Computationally derived rules for persistence of C60 nanowires on recumbent pentacene bilayers

The tendency for C(60) nanowires to persist on two monolayers of recumbent pentacene is studied using molecular dynamics (MD) simulations. A review of existing experimental literature for the tilt angle adopted by pentacene on noble metal surfaces shows that studies cover a limited range from 55° to 90°, motivating simulation studies of essentially the entire range of tilt angles (10°-90°) to predict the optimum surface tilt angle for C(60) nanowire formation. The persistence of a 1D nanowire depends sensitively on this tilt angle, the amount of initial tensile strain, and the presence of surface step edges. At room temperature, C(60) nanowires oriented along the pentacene short axes persist for several nanoseconds and are more likely to occur if they reside between, or within, pentacene rows for ? ≤ ～60°. The likelihood of this persistence increases the smaller the tilt angle. Nanowires oriented along the long axes of pentacene molecules are unlikely to form. The limit of stability of nanowires was tested by raising the temperature to 400 K. Nanowires located between pentacene rows survived this temperature rise, but those located initially within pentacene rows are only stable in the range ?(1) = 30°-50°. Flatter pentacene surfaces, that is, tilt angles above about 60°, are subject to disorder caused by C(60) molecules "burrowing" into the pentacene surface. An initial strain of 5% applied to the C(60) nanowires significantly decreases the likelihood of nanowire persistence. In contrast, any appreciable surface roughness, even by half a monolayer in height of a third pentacene monolayer, strongly enhances the likelihood of nanowire formation due to the strong binding energy of C(60) molecules to step edges.     

Reaction of trimethylchlorosilane in spin-on Silicalite-1 zeolite film

We present a study on the hydrophobization of spin-on Silicalite-1 zeolite films through silylation with trimethylchlorosilane. Microporous and micro-mesoporous Silicalite-1 films were synthesized by spin coating of suspensions of Silicalite-1 nanozeolite crystallized for different times. Ellipsometric porosimetry with toluene and water adsorbates reveals that silylation decreases the porosity and makes the films hydrophobic. The decrease in porosity depends on the exposed surface area in the pores. Water contact angle measurements confirm the hydrophobicity. Fourier transform infrared spectroscopy reveals that the trimethylsilyl groups are chemisorbed selectively on isolated silanols and less on geminal and vicinal silanols due to steric limitations. Time-of-flight secondary-ion mass spectroscopy and in situ ellipsometry analysis of the reaction kinetics show that the silylation is a bulk process occurring in the absence of diffusion limitation. Electrical current leakage on films decreases upon silylation. Silylation with trimethylchlorosilane is shown to be an effective hydrophobization method for spin-on Silicalite-1 zeolite films.     

Capillary electrophoresis as a method for ozone determination in atmospheres

Capillary electrophoresis (CE) is used to quantify nitrate and nitrite extracted from nitrite-impregnated glass fiber filters (IGFF) that are used to monitor ozone in atmospheres. The amount of nitrate produced from conversion of nitrite in the filters is directly related to the amount of ozone passed over the filter. The limit of detection for ozone using the CE method is 1.17 ppml and the method is linear over two orders of magnitude. The effect of the excess nitrite in the IGFF on the limits of detection is discussed. Results from CE analyses of both active and passive filters are presented. The active filter results are compared to ion chromatographic analyses.     

Hydrophobic interaction chromatography of proteins. I. Comparison of selectivity

Currently, the selection of a hydrophobic interaction chromatography (HIC) sorbent for protein separation purposes is entirely based on empirical means. An attempt was made to characterize different HIC sorbents from various manufacturers. The selectivity was determined by isocratic pulse experiments of a set of reference proteins and an algorithm was developed to classify the sorbents according to their selectivity and hydrophobicity. The obtained semi-quantitative parameters take into account the dependence of salt on adsorption. The sorbent characteristics evaluated with the model proteins were compared to the separation of a real feedstock. A good agreement was achieved between the developed evaluation procedure and the separation behaviour of the real feed stock.     

Permselectivity Replication of Artificial Glomerular Basement Membranes in Nanoporous Collagen Multilayers

Basement membranes (BMs) play important roles in many biological functions such as tissue regeneration, cancer proliferation, nutrient/drug delivery, breathing, and many others. While there are many theoretical models, adequate experimental analogs of BMs describing basic physicochemical properties of BM, such as diffusion and permselectivity are not available. Taking BMs found in glomerulus of kidneys as an example, adequate reproduction of their permselectivity requires biomimetic membranes with submicron thickness, high uniformity, nanoscale porosity, and size-selective permeability. Artificial kidney BMs were assembled from poly(acrylic acid) and collagen using layer-by-layer (LBL) assembly technology and display multiple structural similarities with glomerular BMs. Diffusional transport through the artificial BMs faithfully replicate cut-off parameters of kidney membranes. Their utilization in understanding of unique diffusion processes in kidneys, in vitro studies of blood clearance time of small drugs/nanoscale drug carriers and design of more complex organoids including live cells for cancer proliferation studies is anticipated.     

DFT characterization of nanostructured germanium surfaces induced by cobalt atoms

By deposition in ultra‐high vacuum of cobalt on a Ge(111)–c(2 × 8) surface, Mocking et al. obtained a surface reconstruction. In the present paper, we analyse the related atomic structure, proposed by these authors, by means of density functional theory calculations. The surface presents ordered clusters that consist of six Ge atoms arranged in a triangle, lying above three Co atoms. The latter are located at substitutional positions within the top plane of the Ge(111) first bilayer. These clusters are similar to what is obtained on part of the Co‐induced Si(111) surface. For this surface, the clusters are terminated either by six Si atoms or by one, two or three adatoms above the six Si atoms. As the Co–Ge clusters systematically display six protrusions in the scanning tunnelling microscopy measurements by Mocking et al., we investigated why Ge adatoms are not present. Comparison of the Gibbs energy, interatomic distances, as well as charge density indicates that Ge adatoms on top of Co‐Ge clusters are less stable than Si adatoms in the Co‐Si system. Copyright © 2013 John Wiley & Sons, Ltd.     

Structural and Functional Analysis of Bacterial Sulfonosphingolipids and Rosette-Inducing Factor 2 (RIF-2) by Mass Spectrometry-Guided Isolation and Total Synthesis

We have analyzed the abundance of bacterial sulfonosphingolipids, including rosette-inducing factors (RIFs), in seven bacterial prey strains by using high-resolution tandem mass spectrometry (HRMS²) and molecular networking (MN) within the Global Natural Product Social Molecular Networking (GNPS) web platform. Six sulfonosphingolipids resembling RIFs were isolated and their structures were elucidated based on comparative MS and NMR studies. Here, we also report the first total synthesis of two RIF-2 diastereomers and one congener in 15 and eight synthetic steps, respectively. For the total synthesis of RIF-2 congeners, we employed a decarboxylative cross-coupling reaction to synthesize the necessary branched α-hydroxy fatty acids, and the Garner-aldehyde approach to generate the capnine base carrying three stereogenic centers. Bioactivity studies in the choanoflagellate Salpingoeca rosetta revealed that the rosette inducing activity of RIFs is inhibited dose dependently by the co-occurring sulfonosphingolipid sulfobacins D and F and that activity of RIFs is specific for isolates obtained from Algoriphagus.     

Base-specific Photocleavage of DNA Induced by Pazelliptine Sensitization: Study of the Mechanism by Time-resolved Absorption and Fluorescence

The intercalating antitumoral drug pazelliptine (PZE) is able to photosensitize the formation of single- and double-strand breaks in supercoiled plasmid DNA and selective photocleavage at guanine residues is observed. In order to understand the mechanisms of DNA cleavage mediated by the photoexcited drug, singlet and triplet excited-state processes in PZE complexed with poly(dA-dT)-poly(dA-dT), poly(dG-dC)-poly(dG-dC) and calf thymus DNA have been investigated by means of single photon counting fluorescence decay and transient absorption techniques. For each complex, three different binding sites have been identified, due to the existence of different geometric structures of the drug in the ground state. For one type of binding site, a proton transfer reaction occurs in the singlet excited state whatever the nucleic acid environment. In contrast, the relaxation dynamics for the other two sites are found to depend widely upon the type of polynucleotide in which the drug has been intercalated. From the results of this study, we suggest that the photodynamic action of PZE does not originate from excitation of the drug in the environment of G-C base pairs but is initiated from its triplet state that reacts by electron transfer with the adenine bases. The specificity of cleavage could be the result of subsequent reactions leading to guanine oxidation.     

Analysis of aflatoxin B1-lysine adduct in serum using isotope-dilution liquid chromatography/tandem mass spectrometry

A method for quantitative analysis of aflatoxin B1-lysine adduct (B1-Lys) in serum by liquid chromatography using tandem mass spectrometry (LC/MS/MS) is presented. The protein in a 250-microL sample was digested in the presence of a stable-isotope internal standard during a 4-h incubation at 37 degrees C with Pronasetrade mark. B1-Lys and the internal standard were extracted using mixed-mode solid-phase extraction cartridges and eluted with 2% formic acid in methanol. Following evaporation and reconstitution, extracts were injected onto a Luna C-18(2) column and eluted with a step gradient of acetonitrile and 0.06% formic acid. The B1-Lys and the internal standard were detected in a positive ionization selective reaction monitoring mode with a ThermoFinnigan TSQ Quantum triple quadrupole mass spectrometer. Calibration curves were linear for concentrations from 0.05-8.0 ng/mL. The method was validated with aflatoxin B1 dosed rat serum diluted to anticipated high and low concentrations. Total imprecision determined from 30 measurements over 15 days was 5.6% and 9.1%, respectively. Recoveries of 78.8 +/- 6.4% for B1-Lys and 85.4 +/- 12.4% for the internal standard were based on the full extraction and reconstitution processes. The method can be used to quantitate B1-Lys at the 0.5 pg/mg albumin level and is suitable for routine analysis.     

The GROMOS software for biomolecular simulation: GROMOS05

We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization. An overview of GROMOS05 is given, highlighting features not present in the last major release, GROMOS96. The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented.