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     

Synthesis of enantiopure omega-functionalized C15 alpha-amino carboxylates

An efficient route for the synthesis of enantiopure omega-hydroxy, omega-carboxy, omega-oxo, and omega-amino alpha-amino acids and bis-alpha-amino acids was developed. The synthesis of omega-trityloxy delta,epsilon-unsaturated alpha-amino acids was based on the Wittig reaction of methyl (2S)-2-[bis(tert-butoxycarbonyl)amino]-5-oxopentanoate with omega-trityloxy alkylidene triphenylphosphoranes. After hydrogenation, the omega-hydroxy alpha-amino acid was used as starting material for the synthesis of other omega-functionalized alpha-amino acids. The length of the side chain of alpha-amino acids or bis-alpha-amino acids depends on the starting alkanediol or dibromide used to prepare the phosphoranes.     

Ionic liquid crystals derived from the protonation of poly(propylene imine) dendrimers with a cholesterol-based carboxylic acid

The liquid crystalline character of salts resulting from the interaction of poly(propylene imine) dendrimers with 3-cholesteryloxycarbonylpropanoic acid has been studied. The supramolecular structure and consequently the observed liquid crystalline phases are dictated by the degree of protonation of primary amino groups as compared with that of tertiary ones, determined by FTIR spectroscopy in the bulk and by NMR spectroscopy in solution. Glass transition temperatures of the materials are about 38°C. At higher temperatures they are transformed to smectic C* phases while a second-order smectic C phase to smectic A phase transition is observed between 90 and 110°C depending on dendrimer generation. At about 150°C the onset of degradation is observed. The influence of the ionic dendrimeric scaffold on the thermotropic properties is discussed.     

Discarded Oranges and Brewer’s Spent Grains as Promoting Ingredients for Microbial Growth by Submerged and Solid State Fermentation of Agro-industrial Waste Mixtures

The exploitation of various agro-industrial wastes for microbial cell mass production of Kluyveromyces marxianus, kefir, and Saccharomyces cerevisiae is reported in the present investigation. Specifically, the promotional effect of whole orange pulp on cell growth in mixtures consisting of cheese whey, molasses, and potato pulp in submerged fermentation processes was examined. A 2- to 3-fold increase of cell mass was observed in the presence of orange pulp. Likewise, the promotional effect of brewer’s spent grains on cell growth in solid state fermentation of mixtures of whey, molasses, potato pulp, malt spent rootlets, and orange pulp was examined. The cell mass was increased by 3-fold for K. marxianus and 2-fold for S. cerevisiae in the presence of these substrates, proving their suitability for single-cell protein production without the need for extra nutrients. Cell growth kinetics were also studied by measurements of cell counts at various time intervals at different concentrations of added orange pulp. The protein content of the fermented substrates was increased substantially, indicating potential use of mixed agro-industrial wastes of negligible cost, as protein-enriched livestock feed, achieving at the same time creation of added value and waste minimization.     

Thermal Drying of <Emphasis Type="BoldItalic">Lactobacillus delbrueckii</Emphasis> subsp. <Emphasis Type="BoldItalic">bulgaricus</Emphasis> and its Efficient Use as Starter for Whey Fermentation and Unsalted Cheese Making

Lactobacillus bulgaricus grown on whey was dried by a simple thermal drying method at the range 35–55°C and its efficiency for lactic acid fermentation of whey was evaluated. Drying of cells in whey suspension in the examined temperature range did not affect significantly their viability (82–87% survival), indicating a protective effect of whey as both growth and drying medium. The kinetics of fermentation of whey and mixtures of whey/molasses using the dried culture were comparable to those of non-dried cells, and only low pH had a detrimental effect on the fermentation ability of the dried cells. Furthermore, dried L. bulgaricus, free or immobilized on casein coagulates, was used as starter for the production of unsalted hard-type cheese. The effects of the amount of starter culture and the immobilization technique, the evolution of microbial counts, and the sensory properties of the produced cheeses were evaluated during ripening at various temperatures.     

Finite volume schemes for dispersive wave propagation and runup

Finite volume schemes are commonly used to construct approximate solutions to conservation laws. In this study we extend the framework of the finite volume methods to dispersive water wave models, in particular to Boussinesq type systems. We focus mainly on the application of the method to bidirectional nonlinear, dispersive wave propagation in one space dimension. Special emphasis is given to important nonlinear phenomena such as solitary waves interactions, dispersive shock wave formation and the runup of breaking and non-breaking long waves.     

Dark solitons in mode-locked lasers

Dark soliton formation in mode-locked lasers is investigated by means of a power-energy saturation model that incorporates gain and filtering saturated with energy, and loss saturated with power. It is found that general initial conditions evolve (mode-lock) into dark solitons under appropriate requirements also met in experimental observations. The resulting pulses are essentially dark solitons of the unperturbed nonlinear Schr?dinger equation. Notably, the same framework also describes bright pulses in anomalous and normally dispersive lasers.     

New poly(p‐phenylene vinylene) derivatives with two oxadiazole rings per repeat unit: Synthesis,photophysical properties,electroluminescence, and metal ion recognition

Two new poly(p‐phenylene vinylene) derivatives OX1‐PPV and OX2‐PPV bearing two 1,3,4‐oxadiazole rings per repeat unit and a fully conjugated backbone with solubilizing dodecyloxy side groups were synthesized and investigated. The amorphous conjugated polymers had glass‐transition temperature values of 60–75 °C and emitted intense blue or greenish‐blue light in solution with photoluminescence (PL) emission maxima at 379–492 nm and PL quantum yields of 0.41–0.52. In the solid state they emitted yellowish‐green light with PL emission maxima at 533–555 nm. Cyclic voltammetry showed that both conjugated polymers had reversible reduction and irreversible oxidation, making them n‐type materials. The electron affinity of OX2‐PPV was estimated as 2.85 eV whereas that of OX1‐PPV was 2.75 eV. Yellow electroluminescence (EL) was achieved from single‐layer light‐emitting diodes of OX2‐PPV with an EL emission maximum at 555 nm and a brightness of 70 cd/m². Polymer OX2‐PPV, which was functionalized with 2,6‐bis(1,3,4‐oxadiazole‐2‐yl)pyridine, demonstrated sensitivity to various metal ions as a fluorescence‐mode chemosensor. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2112–2123, 2004