A new perspective on beta-sheet structures using vibrational Raman optical activity: from poly(L-lysine) to the prion protein

The vibrational Raman optical activity (ROA) spectrum of a polypeptide in a model beta-sheet conformation, that of poly(l-lysine), was measured for the first time, and the alpha-helix --> beta-sheet transition monitored as a function of temperature in H(2)O and D(2)O. Although no significant population of a disordered backbone state was detected at intermediate temperatures, some side chain bands not present in either the alpha-helix or beta-sheet state were observed. The observation of ROA bands in the extended amide III region assigned to beta-turns suggests that, under our experimental conditions, beta-sheet poly(L-lysine) contains up-and-down antiparallel beta-sheets based on the hairpin motif. The ROA spectrum of beta-sheet poly(L-lysine) was compared with ROA data on a number of native proteins containing different types of beta-sheet. Amide I and amide II ROA band patterns observed in beta-sheet poly(L-lysine) are different from those observed in typical beta-sheet proteins and may be characteristic of an extended flat multistranded beta-sheet, which is unlike the more irregular and twisted beta-sheet found in most proteins. However, a reduced isoform of the truncated ovine prion protein PrP(94-233) that is rich in beta-sheet shows amide I and amide II ROA bands similar to those of beta-sheet poly(L-lysine), which suggests that the C-terminal domain of the prion protein is able to support unusually flat beta-sheets. A principal component analysis (PCA) that identifies protein structural types from ROA band patterns provides a useful representation of the structural relationships among the polypeptide and protein states considered in the study.     

The Pesticide 3-(3,4-Dichlorophenyl)-1,1-dimethylurea (Diuron) Immobilized on Silica Gel Surface

A route for 3-(3,4-dichlorophenyl)-1,1-dimethylurea (diuron) immobilization on silica gel was established after reacting at the first stage the precursor silylant agent 3-trimethoxysilylpropylamine to the support. The pesticide was covalently bonded to available amine groups of the precursor, giving 1.03 mmol of amine per gram of silica. Infrared, (13)C, and (29)Si NMR spectra are in agreement with the proposed reaction between nitrogen of the amine group of the previously anchored silica to carbon on the para-position of the aromatic ring of the pesticide. The immobilization is clearly affected by the presence or absence of disprotonating agent, to give 12.50 and 68.40% reaction yield, respectively; these results were confirmed through elemental analysis. Copyright 2001 Academic Press.     

Molecular dynamics in the smectic a and C phases in a long-chain ferroelectric liquid crystal: 2H NMR, dielectric properties, and a theoretical treatment

In this work, the rotational-diffusion coefficients D(parallel) and D(perpendicular) for the ferroelectric smectogen (+)-(S)-4-[4'-(1-methylheptyloxy)] biphenyl 4-(10-undecenyloxy)benzoate have been studied by means of 2H NMR spectroscopy in the smectic C phase, using a new theoretical approach (Domenici,V.; Geppi, M.; Veracini, C. A. Chem. Phys. Lett. 2003, 382, 518). The analysis of spin-lattice relaxation times has been performed in terms of the diffusional constant and the activation energy of the internal and overall molecular-reorientational motions, and the results are compared to the smectic A (SmA) phase. Moreover, from the 2H NMR data in the SmA phase, the dielectric permittivity and the dielectric relaxation time functions are investigated using a theoretical approach. The longitudinal and transverse components of the real Rchigammaomega and imaginary chigammaomega (gamma = parallel, perpendicular) parts of the complex susceptibility tensor and the nematic-like rotational-viscosity coefficients, lambda2 and lambda5, are calculated.     

The role of rotation in the vibrational relaxation of water by hydrogen molecules

Vibrational relaxation cross sections of the H(2)O(upsilon(2) = 1) bending mode by H(2) molecules are calculated on a recent high-accuracy ab initio potential-energy surface using quasiclassical trajectory calculations. The role of molecular rotation is investigated at a collisional energy of 3500 cm(-1) and it is shown that initial rotational excitation significantly enhances the total (rotationally summed) vibrational relaxation cross sections. A strong and complex dependence on the orientation of the water angular momentum is also observed, suggesting the key role played by the asymmetry of water. Despite the intrinsic limitations of classical mechanics, these exploratory results suggest that quantum approximations based on a complete decoupling of rotation and vibration, such as the widely used vibrational close-coupling (rotational) infinite-order-sudden method, would significantly underestimate rovibrationally inelastic cross sections. We also present some rationale for the absence of dynamical chaos in the scattering process.     

Solid State NMR and TG/MS Study on the Transformation of Methyl Groups During Pyrolysis of Preceramic Precursors to SiOC Glasses

The sol-gel method was used to prepare two different starting gels containing SiCH₃-groups for the preparation of SiOC ceramics. To understand the role of Si—H bonds in the incorporation of carbon into the SiOC network, gels prepared from a 1:2 mixture of triethoxysilane and methyldiethoxysilane (T^HD^H2) and solely methyltriethoxysilane (T^Me) were investigated. Thermogravimetric analysis coupled with mass spectroscopy (TG-MS) in inert atmosphere was performed to attain an insight into the decomposition reactions involved during gel-glass transformation. Samples calcined at different temperatures up to 1000°C were characterized by ²⁹Si and ¹³C magic angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy. The presence of SiH groups in the starting gel allows an efficient conversion of Si—CH₃ groups into CSi₄ sites at lower temperatures. As a result, despite a much lower amount of carbon in the starting T^HD^H2 gel (C/Si = 0.33) compared to the T^Me gel (C/Si = 1), the amount of carbon inserted into the SiOC network of both glasses is equivalent, but the T^Me sample contains the 10 fold amount of free carbon.     

Octasubstituted metal-free phthalocyanine as core of phosphorus dendrimers: a probe for the properties of the internal structure

The synthesis of a new family of phosphorus dendrimers built from an octasubstituted metal-free phthalocyanine core is described up to generation 5. This core is used as a sensor and a probe for analyzing the properties of the internal structure and the influence of each structural part (core, branches, surface) upon the whole structure. UV-visible spectra show both a hyperchromic and bathochromic effect on the Q-bands with increasing generation, indicating that the chromophore is more isolated, and that the dendritic shell mimics a highly polar solvent. There is no evidence for aggregation, except for generation 0, showing again the isolation of the core. However, the dendritic shell is permeable to aqueous acids and bases, as demonstrated by the reversible splitting of the Q-band in an acidic medium (neutral form of the phthalocyanine) and the single Q-band in a basic medium (dianionic form), even for generation 4. The fluorescence quantum yield for the neutral form increases with increasing generation. The dianionic form of generation 0 is poorly fluorescent, whereas generations 3 and 4 (G3 and G4) exhibit better fluorescence. The cores of G3 and G4 are highly sensitive optical sensors for H3O+ and OH-. These experiments are carried out in THF/water mixtures, and the influence of water on the structure has been checked. The hydrodynamic radius of generation 4 is measured by NMR diffusion (pulse gradient spin-echo) experiments. R(H) varies from 35.4 A at 4 mol % of water to 32.5 A at 64 mol % of water in THF, indicating the hydrophobic nature of these dendrimers.     

Multi‐stage high order semi‐Lagrangian schemes for incompressible flows in Cartesian geometries

Efficient transport algorithms are essential to the numerical resolution of incompressible fluid‐flow problems. Semi‐Lagrangian methods are widely used in grid based methods to achieve this aim. The accuracy of the interpolation strategy then determines the properties of the scheme. We introduce a simple multi‐stage procedure, which can easily be used to increase the order of accuracy of a code based on multilinear interpolations. This approach is an extension of a corrective algorithm introduced by Dupont & Liu (2003, 2007). This multi‐stage procedure can be easily implemented in existing parallel codes using a domain decomposition strategy, as the communication pattern is identical to that of the multilinear scheme. We show how a combination of a forward and backward error correction can provide a third‐order accurate scheme, thus significantly reducing diffusive effects while retaining a non‐dispersive leading error term. Copyright © 2016 John Wiley & Sons, Ltd.     

A Monte Carlo error estimator for the expansion of rigid-rotor potential energy surfaces

The computation of rotational energy transfer in nonreactive molecular collisions requires expanding the orientation dependence of the interaction potential over an appropriate complete set of orthonormal functions. We show that the use of random grids for the sampling of the angular geometries combined with the Monte Carlo theorem allows to estimate the mean accuracy on each expansion term determined by a least squares fit. The interest of our approach is illustrated by an application to the H₂O–H₂ system, of great astrophysical interest.