Systematic control of the packing density of self-assembled monolayers using bidentate and tridentate chelating alkanethiols

The structural and interfacial properties of self-assembled monolayers (SAMs) on gold derived from the adsorption of a series of 1,1,1-tris(mercaptomethyl)alkanes (i.e., CH3(CH2)mC[CH2SH]3, where m = 9, 11, 13, 15) were investigated. The new SAMs, which possess uniformly low densities of alkyl chains, were characterized by ellipsometry, contact angle goniometry, and polarization modulation infrared reflection absorption spectroscopy. Additional analysis of the SAMs by X-ray photoelectron spectroscopy permitted a direct calculation of the packing densities of the SAMs on gold. The results as a whole, when compared to those obtained on SAMs generated from normal alkanethiols (CH3(CH2)m+2SH), 2-alkylpropane-1,3-dithiols (CH3(CH2)mCH[CH2SH]2), and 2-alkyl-2-methylpropane-1,3-dithiols (CH3(CH2)mC(CH3)[CH2SH]2) having analogous chain lengths, demonstrate that the 1,1,1-tris(mercaptomethyl)alkanes afford SAMs with alkyl chains having the lowest packing density and least conformational order.     

Grafting from surfaces for "everyone": ARGET ATRP in the presence of air

Atom-transfer radical polymerization (ATRP) is one of the controlled/living radical polymerizations yielding well-defined (co)polymers, nanocomposites, molecular hybrids, and bioconjugates. ATRP, as in any radical process, has to be carried out in rigorously deoxygenated systems to prevent trapping of propagating radicals by oxygen. Herein, we report that ATRP can be performed in the presence of limited amount of air and with a very small (typically ppm) amount of copper catalyst together with an appropriate reducing agent. This technique has been successfully applied to the preparation of densely grafted polymer brushes, poly(n-butyl acrylate) homopolymer, and poly(n-butyl acrylate)-block-polystyrene copolymer from silicon wafers (0.4 chains/nm2). This simple new method of grafting well-defined polymers does not require any special equipment and can be carried out in vials or jars without deoxygenation. The grafting for "everyone" technique is especially useful for wafers and other large objects and may be also applied for molecular hybrids and bioconjugates.     

Characterization of protein conformational states by normal-mode frequencies

Conformational change in polymers including proteins is central to many molecular processes. Defining conformational states, however, remains a difficult and increasingly common problem, with many existing methods based on arbitrary or potentially unrepresentative measures. Furthermore, the expanding length of molecular dynamics simulations and direct observation of transitions between different energy basins suggest that this issue will only become evermore important. Methods commonly used to characterize conformational states include principal component analysis, root-mean-square deviation-based clustering, and geometric measurements such as hinge angles and distances. Here we present a method where the eigenvector frequencies derived from a Gaussian network model (Bahar, I.; Atilgan, A. R.; Erman, B. Folding Des. 1997, 2, 173-181) of a trajectory of structures from a molecular dynamics simulation are used to describe the state of the protein at each time point. We apply the method to three proteins that share the same fold as the type II periplasmic binding proteins: The lysine-arginine-ornithine-binding protein, the glutamine-binding protein, and the ligand-binding domain from the NR1 N-methyl-D-aspartate receptor. We find that the method can distinguish different states in good agreement with a variety of previous analyses and additionally provides information on the dynamic properties of that system at a given time point.     

Smoothed Particle Hydrodynamics Model of Non-Aqueous Phase Liquid Flow and Dissolution

A smoothed particle hydrodynamics model was developed to simulate the flow of mixtures of aqueous and non-aqueous phase liquids in porous media and the dissolution of the non-aqueous phase in the aqueous phase. The model was used to study the effects of pore-scale heterogeneity and anisotropy on the steady state dense non-aqueous phase liquid (DNAPL) saturation when gravity driven DNAPL displaces water from initially water saturated porous media. Pore-scale anisotropy was created by using co-oriented non-overlapping elliptically shaped grains to represent the porous media. After a steady state DNAPL saturation was reached, water was injected until a new steady state DNAPL saturation was reached. The amount of trapped DNAPL was found to be greater when DNAPL is displaced in the direction of the major axes of the soil grains than when it is displaced in the direction of the minor axes of the soil grains. The amount of trapped DNAPL was also found to increase with decreasing initial saturation of the continuous DNAPL phase. For the conditions used in our simulations, the saturation of the trapped DNAPL with a smaller initial DNAPL saturation was more than 3 times larger than the amount of trapped DNAPL with a larger initial saturation. These simulations were carried out assuming that the DNAPL did not dissolve in water. Simulations including the effect of dissolution of DNAPL in the aqueous phase were also performed, and effective (macroscopic) mass transfer coefficients were determined. The U.S. Government’s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

The Container Transshipment Problem: Searching Representation Landscapes with Metaheuristic Algorithms

The container transshipment problem involves scheduling a fleet of lorries to collect and deliver containers of various sizes while minimizing the total distance travelled. The problem originates in the need for logistics companies to solve the problem on a regular basis as part of their daily operations. In this paper, we compare two genetic algorithms tailored to solve this problem based on permutation and bin-packing inspired encodings. Results are presented and analysed in order to evaluate the validity and robustness of the two approaches. As part of the analysis, bounds were calculated to determine how well both GAs perform in absolute terms as well as relative to each other. Of the two GA there is one clear winner, although it is not the one that would have been indicated by previous research. Whilst the winning GA is able to generate significant savings in practice, compared to the optimum there remains room for further improvement.     

Solar neutrino decay

We re-examine the neutrino decay solution to the solar neutrino problem in light of the new data from GALLEX II and Kamiokande III. We compare the experimental data with the solar models of Bahcall and Pinsonneault and Turck-Chieze and find that neutrino decay is ruled out as a solution to the solar neutrino problem at better than the 98% CL even when solar model uncertainties are taken into account.     

Direct on-line hyphenation of capillary liquid chromatography to nuclear magnetic resonance spectroscopy: practical aspects and application to drug metabolite identification

In combining the high peak concentrations of capillary liquid chromatography (CapLC) with the high mass sensitivity of micro scale nuclear magnetic resonance (NMR) the hyphenation of CapLC to micro NMR offers a substantial gain in overall sensitivity. This paper deals with our experiences gained using a commercial CapLC-NMR system which has very recently become available. The limits of detection (SNR > 3) for a test compound of a molecular weight of M 318 were found to be approximately 100 ng (0.35 nmol) within an hour acquisition time and approximately 25 ng over night (85 pmol). Practical aspects such as the feasibility of stopped-flow experiments and sample handling issues are discussed in detail and first possible drug metabolite applications to hepatocyte incubations and direct analysis of plasma samples are presented.     

Modulation techniques and applications in comprehensive two-dimensional gas chromatography (GC x GC)

More than a decade after Phillips' first published work this article reviews recent developments in comprehensive two-dimensional gas chromatography (GC x GC). Special attention is devoted to the further development and diversity of modulation devices. These include heated sweepers, cryofocused modulators, and a variety of diaphragm valve-switching strategies. It is demonstrated that all modulation approaches can be very well suited to GC x GC, depending on the particular application. Diaphragm-valve modulation is very powerful for volatile organic compounds. Slotted heater and cryofocused modulation are preferred for samples that contain non-volatile components. Applications ranging from petroleum to environmental and biological samples are illustrated. Extension of the technique to GC x GC-mass spectrometry (MS) is also discussed and trends for future research activity are pointed out.     

Conversion of distiller's grain into fuel alcohol and a higher-value animal feed by dilute-acid pretreatment

Over the past three decades ethanol production in the United States has increased more than 10-fold, to approx 2.9 billion gal/yr (mid-2003), with ethanol production expected to reach 5 billion gal/yr by 2005. The simultaneous coproduction of 7 million t/yr of distiller's grain (DG) may potentially drive down the price of DG as a cattle feed supplement. The sale of residual DG for animal feed is an important part of corn dry-grind ethanol production economics; therefore, dry-grind ethanol producers are seeking ways to improve the quality of DG to increase market penetration and help stabilize prices. One possible improvement is to increase the protein content of DG by converting the residual starch and fiber into ethanol. We have developed methods for steam explosion, SO₂, and dilute-sulfuric acid pretreatment of DG for evaluation as a feedstock for ethanol production. The highest soluble sugar yields (∼77% of available carbohydrate) were obtained by pretreatment of DG at 140°C for 20 min with 3.27 wt% H₂SO₄. Fermentation protocols for pretreated DG were developed at the bench scale and scaled to a working volume of 809 L for production of hydrolyzed distiller's grain (HDG) for feeding trials. The pretreated DG was fermented with Saccharomyces cerevisiae D₅A, with ethanol yields of 73% of theoretical from available glucans. The HDG was air-dried and used for turkey-feeding trials. The inclusion of HDG into turkey poult (as a model non-ruminant animal) diets at 5 and 10% levels, replacing corn and soybean meal, showed weight gains in the birds similar to controls, whereas 15 and 20% inclusion levels showed slight decreases (−6%) in weight gain. At the conclusion of the trial, no negative effects on internal organs or morphology, and no mortality among the poults, was found. The high protein levels (58–61%) available in HDG show promising economics for incorporation of this process into corn dry-grind ethanol plants.