Fast 3D shape screening of large chemical databases through alignment-recycling

Background  

Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes.     

Determination of lead in the urine of exposed and unexposed adults by extraction and flow-injection/atomic absorption spectrometry

Lead is extracted from urine with ammonium pyrrolidien dithiocrbamate into methyl isobutyl ketone, and 20 μl of the extract is injected into a water carrier stream in a flow-injection/atomic absorption system. The procedure is simple, quick, accurate and reproducible. Recoveries are 96–105%. The mean urine lead contents of 20 unexposed and 20 printing-press lead exposed workers was found to be 39.0 ± 8.3 and 71.7 ± 26.3 μg Pb l^?1, respectively.     

A minimal multiconfigurational technique

A direct minimization method previously presented by the authors is applied here to biconfigurational wave functions. A very moderate increasing in the time by iteration with respect to the one-determinant calculation and good convergence properties have been found. So qualitatively correct studies on singlet systems with strong biradical character can be performed with a cost similar to that required by Hartree-Fock calculations.     

Shaping Solid-State Supramolecular Cavities: Chemically Induced Accordionlike Movement of gamma-Zirconium Phosphate Containing Polyethylenoxide Pillars

The hydrophilic oxygen atoms of polyethylenoxide chains inserted as pillars in gamma-zirconium phosphate form hydrogen bonds with the acid groups of the host. As a result the pillars are almost perpendicular to the gamma layers. Upon changing the pH level of the supernatant solution the hydrogen bonds are broken and the pillars become almost perpendicular to the layers (shown schematically). Thus there is a reversible enlargement-shortening of the interlayer space.     

Synthesis of some dibenzodiazepinone derivatives as potent and m2-selective antimuscarinic compounds

Two series of 5-[[4-[4-(dialkylamino)butyl]-l-cyclohexyl]acetyl], and 5-[(dialkylamino)acyl]-10,11-dihydro-5H- dibenzo[b,e][1,4]diazepin-11-ones were synthesized as potential m2-selective ligands 1,2. Their affinity and selectivity for the muscarinic cholinergic receptor m-AChR subtypes were determined. Replacing a nitrogen with CH in the piperidine ring of 5-[[4-[4-(dialkylamino)butyl]-l-piperidinyl]acetyl]-10,11-dihydro-5H-dibenzo-[b,e][1,4]diazepin-11-ones 3 significantly altered the affinity and selectivity to the muscarinic receptor subtypes.     

TEQ-value determinations of animal feed; emphasis on the CALUX bioassay validation

Polyhalogenated aromatic hydrocarbons, such as polychlorinated dibenzo-p-dioxins are a large and diverse group of environmental pollutants. Their tendency to accumulate in the food chain and their toxicity make monitoring necessary. The reference analysis method is laborious and very expensive, therefore cheap and rapid bioassays have been developed. The chemical-activated luciferase bioassay (CALUX) bioassay uses a recombinant cell line, which responds to dioxins and dioxin-like molecules with Ah receptor (AhR)-dependent induction of firefly luciferase in a dose related response. The CALUX was tested for its use in the screening of feed. Aliquots of 20 g of enriched feed were extracted with a toluene:methanol mixture (20:4 v/v) and extracts were defatted on 33% H₂SO₄ silica columns and purified on carbon columns. Only the dioxin and furan fraction was analysed, the PCB fraction was discarded. The precision of the method is acceptable and in compliance with an R.S.D. <30% as suggested for cell-based bioassays in the Commission Directive 2002/70/EC of July 2002. The results evidence good agreement between TEQ-values obtained by either CALUX or GC–HRMS. The method is now routinely in use for a feed screening programme designed by the Federal Agency for the Safety of the Food chain. Approximately, 25 samples are analysed weekly. From the obtained results approximately 10% was confirmed by GC–HRMS. The false positive ratio is 1% and no false negatives were found, making the use of the CALUX technology advantageous.     

Ring-opening metathesis polymerization (ROMP) of isomerically pure functional monomers and acyclic diene metathesis depolymerization (retro-ADMET) of functionalized polyalkenamers

ROMP and retro-acyclic diene metathesis (ADMET) were used for the synthesis of new functional polymers and functional oligomers, respectively. Purely exo and enantiomerically pure norbornene and 7-oxanorbornene derivatives were prepared using stereospecific synthesis, effective fractionation and high yield condensation reactions. Successful ROMPs of those monomers were performed using either the new carbenic Schrock’s or Grubb’s catalysts or in some cases a classical bicomponent catalyst. New functional polymers such as optically active poly(norbornene-2-carboxylic acid), reactive poly(norbornene-2-azlactone), and side-chain liquid crystal polyoxanorbornenes were fully characterized. On the other hand, successful depolymerizations of 1,4-polyisoprene and of epoxidized 1,4-polybutadiene via cross-metathesis with 4-octene were performed using a stabilized bicomponent catalyst and the Grubb’s catalyst, respectively. Conditions for the controlled synthesis of epoxidized oligobutadienes and of epoxydienic monomers via retro-ADMET were clearly defined.     

Optimization of culture medium and conditions for penicillin acylase production by Streptomyces lavendulae ATCC 13664

The culture medium for Streptomyces lavendulae ATCC 13664 was optimized on a shake-flask scale by using a statistical factorial design for enhanced production of penicillin acylase. This extracellular enzyme recently has been reported to be a penicillin K acylase, presenting also high hydrolytic activity against penicillin V and other natural aliphatic penicillins such as penicillin K, penicillin F, and penicillin dihydroF. The factorial design indicated that the main factors that positively affect penicillin acylase production by S. lavendulae were the concentration of yeast extract and the presence of oligoelements in the fermentation medium, whereas the presence of olive oil in the medium had no effect on enzyme production. An initial concentration of 2.5% (w/v) yeast extract and 3 microg/mL of CuSO4 x 5H2O was found to be best for acylase production. In such optimized culture medium, fermentation of the microorganism yielded 289 IU/L of enzyme in 72 h when employing a volume medium/volume flask ratio of 0.4 and a 300-rpm shaking speed. The presence of copper, alone and in combination with other metals, stimulated biomass as well as penicillin acylase production. The time course of penicillin acylase production was also studied in the optimized medium and conditions. Enzyme production showed catabolite repression by different carbon sources such as glucose, lactose, citrate, glycerol, and glycine.     

Integrated production of ethanol fuel and protein from Coastal Bermudagrass

The herbaceous crops that may provide fermentable carbohydrates for production of fuels and chemicals also contain 10–20% protein. Protein coproduction with biomass-derived fuels and chemicals has important advantages: (1) food and fuel production can be integrated, and (2) protein is a high-value product that may significantly improve overall process economics. We report the results of an integrated approach to producing protein and fermentable sugars from one herbaceous species, Coastal Bermudagrass (CBG). The ammonia fiber explosion (AFEX) process makes possible over 90% conversion of cellulose and hemicellulose to simple sugars (about 650 mg reducing sugars/g dry CBG) at 5 IU cellulase/g vs < 20% conversion for untreated CBG. The AFEX treatment also improves protein extraction from CBG; over 80% protein recovery is possible from AFEX-treated CBG vs about 30% recovery from untreated CBG.     

Use of a55Fe radioisotope for the determination of titanium in laterite samples via energy dispersive X-ray fluorescence

A rapid method for the determination of titanium in geochemical samples using a⁵⁵Fe radioisotope as the extraction source coupled to a Si(Li) detector and a PDP-11.05 computer is described. The relative standard deviation for a thin sample about 100 mg in weight is less than 4% and it is achieved in a fluorescent time of 100 sec. Data are given for the use of two different internal standards, KBrO₃ and K₂Cr₂O₇, the latter being more precise. The values for five international reference standards are in agreement for this method with the reported values. Finally, besides being rapid, no hydrofluoric acid dissolution of fusion is necessary as in atomic absorption and classical methods. This paper was presented at the XX Colloquium Spectroscopium Internationale, 8 Aug.–7. Sept. 1977, Prague, Czechoslovakia.