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.     

Galactose Oxidase models: 19F NMR as a powerful tool to study the solution chemistry of tripodal ligands in the presence of copper(II)

In copper(ii) complexes of tripodal ligands, the protonation state of the phenol moiety, and its position (axial vs. equatorial), are easily assessed by (19)F NMR.     

Photofragmentation of the fluorene cation: II. Determination of the H-loss energy-dependent rate constant

The hydrogen-loss channel, induced by sequential multiphoton absorption, of the vapor-phase fluorene cation was investigated using a pulsed supersonic molecular beam, a time-of-flight mass spectrometer, and pulsed nanosecond lasers. Our new method leads to the determination of the absolute absorption cross section. Its attenuation with the number of absorbed photons has been approximated by means of statistical models. A model-free determination of the evolution of the dissociation rate constant in a relatively large energy range was obtained by solving the set of coupled differential kinetic equations numerically. Particular attention was focused on the data analysis techniques. The free fit of these rate constants is close to the photothermodissociation statistical model, but shows a discrepancy with the Rice and Ramsperger and Kassel model mainly at high energy. The resulting activation energy is in agreement with both that deduced from the ab initio calculations and that from the tight-binding energy potential surface model.     

Nature of the chemical bond in protonated methane

Protonated methane, CH(5)(+), is a key reactive intermediate in hydrocarbon chemistry and a borderline case for chemical structure theory, being the simplest example of hypercoordinated carbon. Early quantum mechanical calculations predicted that the properties of this species could not be associated with only one structure, because it presents serious limitations of the Born-Oppenheimer approximation. However, ab initio molecular dynamics and diffusion Monte Carlo calculations showed that the most populated structure could be pictured as a CH(3) tripod linked to a H(2) moiety. Despite this controversy, a model for the chemical bonds involved in this ion still lacks. Here we present a modern valence bond model for the electronic structure of CH(5)(+). The chemical bond scheme derived directly from our calculations pictures this ion as H(3)C...H(2)(+). The fluxionality can be seen as the result of a proton transfer between C-H bonds. A new insight on the vibrational bands at approximately 2400 and approximately 2700 cm(-1) is suggested. Our results show that the chemical bond model can be profitably applied to such intriguing systems.