"Exact" surface free energies of iron surfaces using a modified embedded atom method potential and lambda integration

Previously a new universal lambda-integration path and associated methodology was developed for the calculation of "exact" surface and interfacial free energies of solids. Such a method is in principle applicable to any intermolecular potential function, including those based on ab initio methods, but in previous work the method was only tested using a relatively simple embedded atom method iron potential. In this present work we apply the new methodology to the more sophisticated and more accurate modified embedded atom method (MEAM) iron potential, where application of other free- energy methods would be extremely difficult due to the complex many-body nature of the potential. We demonstrate that the new technique simplifies the process of obtaining "exact" surface free energies by calculating the complete set of these properties for the low index surface faces of bcc and fcc solid iron structures. By combining these data with further calculations of liquid surface tensions we obtain the first complete set of exact surface free energies for the solid and liquid phases of a realistic MEAM model system. We compare these predictions to various experimental and theoretical results.     

Lipase-catalyzed solvent-free transesterification of wood sterols

Eighteen commercial lipase preparations, either immobilized or crude enzyme powders, were screened for the transesterification of wood sterols. The reactions were carried out in a solvent-free system, at the optimum temperature of the enzyme preparations as reported by the manufacturer and at the pressure of 2 mbar, with 5 or 10% in weight of the enzyme relative to the wood sterol content of the reacting mixture. Methyl esters of sunflower fatty acids were used as transesterifying agent. Of all the enzymes assayed, only Lipase TL from Pseudomonas stutzeri PL-836 (Meito Sangyo) exhibited any significant transesterifying capacity, 85 and 95% of conversion after 2 and 8 h of reaction, respectively, when 10% in weight of enzyme was used.     

Protein deformation of lipid hybrid bilayer membranes studied by sum frequency generation vibrational spectroscopy

Structural deformations of lipid hybrid bilayer membranes induced by signal peptideless (SPL) proteins have been studied for the first time using the inherently surface specific nonlinear optical technique of sum frequency generation vibrational spectroscopy. Specifically, deformations of 1,2-distearoylphosphatidylglycerol(DSPG) membranes induced by interaction with FGF-1, a SPL protein which is released asa function of cellular stress through a nonclassical pathway, have been investigated. FGF-1 was found to induce lipid alkyl chain deformations in previously highly ordered DSPG membranes at the extremely low concentration of 1 nM at 60 degrees C. The deformation process was shown to exhibit a degree of reversibility upon removal of the protein by rinsing with buffer solution.     

Representation of the molecular topology of cyclical structures by means of cycle graphs. 3. Hierarchical model of screening of chemical databases

The increase in the size and complexity of chemical databases necessitates the proposal and development of efficient methods of classification and recovery of information, which supposes proposal of a model of classification of database records and the use of a compatible model of screening for inspection of clusters and recovery of the molecules that satisfy the search criterion. The cycle graphs model based on consideration of all the cycles and chains (and equivalent cycles and chains) present in the molecular structure has been proven appropriate for classification of chemical databases, giving rise to a generation of different classification levels depending on the structural elements (cycles and chains) that are considered. In this paper we propose a screening model, compatible with the cycle graphs model, based on a hierarchy of levels of abstraction. The set of molecules that satisfies a screening model (or selection criterion) diminishes as we advance in the hierarchy of levels of the model, which allows filtering of records and, therefore, an increase in the efficiency of the screening process. In the following work of this series we describe and validate the screening tool developed.     

A mixed ladderane/n-alkyl glycerol diether membrane lipid in an anaerobic ammonium-oxidizing bacterium

A novel glycerol diether containing ladderane and tetradecyl moieties has been identified in an anaerobic ammonium-oxidizing bacterium by GC/MS and high-field NMR spectroscopy.     

Novel antibiotics: second generation macrocyclic peptides designed to trap Holliday junctions

Described are the syntheses of 15 macrocyclic peptides designed to trap Holliday junctions (HJs) in bacteria during site-specific and homologous recombination. This leads to inhibiting bacterial growth. These second generation macrocycles were based on the C-2 symmetrical HJ. They were synthesized using a strategy that permits elucidation of the amino acid role in binding HJs. The syntheses of these macrocycles are an important step in the development of a new class of antibiotics.     

PCR-based detection of gene transfer vectors: application to gene doping surveillance

Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR.     

Development of an HPLC-NMR method for the determination of PAHs in soil samples - a comparison with conventional methods

A hyphenated HPLC-(1)H NMR method for the identification and quantification of PAHs in soil samples has been developed and applied to a PAH reference sample provided by the Federal Institute for Materials Research and Testing (BAM, Berlin, Germany). The results were compared with those obtained by HPLC-DAD, HPLC-F, and GC-MS analyses of the same sample.     

Time evolution studies of the H2O/quartz interface using sum frequency generation, atomic force microscopy, and molecular dynamics

Many interfacial studies on solid surfaces, for example, quartz/water, assume that a standard cleaning procedure regenerates the surface reproducibly. In the reported work, the results of two surface specific techniques, sum frequency generation (SFG) spectroscopy and atomic force microscopy, show that the effects of prolonged exposure to Nanopure water and to pH 10 NaOH are distinctly different. In conjunction with the experimental data, molecular mechanics is used to correlate the SFG spectral frequencies to the hydrogen stretching vibrations of the surface-bound water molecules. It is found that after 17 days of soaking in water, water molecules penetrate into the SiO2 matrix to produce a swollen and amorphous layer; it is likely that broken Si-O bonds from the polishing process serve as nucleation sites for hydration and swelling. Disorder introduced in the interfacial water layer is detected by the rising intensity of the weakly hydrogen-bonded SFG peak at 3450 cm(-1). Dominance of the 3450 cm(-1) is absent in a pH 10, NaOH-soaked quartz disk, indicating that the strong hydrogen-bonded network in water remains intact.     

Brønsted Acid Assisted Regio‐ and Enantioselective Direct O‐Nitroso Aldol Reaction Catalysed by α,α‐Diphenylprolinol Trimethylsilyl Ether

In the presence of p‐nitrobenzoic acid, the O‐nitroso aldol reaction of nitrosobenzene with enolisable aldehydes may be promoted by commercially available α,α‐diphenylprolinol trimethylsilyl ether. The reaction proceeds with good yields and essentially complete enantioselectivity, with catalyst loadings in the 5–10 mol % range. The resulting α‐oxyaldehyde adducts may be transformed in situ into α‐oxyimines, which provide 1,2‐amino alcohols upon treatment with Grignard reagents, in good overall yield (45–59 %) and with typical diastereomeric ratios ≥95:5.