Changing the diffusion mechanism of Ge-Si dimers on Si(001) using an electric field

We change the diffusion mechanism of adsorbed Ge-Si dimers on Si(001) using the electric field of a scanning tunneling microscope tip. By comparing the measured field dependence with first-principles calculations we conclude that, in negative field, i.e., when electrons are attracted towards the vacuum, the dimer diffuses as a unit, rotating as it translates, whereas, in positive field the dimer bond is substantially stretched at the transition state as it slides along the substrate. Furthermore, the active mechanism in positive fields facilitates intermixing of Ge in the Si lattice, whereas intermixing is suppressed in negative fields.     

Dynamic combinatorial libraries of metalloporphyrins: templated amplification of disulfide-linked oligomers

Disulfide-linked cyclic porphyrin oligomers from dimer to tetramer can be selected and amplified virtually quantitatively from a dynamic combinatorial library using bis-thiol substituted zinc(II) porphyrin units with appropriate amine donor templates.     

NMR-Based amide hydrogen-deuterium exchange measurements for complex membrane proteins: development and critical evaluation

A method for measuring site-specific amide hydrogen-deuterium exchange rates for membrane proteins in bilayers is reported and evaluated. This method represents an adaptation and extension of the approach of Dempsey and co-workers (Biophys. J. 70, 1777-1788 (1996)) and is based on reconstituting (15)N-labeled membrane proteins into phospholipid bilayers, followed by lyophilization and rehydration with D(2)O or H(2)O (control). Following incubation for a time t under hydrated conditions, samples are again lyophilized and then solubilized in an organic solvent system, where (1)H-(15)N HSQC spectra are recorded. Comparison of spectra from D(2)O-exposed samples to spectra from control samples yields the extent of the H-D exchange which occurred in the bilayers during time t. Measurements are site specific if specific (15)N labeling is used. The first part of this paper deals with the search for a suitable solvent system in which to solubilize complex membrane proteins in an amide "exchange-trapped" form for NMR quantitation of amide peak intensities. The second portion of the paper documents application of the overall procedure to measuring site-specific amide exchange rates in diacylglycerol kinase, a representative integral membrane protein. Both the potential usefulness and the significant limitations of the new method are documented.     

Single molecule spectroscopy studies of diffusion in mesoporous silica thin films

Single molecule spectroscopy is applied in studies of diffusion and surface adsorption in sol-gel-derived mesoporous silica thin films. Mesoporous films are obtained by spin casting surfactant-templated sols onto glass substrates. Small-angle X-ray diffraction results are consistent with hexagonally ordered mesophases in as-synthesized (i.e., surfactant-containing) films. Upon calcination, a 30% contraction and disordering of these structures occurs. Nile Red is used as a fluorescent probe of both the as-synthesized and calcined films. It is loaded into the samples at subnanomolar levels either prior to spin casting or after calcination. Fluorescence imaging and single-point fluorescence time transients show the dye molecules to be relatively mobile in the as-synthesized samples. In contrast, the molecules appear entrapped at fixed locations in dry calcined films. In calcined films rehydrated under high humidity conditions, the Nile Red molecules again become mobile. Time transients obtained from the as-synthesized and rehydrated samples provide clear evidence for frequent reversible adsorption of the dye to the silica surfaces. Autocorrelations of the time transients provide quantitative data on the mean diffusion coefficients (D = 2.4 x 10(-10) and 2.6 x 10(-10) cm2/s) and mean desorption times (1/k = 25 and 40 s) for the as-synthesized and rehydrated films, respectively. The results prove both water and surfactant play important roles in governing matrix interactions and mass transport.     

Quantitation of acrylamide in food products by liquid chromatography/mass spectrometry

A simple and inexpensive liquid chromatography/mass spectrometry (LC/MS) method was developed for the quantitation of acrylamide in various food products. The method involved spiking the isotope-substituted internal standard (1-C13 acrylamide) onto 6.00 g of the food product, adding 40 mL distilled/deionized water, and heating at 65 degrees C for 30 min. Afterwards, 10 mL ethylene dichloride was added and the mixture was homogenized for 30 s and centrifuged at 2700 x g for 30 min, and then 8 g supernatant was extracted with 10, 5, and 5 mL portions of ethyl acetate. The extracts were combined, dried with sodium sulfate, and concentrated to 100-200 microL. Acrylamide was determined by analysis of the final extract on a single quadrupole, bench-top mass spectrometer with electrospray ionization, using a 2 mm id C18 column and monitoring m/z = 72 (acrylamide) and m/z = 73 (internal standard). For difficult food matrixes, such as coffee and cocoa, a solid-phase extraction cleanup step was incorporated to improve both chromatography and column lifetime. The method had a limit of quantitation of 10 ppb, and coefficients of determination (r2) for calibration curves were typically better than 0.998. Acceptable spike recovery results were achieved in 11 different food matrixes. Precision in potato chip analyses was 5-8% (relative standard deviation). This method provides an LC/MS alternative to the current LC/MS/MS methods and derivatization gas chromatography/mass spectrometry methods, and is applicable to difficult food products such as coffee, cocoa, and high-salt foods.     

Puroindoline-a, a lipid binding protein from common wheat, spontaneously forms prolate protein micelles in solution

The self-assembly in solution of puroindoline-a (Pin-a), an amphiphilic lipid binding protein from common wheat, was investigated by small angle neutron scattering, dynamic light scattering and size exclusion chromatography. Pin-a was found to form monodisperse prolate ellipsoidal micelles with a major axial radius of 112 ± 4.5 ? and minor axial radius of 40.4 ± 0.18 ?. These protein micelles were formed by the spontaneous self-assembly of 38 Pin-a molecules in solution and were stable over a wide pH range (3.5-11) and at elevated temperatures (20-65 °C). Pin-a micelles could be disrupted upon addition of the non-ionic surfactant dodecyl-β-maltoside, suggesting that the protein self-assembly is driven by hydrophobic forces, consisting of intermolecular interactions between Trp residues located within a well-defined Trp-rich domain of Pin-a.     

Disulfide-strapped porphyrins for monolayer formation on gold

Porphyrins with a disulfide-containing strap have been prepared as an alternative to dithiols for self-assembled monolayer formation on gold surfaces. The strapped porphyrins have the advantage of greater air stability than their dithiol analogues. Cis and trans atropisomers of a strapped porphyrin were isolated. Gold electrodes modified with dithiol and disulfide porphyrins were not identical as evidenced by contact angle or electrochemical measurements.     

Correlation between host-guest binding and host amplification in simulated dynamic combinatorial libraries

We present a versatile computer model of diverse dynamic combinatorial libraries, and examine how molecular recognition between library members and a template can be used to amplify the best binders. The correlation between host-guest binding and amplification was examined for a set of 50 libraries with >300 components each over a wide range of template and building block concentrations. Depending on these concentrations correlations vary from poor (when using a large excess of template) to good (for very dilute libraries and/or substoichiometric template concentrations), highlighting the need to choose the experimental conditions for dynamic combinatorial libraries thoughtfully.