Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

TOSAR – A Topological Method for the Representation of Synthetic and Analytical Relations of Concepts

In mechanized systems used for searching in literature stores there is a steadily growing necessity not only to be able to formulate concepts as a search condition but also the characteristic connections under which these concepts appear in the inquiry. In this way the precision of the mechanized literature search is considerably increased. TOSAR has been developed in order to improve computerized literature searching in this respect.     

Characterization and separation of Al13 species using gel-filtration chromatography

A polyaluminum chloride (PAC) sample was prepared using a slow alkaline titration method. The Bio-Gel P-100 gel column chromatographic technique was used to separate and characterize the various forms of aluminum present in the prepared PAC solution. The effluents from a gel column were monitored using online chemical method: Al-Ferron timed complexation spectrophotometry and by ²⁷Al nuclear magnetic resonance (NMR) spectroscopy. Effects of different experimental conditions such as eluent flow rate, ionic strength and pH on separation of Al₁₃ were investigated. Experimental results indicated that molecule size exclusion was not the only parameter affecting the column chromatographic separation efficiency of Al₁₃ but molecule charge as well. Reducing the eluent flow rate, increasing the ionic strength and suitable pH resulted in increase in the separation efficiency. Experimental results clearly indicated that by varying the experimental conditions, it is possible to produce pure Al₁₃ species using a gel column chromatographic technique.     

Bienzymatic analytical microreactors for glucose, lactate, ethanol, galactose and l-amino acid monitoring in cell culture media

A new alternative method for bioprocess monitoring based on bienzymatic analytical microreactors integrated in a flow injection analysis (FIA) system is described. Glucose-, alcohol-, lactate-, galactose- and l-amino acid oxidases (GO, AO, LacO, GalO and LAAO) and horseradish peroxidase (HRP) are immobilized on controlled pore glass (CPG) and used for the development of glucose, ethanol, lactate, galactose and amino acid sensors. The analytical methodology is based on HRP catalysed reaction of hydrogen peroxide produced by oxidases with phenol-4-sulfonic acid and 4-aminoantipyrine. The immobilized enzymes are characterized and used for preparation of the packed bed analytical microreactors. Shelf life and operational stability of the microeactors are determined. GO/HRP, AO/HRP and LAAO/HRP microreactors showed excellent shelf life, they could be stored and reused for more than 6 months with no or very little activity loss, while GalO/HRP and LacO/HRP could be stored for shorter periods of time (10-20 days). Operational stability of GO and LacO microreactors was very good: an equivalent to 16,900 FIA injections of 25 μl to a LacO microreactor resulted in loss of half of its activity, immobilized GO was so stable that it was impossible to evaluate enzyme halflife. Immobilized GalO and LAAO lose their operational activity much faster: approximately 1400 and 8000 FIA injections of the respective substrate solution in a FIA set-up resulted in 50% activity loss. The methods with all the described microreactors were successfully validated using off-line samples from S. cerevisiae, E. coli and mesenchymal stem cell cultures with HPLC as the reference method.     

A simple flow injection-reduced volume column system for hemoglobin typing

A flow injection (FI)-reduced volume column system was developed for hemoglobin (Hb) typing to be used as an initial screening method for thalassemia. The column was packed with 140 μl diethylaminoethyl (DEAE)-Sephadex A-50 ion exchange beads. Hb can be separated using Tris–HCl buffer solution with pH gradient 8.5–6.5 and then monitored spectrophotometrically at 415 nm. The hemolysate of 40 blood samples from packed red cells were screened for thalassemia by determining the amount of HbA₂ and HbE present. The proposed system was able to predict positive test results from those samples with β, E-trait and EE homozygous thalassemia, Hb types that were independently identified following the conventional method at the hospital laboratory. Advantages of the proposed system over the conventional column technique include low amount of reagents and blood sample needed, short analysis time and low cost. Each analysis required only 80 μl of 50 times diluted packed cells, which is equivalent to 1.6 μl undiluted packed cells, and it can be completed in only 35 min. This simple FI-reduced volume column system was demonstrated to be an economic alternative system for Hb typing to initially screen some types of thalassemia such as β-trait, E-trait and EE-homozygous which are commonly found in Thailand.     

Capillary gas chromatography of pesticide residues in foods: Application of a split/splitless inlet system

Residue mixtures of pesticides in foods which were difficult to separate by packed-column gas chromatography were determined by capillary gas chromatography and electron capture detection. Manual injections of sample and reference standard were made with a 10 μL syringe on a septum-enclosed, split/ splitless inlet system. Optimal peak height repeatability (± 3%( was achieved with three-μL injections which were made within time periods of four hours or less. The average linearity coefficient (slope( obtained for detector response as a function of solution concentration was 1.1.     

Rapid and high-resolution analysis of geometric polyprenol homologues by connected octadecylsilylated monolithic silica columns in high-performance liquid chromatography

A Chromolith Performance octadecylsilyl (ODS) monolithic silica column (Merck) was compared with a conventional microparticulate ODS-bonded silica column in the high-performance liquid chromatography separation of natural polyprenols. A system comprising two connected monolithic columns afforded an equivalent separation at half the analysis time of the conventional method. Furthermore, ten connected columns achieved a tremendously high-resolution separation, in which the complicated series of homologous polyprenols with geometric isomerism were fully separated.     

Separation and sensitive determination of arsenic species (As/As) using the yeast-immobilized column and hydride generation in ICP–AES

Inorganic arsenic was separated using the yeast-immobilized column. Saccharomyces cerevisiae was covalently bonded unto the controlled pore glass, which showed selective preconcentration of As⁵⁺ over As³⁺. The effluent was directly connected to hydride generation (HG) to increase sensitivity. The optimum pH condition for the retainment of arsenic at the column was 7. As⁵⁺ and As³⁺ were completely separated in a few minutes with the flow rate of 1.5 ml min⁻¹. Three molars of nitric acid was adequate both for the elution of As⁵⁺ and hydride generation. The accuracy of the technique was tested with NIST SRMs. Quantitative analysis of arsenic species for herbicide, pesticide, and cigarette were performed, and the results showed good agreements with the suggested values. Yeast-immobilized column-HG-ICP showed a promising future for the arsenic speciation study.     

大口径厚液膜毛细管柱的制备

制备出了内径从0.46～0.74mm、液膜厚度从0.9～5.6μm的SE-54大口径厚液膜玻璃毛细管柱,并对它们的性能进行了评价。对低沸点的C_1-C_4烃进行了初步分离。     

Advances in two-dimensional GC with glass capillary columns

A versatile two-dimensional gas chromatograph is described, consisting of 2 separate ovens, one intermediate trap, an auxiliary inlet, and the necessary hardware to effect off-line switching according to the principle of Deans. The unit has been designed for use with high resolution glass capillary columns. The performance of individual instrumental components was critically evaluated. Results showed that low dead volume glass to metal connections were required in the manifold and detector lines to minimize extra-column effects. The mass of the intermediate trap must be low to allow rapid heating. Operational parameters are discussed and examples of some applications are shown.