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})

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

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

Rapid IRMPD analysis for glycomics

Infrared vibrational spectroscopy in the gas phase has emerged as a powerful tool to determine complex molecular structures with Angstrom accuracy. Among the different approaches IRMPD (InfraRed Multiple Photon Dissociation), which requires the use of an intense pulsed tunable laser in the IR domain, has been broadly applied to the study of complex (bio)molecules. Recently, it also emerged as a highly relevant approach for analytical purposes especially in the field of glycomics in which structural analysis is still a tremendous challenge. This opens the perspective to develop new analytical tools allowing for the determination of molecular structures with atomic precision, and to address advanced questions in the field. However, IRMPD experiments require either non commercial equipments and long acquisition time which limits the data output. Here we show that it is possible to improve the IRMPD performances by optimizing the combination between a LTQ XL mass spectrometer and a high repetition tunable laser Firefly. Two orders of magnitude are gained with this approach compared to usual experiments ultimately leading to a completely resolved spectrum acquired in less than one minute. These results open the way to many new applications in glycomics with the possibility to include IRMPD in complex analytical workflows

O -Acetylated sugars in the gas phase: stability, migration, positional isomers and conformation

O-acetylations are functional modifications which can be found on different hydroxyl groups of glycans and which contribute to the fine tuning of their biological activity. Localizing the acetyl modifications is notoriously challenging in glycoanalysis, in particular because of their mobility: loss or migration of the acetyl group may occur through the analytical workflow. Whereas migration conditions in the condensed phase have been rationalized, little is known about the suitability of Mass Spectrometry to retain and resolve the structure of O-acetylated glycan isomers. Here we use the resolving power of infrared ion spectroscopy in combination with ab initio calculation to assess the structure of O-acetylated monosaccharide ions in the gaseous environment of a mass analyzer. N-acetyl glucosamines were synthetized with an O-acetyl group in positions 3 or 6, respectively. The protonated ions produced by electrospray ionization were observed by mass spectrometry and their vibrational fingerprints were recorded in the 3 $μ$m range by IRMPD spectroscopy (InfraRed Multiple Photon Dissociation). Experimentally, the isomers show distinctive IR fingerprints. Additionally, ab initio calculations confirm the position of the O-acetylation and resolve their gas phase conformation. These findings demonstrate that the position of O-acetyl groups is retained through the transfer from solution to the gas phase, and can be identified by IRMPD spectroscopy

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

Secondary structures of short peptide chains in the gas phase: Double resonance spectroscopy of protected dipeptides

Contains fulltext : 98874.pdf (publisher's version ) (Open Access

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