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.     

Enantioselective synthesis of 3(S)-hydroxy polygodial derivatives and evaluation of their vanilloid activity

The enantioselective synthesis of 3(S)-hydroxy polygodial and its acetyl derivative is described. The construction of the 3-hydroxy drimane skeleton was based on the titanium-catalyzed radical cyclization of (10S)-10, 11-epoxy-farnesyl acetate. Only underivatized 3(S)-hydroxy polygodial showed activity in assays on VR1 vanilloid receptor in HEK cells transfected with the human VR1.     

Separation of benzene from alkanes by solvent extraction with 1-ethylpyridinium ethylsulfate ionic liquid

The (liquid + liquid) equilibrium (LLE) data for ternary mixtures {alkane + benzene + 1-ethylpyridinium ethylsulfate ([EPy][EtSO₄])} at T = (283.15 and 298.15) K and atmospheric pressure are presented. The alkanes used were hexane and heptane. The cloud point method was used to determinate the binodal curve, and the tie-line compositions were obtained by density measurements. The LLE data obtained were used to calculate distribution coefficients and selectivity values. The consistency of tie-line data was ascertained by applying the Othmer-Tobias and Hand equations. Correlation of the experimental tie-lines was conducted through the use of NRTL equation, which provides good correlation of the experimental data.The results show that [EPy][EtSO₄] can be used as an alternative solvent in liquid extraction processes for the removal of benzene from its mixtures with alkanes.     

The use of multivariate modelling of near infra-red spectra to predict the butter fat content of spreads

In order to obtain a rapid method that can detect adulteration of butter fats with cheaper vegetable fats, the use of NIR spectroscopy and multivariate modelling was explored. For model building and validation, an extensive set of samples was collected, consisting of 152 butter samples, 42 oils and 200 blends thereof. Variations in butter fat composition are reflected in distinct NIR spectral regions. Principal components analysis and partial least square discriminant analysis was used to inspect the variation within the sample set. As reference values for training partial least squares models, butter fat levels as declared by suppliers were taken, as well as C4:0 fatty acid levels as measured directly by GC. All samples were used for training, except for 100 blends, which were used later for validation. Different pre-processing and PLS approaches were explored, resulting in models that had a RMSEPs for butter fat and C4:0 fatty acid level in the range of 4.3-8.2 and 0.33-0.38% (w/w), respectively. The performance of NIR in assessment of C4:0 fatty acid levels is lower as for GC, but this disadvantage is outweighed by shorter measurement times and the lower skill levels required. Furthermore NIR is able to assess overall levels of butter fat, in addition to the indirect indicator provided by the C4:0 fatty acid level.