TD-DFT Performance for the Visible Absorption Spectra of Organic Dyes: Conventional versus Long-Range Hybrids.

The π → π* transitions of more than 100 organic dyes from the major classes of chromophores (quinones, diazo, ...

A method to assess the lysosomal residence of proteins in cultured cells.

Analytical subcellular fractionation is playing an increasingly important role in proteomic studies to identify and validate components of cellular organelles. For lysosomes, definitive studies in this area have been restricted to rodent tissues due to technical constraints. Our goal was to design a quantitative assay that would allow clear demonstration of lysosomal localization in cultured human cells.

An analytical derivative procedure for the calculation of vibrational Raman optical activity spectra.

We present an analytical time-dependent Hartree-Fock algorithm for the calculation of the derivatives of the electric dipole-magnetic dipole polarizability with respect to atomic Cartesian coordinates. Combined with analogous procedures to determine the derivatives of the electric dipole-electric dipole and electric dipole-electric quadrupole polarizabilities, it enables a fully analytical evaluation of the three frequency-dependent vibrational Raman optical activity (VROA) invariants within the harmonic approximation. The procedure employs traditional non-London atomic orbitals, and the gauge-origin dependence of the VROA intensities has, therefore, been assessed for the commonly used aug-cc-pVDZ and rDPS:3-21G basis sets.

Circular dichroism of helical structures using semiempirical methods.

A general semiempirical scheme has been elaborated to simulate circular dichroism (CD) spectra of supramolecular systems. This approach adopts the analytical method of Beck and Hohlneicher [Theor. Chem.

Time dependent density functional theory investigation of the resonance Raman properties of the julolidinemalononitrile push-pull chromophore in various solvents.

The absorption and resonance Raman spectra have been investigated for the first excited state of the julolidinemalononitrile push-pull chromophore in cyclohexane, dichloromethane, and acetonitrile by means of time dependent density functional theory calculations. The effect of nonlocal exchange has been considered by using three different hybrid exchange-correlation functionals containing 20%, 35%, and 50% of exact Hartree-Fock exchange. The interactions with the solvent have been described by the polarizable continuum model.

Revisiting the relationship between the bond length alternation and the first hyperpolarizability with range-separated hybrid functionals.

We monitor the influence of the bond length alternation (BLA) modification on the static electronic polarizability and first hyperpolarizability of two polymethineimine oligomers. Four theoretical approaches are compared: HF, PBE0, LC-omegaPBE, and MP2. For the dodecamer, both HF and PBE0 are unable to foresee even the qualitative evolution of the first hyperpolarizability when varying the BLA.

Switchable reflector in the Panamanian tortoise beetle Charidotella egregia (Chrysomelidae: Cassidinae).

The tortoise beetle Charidotella egregia is able to modify the structural color of its cuticle reversibly, when disturbed by stressful external events. After field observations, measurements of the optical properties in the two main stable color states and scanning electron microscope and transmission electron microscope investigations, a physical mechanism is proposed to explain the color switching of this insect. It is shown that the gold coloration displayed by animals at rest arises from a chirped multilayer reflector maintained in a perfect coherent state by the presence of humidity in the porous patches within each layer, while the red color displayed by disturbed animals results from the destruction of this reflector by the expulsion of the liquid from the porous patches, turning the multilayer into a translucent slab that leaves an unobstructed view of the deeper-lying, pigmented red substrate.

Assessment of long-range corrected functionals performance for n-->pi* transitions in organic dyes.

The first n-->pi* transitions of 18 nitroso and 16 thiocarbonyl dyes have been computed by time-dependent density functional theory (TD-DFT) using pure as well as global and range-separated hybrid functionals. It turns out that the accuracy of all hybrids is relatively similar, i.e.

Finite-Field Spin-Flip Configuration Interaction Calculation of the Second Hyperpolarizabilities of Singlet Diradical Systems.

Ab initio spin-flip configuration interaction (SF-CI) methods with the finite-field (FF) scheme are applied to the calculation of static second hyperpolarizabilities (γ) of several singlet diradical systems, i.e., the model H2 molecule under dissociation, p-quinodimethane, o-quinoid five-membered ring, and 1,4-bis(imidazole-2-ylidene)cyclohexa-2,5-diene (BI2Y) models.

Mutations of the quorum sensing-dependent regulator VjbR lead to drastic surface modifications in Brucella melitensis.

Successful establishment of infection by bacterial pathogens requires fine-tuning of virulence-related genes. Quorum sensing (QS) is a global regulation process based on the synthesis of, detection of, and response to small diffusible molecules, called N-acyl-homoserine lactones (AHL), in gram-negative bacteria. In numerous species, QS has been shown to regulate genes involved in the establishment of pathogenic interactions with the host.

TD-DFT investigation of diarylethene dyes with cyclopentene, dihydrothiophene, and dihydropyrrole bridges.

We have investigated the visible spectra of closed-ring diarylethenes presenting cyclopentene, dihydrothiophene, and dihydropyrrole bridging structures. Our simulations have been performed with an ab initio time-dependent density functional theory approach that takes into account bulk environmental effects. The computed lambda(max) agree qualitatively with experiment, and once a simple statistical treatment is performed, a quantitative agreement is reached.

First hyperpolarizability of polymethineimine with long-range corrected functionals.

Using the long-range corrected (LC) density functional theory (DFT) scheme introduced by Iikura et al. [J. Chem.

Orange reflection from a three-dimensional photonic crystal in the scales of the weevil Pachyrrhynchus congestus pavonius (Curculionidae).

The three-dimensional structure that causes the coloration of the tropical weevil Pachyrrhynchus congestus pavonius was studied, using a combination of electron microscopy, optical spectroscopy, and numerical modeling. The orange scales that cover the colored rings on the animal's body were opened, to display the structure responsible for the coloration. This structure is a three-dimensional photonic polycrystal, each grain of which showing a face-centered cubic symmetry.

Assessment of the efficiency of long-range corrected functionals for some properties of large compounds.

Using the long-range correction (LC) density functional theory (DFT) scheme introduced by Iikura et al. [J. Chem.

Ab initio studies of the lambda(max) of naphthoquinones dyes.

Using a state-of-the-art time-dependent density functional (TD-DFT) approach that includes the explicit consideration of bulk medium effects on both the ground-state geometry and the electronic spectrum, we have determined the lambda(max) of 86 naphthoquinones (NQ) dyes in various solvents for a total of 151 cases. In most cases, TD-DFT provides the correct ordering of transitions for substituted NQ dyes. Comparisons with experimental values lead to a mean signed error of -7.

Recruitment of P-TEFb (Cdk9-Pch1) to chromatin by the cap-methyl transferase Pcm1 in fission yeast.

Capping of nascent pre-mRNAs is thought to be a prerequisite for productive elongation and associated serine 2 phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (PolII). The mechanism mediating this link is unknown, but is likely to include the capping machinery and P-TEPb. We report that the fission yeast P-TEFb (Cdk9-Pch1) forms a complex with the cap-methyltransferase Pcm1 and these proteins colocalise on chromatin.

Wide angular range operation of a dielectric multilayer film with a photonic-crystal-type defect.

Light can tunnel through a high-reflectivity dielectric multilayer film when a photonic-crystal-type defect is introduced in the structure, which is useful for optical signal processing. We consider chirped structures with a defect in layer thickness for which high reflectivity is achieved over a broad wavelength range except within a narrow spectral window. The useful transmission window, while it shifts toward shorter wavelengths as the angle of incidence of the light beam is increased, does not, in general, survive; i.

Preparation of organic nanoparticles using microemulsions: their potential use in transdermal delivery.

Organic nanoparticles of cholesterol and retinol have been synthesized in various AOT (Aerosol OT; sodium bis(2-ethylhexyl) sulfosuccinate)/heptane/water microemulsions by direct precipitation of the active principle in the aqueous cores. The nanoparticles are observed by transmission electron microscopy (TEM) using the adsorption of a contrasting agent, such as iodine vapor. The size of the nanoparticles can be influenced, in principle, by the concentration of the organic molecules and the diameter of the water cores, which is related to the ratio R=[H2O]/[surfactant].

Finite-difference calculation of the Green's function of a one-dimensional crystal: application to the Krönig-Penney potential.

We present a finite-difference scheme for computing the Green's function of a one-dimensional crystal. The method enables one to derive the band structure and the density of states of this type of structures, whatever the particular values of the potential energy. The technique also enables one to compute the influence of defects on the density of states and on the scattering of the eigenstates of the crystal.

Investigation of the UV/visible absorption spectra of merocyanine dyes using time-dependent density functional theory.

The visible spectral properties of a set of merocyanine dyes have been determined experimentally and compared to theoretical estimates calculated using time-dependent density functional theory. Three families of merocyanines have been investigated. The merocyanines of the first class contain the 4-thiazolidinone, 2-thioxo group in resonance with different donor groups.

Lysosomes and Fas-mediated liver cell death.

A number of studies, mostly performed ex vivo, suggest that lysosomes are involved in apoptosis as a result of a release of their cathepsins into the cytosol. These enzymes could then contribute to the permeabilization of the outer mitochondrial membrane; they could also activate effector caspases. The present study aims at testing whether the membrane of liver lysosomes is disrupted during Fas-mediated cell death of hepatocytes in vivo, a process implicated in several liver pathologies.

Density functional theory investigation of the polarizability and second hyperpolarizability of polydiacetylene and polybutatriene chains: treatment of exact exchange and role of correlation.

The static polarizability and second hyperpolarizability of increasingly large polydiacetylene and polybutatriene (PBT) chains have been evaluated using the optimized effective potential for exact exchange (OEP-EXX) method developed by Yang and Wu [Phys. Rev. Lett.

Do sewage treatment plant discharges substantially impair fish reproduction in polluted rivers?

Sewage treatment plants are frequently associated with the release of xenobiotics and, consequently, with alterations of the reproductive function induced by many of these substances in aquatic organisms. In order to assess the impacts of sewage treatment plant (STP) discharges in polluted rivers, two sentinel species (gudgeon Gobio gobio and stoneloach Barbatula barbatula) were caught during their reproductive cycle upstream and downstream two STPs (STP1--Goffontaine, STP2--Wegnez). Gonadosomatic index, histological (testicular and ovarian stages, atretic follicles, intersexuality) and endocrine (sex steroids, aromatase activity, alkali-labile phosphorus) parameters were assayed.