Heterocyclic rearrangements. N,N-diphenylhydrazones,oximes and O-methyloximes of 3-benzoyl-5-phenyl-1,2,4-oxadiazole

The behaviour of (E)- and (Z)-N,N-diphenylhydrazones and O-Methyloximes of 3-benzoyl-5-phenyl-1,2,4-oxadiazole has been studied. When refluxed in benzene, or in dioxane-water (1:1), the (Z)-N,N-diphenylhydrazone 8Z gave the indazole 11 or the substituted semicarbazide 12 , respectively. The O-methyloxime 14Z did not give any rearrangement. A criticism of the oximation reaction of 3-benzoyl-5-phenyl-1,2,4-oxadiazole is also reported.     

XAS investigation of tantalum and niobium in nanostructured TiO2 anatase

Sol-gel routes were used to prepare Ta 10 at% and Nb 5 at% and 10 at% doped titania nanosized powders. When fired between 410°C and 850°C the doped titania powders are in the anatase phase; further heating up to 1050°C is required to obtain the rutile phase. The presence of dopant atoms delays the rate of transformation as compared with pure titania powders. Doping also affects the rate of grain growth and increases the conductance response to gas. To better understand the role played by dopant atoms in inhibiting both phase transformation to rutile and grain growth, X-ray Absorption Spectroscopy measurements were performed at the L_III-L_I absorption edges of Ta and Nb K absorption edge. Analysis was restricted to the anatase phase because the transformation to rutile phase, obtained by firing at 1050°C, is accompanied by the formation of undesired Ta and Nb oxides (Ta₂O₅ and Nb₂TiO₇, respectively). Extended X-ray Absorption Fine Structure and X-ray Absorption Near-Edge Spectroscopy analysis results indicate that in nanostructured anatase both tantalum and niobium atoms substitute Ti cations with +5 valence state.     

Developpement de la methode thermique de mesure de la tension superficielle liquide-solide

A thermal method connects the solid-liquid surface tension/s of a substance to its triple point temperature depression. Here a practical process for application of this method is described. A previous determination of the thickness of the condensate layer which does not freeze near the wall of the porous material is no longer necessary. The process is applied to some organic substances and to a metal (indium).

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Zusammenfassung Eine thermische Methode ermöglicht die Oberflächenspannung/s einer Substanz mit der Erniedrigung der Tripelpunkttemperatur in Bezug zu bringen. Eine vorangehende Bestimmung der Dicke der Kondensatschicht, deren Aggregatzustand sich bei Kontakt mit dem porösen Material nicht ändert, ist überflüssig. Die Methode wird auf einige organische Verbindungen und ein Metall (Indium) angewandt.

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Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations

The intrinsically disordered protein alpha-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of alpha-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of alpha-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.     

Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases

The biological function of the aspartic protease from HIV-1 has recently been related to the conformational flexibility of its structural scaffold. Here, we use a multistep strategy to investigate whether the same mechanism affects the functionality in the pepsin-like fold. (i) We identify the set of conserved residues by using sequence-alignment techniques. These residues cluster in three distinct regions: near the cleavage-site cavity, in the four beta-sheets cross-linking the two lobes, and in a solvent-exposed region below the long beta-hairpin in the N-terminal lobe. (ii) We elucidate the role played by the conserved residues for the enzymatic functionality of one representative member of the fold family, the human beta-secretase, by means of classical molecular dynamics (MD). The conserved regions exhibit little overall mobility and yet are involved into the most important modes of structural fluctuations. These modes influence the substrate-catalytic aspartates distance through a relative rotation of the N- and C-terminal lobes. (iii) We investigate the effects of this modulation by estimating the reaction free energy at different representative substrate/enzyme conformations. The activation free energy is strongly affected by large-scale protein motions, similarly to what has been observed in the HIV-1 enzyme. (iv) We extend our findings to all other members of the two eukaryotic and retroviral fold families by recurring to a simple, topology-based, energy functional. This analysis reveals a sophisticated mechanism of enzymatic activity modulation common to all aspartic proteases. We suggest that aspartic proteases have been evolutionarily selected to possess similar functional motions despite the observed fold variations.     

Axial Imidazole Distortion Effects on the Catalytic and Binding Properties of Chelated Deuterohemin Complexes

The effect of strain in the axial coordination of imidazole to the heme has been studied in the chelate complexes deuterohemin-histidine (DH-His) and deuterohemin-alanylhistidine (DH-AlaHis). Molecular mechanics calculations indicate that three types of distortion of the axial ligand occur in DH-His, due to the relatively short length of the arm carrying the donor group: tilting off-axis, tipping, and inclination of the imidazole plane with respect to the axial Fe-N bond. The effects of tilting (Deltagamma approximately 10 degrees ) and inclination of the imidazole ring (Deltadelta approximately 17 degrees ) are dominant, while tipping is small and is probably of little importance here. By contrast, the axial imidazole coordination is normal in DH-AlaHis and other computed deuterohemin-dipeptide or -tripeptide complexes where histidine is the terminal residue, the only exception being DH-ProHis, where the rigidity of the proline ring reduces the flexibility of the chelating arm. The distortion in the axial iron-imidazole bond in DH-His has profound and negative influence on the binding and catalytic properties of this complex compared to DH-AlaHis. The former complex binds more weakly carbon monoxide, in its reduced form, and imidazole, in its oxidized form, than the latter. The catalytic efficiency in peroxidative oxidations is also reduced in DH-His with respect to DH-AlaHis. The activity of the latter complex is similar to that of microperoxidase-11, the peptide fragment incorporating the heme that results from hydrolytic cleavage of cytochrome c.     

Cation-crown ether complex formation in water. II. Alkali and alkaline earth cations and 12-crown-4, 15-crown-5, and 18-crown-6

The stability constants and the partial molal volume and isentropic partial molal compressibility changes of complex formation between cations and crown ethers in water at 25°C are presented. The cations involved are Na⁺, K⁺, Rb⁺, Cs⁺, Ca²⁺, and Ba²⁺, and the crown ethers are 12-crown-4, 15-crown-5, and 18-crown-6. Values of V of complex formation have been discussed in terms of two simple models, one based on the scaled particle theory, and the others on the Drude-Nernst continuum model. The results indicate that the charge of the potassium cation in 18-crown-6 is especially well screened from the water. On this basis hydration numbers of complexed cations have been calculated. This shows that the size of the cation compared to the crown ether hole is important for the contacts between complexed cations and water.     

Two new marine sediment standard reference materials (SRMs) for the determination of organic contaminants

Two new marine sediment standard reference materials (SRMs), SRM 1941b Organics in Marine Sediment and SRM 1944 New York/New Jersey Waterway Sediment, have been recently issued by the National Institute of Standards and Technology (NIST) for the determination of organic contaminants including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyl (PCB) congeners, and chlorinated pesticides. Both sediment SRMs were analyzed using multiple analytical methods including gas chromatography/mass spectrometry (GC/MS) on columns with different selectivity, reversed-phase liquid chromatography with fluorescence detection (for PAHs only), and GC with electron capture detection (for PCBs and pesticides only). SRM 1941b has certified concentrations for 24 PAHs, 29 PCB congeners, and 7 pesticides, and SRM 1944 has certified concentrations for 24 PAHs, 29 PCB congeners, and 4 pesticides. Reference concentrations are also provided for an additional 58 (SRM 1941b) and 39 (SRM 1944) PAHs, PCB congeners, and pesticides. SRM 1944, which was collected from multiple sites within New York/New Jersey coastal waterways, has contaminant concentrations that are generally a factor of 10–20 greater than SRM 1941b, which was collected in the Baltimore (Maryland) harbor. These two SRMs represent the most extensively characterized marine sediment certified reference materials available for the determination of organic contaminants.Electronic Supplementary Material Supplementary material is available in the online version of this article at . A link in the frame on the left on that page takes you directly to the supplementary material.     

Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations

Collagen-like peptides of the type (Pro-Pro-Gly)(10) fold into stable triple helices. An electron-withdrawing substituent at the H(gamma)(3) ring position of the second proline residue stabilizes these triple helices. The aim of this study was to reveal the structural and energetic origins of this effect. The approach was to obtain experimental NMR data on model systems and to use these results to validate computational chemical analyses of these systems. The most striking effects of an electron-withdrawing substituent are on the ring pucker of the substituted proline (Pro(i)) and on the trans/cis ratio of the Xaa(i-1)-Pro(i) peptide bond. NMR experiments demonstrated that N-acetylproline methyl ester (AcProOMe) exists in both the C(gamma)-endo and C(gamma)-exo conformations (with the endo conformation slightly preferred), N-acetyl-4(R)-fluoroproline methyl ester (Ac-4R-FlpOMe) exists almost exclusively in the C(gamma)-exo conformation, and N-acetyl-4(S)-fluoroproline methyl ester (Ac-4S-FlpOMe) exists almost exclusively in the C(gamma)-endo conformation. In dioxane, the K(trans/cis) values for AcProOMe, Ac-4R-FlpOMe, and Ac-4S-FlpOMe are 3.0, 4.0, and 1.2, respectively. Density functional theory (DFT) calculations with the (hybrid) B3LYP method were in good agreement with the experimental data. Computational analysis with the natural bond orbital (NBO) paradigm shows that the pucker preference of the substituted prolyl ring is due to the gauche effect. The backbone torsional angles, phi and psi, were shown to correlate with ring pucker, which in turn correlates with the known phi and psi angles in collagen-like peptides. The difference in K(trans/cis) between AcProOMe and Ac-4R-FlpOMe is due to an n-->pi interaction associated with the Bürg-Dunitz trajectory. The decrease in K(trans/cis) for Ac-4S-FlpOMe can be explained by destabilization of the trans isomer because of unfavorable electronic and steric interactions. Analysis of the results herein along with the structures of collagen-like peptides has led to a theory that links collagen stability to the interplay between the pyrrolidine ring pucker, phi and psi torsional angles, and peptide bond trans/cis ratio of substituted proline residues.     

Reaction of trans-[Pt(H)2(PCy3)2] with C60 reductive elimination of H2 and formation of [Pt(PCy3)2(η-C60)]

Reaction of trans-[Pt(H)₂(PCy₃)₂], 1, with [60]fullerene at room temperature affords [Pt(PCy₃)₂(η²-C₆₀)], 2, in nearly quantitative yield. The most probable reaction pattern is the insertion of a fullerene 6,6 junction onto a Pt-H bond yielding an η¹ alkyl derivative which, after hydrogen extrusion, gives 2. On the other hand, addition of 1 to different electron-deficient olefins, such as dimethyl maleate and fumarate, furnishes mixtures of both η¹ metal—alkyl and η² metal—olefin derivatives. If tetrachloroethylene is used as 2π component, trans-[PtCl(H)(PCy₃)₂] forms exclusively.