iGVPT2 : an interface to computational chemistry packages for anharmonic corrections to vibrational frequencies

iGVPT2 is a program for computing anharmonic corrections to vibration frequencies, based on force field expansion of the potential energy surface in normal mode coordinates. It includes second order vibrational perturbation theory (VPT2) algorithm and its derived methods (VPT2+K, DCPT2, HDCPT2). iGVPT2 is interfaced with several computation chemistry packages to compute the potential energies and dipoles derivatives. The second, third and quartic derivatives can be computed at the same level of theory but they can be also computed using different methods via one or two computational packages. iGPVT2 includes also a very fast hybrid QM//MM approach for biomolecules. It is provided free-of-charge for non-commercial research (see \url{https://sites.google.com/site/allouchear/igvpt2})

Mass spectrometry hybridized with gas-phase InfraRed spectroscopy for glycan sequencing

International audiencePrecise structural differentiation of often isomeric glycans is important given their roles in numerous biological processes. Mass spectrometry (MS) (and tandem MS) is one of the analytical techniques at the forefront of glycan analysis given its speed, sensitivity in producing structural information as well as the fact it can be coupled to other orthogonal analytical techniques such as liquid chromatography (LC) and ion mobility spectrometry (IMS). This review describes another family of techniques that are more commonly being hybridized to MS(/MS) namely gas-phase infrared (IR) spectroscopy, whose rise is in part due to the development and improved accessibility of tunable IR lasers. Gas-phase IR can often differentiate fine isomeric differences ubiquitous within carbohydrates that MS may be 'blind' to. There are also examples of cryogenic gas-phase IR spectroscopy with much greater spectral resolution as well as hybridizing with separative methods (LC, IMS). Furthermore, collision-induced dissociation (CID) product ions can also be probed by IR, which may be beneficial to deconvolute spectra, aid analysis and build spectral libraries, thus generating novel opportunities for fragment-based approaches to analyze glycans

The structure and energetics of 3^3He and 4^4He nanodroplets doped with alkaline earth atoms

We present systematic results, based on density functional calculations, for the structure and energetics of $^3$He and $^4$He nanodroplets doped with alkaline earth atoms. We predict that alkaline earth atoms from Mg to Ba go to the center of $^3$He drops, whereas Ca, Sr, and Ba reside in a deep dimple at the surface of $^4$He drops, and Mg is at their center. For Ca and Sr, the structure of the dimples is shown to be very sensitive to the He-alkaline earth pair potentials used in the calculations. The $5s5p\leftarrow5s^2$ transition of strontium atoms attached to helium nanodroplets of either isotope has been probed in absorption experiments. The spectra show that strontium is solvated inside $^3$He nanodroplets, supporting the calculations. In the light of our findings, we emphasize the relevance of the heavier alkaline earth atoms for analyzing mixed $^3$He-$^4$He nanodroplets, and in particular, we suggest their use to experimentally probe the $^3$He-$^4$He interface.Comment: Typeset using Revtex, 20 pages and 8 Postscript file

Beneficial Effects of Remifentanil Against Excitotoxic Brain Damage in Newborn Mice

Background: Remifentanil, a synthetic opioid used for analgesia during cesarean sections, has been shown in ex vivo experiments to exert anti-apoptotic activity on immature mice brains. The present study aimed to characterize the impact of remifentanil on brain lesions using an in vivo model of excitotoxic neonatal brain injury.Methods: Postnatal day 2 (P2) mice received three intraperitoneal injections of remifentanil (500 ng/g over a 10-min period) or saline just before an intracortical injection of ibotenate (10 μg). Cerebral reactive oxygen species (ROS) production, cell death, in situ labeling of cortical caspase activity, astrogliosis, inflammation mediators, and lesion size were determined at various time points after ibotenate injection. Finally, behavioral tests were performed until P18.Results: In the injured neonatal brain, remifentanil significantly decreased ROS production, cortical caspase activity, DNA fragmentation, interleukin-1β levels, and reactive astrogliosis. At P7, the sizes of the ibotenate-induced lesions were significantly reduced by remifentanil treatment. Performance on negative geotaxis (P6-8) and grasping reflex (P10-12) tests was improved in the remifentanil group. At P18, a sex specificity was noticed; remifentanil-treated females spent more time in the open field center than did the controls, suggesting less anxiety in young female mice.Conclusions:In vivo exposure to remifentanil exerts a beneficial effect against excitotoxicity on the developing mouse brain, which is associated with a reduction in the size of ibotenate-induced brain lesion as well as prevention of some behavioral deficits in young mice. The long-term effect of neonatal exposure to remifentanil should be investigated

Mesure de dipôle électrique en phase gazeuse ; application aux agrégats et aux biomolécules

This manuscript discusses permanent electric dipole measurements of gas phase molecules and molecular complexes. The permanent electric dipole characterizes the distribution of charges in the ground state of the molecule; it depends on the internal charge transfers and on the geometric structure of the system. Measurements were performed with a molecular beam deflection setup (analogue to the Stern & Gerlach experiment) coupled with a laser vaporization/desorption source. We have studied three categories of systems: fullerene-metal clusters, one excess electron alkali halide clusters and polypeptides.Cette thèse décrit la mesure du dipôle électrique permanent de molécules et de complexes moléculaires en phase gazeuse. Le dipôle électrique caractérise la distribution de charge dans l'état fondamental de la molécule, il dépend des transferts de charge internes et de la géométrie du système. Les mesures sont réalisées gr`ace une source vaporisation/désorption laser couplée à un montage de déflexion de jet moléculaire dans un champ électrique intense et inhomogne (similaire à l'expérience de Stern & Gerlach). Trois familles de systèmes ont ainsi été étudiées : des agrégats mixtes fullerènes-métal, des agrégats d'halogénures d'alcalins à un électron en excès et des polypeptides

Mesure de dipôle électrique en phase gazeuse (application aux agrégats et aux biomolécules)

Cette thèse décrit la mesure du dipôle électrique permanent de molécules et complexes moléculaires en phase gazeuse. Le dipôle électrique caractérise la distribution de charge dans l'état fondamental de la molécule, il dépend des transferts de charge internes et de la géométrie du système. Les mesures sont réalisées grâce à une source à vaporisation/désorption laser couplée à un montage de déflexion de jet moléculaire dans un champ électrique intense et inhomogène (similaire a l'expérience de Stern & Gerlach). Trois familles de systèmes ont ainsi été étudiées : des agre gats mixtes fullerènes-métal, des agrégats d'halogénures d'alcalins à un électron en excès et des polypeptidesLYON1-BU.Sciences (692662101) / SudocSudocFranceF

Fucose migration: where to ?

Fucose is a ubiquitous monosaccharide linked to the core of major classes of glycans and the identification of fucose location is one critical bottleneck in glycomics. This is due to the remarkable inclination of the fucosyl residue to migrate to neighboring throughout mass spectrometric analysis. Such molecular rearrangements first reported in the 90’s and called “internal residue loss” can be mistaken for diagnostic fragments and lead to false assignment of the position of fucose on the glycan core. While a variety of misleading fucosylated fragments has been observed for glycan standards, the exact molecular structure of fucosylated products after rearrangement remains elusive and their formation unpredictable. This constitutes a major obstacle to the sequencing of fucosylated glycans. Using Infrared ion spectrosopy, we resolve the molecular structure of fucosylated fragments of four Lewis and Blood Group H antigen trisaccharides. Our findings suggest that fucose migration, which was reported decades ago, results in fragment ions, which can be fully characterized. Additionally we report a new type of fucose migration, which does not feature any internal residue loss and therefore had not been previously detected by mass spectrometry: it consists of a local type of migration, where the fucose remains on the initial residue with a change of regiochemistry. Therefore, such glycan fragments previously regarded as diagnostic carry previously undetected molecular rearrangements. Infrared ion spectroscopy enables molecular characterization of glycan fragments and this knowledge is essential to the interpretation of glycomics data, as well as the understanding of the processes underlying Mass Spectrometry analysis

Légitimer les politiques de la biodiversité. Droit, science et participation dans les aires protégées françaises

National audienceCe chapitre d'ouvrage propose une lecture de la trajectoire des politiques françaises de la biodiversité en s'appuyant de manière privilégiée sur l'évolution des espaces naturels protégés. Il entend montrer que cette trajectoire est régie par deux modèles principaux en interaction, un modèle rationnel-légal historiquement dominant et un modèle participatif plus récent. Le modèle rationnel-légal est fondé sur l'articulation d'un impératif scientifique de connaissance et de textes juridiques visant à préserver la nature. Le modèle participatif, qui prend de l'ampleur dans les années 1990, se traduit par une revalorisation du local et une extension des acteurs pris en compte. Née dans la communauté scientifique dans une logique d'alerte et incluant les hommes et leurs activités, la notion de biodiversité peut servir de point d'appui à l'un et à l'autre. Ces deux modèles entretiennent des relations complexes, faites de tensions et de tentatives d'articulation, qu'illustrent l'essor des sciences participatives et la diffusion de concepts comme celui de services écosystémiques. L'article s'interroge en conclusion sur l'avenir des politiques de la biodiversité : ce fondement intrinsèque sur deux modèles en interaction est-il une spécificité des politiques publiques de la biodiversité ? Si leur trajectoire tient aux fluctuations de l'équilibre entre ces deux modèles, comment cet équilibre est-il susceptible d'évoluer à l'avenir