Chlorofluoroiodomethane as a potential candidate for parity violation measurements

CHFClI is among the more favorable molecules for parity violation (PV) measurements in molecules. Despite the fact that calculated PV effects are two orders of magnitude smaller than in some organometallic compounds, CHFClI displays interesting features which could make possible a new experimental PV test on this molecule. Indeed, ultrahigh resolution spectroscopy using an ultrastable CO(2) laser is favored by several intrinsic properties of this molecule. For example, the high vapor pressure of CHFClI allows investigation by supersonic beam spectroscopy. Indeed, the spectroscopic constants have been accurately determined by microwave and millimetre wave spectroscopy. This is important for the subsequent selection of an appropriate absorption band of CHFClI that could be brought to co?ncide with the absorption of CO(2). Partially resolved (+)- and (-)-CHFClI enantiomers with respectively 63.3 and 20.5% ee's have been recently prepared and analyzed by molecular recognition using chiral hosts called cryptophanes. Finally, the S-(+)/R-(-) absolute configuration was ascertained by vibrational circular dichro?sm (VCD) in the gas phase.     

Water dynamics in ionomer membranes by field-cycling NMR relaxometry

The dynamic behavior of water within two types of ionomer membranes, Nafion and sulfonated polyimide, has been investigated by field-cycling nuclear magnetic relaxation. This technique, applied to materials prepared at different hydration levels, allows the proton motion on a time scale of microseconds to be probed. The NMR longitudinal relaxation rate R(1) measured over three decades of Larmor angular frequencies omega is particularly sensitive to the host-water interactions and thus well-suited to study fluid dynamics in restricted geometries. In the polyimide membranes, we have observed a strong dispersion of R(1)(omega) following closely a 1/square root omega law in a low-frequency range (correlation times from 0.1 to 10 micros). This is indicative of a strong interaction of water with "interfacial" hydrophilic groups of the polymeric matrix (wetting situation). Variations of the relaxation rates with water uptake reveal a two-step hydration process: solvation and formation of disconnected aqueous clusters near polar groups, followed by the formation of a continuous hydrogen bond network. On the contrary, in the Nafion we observed weak variations of R(1)(omega) at low frequencies. This is typical of a nonwetting behavior. At early hydration stages, R(1)(omega) evolves logarithmically, suggesting a confined bidimensional diffusion of protons in the microsecond time range. Such an evolution is lost at higher swelling where a plateau related to three-dimensional diffusion is observed.     

Molecular dynamics simulations of electron-alkali cation pairs in bulk water

The structural, dynamic, and thermodynamic properties of an excess electron interacting with an alkali cation (Na+, K+, Li+) in bulk water were investigated by means of a mixed quantum-classical molecular dynamics simulation technique. This study includes a reparametrization of the electron-cation pseudopotentials. The free energy calculations for all three systems show that a contact electron-cation pair can be observed, which is either as stable as the dissociated pair (Li+) or more stable by only a few kT (Na+, K+). Given that the dissociation barrier is also quite small, we suggest that the average cation-electron distance in the experiments at room temperature will not depend on this free energy profile but rather on the minimization of the Coulombic repulsive interaction between like charges in the solvent medium. This enables us to compare the present molecular dynamics simulations with the spectroscopic data obtained for different ionic strengths. The overall trend of the UV-vis hydrated absorption spectra, namely, the shift toward shorter wavelengths at high ionic strengths, is fairly well reproduced. This confirms our hypothesis of statistical distribution of the cations and solvated electrons.     

Solvation parameters. 2. A simplified molecular topology to generate easily optimized values

This paper describes a generalized method to establish the values of the five solvation parameters of solutes, which reflect, together with the five solvation parameters of solvents, the intermolecular forces involved in solutions and in some biological phenomena. The tool applied for this purpose is a simplified molecular topology (SMT), which principally takes into account, for each atom of a molecule, its nature, the nature of its bonds, and in some cases the nature of its first neighbors. The learning material used to weight the molecular features generated by SMT are two sets of experimentally determined solvation parameters, established in a previous work (Laffort et al. J. Chromatogr., A 2005, 1100, 90-107).     

The pharmacophore kernel for virtual screening with support vector machines

We introduce a family of positive definite kernels specifically optimized for the manipulation of 3D structures of molecules with kernel methods. The kernels are based on the comparison of the three-point pharmacophores present in the 3D structures of molecules, a set of molecular features known to be particularly relevant for virtual screening applications. We present a computationally demanding exact implementation of these kernels, as well as fast approximations related to the classical fingerprint-based approaches. Experimental results suggest that this new approach is competitive with state-of-the-art algorithms based on the 2D structure of molecules for the detection of inhibitors of several drug targets.     

New methods for ligand-based virtual screening: use of data fusion and machine learning to enhance the effectiveness of similarity searching

Similarity searching using a single bioactive reference structure is a well-established technique for accessing chemical structure databases. This paper describes two extensions of the basic approach. First, we discuss the use of group fusion to combine the results of similarity searches when multiple reference structures are available. We demonstrate that this technique is notably more effective than conventional similarity searching in scaffold-hopping searches for structurally diverse sets of active molecules; conversely, the technique will do little to improve the search performance if the actives are structurally homogeneous. Second, we make the assumption that the nearest neighbors resulting from a similarity search, using a single bioactive reference structure, are also active and use this assumption to implement approximate forms of group fusion, substructural analysis, and binary kernel discrimination. This approach, called turbo similarity searching, is notably more effective than conventional similarity searching.     

Integrated microfluidic devices with enhanced separation performance: application to phosphoproteome analyses of differentiated cell model systems

This work reports on the application of a microfluidic device integrating nanoscale LC to nanoelectrospray MS (nano-LC-chip-MS) for the analysis of complex protein digests. Peak profile analyses of more than 700 peptide ions, reproducibly detected across replicate nano-LC-chip-MS runs (n = 5), indicated that the system provided RSD values of 0.24% on retention time, +/- 30 ppm on m/z measurement and +/- 30% variation on intensity over three orders of magnitude. RP adsorbant media with different alkyl chains and particle size packed in both trapping and separation channels were investigated to improve the chromatographic performance of this system. A two-fold improvement in chromatographic peak capacity was achieved using microfluidic devices comprising a 5 mircrom C3 trap with 2.5 microm C18 trap separation channel compared to the traditional 5 microm C18 stationary phase. Enhanced sample selectivity for the identification of phosphopeptides was obtained by combining immobilized metal affinity media prior to peptide separation on the RP microfluidic device. This system was evaluated in the context of differential phosphoproteome analyses to identify changes in signaling events and protein expression of human monocytes following the administration of phorbol ester.     

New theoretical and experimental infrared results on formaldehyde in solution

An extension of our combined procedure to determine a complete quartic force field and to resolve a vibrational problem thanks to a variational treatment is proposed for quantitative calculations of vibrational spectra in solution. Energies and gradients are obtained through a polarizable continuum model (PCM), the so-called self-consistent isodensity (SCI)-PCM. We present in this paper new experimental results dealing with formaldehyde in solution in cyclohexane, chloroform, THF, acetonitrile, DMSO and water; the obtained vibrational spectra are then compared with CCSD(T)/cc-pVQZ calculations. In addition, density functional theory (DFT) calculations have been carried out with the aim of both anticipating and positioning these approaches for larger sized molecules.     

NMR diffusion and nuclear Overhauser investigation of the hydration properties of thymine: influence of the methyl group

The absence of preferential hydration in thymine and its lowest water accessibility with respect to uracil were evidenced by NMR diffusion and HOESY experiments; the hydration differences observed between these pyrimidine bases were attributed to the electronic rather than steric properties of the methyl group.     

A star-shaped triphenylamine pi-conjugated system with internal charge-transfer as donor material for hetero-junction solar cells

Introduction of dicyanovinyl groups on a triphenylamine-based conjugated system leads to an intramolecular charge transfer which extends the spectral response and raises the open-circuit voltage of the resulting hetero-junction solar cells.