochemistry of some ferrocenyl-n-alkanethiol derivatives on gold

Three ferrocenyl-alkanethiol derivatives with different functional groups linking ferrocene to an alkanethiol chain have been synthesized and characterized electrochemically in bulk solution and in self-assembled monolayer films on gold electrodes. Relative affinities of the ferrocenyl-alkanethiols and of the corresponding n-alkanethiols for the electrode surface were evaluated by the competitive self-assembly method. The affinity of the ferrocenyl-alkanethiols for the surface, relative to that of the corresponding alkanethiols, is a function of the polarity of the functional group linking ferrocene to the alkanethiol chain. In general, nonpolar linking groups (methylene) show a stronger affinity for the surface than do polar groups (carboxamides) and especially charged groups (quaternary ammonium salts). It is postulated that electrostatic effects are critically important during self-assembly. Redox potentials for the three ferrocenyl-alkanethiol derivatives scale approximately with the electron donating/withdrawing effects of the functional groups on the cyclopentadiene rings. However, redox potentials for the surface-confined molecules are consistently more positive than for the identical molecules in bulk solution.     

Interfacial electron-transfer kinetics of ferrocene through oligophenyleneethynylene bridges attached to gold electrodes as constituents of self-assembled monolayers: observation of a nonmonotonic distance dependence

The standard heterogeneous electron-transfer rate constants (k(n)0) between substrate gold electrodes and the ferrocene redox couple attached to the electrode surface by variable lengths of substituted or unsubstituted oligophenyleneethynylene (OPE) bridges as constituents of mixed self-assembled monolayers were measured as a function of temperature. The distance dependences of the unsubstituted OPE standard rate constants and of the preexponential factors (An) obtained from an Arrhenius analysis of the unsubstituted OPE k(n)0 versus temperature data are not monotonic. This surprising result, together with the distance dependence of the substituted OPE preexponential factors, may be assessed in terms of the likely conformational variability of the OPE bridges (as a result of the low intrinsic barrier to rotation of the phenylene rings in these bridges) and the associated sensitivity of the rate of electron transfer (and, hence, the single-molecule conductance which may be estimated using An) through these bridges to the conformation of the bridge. Additionally, the measured standard rate constants were independent of the identity of the diluent component of the mixed monolayer, and using an unsaturated OPE diluent has no effect on the rate of electron transfer through a long-chain alkanethiol bridge. These observations indicate that the diluent does not participate in the electron-transfer event.     

Integration of enzyme kinetic models and isotopomer distribution analysis for studies of <Emphasis Type="Italic">in situ</Emphasis>cell operation

A current trend in neuroscience research is the use of stable isotope tracers in order to address metabolic processes in vivo. The tracers produce a huge number of metabolite forms that differ according to the number and position of labeled isotopes in the carbon skeleton (isotopomers) and such a large variety makes the analysis of isotopomer data highly complex. On the other hand, this multiplicity of forms does provide sufficient information to address cell operation in vivo. By the end of last millennium, a number of tools have been developed for estimation of metabolic flux profile from any possible isotopomer distribution data. However, although well elaborated, these tools were limited to steady state analysis, and the obtained set of fluxes remained disconnected from their biochemical context. In this review we focus on a new numerical analytical approach that integrates kinetic and metabolic flux analysis. The related computational algorithm estimates the dynamic flux based on the time-dependent distribution of all possible isotopomers of metabolic pathway intermediates that are generated from a labeled substrate. The new algorithm connects specific tracer data with enzyme kinetic characteristics, thereby extending the amount of data available for analysis: it uses enzyme kinetic data to estimate the flux profile, and vice versa, for the kinetic analysis it uses in vivo tracer data to reveal the biochemical basis of the estimated metabolic fluxes.     

Li+ transport in lithium sulfonylimide-oligo(ethylene oxide) ionic liquids and oligo(ethylene oxide) doped with LiTFSI

The Li+ environment and transport in an ionic liquid (IL) comprised of Li+ and an anion of bis(trifluoromethanesulfonyl)imide anion (TFSI-) tethered to oligoethylene oxide (EO) (EO(12)TFSI-/Li+) were determined and compared to those in a binary solution of the oligoethylene oxide with LiTFSI salt (EO(12)/LiTFSI) by using molecular dynamics (MD) simulations and AC conductivity measurements. The latter revealed that the AC conductivity is 1 to 2 orders of magnitude less in the IL compared to the oligoether/salt binary electrolyte with greater differences being observed at lower temperatures. The conductivity of these electrolytes was accurately predicted by MD simulations, which were used in conjunction with a microscopic model to determine mechanisms of Li+ transport. It was discerned that structure-diffusion of the Li+ cation in the binary electrolyte (EO(12)/LiTFSI-) was similar to that in EO(12)TFSI-/Li+ IL at high temperature (>363 K), thus, one can estimate conductivity of IL at this temperature range if one knows the structure-diffusion of Li+ in the binary electrolyte. However, the rate of structure-diffusion of Li+ in IL was found to slow more dramatically with decreasing temperature than in the binary electrolyte. Lithium motion together with EO(12) solvent accounted for 90% of Li+ transport in EO(12)/LiTFSI-, while the Li+ motion together with the EO(12)TFSI- anion contributed approximately half to the total Li+ transport but did not contribute to the charge transport in IL.