Determination of synthetic polypeptide conformations and molecular geometrical parameters by nonaqueous CE

The aim of this work was to study changes in homopolypeptide chain conformation as a function of the number of residues by the modeling of the electrophoretic mobility. For this purpose, the frictional coefficients of poly(N(epsilon)-trifluoroacetyl-L-lysine) with different number of residues (up to 11) were determined from the absolute ionic mobilities and modeled by the hydrodynamic frictional coefficient of an equivalent cylinder. This approach allowed determination of geometrical parameters of the polypeptide chain in a liquid phase (nonaqueous solution of the BGE). The fact that the BGE and analyte are dissolved in mixed (methanol-ACN) organic solvent implied to take into account different effects and corrections that are generally not considered in aqueous solvent: namely, the effect of ion-pairs between constituents of the BGE for the calculation of the ionic strength, the effect of ion-pairs between the solutes and the electrolyte counterions and the correction due to the dielectric friction (Hubbard-Onsager equations). In addition, the influence of the ionic strength on the electrophoretic mobility was corrected using the Pitts equation, and the effect of lateral charges due to a slight deprotonation of the -NH- group in the lateral chain was also considered. From this modeling, molecular geometrical parameters relative to the linear and helico?dal conformations were obtained with very good correlation coefficients. Interestingly, this work also points out that the use of ionic mobility modeling for extracting molecular geometrical parameters can also be applied to end-charged polypeptides with slightly charged lateral chains (3% of elementary charge per residue).     

N-heterocyclic carbene and phosphine ruthenium indenylidene precatalysts: a comparative study in olefin metathesis

Kinetic studies on ring-closing metathesis of unhindered and hindered substrates using phosphine and N-heterocyclic carbene (NHC)-containing ruthenium-indenylidene complexes (first and second generation precatalysts, respectively) have been carried out. These studies reveal an appealing difference, between the phosphine and NHC-containing catalysts, associated with a distinctive rate-determining step in the reaction mechanism. These catalysts have been compared with the benzylidene generation catalysts and their respective representative substrates. Finally, the reaction scope of the two most interesting precatalysts, complexes that contain tricyclohexylphosphine and 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene (SIMes), has been investigated for the ring-closing and enyne metathesis for a large range of olefins. Owing to their high thermal stability, the SIMes-based indenylidene complexes were more efficient than their benzylidene analogues in the ring-closing metathesis of tetrasubstituted dienes. Importantly, none of the indenylidene precatalysts were found to be the most efficient for all of the substrates, indeed, a complementary complex-to-substrate activity relationship was observed.     

2,2'-Biphosphinines and 2,2'-bipyridines in homoleptic dianionic Group 4 complexes and neutral 2,2'-biphosphinine Group 6 d(6) metal complexes: octahedral versus trigonal-prismatic geometries

The geometric and electronic structure of formally d(6) tris-biphosphinine [M(bp)(3)](q) and tris-bipyridine [M(bpy)(3)](q) complexes were studied by means of DFT calculations with the B3LYP functional. In agreement with the available experimental data, Group 4 dianionic [M(bp)(3)](2-) complexes (1P-3P for M=Ti, Zr, and Hf, respectively) adopt a trigonal-prismatic (TP) structure, whereas the geometry of their nitrogen analogues [M(bpy)(3)](2-) (1N-3N) is nearly octahedral (OC), although a secondary minimum was found for the TP structures (1N'-3N'). The electronic factors at work in these systems are discussed by means of an MO analysis of the minima, MO correlation diagrams, and thermodynamic cycles connecting the octahedral and trigonal-prismatic limits. In all these complexes, pronounced electron transfer from the metal center to the lowest lying pi* ligand orbitals makes the d(6) electron count purely formal. However, it is shown that the bp and bpy ligands accommodate the release of electron density from the metal in different ways because of a change in the localization of the HOMO, which is a mainly metal-centered orbital in bp complexes and a pure pi* ligand orbital in bpy complexes. The energetic evolution of the HOMO allows a simple rationalization of the progressive change from the TP to the OC structure on successive oxidation of the [Zr(bp)(3)](2-) complex, a trend in agreement with the experimental structure of the monoanionic complex. The geometry of Group 6 neutral complexes [M(bp)(3)] (4P and 5P for M=Mo and W, respectively) is found to be intermediate between the TP and OC limits, as previously shown experimentally for the tungsten complex. The electron transfer from the metal center to the lowest lying pi* ligand orbitals is found to be significantly smaller than for the Group 4 dianionic analogues. The geometrical change between [Zr(bp)(3)](2-) and [W(bp)(3)] is analyzed by means of a thermodynamic cycle and it is shown that a larger ligand-ligand repulsion plays an important role in favoring the distortion of the tungsten complex away from the TP structure.     

Dehydrogenation of aromatic molecules under a scanning tunneling microscope: pathways and inelastic spectroscopy simulations

We have performed a theoretical study on the dehydrogenation of benzene and pyridine molecules on Cu(100) induced by a scanning tunneling microscope (STM). Density functional theory calculations have been used to characterize benzene, pyridine, and different dehydrogenation products. The adiabatic pathways for single and double dehydrogenation have been evaluated with the nudge elastic band method. After identification of the transition states, the analysis of the electronic structure along the reaction pathway yields interesting information on the electronic process that leads to H-scission. The adiabatic barriers show that the formation of double dehydrogenated fragments is difficult and probably beyond reach under the actual experimental conditions. However, nonadiabatic processes cannot be ruled out. Hence, in order to identify the final dehydrogenation products, the inelastic spectra are simulated and compared with the experimental ones. We can then assign phenyl (C6H5) and alpha-pyridil (alpha-C5H4N) as the STM-induced dehydrogenation products of benzene and pyridine, respectively. Our simulations permit us to understand why phenyl, pyridine, and alpha-pyridil present tunneling-active C-H stretch modes in opposition to benzene.     

Double plasma mirror for ultrahigh temporal contrast ultraintense laser pulses

We present and characterize a very efficient optical device that employs the plasma mirror technique to increase the contrast of high-power laser systems. Contrast improvements higher than 10(4) with 50% transmission are shown to be routinely achieved on a typical 10 TW laser system when the pulse is reflected on two consecutive plasma mirrors. Used at the end of the laser system, this double plasma mirror preserves the spatial profile of the initial beam, is unaffected by shot-to-shot fluctuations, and is suitable for most high peak power laser systems. We use the generation of high-order harmonics as an effective test for the contrast improvement produced by the double plasma mirrors.     

Trace-level determination of pyrethroid,neonicotinoid and carboxamide pesticides in beeswax using dispersive solid-phase extraction followed by ultra-high-performance liquid chromatography-tandem mass spectrometry

The aim of the work was to develop an analytical procedure able to quantify traces of 13 neonicotinoids and pyrethroids as well as carboxamide in beeswax at low levels (ng g^?1) to evaluate the contamination. For this purpose, an efficient sample preparation procedure was developed based on solid–liquid extraction using dispersive diatomaceous earth and acetonitrile. This step was followed by a selective and sensitive analysis based on ultra-high-performance liquid chromatography coupled to tandem mass spectrometry (ESI-MS/MS). This analytical procedure was validated based on International Conference on Harmonization guidelines. The limits of quantification ranged from 1 ng g^?1 (thiamethoxam, clothianidin, imidacloprid, acetamiprid, thiacloprid and boscalid) to 40 ng g^?1 (lambda-cyhalothrin). The method was then successfully applied to 60 samples of beeswax collected in several areas of France. The presence of thiacloprid, boscalid, imidacloprid and deltamethrin in beeswax was confirmed. The most frequently quantified pesticide was boscalid.     

Differential MRI diagnosis between brain abscesses and necrotic or cystic brain tumors using the apparent diffusion coefficient and normalized diffusion-weighted images

Magnetic Resonance Diffusion-Weighted Imaging (DWI) has been reported to be helpful for the differential diagnosis between abscesses and cystic/necrotic brain tumors. However the number of patients is still limited, and the sensitivity and specificity of the method remain to be confirmed. The primary purpose of this study was to investigate a larger sample of patients, all investigated under the same experimental conditions, in order to obtain statistically significant data. Moreover, there is no consensus about the appropriate values of b required to use to make an accurate diagnosis from DWI. The secondary purpose of this study was to determine the discriminating threshold b values for raw diffusion-weighted images and for normalized diffusion-weighted images. On the basis of 14 abscesses, 10 high-grade gliomas and 2 metastases, we show that the calculation of accurate Apparent Diffusion Coefficient (ADC) values gives a specificity rate of 100%. Without ADC calculation, we show that image normalization is required to make an accurate differential diagnosis, and we highlight the ability of DWI to discriminate between brain abscesses and cystic/necrotic brain tumors using normalized signal intensity at lower b values (503 s/mm(2)) than usual.     

Identification of the EPR signal of S₂⁻ in green ultramarine pigments

Green and blue ultramarine pigments are characterized by the sodalite structure Na(6)(Al(6)Si(6)O(24)) and colored inserted species. These chromophores are sulfur species: S(3)(-) (blue) and S(2)(-) (yellow). Both radicals are encapsulated inside the β-cages. They contribute to the EPR spectrum of ultramarine pigments. The well-known strong EPR signal observed in all ultramarine pigments Continuous-Wave (CW) spectra has long been assigned to S(3)(-) (g = 2.029). In contrast, the S(2)(-) contribution is still subject to controversy because its signal in ultramarine pigments was not resolved even at low temperature in CW-EPR experiments. In this study, we identify unambiguously for the first time by CW-EPR and field sweep-echo detected (FS-ED) EPR the signal of S(2)(-) in ultramarine pigments and we determine its tensor components: g(1) = 2.69(6), g(2) = 2.03(4) and g(3) = 1.86(4).     

Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction

We carried out a prospective evaluation of the utility of the SIE (solvation interaction energy) scoring function for virtual screening and binding affinity prediction. Since experimental structures of the complexes were not provided, this was an exercise in virtual docking as well. We used our exhaustive docking program, Wilma, to provide high-quality poses that were rescored using SIE to provide binding affinity predictions. We also tested the combination of SIE with our latest solvation model, first shell of hydration (FiSH), which captures some of the discrete properties of water within a continuum model. We achieved good enrichment in virtual screening of fragments against trypsin, with an area under the curve of about 0.7 for the receiver operating characteristic curve. Moreover, the early enrichment performance was quite good with 50% of true actives recovered with a 15% false positive rate in a prospective calculation and with a 3% false positive rate in a retrospective application of SIE with FiSH. Binding affinity predictions for both trypsin and host-guest complexes were generally within 2 kcal/mol of the experimental values. However, the rank ordering of affinities differing by 2 kcal/mol or less was not well predicted. On the other hand, it was encouraging that the incorporation of a more sophisticated solvation model into SIE resulted in better discrimination of true binders from binders. This suggests that the inclusion of proper Physics in our models is a fruitful strategy for improving the reliability of our binding affinity predictions.