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})

Les recherches contemporaines en géographie rurale : territoires, ressources et pratiques du terrain

International audienceCe texte est une synthèse des réflexions partagées par les doctorants présents lors d'une journée organisée à Montpellier, le 26 mars 2009, par la commission française de géographie rurale. Il pose la question de la spécificité des recherches géographiques sur les espaces ruraux à partir de trois entrées épistémologiques et méthodologiques : le territoire, les ressources et la pratique du terrain. Les regards croisés des huit contributeurs, enrichis de leurs propres expériences de recherche et d'une journée commune de terrain, montrent que les problèmes de délimitation des territoires d'étude, de caractérisation des ressources locales et de méthodologie d'investigation préoccupent les jeunes chercheurs géographes

Caractérisation structurale et séquençage de carbohydrates par spectroscopie infrarouge intégrée à la spectrométrie de masse

Sequencing techniques have been established for proteins and DNA and have revolutionised modern biology but similar technique do not exist for carbohydrates due to their unique complexity. In this context, we have built an instrument coupling vibrational spectroscopy and mass spectrometry (MS/IR) dedicated to the structural characterization of carbohydrates.In this thesis, we have shown that the IR signature is a powerful metric which is able to resolve simultaneously all carbohydrate isomerisms: the monosaccharide content, the position of functional modifications, the regiochemistry and the stereochemistry of the glycosidic linkage. Then the conservation of the molecular structure of MS fragments has been revealed on disaccharide fragments. Following this demonstration we have established the carbohydrate sequencing rules using MS/IR and applied them for the determination of the sequence of different oligosaccharides.Finally the potential of the IRMPD spectroscopy in the Far-IR range is explored for anomers, isomers and conformations resolution as well as the utilisation of a two colors infrared spectroscopy or the coupling with an HPLC instrumentDes techniques de séquençage existent pour les biopolymères comme les protéines et l'ADN et ont permis de révolutionner la biologie moderne. Toutefois, des techniques similaires dédiées au séquençage des carbohydrates n'ont pas encore été développées à cause de la complexité de cette classe de biomolécules. Dans ce contexte, nous avons construit un instrument couplant spectroscopie vibrationnelle et spectrométrie de masse (MS/IR) afin de caractériser la structure des carbohydrates grâce à leur signature infrarouge.Dans cette thèse, nous avons démontré que cette métrique permet de différencier les différentes isoméries présentes dans la classe des carbohydrates : la nature des monosaccharides, la position des modifications fonctionnelles ainsi que la régio- et la stéréochimie de la liaison glycosidique. Ensuite la conservation de la structure moléculaire des ions après fragmentation a été démontrée sur des fragments de disaccharides permettant ainsi d'établir les règles du séquençage de carbohydrates par MS/IR. Cette méthode a ensuite été appliquée sur différents oligosaccharides.Enfin dans la dernière partie de ce manuscrit, le potentiel de la spectroscopie IRMPD dans l'infrarouge lointain est exploré pour la résolution des anomères, des isomères et des conformations. Finalement deux approches permettant une séparation en masse et en isomère en amont de l'analyse spectroscopique sont proposées : spectroscopie IRMPD 2 couleurs ou couplage avec la chromatographie liquid

Structural characterization and sequencing of carbohydrates by IR spectroscopy integrated into mass spectrometry

Des techniques de séquençage existent pour les biopolymères comme les protéines et l'ADN et ont permis de révolutionner la biologie moderne. Toutefois, des techniques similaires dédiées au séquençage des carbohydrates n'ont pas encore été développées à cause de la complexité de cette classe de biomolécules. Dans ce contexte, nous avons construit un instrument couplant spectroscopie vibrationnelle et spectrométrie de masse (MS/IR) afin de caractériser la structure des carbohydrates grâce à leur signature infrarouge.Dans cette thèse, nous avons démontré que cette métrique permet de différencier les différentes isoméries présentes dans la classe des carbohydrates : la nature des monosaccharides, la position des modifications fonctionnelles ainsi que la régio- et la stéréochimie de la liaison glycosidique. Ensuite la conservation de la structure moléculaire des ions après fragmentation a été démontrée sur des fragments de disaccharides permettant ainsi d'établir les règles du séquençage de carbohydrates par MS/IR. Cette méthode a ensuite été appliquée sur différents oligosaccharides.Enfin dans la dernière partie de ce manuscrit, le potentiel de la spectroscopie IRMPD dans l'infrarouge lointain est exploré pour la résolution des anomères, des isomères et des conformations. Finalement deux approches permettant une séparation en masse et en isomère en amont de l'analyse spectroscopique sont proposées : spectroscopie IRMPD 2 couleurs ou couplage avec la chromatographie liquideSequencing techniques have been established for proteins and DNA and have revolutionised modern biology but similar technique do not exist for carbohydrates due to their unique complexity. In this context, we have built an instrument coupling vibrational spectroscopy and mass spectrometry (MS/IR) dedicated to the structural characterization of carbohydrates.In this thesis, we have shown that the IR signature is a powerful metric which is able to resolve simultaneously all carbohydrate isomerisms: the monosaccharide content, the position of functional modifications, the regiochemistry and the stereochemistry of the glycosidic linkage. Then the conservation of the molecular structure of MS fragments has been revealed on disaccharide fragments. Following this demonstration we have established the carbohydrate sequencing rules using MS/IR and applied them for the determination of the sequence of different oligosaccharides.Finally the potential of the IRMPD spectroscopy in the Far-IR range is explored for anomers, isomers and conformations resolution as well as the utilisation of a two colors infrared spectroscopy or the coupling with an HPLC instrumen

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

Lasers and ion mobility: new additions to the glycosaminoglycanomics toolkit

International audienceGlycosaminoglycans are biopolymers present in mammalian cells or in the extracellular matrix. To address their structure, the nature of the hexuronic acids and the position of sulfate groups must be determined. Tandem mass spectrometry using collision induced dissociation or electron-based fragmentation techniques, is a well-established approach for the identification of glycans but suffers from the frequent lack of diagnostic fragments in the case of glycosaminoglycans. This review presents alternative fragmentation techniques, namely photofragmentation in the IR and the UV ranges. Alternative approaches based on the direct analysis of the molecular structure, including ion mobility spectrometry and ion spectroscopies are reviewed. The potential of future multidimensional workflows for glycosaminoglycanomics is discussed

Fast and accurate hybrid QM//MM approach for computing anharmonic corrections to vibrational frequencies

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Conformational preferences of protonated N -acetylated hexosamines probed by InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy and ab initio calculations

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Spectroscopic diagnostic for the ring-size of carbohydrates in the gas phase: furanose and pyranose forms of GalNAc

International audienceHexoses are mainly found in nature in the pyranose form (6-membered ring). Yet, furanose forms (5-membered ring) are observed in some rare polysaccharides. Using IRMPD spectroscopy (InfraRed Multiple Photon Dissociation), we propose a straightforward diagnostic of the ring-size of N-acetyl galactosamine ions. The furanose form of N-acetyl galactosamine was synthesized and its protonated ion was isolated in an ion trap to measure its gas phase vibrational spectrum by IRMPD. Comparison with the IRMPD spectrum of its pyranose counterpart reveals that they have distinctive optical fingerprints. This new MS-based diagnostic opens the way to facile identification of the ring-size in oligosaccharides. Our experimental data also provide new insights to support the theoretical description of the conformational behavior of the furanose ring, which is notoriously more flexible than the pyranose form but remains difficult to assess

Ion spectroscopy of heterogeneous mixtures: IRMPD and DFT analysis of anomers and conformers of monosaccharides

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