Time-dependent density functional theory investigation of the absorption, fluorescence, and phosphorescence spectra of solvated coumarins.

Using time-dependent density functional theory (TD-DFT) and the polarizable continuum model, we have computed the electronic transitions of a large panel of coumarin dyes in their enol, keto, cationic, and anionic forms. Several processes have been studied: absorption, fluorescence, 0-0 phosphorescence, and triplet-triplet excitations. For each process, detailed comparison with experimental data has been carried out.

Theoretical determination of the vibrational Raman optical activity signatures of helical polypropylene chains.

Raman and vibrational Raman optical activity (VROA) spectra of helical conformers of polypropylene chains are simulated using ab initio methods to unravel the relationships between the vibrational signatures and the primary and secondary structures of the chains. For a polypropylene chain containing three units, conformational effects are shown to lead to more acute signatures for VROA than for Raman spectra. In addition to regular polypropylene chains, which can display right and left helicities with the same probability, chirality and therefore helicity are enforced by substituting one chain end with a phenyl group.

FtcR is a new master regulator of the flagellar system of Brucella melitensis 16M with homologs in Rhizobiaceae.

The flagellar regulon of Brucella melitensis 16M contains 31 genes clustered in three loci on the small chromosome. These genes encode a polar sheathed flagellum that is transiently expressed during vegetative growth and required for persistent infection in a mouse model. By following the expression of three flagellar genes (fliF, flgE, and fliC, corresponding to the MS ring, hook, and filament monomer, respectively), we identified a new regulator gene, ftcR (flagellar two-component regulator).

Theoretical investigation of the second-order nonlinear optical properties of helical pyridine-pyrimidine oligomers.

The structure and second-order nonlinear optical properties of a series of helical pyridine-pyrimidine oligomers recently synthesized by Barboiu and Lehn have been investigated theoretically by combining molecular mechanics and quantum chemistry approaches. In the absence of substituents, the hyper-Rayleigh scattering response (betaHRS) and the projection of the first hyperpolarizability on the dipole moment (beta||) exhibit periodic variations with chain length, but these nonlinear optical responses remain small. The first hyperpolarizabilities can, however, be enhanced by adding substituents.

Theoretical investigation on 1H and 13C NMR chemical shifts of small alkanes and chloroalkanes.

Using density functional theory (DFT) with the B3LYP, PBE, and PBE0 exchange-correlation functionals as well as the Moller-Plesset second-order perturbation theory (MP2) combined with a series of rather extended basis sets, 1H and 13C chemical shifts of small alkanes and chloroalkanes (with different numbers of chlorine atoms on specific positions) have been simulated and compared to experimental data. For the 1H chemical shifts, theory tends to reproduce experiment within the limits of the experimental errors. In the case of 13C chemical shift, the differences between theory and experiment increase monotonically with the number of chlorine atoms and exhibit a deviation from additivity.

Recursive partitioning for the prediction of cytochromes P450 2D6 and 1A2 inhibition: importance of the quality of the dataset.

The purpose of this study was to explore the use of detailed biological data in combination with a statistical learning method for predicting the CYP1A2 and CYP2D6 inhibition. Data were extracted from the Aureus-Pharma highly structured databases which contain precise measures and detailed experimental protocol concerning the inhibition of the two cytochromes. The methodology used was Recursive Partitioning, an easy and quick method to implement.

Structure-based pharmacophore of COX-2 selective inhibitors and identification of original lead compounds from 3D database searching method.

A four-point pharmacophore of COX-2 selective inhibitors was derived from a training set of 16 compounds, using the Catalyst program. It consists of a H bond acceptor, two hydrophobic groups and an aromatic ring, in accordance with SAR data of the compounds and with topology of the COX-2 active site. This hypothesis, combined with exclusion volume spheres representing important residues of the COX-2 binding site, was used to virtually screen the Maybridge database.

Repression of ergosterol level during oxidative stress by fission yeast F-box protein Pof14 independently of SCF.

We describe a new member of the F-box family, Pof14, which forms a canonical, F-box dependent SCF (Skp1, Cullin, F-box protein) ubiquitin ligase complex. The Pof14 protein has intrinsic instability that is abolished by inactivation of its Skp1 interaction motif (the F-box), Skp1 or the proteasome, indicating that Pof14 stability is controlled by an autocatalytic mechanism. Pof14 interacts with the squalene synthase Erg9, a key enzyme in ergosterol metabolism, in a membrane-bound complex that does not contain the core SCF components.

Ab initio tools for the accurate prediction of the visible spectra of anthraquinones.

The UV/vis absorption spectra of 101 anthraquinones solvated in two protic solvents (methanol and ethanol) has been theoretically predicted using the time-dependent density functional theory (TD-DFT) for the excited state calculations and the polarizable continuum model (PCM) for evaluating bulk solvent effects. Two functionals (B3LYP and PBE0) have been used and they provide similar mean absolute deviations (approximately 0.09 eV) but mean signed errors presenting opposite signs.

Similarity measures based on Gaussian-type promolecular electron density models: alignment of small rigid molecules.

Various molecular similarity measures (overlap, Coulomb, kinetic, electrostatic energy) and similarity indices (Carbó, Hodgkin-Richards, Kulczynski, Shape Tanimoto) are applied to the superposition of 3D promolecular electron density (PED) distributions. The original aspect of the paper lies in the consideration of smoothed PEDs, which allow to decrease the number of local solutions to a superposition problem, together with the use of the less common kinetic and electrostatic energy similarity measures. Results are obtained for a family of five rigid endothiapepsin ligands that were already considered in previous applications, based on graph representations of their PED.

Adsorption of fumaramide [2]rotaxane and its components on a solid substrate: a coverage-dependent study.

The coverage-dependent adsorption on Au(111) of a fumaramide [2]rotaxane and its components, a benzylic amide macrocycle and a fumaramide thread, is studied using high-resolution electron energy loss spectroscopy (HREELS). Up to monolayer coverage, the relative intensity of out-of-plane to in-plane phenyl ring vibrational modes indicates that the macrocycle adopts an orientation with the phenyl rings largely parallel to the surface. The formation of a chemisorption bond is evidenced by the presence of a Au-O stretching vibration.

Charge carriers in few-layer graphene films.

The nature of the charge carriers in 2D few-layer graphites (FLGs) has been recently questioned by transport measurements [K. S. Novoselov, Science 306, 666 (2004)10.

Mechanism of formation of inorganic and organic nanoparticles from microemulsions.

This chapter essentially deals with the preparation of nanoparticles using microemulsions. The preparation of inorganic nanoparticles--Ni2B, Pt, Au, Pt-Au, AgX--and the synthesis of organic nanoparticles--cholesterol, rhovanil, rhodiarome--are systematically studied as a function of the concentration of the precursor molecules, the size of the inner water cores, and the manner of mixing the various solutions. Two different behaviors are observed in the various systems.

Ab initio investigation of the n --> pi* transitions in thiocarbonyl dyes.

The n --> pi* transitions in more than 100 thiocarbonyl dyes have been calculated with an ab initio procedure relying on the combination of time-dependent density functional theory (TD-DFT) for evaluating excited states and the polarizable continuum model (PCM) for modeling the bulk solvent effects on both the geometrical and electronic structures. Two hybrid functionals (B3LYP and PBE0) and several basis sets, some including f polarization functions, have been used. B3LYP provides the most accurate raw estimates, but once simple linear regression is performed, both functionals give similar results with a small advantage for PBE0.

Electrode surface modification by a spirobifluorene derivative. An XPS and electrochemical investigation.

Ordered thin layers of a spirobifluorene derivative containing an amino group were formed by grafting them onto a self-assembled monolayer (SAM) of 11-mercaptoundecanoic acid (11-MUA) on gold. Either physical (H-bonding) or chemical bonding (activated by EDCl) was investigated. X-ray photoelectron spectroscopy and electrochemical impedance spectroscopy confirmed that both methods can be used to effectively graft 2-amino-9,9'-spirobifluorene molecules onto the SAM surface, giving high surface coverages, with a significantly higher packing in the case of chemisorbed films.

Evaluation of alternative sum-over-states expressions for the first hyperpolarizability of push-pull pi-conjugated systems.

A dipolar-free sum-over-states expression for the diagonal components of the first hyperpolarizability (beta) tensor has been proposed by Kuzyk [Phys. Rev. A 72, 053819 (2005)] as an alternative to the traditional expression.

Ab initio assessment of the first hyperpolarizability of saturated and unsaturated polyaminoborane/polyphosphinoborane copolymers.

The linear and nonlinear optical properties of trans-cisoïd saturated and unsaturated polyaminoborane/polyphosphinoborane alternating copolymers are studied at the MP2/6-311G(2d)//PBE0/6-31G(2d) level of approximation, by using the increasingly large oligomer series methodology. We report the evolution with chain length of geometry parameters, partial atomic charges, electric dipole moments, polarizabilities and first hyperpolarizabilities of both phosphorus- and nitrogen-terminated chains. It turns out that for the saturated copolymer, linear and nonlinear optics properties of the saturated copolymer correspond to an average of the response of polyaminoborane and polyphosphinoborane.

Second-order Møller-Plesset evaluation of the bond length alternation of several series of linear oligomers.

We investigate, at the second-order Møller-Plesset level, the bond length alternation of 30 series of increasingly long linear oligomers for a total of more than 250 compounds, polyacetylene, polymethineimine, polyphosphinoborane, polyaminoborane, polyphosphazene, etc., for which, often for the first time, an accurate estimate of the polymeric bond length alternation is given. The variations induced either by chemical substitution of the backbone atoms or conformational modifications are discussed.

Experimental and theoretical investigation of the Raman and hyper-Raman spectra of acetonitrile and its derivatives.

The Raman and hyper-Raman spectra of acetonitrile and its deuterated analog have been investigated by combining experimental analysis and theoretical interpretation. It has been observed that the Raman spectra can easily be reproduced at both the Hartree-Fock and Moller-Plesset second-order levels of approximation and that for these fundamental transitions, inclusion of anharmonicity effects is not essential. On the other hand, the hyper-Raman spectra are more difficult to simulate and interpret.

TD-DFT investigation of the UV spectra of pyranone derivatives.

The UV absorption spectra of more than 80 substituted coumarins and chromones have been investigated with the PCM-TD-DFT theoretical scheme using three hybrid functionals (O3LYP, B3LYP, and PBE0) and taking into account methanol or ethanol solvation effects. For most of the studied derivatives, there are at least two allowed excited states presenting a strong oscillator strength in the UV region. The first allowed excitation is associated to a HOMO-LUMO transition whereas the second corresponds to a transition from the HOMO-1 to the LUMO.

Dispersion of carbon nanotubes using organic solvents.

Phenyl ethyl alcohol was used for fast and stable dispersion of carbon nanotubes. This solvent, more effective than ethanol and toluene, allows easy dispersion of carbon nanotubes for TEM characterization. For TEM grids prepared at high dilution, it is possible to observe each tube separately.

Excitation spectra of nitro-diphenylaniline: accurate time-dependent density functional theory predictions for charge-transfer dyes.

Using time-dependent density functional theory (TD-DFT) and the polarizable continuum model (PCM), we have computed the absorption spectra of nitro-diphenylamine dyes. It turns out that the 6-311+G(2d,p) and 6-311G(d,p) basis sets provide, respectively, almost perfectly converged excitation spectra and geometries. Using the PBE0 hybrid functional, we obtain a valuable correlation between PCM-TD-DFT and experimental lambdamax with mean signed/absolute deviations of -4 nm (0.

Spectral filtering of visible light by the cuticle of metallic woodboring beetles and microfabrication of a matching bioinspired material.

Samples of the cuticle taken from the body of Buprestidae Chrysochroa vittata have been studied by scanning electron microscopy and optical reflectance measurements, related to numerical simulations. The cause of the metallic coloration of the body of these insects is determined to be the structure of the hard carapace constructed as a stack of thin chitin layers separated by very thin irregular air gaps. In particular the change of color as a function of the observation angle is elucidated in terms of an infinite photonic-crystal model, confirmed by finite multilayer calculations.

Expression of lysosome-associated membrane protein 1 (Lamp-1) and galectins in human keratinocytes is regulated by differentiation.

Lysosomes and their components are suspected to be involved in epidermal differentiation. In this study, lysosomal enzyme activities, expression of the lysosome-associated membrane protein 1 (Lamp-1) and expression of the epidermal galectins-1, -3 and -7 were investigated in human keratinocytes cultured at different cell densities (subconfluence, confluence and postconfluence) in order to induce differentiation. Detected by Western blot and immunofluorescence, Lamp-1 expression is transiently upregulated at culture confluence, but reduced at postconfluence.