Molecular dynamics of polystyrene model molecules: Solvent effects on intramolecular excimer formation in 2,4-diphenylpentanes

Intramolecular excimer formation in 2,4-diphenylpentanes has been examined in a homologous series of alkanes, in ethanol and in mixtures of ethanol, ethylene glycol and glycerol. The ratio of the emission intensities of dimer and monomer (I_D/I_M) is not affected in low viscosity solvents but, above 4 cP, viscosity effects are discernible and a relationship of the form I_D/I_M = Aη^?2 is obeyed. In methylene chloride, only the dl molecule exhibits a decrease of the efficiency of excimer sampling. The temperature dependence of I_D/I_M in isooctane and methylene chloride has been interpreted in terms of the activation energy of the excimer sampling.     

Peptidomic analysis of the larval Drosophila melanogaster central nervous system by two-dimensional capillary liquid chromatography quadrupole time-of-flight mass spectrometry

Peptides are the largest class of signalling molecules found in animals. Nevertheless, in most proteomic studies peptides are overlooked since they literally fall through the mazes of the net. In analogy with proteomics technology, where all proteins expressed in a cell or tissue are analyzed, the peptidomic approach aims at the simultaneous visualization and identification of the whole peptidome of a cell or tissue, i.e. all expressed peptides with their post-translational modifications. In this paper we describe the analysis of the larval fruit fly central nervous system using two-dimensional capillary liquid chromatography/quadrupole time-of-flight tandem mass spectrometry (LC/Q-TOF-MS/MS. Using the central nervous systems of only 50 larval Drosophila as starting material, we identified 38 peptides in a single analysis, 20 of which were not detected in a previous study that reported on the one-dimensional capillary LC/MS/MS analysis of the same tissue. Among the 38 sequenced peptides, some originate from precursors, such as the tachykinin and the IFamide precursor that were entirely missed in the first study. This clearly demonstrates that the two-dimensional capillary LC approach enhances the coverage of the peptidomic analysis.     

Unsteady-State Flow of Flexible Polymers in Porous Media

In this paper we report an investigation of the unsteady-state flow of polymer solutions through granular porous media. The experiments were performed using high-molecular-weight nonionic and anionic polyacrylamides dissolved in water containing NaCl and model porous media obtained by packing silicon carbide (SiC) grains having a narrow grain size distribution. Before injection in porous media, the polymer solutions were carefully filtered according to a method that was proved to be efficient in removing any possibly remaining microgels. The SiC grain surface was passively oxidized by a controlled thermal treatment in order to obtain a surface partially covered by a thin silica layer having adsorption properties similar to those of quartzitic sand. By packing SiC grains of different sizes, porous media having identical adsorption properties and well-known pore throats sizes can be obtained with a good reproducibility. Parameters investigated include pore size, velocity gradient, polymer concentration, and adsorption energy. A striking unsteady-state flow behavior (pressure build-up at constant flow rate) is observed when three conditions are fulfilled: (a) the velocity gradient is larger than that known to be able to induce a coil-stretch transition, (b) the polymer adsorbs on the pore surfaces, and (c) the length of stretched macromolecules is larger than the effective pore throat diameter. When one of these conditions is not satisfied the flow remains steady. These observations are interpreted by a mechanism involving the adsorption and bridging across pore restrictions of elongated chains. We propose to refer to this peculiar mode of polymer adsorption as bridging adsorption. Copyright 2001 Academic Press.     

Molecular dynamics assignment of NMR correlation times to specific motions in a "basket-handle porphyrin" heme

Iron (II) basket-handle porphyrins (BHP) are a series of encumbered heme models designed several years ago to mimic the ligand binding site of hemoproteins. Contrary to expectations, kinetic investigations have revealed that the k(on) rates for CO and/or O2 binding were only marginally affected by the assumed central steric hindrance of the iron atom. Thus, it was hypothesized that the internal dynamics of the molecule might be at the origin of the poor steric protection. To address this issue, measurements of nuclear magnetic resonance relaxation rates, fluorescence anisotropy experiments, and molecular dynamics simulations were undertaken. The size of BHP is small enough to allow the simulation in explicit chloroform with an almost complete sampling of the conformational space. The order parameters calculated from the MD trajectory compare well with the NMR experimental data and the predicted rotational correlation time corresponding to the Brownian motion of the molecule is in good agreement with the fluorescence measurements. Moreover, combining the results obtained using the three techniques allows the attribution of each internal NMR correlation time to a particular internal motion, revealing that even such medium-sized molecules are able to display quite complex internal dynamics. In particular, the handle phenyls that were assumed to sandwich the porphyrin have in fact a vanishing probability to be found in the proximity of the iron atom. They are therefore unable to reduce ligand accessibility significantly, which may explain the behavior of the k(on) rates.     

Selective catalytic hydrogenation of the trans,trans isomer from a mixture of 2,4-hexadienes.

trans, trans-2,4-hexadiene is quantitatively converted into cis-3-hexene by photoinduced hydrogenation catalyzed by chromium carbonyl complexes in presence of acetone which allows both acceleration and selectivity.     

Synthesis and characterisation of Hf(thd)2X2 derivatives [X = N(SiMe3)2, OSiMe3 and OSiBuMe2] as precursors for MOCVD of hafnium silicate films

Hafnium β-diketonatochlorides HfCl₂(thd)₂ (1), HfCl(thd)₃ (2) as well as β-diketonato-silylamide and/or siloxide derivatives of 1 namely Hf(thd)₂[N(SiMe₃)₂]₂ (3), Hf(thd)₂(OSiMe₃)₂ (4) and Hf(thd)₂(OSi^tBuMe₂)₂ (5) (thd = 2,2,6,6-tetramethyl-3,5-heptanedionate) were synthesized and characterized by elemental analysis, FT-IR, ¹H NMR and TGA. 2 and 5 were also characterized by single-crystal X-ray diffraction. The siloxide ligands are in cis position for 5 and exert a strong trans effect. The new volatile compounds were tested as single-source precursors for the deposition of HfSi_xO_y films by pulsed liquid injection MOCVD on Si(1 0 0) and R plane sapphire. The as-deposited at 600–800 °C films were essentially amorphous, Hf-rich (Hf/Hf + Si = 0.7–0.85) and smooth.     

Promotion of sugar-lectin recognition through the multiple sugar presentation offered by regioselectively addressable functionalized templates (RAFT): a QCM-D and SPR study

The investigation of recognition events between carbohydrates and proteins, especially the understanding of how spatial factors and binding avidity are correlated, remains a great interest for glycobiology. In this context we have investigated by nanogravimetry (QCM-D) and surface plasmon resonance (SPR), the kinetics and thermodynamics of the interaction between concanavalin A (Con A) and various neoglycopeptide ligands of low molecular weight. Regioselectively addressable functionalized templates (RAFT) have been used as scaffolds for the design of multivalent neoglycopeptides bearing thiol or biotin functions for their anchoring on transducer surfaces. Although these multivalent neoglycopeptide ligands cannot span multiple binding sites within the same Con A protein, they have increased activities relative to their monovalent counterpart. Our results emphasize that the multivalent RAFT ligands function by clustering several lectins, which leads to enhanced affinities.     

Recognition of cyclic, acyclic, exocyclic, and spiro acetals via structurally diagnostic ion/molecule reactions with the (CH3)2N-C(+)=O acylium ion

Reactions of the model acylium ion (CH3)2N-C(+)=O with acyclic, exocyclic, and spiro acetals of the general formula R(1)O-CR(3)R(4)-OR(2) were systematically evaluated via pentaquadrupole mass spectrometry. Characteristic intrinsic reactivities were observed for each of these classes of acetals. The two most common reactions observed were hydride and alkoxy anion [R(1)O(-) and R(2)O(-)] abstraction. Other specific reactions were also observed: (a) a secondary polar [4(+) + 2] cycloaddition for acetals bearing alpha,beta-unsaturated R(3) or R(4) substituents and (b) OH(-) abstraction for exocyclic and spiro acetals. These structurally diagnostic reactions, in conjunction with others observed previously for cyclic acetals, are shown to reveal the class of the acetal molecule and its ring type and substituents and to permit their recognition and distinction from other classes of isomeric molecules.