Competitive Gold‐Promoted Meyer–Schuster and oxy‐Cope Rearrangements of 3‐Acyloxy‐1,5‐enynes: Selective Catalysis for the Synthesis of (+)‐(S)‐γ‐Ionone and (−)‐(2S,6 R)‐cis‐γ‐Irone

We report a simple, highly stereoselective synthesis of (+)‐(S)‐γ‐ionone and (‐)‐(2S,6R)‐cis‐γ‐irone, two characteristic and precious odorants; the latter compound is a constituent of the essential oil obtained from iris rhizomes. Of general interest in this approach are the photoisomerization of an endo trisubstituted cyclohexene double bond to an exo vinyl group and the installation of the enone side chain through a [(NHC)Au^I]‐catalyzed Meyer–Schuster‐like rearrangement. This required a careful investigation of the mechanism of the gold‐catalyzed reaction and a judicious selection of reaction conditions. In fact, it was found that the Meyer–Schuster reaction may compete with the oxy‐Cope rearrangement. Gold‐based catalytic systems can promote either reaction selectively. In the present system, the mononuclear gold complex [Au(IPr)Cl], in combination with the silver salt AgSbF₆ in 100:1 butan‐2‐one/H₂O, proved to efficiently promote the Meyer–Schuster rearrangement of propargylic benzoates, whereas the digold catalyst [{Au(IPr)}₂(μ‐OH)][BF₄] in anhydrous dichloromethane selectively promoted the oxy‐Cope rearrangement of propargylic alcohols.     

Tenth Peregrine breather solution to the NLS equation

In this paper we construct a particularly important solution to the focusing NLS equation, namely a Peregrine breather of the rank 10 which we call, P₁₀$P_{10}$ breather. The related explicit formula is given by the ratio of two polynomials of degree 110 with integer coefficients times trivial exponential factor. This formula drastically simplifies for the “initial values” namely for t=0$t=0$ or x=0$x=0$. This formula confirms a general conjecture saying that between all quasi-rational solutions of the rank N$N$ fixed by the condition that its absolute value tends to 1 at infinity and its highest maximum is located at the point (x=0,t=0)$(x=0,t=0)$, the P_N$P_N$ breather is distinguished by the fact that P_N(0,0)=2N+1$P_N(0,0)=2N+1$ and, in the aforementioned class of quasi-rational solutions, it is an absolute maximum. At the end we also make a few remarks concerning the rational deformations of P₁₀$P_{10}$ breather involving 2N−2$2N-2$ free real parameters chosen in a way that P_N$P_N$ breather itself corresponds to the zero values of these parameters although we have no intention to discuss the properties of these deformations here.     

Pairwise decomposition of an MMGBSA energy function for computational protein design

Computational protein design (CPD) aims at predicting new proteins or modifying existing ones. The computational challenge is huge as it requires exploring an enormous sequence and conformation space. The difficulty can be reduced by considering a fixed backbone and a discrete set of sidechain conformations. Another common strategy consists in precalculating a pairwise energy matrix, from which the energy of any sequence/conformation can be quickly obtained. In this work, we examine the pairwise decomposition of protein MMGBSA energy functions from a general theoretical perspective, and an implementation proposed earlier for CPD. It includes a Generalized Born term, whose many‐body character is overcome using an effective dielectric environment, and a Surface Area term, for which we present an improved pairwise decomposition. A detailed evaluation of the error introduced by the decomposition on the different energy components is performed. We show that the error remains reasonable, compared to other uncertainties. © 2014 Wiley Periodicals, Inc.     

Evaluation of DNA Force Fields in Implicit Solvation

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models.     

An improved error bound for a finite element approximation of a model for phase separation of a multi-component alloy

Using the approach of Rulla (1996 SIAM J. Numer. Anal. 33, 68-87)for analysing the time discretization error and assuming moreregularity on the initial data, we improve on the error boundderived by Barrett and Blowey (1996 IMA J. Numer. Anal. 16,257-287) for a fully practical piecewise linear finite elementapproximation with a backward Euler time discretization of amodel for phase separation of a multi-component alloy.     

TPD and ITPD study of materials used as chemoresistive gas sensors

Temperature-programmed desorption (TPD) and a differential form of it, called intermittent temperature-programmed desorption (ITPD), turned out to be powerful characterising techniques for chemoresistive materials applied to gas sensing. We investigated samples of SnO₂, TiO₂ and solid solutions of them (Ti_xSn_1 ? xO₂). TPD and ITPD experiments were carried out in vacuum, with samples previously treated in pure O₂ (100 Torr, 500 °C, 30 min). Amounts of desorbed O₂ corresponded for all Ti-containing samples to less than 10% of a compact monolayer of ions O^2?. Corresponding values of the apparent activation energy of desorption (E_app) were calculated directly from the Arrhenius plots for each partial TPD and ranged from about 100 to 330 kJ mol^? 1 (1.16 to 3.82 eV).     

Identification of phosphorylation sites of equine β‐casein isoforms

Equine β‐casein is phosphorylated at variable degrees and isoforms carrying 3 to 7 phosphate groups (3P–7P) have been found in milk, but the phosphorylated amino acid residues of each isoform are not yet identified. In the present work, the different phosphorylation variants were first isolated by ion‐exchange chromatography and then hydrolysed by trypsin to generate caseinophosphopeptides (CPPs), each containing all the potential phosphorylation sites. The equine CPPs were prepared by metal oxide affinity chromatography, a method based on the affinity of phosphate groups towards titanium dioxide immobilized onto a micro‐column. This method turned out to be an efficient tool to separate the CPPs Arg¹–Lys³⁴ and Glu⁴–Lys³⁴ from non‐phosphorylated peptides. Purification was achieved by reversed‐phase high‐performance liquid chromatography (RP‐HPLC) and each CPP was hydrolyzed by endoproteinase Glu‐C. Finally, the digests were analyzed by RP‐HPLC/electrospray ionization mass spectrometry (RP‐HPLC/ESI‐MS) and identified by nano‐electrospray ionization tandem mass spectrometry (nESI‐MS/MS) to locate the phosphorylated sites of the β‐casein isoforms 4P–7P with accuracy. Thus, the isoform 4P was found to be phosphorylated on residues Ser⁹, Ser²³, Ser²⁴, and Ser²⁵. Addition of phosphate groups on Ser¹⁸, Thr¹², and Ser¹⁰ led to the formation of the isoforms 5P–7P, respectively. The results indicated that the in vivo phosphorylation of the equine β‐casein follows a sequential way and is not randomly performed. Copyright © 2010 John Wiley & Sons, Ltd.     

The Fifth Order Peregrine Breather and Its Eight-Parameter Deformations Solutions of the NLS Equation

We construct here explicitly new deformations of the Peregrine breather of order 5 with 8 real parameters. This gives new families of quasi-rational solutions of the NLS equation and thus one can describe in a more precise way the phenomena of appearance of multi rogue waves. With this method, we construct new patterns of different types of rogue waves. We get at the same time, the triangular configurations as well as rings isolated. Moreover, one sees appearing for certain values of the parameters, new configurations of concentric rings.     

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