Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

CO Oxidation on Cu/MgO-SiO2 Sol-Gel Derived Catalysts

Sol-gel Cu//MgOSiO₂ catalysts were prepared gelling tetraethoxysilane (TEOS), magnesium ethoxide and copper acetylacetonate at pH 3 and pH 9. The catalysts shown specific surface areas ca. 500 m²/g and 140 m²/g for pH 9 and pH 3 preparations respectively. Si(OH) and Si(OH)₂ hydroxy groups were observed by MAS-RMN spectroscopy in both preparations. CO₂-TPD and NH₃-TPD desorption thermograms showed that acid and basic sites were formed on the catalysts surface. It has been found that the catalysts having the highest density of basic sites were the catalysts showing the highest activity for the CO oxidation. It is proposed that the catalytic activity depends of the relative Cu⁼¹/Cu⁼² stability given by the support acidity.     

A new technique for the identification of chloride ions by the formation of chromyl chloride

Summary A new technique is described for the identification of the chloride ion through the formation of chromyl chloride, based on the extraction of the latter with carbon tetrachloride. The identification limit is 2g of chloride. It is possible to carry out the test in the presence of many other anions, including fluoride, which cannot be present when the traditional distillation technique is employed.

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Zusammenfassung Vorgeschlagen wird eine neue Technik zum Chloridnachweis durch Bildung von Chromylchlorid. Dieser Nachweis beruht auf der Extraktion des Chromylchlorids mit Tetrachlorkohlenstoff. Die Nachweisgrenze liegt bei 2g Chlorid, wobei die Möglichkeit besteht, den Test auch in Gegenwart von Fluorid durchzuführen, das bei Anwendung der üblichen Destillationsmethoden nicht anwesend sein darf.

     

Benzylic cleavage and McLafferty rearrangement under electron ionization conditions in the fragmentation of 5,6-dialkyl-2, 4-diarylpyrimidines

Several 5,6-dialkyl-2,4-diarylpyrimidines were prepared and their electron ionization (EI) mass spectra reported. The benzylic cleavage takes place easily together with an important McLafferty rearrangement. The involvement of the nitrogen atom appears to be important in the fragmentation of 5-methyl-substituted pyrimidines. In contrast, the 6-methyl-substituted pyrimidines undergo benzylic cleavage without hydrogen transfer. Thus, the difference in the mass spectrometric behaviour allows the identification of these isomeric compounds which, in contrast, exhibit only small differences in their NMR spectra. Copyright 1999 John Wiley & Sons, Ltd.     

Certified reference material for the quality control of EDTA- and DTPA-extractable trace metal contents in calcareous soil (CRM 600)

Single extraction tests are commonly used to study the eco-toxicity and mobility of metals in soils, e.g. to assess the bioavailable metal fraction (and thus to estimate the related phyto-toxic and nutritional deficiency effects) and the environmentally accessible trace metals upon disposal of e.g. sediment on to a soil (e.g. contamination of ground waters). However, the lack of uniformity in the different procedures does not allow the results to be compared worldwide nor the procedures to be validated. This paper describes the interlaboratory testing of EDTA- and DTPA-extraction procedures for soil analysis, followed by the preparation of a calcareous soil reference material (CRM 600), the homogeneity and stability studies and the analytical work performed for the certification of the EDTA- and DTPA- extractable contents of some trace metals (following the standardized extraction procedures). Received: 21 May 1997 / Revised: 4 July 1997 / Accepted: 9 July 1997     

Determination of fluoride in complex liquid matrices by electrothermal atomic absorption spectrometry with in-furnace oxygen-assisted ashing

A new chemical method is reported for the determination of total fluoride in complex liquids and suspensions, such as fruit juices, urine, serum and blood. It is based on the formation of the A1F radical in a graphite furnace afterin situ oxygen-assisted ashing of the untreated sample. The absorbance of this radical is measured at 227.45 nm. The method is relatively easy to use and provides a low detection limit (14 ng/ml) and reasonable reproducibility (5–10%).     

Selective palladium-catalyzed cocyclotrimerization of arynes with dimethyl acetylenedicarboxylate: A versatile method for the synthesis of polycyclic aromatic hydrocarbons

Benzyne (1a) and the substituted derivatives 4,5-difluorobenzyne (1b) and 3-methoxybenzyne (2) undergo chemoselective palladium-catalyzed [2 + 2 + 2]-cocyclotrimerization with dimethyl acetylenedicarboxylate (DMAD) to afford the corresponding phenanthrenes and/or naphthalenes. The major products are phenanthrenes if Pd(PPh(3))(4) is used as the catalyst, naphthalenes if Pd(2)(dba)(3) is used. When the method is applied to polycyclic arynes 3-6, which are generated from the corresponding o-trimethylsilylaryl triflates, the same reactivity pattern is observed: the reaction can be selectively directed either toward the cocyclization of one molecule of aryne and two molecules of alkyne or to the reaction of two molecules of aryne with one molecule of alkyne, by appropriate choice of the palladium catalyst. The synthesis of polycyclic aromatic compounds 33-39 using this methodology is reported.     

Core/valence partition and relativistic effects in effective potentials for transition metals

Two different versions, relativistic and nonrelativistic, of the “shape-consistent” effective potential (EP ) formalism are analyzed in ab initio calculations for transition metals. The influence of alternative core/valence partitions on the reliability of the procedure is discussed. The accuracy of EP results for transition metals is shown to depend on adequate choices of the valence subspace and proper inclusion of relativistic effects.