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1. Syntheses and Electrochemical and EPR Studies of Porphyrins Functionalized with Bulky Aromatic Amine Donors

Author

Mary-Ambre Carvalho, Khalissa Merahi, Julien Haumesser, Ana Mafalda Vaz Martins Pereira, Nathalie Parizel, Jean Weiss, Maylis Orio, Vincent Maurel, Laurent Ruhlmann, Sylvie Choua, and Romain Ruppert

Subjects
porphyrinoids, phenothiazine, radical cation, EPR spectroscopy, ENDOR, HYSCORE, Organic chemistry, QD241-441
Abstract

A series of nickel(II) porphyrins bearing one or two bulky nitrogen donors at the meso positions were prepared by using Ullmann methodology or more classical Buchwald–Hartwig amination reactions to create the new C-N bonds. For several new compounds, single crystals were obtained, and the X-ray structures were solved. The electrochemical data of these compounds are reported. For a few representative examples, spectroelectrochemical measurements were used to clarify the electron exchange process. In addition, a detailed electron paramagnetic resonance (EPR) study was performed to estimate the extent of delocalization of the generated radical cations. In particular, electron nuclear double resonance spectroscopy (ENDOR) was used to determine the coupling constants. DFT calculations were conducted to corroborate the EPR spectroscopic data.

Published
2023
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2. ORR activity of metalated phenanthroline-strapped porphyrin adsorbed on carbon nanotubes

Author

Jean Weiss, Renaud Cornut, Bruno Jousselme, Stéphane Campidelli, Jennifer A. Wytko, Manel Hanana, Christophe Kahlfuss, CEA, Université Paris-Saclay (CEA), Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE29-0027,MAGMA,Propriétés Magnétiques du Graphène Fonctionnalisé par des Assemblages Moléculaires Bidimensionnels(2016), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
Oxygen reduction, Phenanthroline, Carbon nanotubes, Carbon nanotube, Électrocatalyse, [CHIM.INOR]Chemical Sciences/Inorganic chemistry, 010402 general chemistry, 01 natural sciences, law.invention, Porphyrin, chemistry.chemical_compound, Adsorption, law, Porphyrine, Polymer chemistry, [CHIM]Chemical Sciences, Electrical and Electronic Engineering, Nanotubes de carbone, Energy, 010405 organic chemistry, Réduction de l'oxygène, Building and Construction, 0104 chemical sciences, chemistry, Énergie, Electrocatalysis
Abstract

International audience; Developing efficient noble metal-free systems for electrocatalysis and the reduction of oxygen (ORR) is crucial for hydrogen economy. Bioinspired hybrids combining iron or copper/iron porphyrins with multiwalled carbon nanotubes were tested for ORR using a rotating ring-disk electrode at pH 13 to 8. The porphyrin-nanotube hybrids exhibited better electrocatalytic properties than their constituents alone due to the electrical network formed by the nanotubes, and they reduced oxygen via a four-electron pathway to produce water. Whereas the presence of Cu was not mandatory to reduce oxygen, its presence improved ORR activity and decreased the overpotential compared to monometalic (iron porphyrin) hybrids.; La conception de matériaux sans métaux nobles pour la réaction de réduction de l'oxygène (ORR) est cruciale pour le développement d'une économie basée sur l'hydrogène. Ici, des matériaux hybrides bioinspirés à base de porphyrines métallées et de nanotubes de carbone multi-parois ont été testés pour l'ORR avec un système d'électrode disque-anneau entre pH 8 et 13. Les matériaux hybrides présentent systématiquement de meilleures propriétés électrocatalytiques que celles de leurs constituants pris individuellement et permettent de réduire l'oxygène par un processus à quatre électrons. La présence du cuivre dans les hybrides n'est pas obligatoire mais elle améliore légèrement les propriétés électrocatalytiques.

Published
2021

3. MAPYRO: the French Fellowship of the Pyrrolic Macrocyclic Ring

Author

Bernard Boitrel, Jean Weiss, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Strasbourg, and Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[CHIM]Chemical Sciences, Building and Construction, Electrical and Electronic Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

4. A New Phenanthroline Ligand and the Spontaneous Resolution of its Homoleptic Copper(I) Complex

Author

Vincent Silber, Jean-Claude Chambron, Lydia Karmazin, Romain Ruppert, Jordan L. Appleton, Jean Weiss, Corinne Bailly, Institut de Chimie de Strasbourg, and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
010405 organic chemistry, Ligand, Phenanthroline, Organic Chemistry, Resolution (electron density), chemistry.chemical_element, 010402 general chemistry, 01 natural sciences, Copper, 0104 chemical sciences, chemistry.chemical_compound, Crystallography, chemistry, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry, Homoleptic, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

5. Revealing the morphology and the magnetic properties of single buried cobalt-ZnTPP hybrid interfaces by ferromagnetic nuclear resonance spectroscopy

Author

Jennifer A. Wytko, Jacek Arabski, Garen Avedissian, Christian Meny, Jean Weiss, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), Université de Strasbourg (UNISTRA)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, and Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)

Subjects
Materials science, Spintronics, chemistry.chemical_element, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, Magnetic anisotropy, symbols.namesake, Chemical bond, Ferromagnetism, chemistry, Chemical physics, 0103 physical sciences, symbols, Molecule, van der Waals force, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 010306 general physics, 0210 nano-technology, Spectroscopy, Cobalt
Abstract

International audience; The deeply buried, yet most important part of any spintronic device is the interface. This is even more interesting and much more complex when soft, light materials like organic molecules are in contact with an inorganic metallic electrode. Hence, exceptional care is required to better understand the phenomena driven by this type of organic/inorganic interfaces. To this end, ferromagnetic nuclear resonance (FNR) spectroscopy studies were performed to investigate the morphology and the magnetic properties of the hybrid organic-inorganic interfaces when zinc tetra-phenyl porphyrin (ZnTPP) molecules are at the vicinity of ferromagnetic metallic cobalt (Co) layers. The FNR experimental results show that when ZnTPP is deposited on top of Co the resulting interface is smoother and sharper compared to the more extended interface obtained when Co is deposited on top of ZnTPP. The shape of the spectra suggests that no chemical bonds take place between the interfacial Co atoms and the ZnTPP molecules and that interactions at the interfaces are governed by weak van der Waals forces. Finally, FNR also showed that the magnetic anisotropy at the Co-ZnTPP hybrid interfaces is reduced compared to the magnetic anisotropy of the Co atoms inside the Co films.

Published
2020

6. Probing the Growth of Organic Molecular Films Embedded between Cobalt and Iron Electrodes: Ferromagnetic Nuclear Resonance Approach

Author

Christian Meny, Jacek Arabski, Jean Weiss, Garen Avedissian, Jennifer A. Wytko, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), and univOAK, Archive ouverte

Subjects
Materials science, Nanostructure, Supramolecular chemistry, Aucun, chemistry.chemical_element, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Biomaterials, chemistry.chemical_compound, Molecular film, Monolayer, Electrochemistry, [CHIM.MATE] Chemical Sciences/Material chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Porphyrin, 0104 chemical sciences, Electronic, Optical and Magnetic Materials, Solid-state nuclear magnetic resonance, Ferromagnetism, chemistry, Chemical physics, 0210 nano-technology, Cobalt
Abstract

Physical properties of magnetic nanostructures and devices strongly depend on the morphological characteristics of their various components. This is especially true and becomes particularly complex in hybrid nanostructures, where soft organic molecules are at the vicinity of ferromagnetic metallic films. The supramolecular architecture of molecular films embedded between iron (Fe) and cobalt (Co) layers, has been investigated by ferromagnetic nuclear resonance (FNR). In such sample architecture, the presence of pin holes in the organic layers is detected by FNR contributions in a specific spectral range. The methodology that has been developed allows probing the continuity and packing of zinc tetra-phenyl porphyrin (ZnTPP) molecular films between the Co and Fe films. The experimental results suggest that, regardless of the nature of the ferromagnetic under-layer, at least 15 monolayers of ZnTPP are necessary to form continuous and pin-hole free molecular films. In addition, quantitative analyses show that ZnTPP layers exhibit distinct morphologies that are dependent on the nature of the ferromagnetic metallic under-layer.

Published
2020

7. Case studies of the radical cation reactivity in meso-aryl and octaethyl porphyrins

Author

Raphaël Lamare, Romain Ruppert, Jean Weiss, Laurent Ruhlmann, Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Laboratoire de Chimie Quantique, Centre National de la Recherche Scientifique (CNRS), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
Access route, 010405 organic chemistry, Chemistry, Aryl, Cationic polymerization, General Chemistry, 010402 general chemistry, 01 natural sciences, Porphyrin, Medicinal chemistry, 0104 chemical sciences, 3. Good health, chemistry.chemical_compound, Radical ion, Nucleophile, Reactivity (chemistry), [CHIM.OTHE]Chemical Sciences/Other
Abstract

The reactivity of porphyrin radical cationic species derived from octaethyl porphyrin (OEP) or meso-aryl porphyrins with nucleophiles, envisioned as an access route to elaborate porphyrin dimers, has been studied and optimized in the case of OEP. Standardized conditions have been applied to various spacers to show that the success of the reaction is mostly nucleophile dependent and that the method has little chances to yield non-linear bis-porphyrins.

Published
2019

8. Modelling haemoproteins: Porphyrins and cyclodextrins as sources of inspiration

Author

Hiroaki Kitagishi, Jennifer A. Wytko, Maxime Vonesch, Koji Kano, Jean Weiss, Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Doshisha University [Kyoto], and Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC)

Subjects
Hemeproteins, Models, Molecular, Porphyrins, 010402 general chemistry, Ligands, 01 natural sciences, Catalysis, chemistry.chemical_compound, Cucurbituril, Materials Chemistry, Molecule, [CHIM]Chemical Sciences, Reactivity (chemistry), [CHIM.COOR]Chemical Sciences/Coordination chemistry, Solubility, Cyclodextrins, Molecular Structure, 010405 organic chemistry, Ligand, Chemistry, Metals and Alloys, Cavitand, Water, General Chemistry, Combinatorial chemistry, Porphyrin, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, Covalent bond, Ceramics and Composites, Hydrophobic and Hydrophilic Interactions
Abstract

International audience; The association of hydrophobic cavities with porphyrin derivatives has been used to mimic haemoproteinstructures. The most employed cavity in this field is b-cyclodextrin (b-CD) and scaffolds combining beta-CDs and porphyrinsare expected to inspire the combination of porphyrins and cucurbiturils in a near future. Aside from providing watersolubility to various porphyrinic structures, the beta-CD framework can also modulate and control the reactivity of the metalcore of the porphyrin. After a general introduction of the challenges faced in the field of haemoprotein models and thebinding behavior of beta-CDs, the article will discuss covalent and non-covalent association of porphyrins with beta-CDs. In eachapproach, the role of the CD differs according to the relative position of the concave CD host, either directly controlling thebinding and transformation of a substrate on the metalloporphyrin or playing a dual role of controlling the water solubilityand selecting the axial ligand of the metal core. The discussion will be of interest to the cucurbituril community as well asto the cavitand community as the information provided should be useful for the design of haemoprotein mimics usingcucurbiturils (CBs).

Published
2019

9. Light triggers molecular shuttling in rotaxanes: control over proximity and charge recombination

Author

Dirk M. Guldi, Jean Weiss, Koji Oohora, Maxime Vonesch, Stéphane Campidelli, Jennifer A. Wytko, Ayumu Ogawa, Mareike Bechtold, Takashi Hayashi, Maximilian Wolf, Inorganic Chemistry, Department of Chemistry and Pharmacy & Interdisciplinary Center for Molecular Materials (ICMM) (ICMM), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka University [Osaka], Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Karlsruhe Institute of Technology (KIT), Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN UMR 3685), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), JSPS KAKENHI (Grant Number JP15H05804 in Innovative Areas 'Precisely Designed Catalysts with Customized Scaffolding'), Deutsche Forschungsgemeinschat DFG (SFB953 Synthetic Carbon Allotropes), the State of Bavaria (SolTech), ANR-14-JTIC-0002,MECANO,Ingenierie moléculaire et assemblages contrôlés de nanoobjets fonctionnels à base de porphyrines(2014), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
Fullerene, Materials science, Chemistry & allied sciences, 010402 general chemistry, Photochemistry, 01 natural sciences, chemistry.chemical_compound, Ultrafast laser spectroscopy, polycyclic compounds, Physics::Atomic and Molecular Clusters, Directionality, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Physics::Biological Physics, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], 010405 organic chemistry, Charge (physics), General Chemistry, Porphyrin, 0104 chemical sciences, Condensed Matter::Soft Condensed Matter, Zinc porphyrin, Solvent, Chemistry, chemistry, ddc:540, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Recombination
Abstract

The lifetime of a charge separated state is enhanced by the effects of solvent polarity and the coordination controlled shuttling of a dumbbell in a porphyrin/fullerene rotaxane., We present the synthesis of novel rotaxanes based on mechanically interlocked porphyrins and fullerene and their advanced investigations by means of photophysical measurements. To this end, a fullerene-capped dumbbell-type axle containing a central triazole was threaded through strapped (metallo)porphyrins—either a free-base or a zinc porphyrin. Femtosecond-resolved transient absorption measurements revealed charge-separation between the porphyrin and fullerene upon light excitation. Solvent polarity and solvent coordination effects induced molecular motion of the rotaxanes upon charge separation and enabled, for the first time, subtle control over the charge recombination by enabling and controlling the directionality of shuttling.

Published
2019
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10. Controlled Growth of Porphyrin Wires at a Solid‐Liquid Interface

Author

Jean Weiss, Yoshihiro Kikkawa, Christophe Kahlfuss, Jennifer A. Wytko, Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), and National Institute of Advanced Industrial Science and Technology (AIST)

Subjects
010405 organic chemistry, Atomic force microscopy, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Interface (computing), Organic Chemistry, 010402 general chemistry, 01 natural sciences, Biochemistry, Porphyrin, Catalysis, 0104 chemical sciences, Inorganic Chemistry, Molecular wire, chemistry.chemical_compound, chemistry, Chemical engineering, Drug Discovery, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Self-assembly, Physical and Theoretical Chemistry, Solid liquid
Abstract

International audience; Bis(zinc porphyrin) scaffolds bearing C8 or C18 alkyl chains and imidazole end groups self‐assembled in a head‐to‐tail fashion into multi‐porphyrin assemblies on both HOPG and mica. Due to weaker molecule surface‐interactions, longer arrays formed on mica than on HOPG. In both cases, it was essential first to generate monomers that were drop casted on the surface, then to allow time for the bis(zinc porphyrins) to assemble. Although thicker fibrous assemblies were observed with the C8 alkyl substituents than with the longer chains, noncovalent assemblies up to 1 μm long were observed for each molecule. These investigations provide a reproducible, noncovalent method to grow porphyrin arrays that may be of interest in molecular electronics for charge transport.

Published
2019

11. Stable isoporphyrin copolymer: Electrochemical mechanism and behavior and photovoltaic properties

Author

Sylvie Choua, Helen Ibrahim, Jean Weiss, Nolwenn Le Breton, Moussa Boudiaf, Antoine Bonnefont, Vasilica Badets, Michel Goldmann, Laurent Ruhlmann, Raphaël Lamare, Yiming Liang, Embarek Bentouhami, Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
Photocurrent, Materials science, General Chemical Engineering, 02 engineering and technology, Quartz crystal microbalance, 010402 general chemistry, 021001 nanoscience & nanotechnology, Photochemistry, 01 natural sciences, 7. Clean energy, Porphyrin, 0104 chemical sciences, Dielectric spectroscopy, Dication, chemistry.chemical_compound, chemistry, Radical ion, Hexafluorophosphate, Electrochemistry, Copolymer, 0210 nano-technology, [CHIM.OTHE]Chemical Sciences/Other
Abstract

Two types of porphyrin copolymer thin films were obtained by electropolymerization of zinc-5,15-bis(p-tolyl)porphyrin. Electrogenerated porphyrin radical cation and dication are powerful electrophiles which can rapidly react with 1,1″-(1,3-propanediyl)bis-4,4′-bipyridinium hexafluorophosphate salt (bpy+–(CH2)3–+bpy·2PF6−) as nucleophiles to form copolymers containing stable isoporphyrin radicals or porphyrins, depending of the applied upper potential limit (1.0 V versus 1.6 V). Electrochemical routes leading to these electroactive copolymers are discussed and the unusual redox properties of copolymers containing stable isoporphyrin radicals are studied. The electropolymerization of the two copolymers was monitored by electrochemical quartz crystal microbalance (EQCM). The copolymers were characterized by UV–Vis–NIR spectroscopy, X-ray photoelectron spectroscopy (XPS), electrochemistry, electron spin resonance (ESR) and atomic force microscopy (AFM). Their electrical properties have been studied by electrochemical impedance spectroscopy and their photovoltaic performances have been investigated by photocurrent transient measurements under visible-NIR light irradiation. The isoporphyrin radical copolymer exhibited considerably better photocurrent generation when compared to the porphyrin copolymer.

Published
2018

12. Ring-Oxidized Zinc(II) Phthalocyanine Cations: Structure, Spectroscopy, and Decomposition Behavior

Author

Romain Ruppert, Sylvie Choua, Wen Zhou, Jean Weiss, Jennifer A. Wytko, Declan McKearney, Daniel B. Leznoff, Yumeela Ganga-Sah, Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Laboratoire de Chimie Quantique, Centre National de la Recherche Scientifique (CNRS), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
010405 organic chemistry, Dimer, chemistry.chemical_element, Protonation, Zinc, 010402 general chemistry, 01 natural sciences, 3. Good health, 0104 chemical sciences, Inorganic Chemistry, Solvent, chemistry.chemical_compound, Crystallography, Monomer, chemistry, Phthalocyanine, Physical and Theoretical Chemistry, Acetonitrile, [CHIM.OTHE]Chemical Sciences/Other, Tetrahydrofuran
Abstract

A bromonium oxidizing agent was used to produce a ring-oxidized zinc phthalocyanine (PcZn), [PcZn(solvent)]•2[BArF4]2 (1·solvent), in good yield. This material is dimeric in the solid state with one axially coordinated solvent [tetrahydrofuran (THF) or 1,2-dimethoxyethane (DME)] and close intradimer ring–ring distances of 3.18 and 3.136 A (THF and DME respectively); this proximity facilitates strong antiferromagnetic coupling to yield diamagnetic dimers. 1·THF is present in solution as a monomer and a dimer. In CH2Cl2, the dimer is favored above 0.1 mM, and it is almost exclusively present in solvents with a high dielectric constant such as acetonitrile. The material 1·THF/DME decomposes in DME to a meso-nitrogen-protonated species, [HPcZn(DME)2][BArF4] (2), which was isolated and represents the first example of such a structurally characterized, protonated, unsubstituted PcM complex. A partially oxidized dimer or “pimer” [(PcZn(DME))2]•[BArF4] (3) was also structurally characterized and has a intradimer ...

Published
2018

13. Development of an electron paramagnetic resonance methodology for studying the photo-generation of reactive species in semiconductor nano-particle assembled films

Author

Youcef Messai, Olivier Felix, Jean Weiss, Gero Decher, Philippe Turek, David Martel, Marek Twardoch, Djamel Eddine Mekki, Yannick Hoarau, Bertrand Vileno, Institut Charles Sadron (ICS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Badji Mokhtar Annaba (UBMA), RENARD (TGE Réseau National de RPE interdisciplinaire - 3443 ), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Strasbourg (UNISTRA)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Descartes - Paris 5 (UPD5)-Université de Lille-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, International Center for Frontier Research in Chemistry [Strasbourg, France] (icFRC), Martel, David, Institut de Mécanique des Fluides et des Solides (IMFS), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), RENARD (TGE Réseau National de RPE interdisciplinaire - 3443), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-FR-CNRS 3443-Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Lille-Sorbonne Université (SU)-Aix Marseille Université (AMU)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-FR-CNRS 3443-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)

Subjects
Materials science, education, Biophysics, Nanoparticle, Nanotechnology, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, nano-particle, law.invention, modelling, Condensed Matter::Materials Science, law, Thin film, Physical and Theoretical Chemistry, Electron paramagnetic resonance, Molecular Biology, ComputingMilieux_MISCELLANEOUS, [PHYS]Physics [physics], business.industry, Chimie/Matériaux, technology, industry, and agriculture, kinetic of photo-generated species, semiconductor, 021001 nanoscience & nanotechnology, Condensed Matter Physics, [PHYS.COND.CM-MS] Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], 0104 chemical sciences, Semiconductor, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Condensed Matter::Strongly Correlated Electrons, EPR, 0210 nano-technology, business
Abstract

International audience; An experimental approach involving electron paramagnetic resonance is proposed for studying photogenerated reactive species in semiconductor nano-particle-based films deposited on the internal wall of glass capillaries. This methodology is applied here to nano-TiO2 and allows a semiquantitative analysis of the kinetic evolutions of radical production using a spin scavenger probe.

Published
2018

14. Fluorescence Commutation and Surface Photopatterning with Porphyrin Tetradithienylethene Switches

Author

Julien Boixel, Jean Weiss, Jennifer A. Wytko, Agostino Galanti, Paolo Samorì, Thomas Biellmann, Véronique Guerchais, Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Institut de Science et d'ingénierie supramoléculaires (ISIS), Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Agence Nationale de la Recherche through the Labex projects CSC within the Investissement d'Avenir program [ANR-10-LABX-0026 CSC, ANR-10-120 IDEX-0002-02], International Center for Frontier Research in Chemistry [JWe-CSC-0001], Universite de Strasbourg, Centre National de la Recherche Scientifique, Universite de Rennes, European Commission through the Marie Sklodowska-Curie project ITN project iSwitch [GA-642196], ANR-10-IDEX-0002,UNISTRA,Par-delà les frontières, l'Université de Strasbourg(2010), European Project: 642196,H2020,H2020-MSCA-ITN-2014,iSwitch(2015), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
010405 organic chemistry, photopatterning, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Organic Chemistry, Free base, porphyrinoids, General Chemistry, Confocal scanning microscopy, 010402 general chemistry, Photochemistry, photochromism, 01 natural sciences, Fluorescence, Porphyrin, Catalysis, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry.chemical_compound, Photochromism, chemistry, dithienylethene, Polystyrene, fluorescence, Absorption (chemistry), Luminescence
Abstract

International audience; Four tetradithienylethene (DTE) substituted porphyrins, the free base 1H(2), and three metal derivatives (1Zn, 1Co, 1Ni), were synthesized and studied. These dyads, for which the DTE units are connected to the porphyrin's meso positions via a meta-phenyl spacer, exhibit reversible photochromic properties in all cases, with conversion to the photostationary state (PSS) up to 88%, as confirmed by absorption and NMR spectroscopies. Compounds1H(2) and 1Zn are fluorescent in solution and display a red emission. Upon irradiation with UV light to trigger the closing of the DTEs, the fluorescence of both the free base and zinc porphyrin was very efficiently quenched in solution. The reversible, photo-switching of luminescence was retained in a tetra-DTE free-base porphyrin-doped polystyrene film, for which photo-patterning was demonstrated by confocal scanning microscopy. The tunable fluorescent properties of this multi-DTE framework render this compound of interest as a photo-rewritable fluorescent ink.

Published
2018

15. A Highly Stable Organic Radical Cation

Author

Monika Stolar, Thomas Baumgartner, Sylvie Choua, Christophe Gourlaouen, Corinne Boudon, Jennifer A. Wytko, Nolwenn Le Breton, Mathilde Berville, Jean Weiss, Laurent Ruhlmann, Jimmy Richard, Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), and York University [Toronto]

Subjects
[CHIM.ORGA]Chemical Sciences/Organic chemistry, Organic Chemistry, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, Photochemistry, 01 natural sciences, Biochemistry, 0104 chemical sciences, Reduction (complexity), chemistry.chemical_compound, chemistry, Radical ion, Surface modification, Physical and Theoretical Chemistry, 0210 nano-technology, Derivative (chemistry)
Abstract

Functionalization of a methylviologen with four methyl ester substituents significantly facilitates the first two reduction steps. The easily generated radical cation shows markedly improved air stability compared to the parent methylviologen, making this derivative of interest in organic electronic applications.

Published
2018

16. Trapping Nanostructures on Surfaces through Weak Interactions

Author

Yoshihiro Kikkawa, Masatoshi Kanesato, Ismail Hijazi, Antoine Goujon, Stéphane Campidelli, Jennifer A. Wytko, Matthieu Koepf, Jean Weiss, Vivien Rauch, Institut de Chimie de Strasbourg, Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), National Institute of Advanced Industrial Science and Technology (AIST), Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN UMR 3685), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), and Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN)

Subjects
chemistry.chemical_classification, Organic Chemistry, General Chemistry, Polyethylene glycol, [CHIM.MATE]Chemical Sciences/Material chemistry, Evaporation (deposition), Catalysis, chemistry.chemical_compound, Molecular wire, chemistry, Highly oriented pyrolytic graphite, Chemical engineering, Organic chemistry, Self-assembly, Mica, Methylcyclohexane, Alkyl
Abstract

International audience; The assembly of imidazole-functionalized phenan-throline-strapped zinc porphyrins (ZnPorphen)w ith alkyl or polyethylene glycol (PEG) side chains was studied in solution and by AFM after casting on highly oriented pyrolytic graphite (HOPG) or mica. The natureo ft he solvent and its evaporation time influenced the morphology of the objectso b-served.O nH OPG, short rods of about 100 nm were observed after fast evaporation of solutions of the alkyl derivatives in CHCl 3 ,T HF,o rp yridine, whereas islands of aligned rows of longer wires were obtained from methylcyclohexane (MCH). Slow evaporation of MCH led to at hree-dimensional assembly. The PEG porphyrin assembled into short wires on HOPG or fibers on mica after slow evaporation of solutions in THF.T his study shows the role of surface–molecule interactions in the interfacial assembly of ZnPorphen derivatives and contributes to understanding the parameters that control their noncovalent assembly into molecular wires on as urface.

Published
2015

17. Hydrogen-Bond Controlled π-Dimerization in Viologen-Appended Calixarenes: Revealing a Subtle Balance of Weak Interactions

Author

Jean Weiss, Eric Saint-Aman, Christophe Bucher, Jennifer A. Wytko, Anne Milet, Christophe Kahlfuss, Département de Chimie Moléculaire - Chimie Inorganique Redox Biomimétique (DCM - CIRE), Département de Chimie Moléculaire (DCM), Université Joseph Fourier - Grenoble 1 (UJF)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Département de Chimie Moléculaire - Chimie Théorique (DCM - CT), Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Département de Chimie Moléculaire - Chimie Inorganique Redox (DCM - CIRE), Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
010405 organic chemistry, Chemistry, Hydrogen bond, Radical, Organic Chemistry, Viologen, Orbital overlap, 010402 general chemistry, 01 natural sciences, Biochemistry, 3. Good health, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Crystallography, Intramolecular force, Calixarene, medicine, Physical and Theoretical Chemistry, ComputingMilieux_MISCELLANEOUS, medicine.drug
Abstract

The intramolecular π-dimerization between two 4,4'-bipyridinium cation radicals directly connected to the wide rim of a calixarene is described. The ability of a phenol-containing calixarene to dimerize in its two-electron-reduced state depends on a subtle balance of weak interactions associated with hydrogen bond formation on the lower rim and orbital overlap between π-radicals on the upper rim.

Published
2015

18. 1D and 3D surface-assisted self-organization

Author

Jennifer A. Wytko, Frédéric Chérioux, Jean Weiss, Matthieu Koepf, Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), and Université de Franche-Comté (UFC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Technologie de Belfort-Montbeliard (UTBM)

Subjects
Surface (mathematics), Self-organization, Nanostructure, Chemistry, Plane (geometry), [CHIM.ORGA]Chemical Sciences/Organic chemistry, Molecular electronics, Nanotechnology, 02 engineering and technology, [CHIM.INOR]Chemical Sciences/Inorganic chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, Characterization (materials science), Inorganic Chemistry, Materials Chemistry, Self-assembly, Physical and Theoretical Chemistry, Layer (object-oriented design), 0210 nano-technology
Abstract

International audience; In view of the many potential applications for functional hybrid interfaces, the controlled assembly of sophisticated structures on surfaces is a current challenge for chemists. Applications can be foreseen in fields such as molecular electronics, spintronics, sensors, catalysis and even synthesis. Independent of their functional nature, the characterization of nano-objects usually involves their deposition on surfaces. Whereas the formation of 2D networks on a surface corresponds to the association of scaffolds of the same dimensionality, 1D and 3D self-organized materials clearly differ from the 2D nature of the support. Unless necessary, organized 2D networks will not be examined in detail, as this subject has been periodically reviewed elsewhere. In this review, concepts originating from the 2D organization, but leading to the surface-assisted production of organized 1D and 3D self-assemblies will be examined and illustrated by selected recent examples from the literature. Three roles can be played by the surface. First, the surface can simply serve as an inert foundation for the organization of the functional layer, which is controlled by molecule-molecule interactions only. Second, the surface can be considered as a template by adding specific constraints to the assembly of the building blocks, restricting their conformational freedom and thus confining the growth in a surface plane or directing the growth of the nanostructures along specific symmetry axes (epitaxy) or surface defects and heterogeneities (step edges). This case seems the most conceptually advanced and has already led to integration of self-assembled materials into devices by using preferred orientations of the surface to align molecules in given directions, for example between interdigitated electrodes. Third, the surface itself can be a source of constituents, or adatoms, of the assembly and can alter the electronic structure of the building blocks, thus directly participating in the assembly process and final function of the structures. The latter case is more scarcely spread over different explorative works in which the major road maps are the successive growth of layers into three dimensions from a preorganized two dimensional (molecular) adlayer, as well as surface-induced reactions within an organized layer.

Published
2012

19. Toward Generic Models of Hemoproteins

Author

Corinne Boudon, Mamadou Lo, Jennifer A. Wytko, Dinesh Mahajan, Jean Weiss, Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), and Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Hemeproteins, Models, Molecular, Hemeprotein, Metalloporphyrins, Pyridines, Stereochemistry, chemistry.chemical_element, Zinc, Resorcinol, Crystallography, X-Ray, Ligands, 010402 general chemistry, Ferric Compounds, 01 natural sciences, Biochemistry, chemistry.chemical_compound, Pyridine, medicine, Molecule, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Physical and Theoretical Chemistry, Molecular Structure, 010405 organic chemistry, Organic Chemistry, Resorcinols, Porphyrin, 0104 chemical sciences, 3. Good health, Claisen rearrangement, chemistry, Ferric, Phenanthrolines, medicine.drug
Abstract

The versatility of a resorcinol-substituted phenanthroline-strapped porphyrin was enhanced by appending allyl chains via a double Claisen rearrangement. Two pyridine arms were then appended to the resorcinol oxygens. This multifunctional porphyrin is a suitable generic building block for the preparation of liposoluble heme protein models. X-ray characterization of the pentacoordinated zinc complex and the binding of a sixth imidazole ligand to the ferric complex both suggest a facilitated access to an empty distal site.

Published
2009

20. Intrinsic structure of acoustic emission events during jerky flow in an Al alloy

Author

Jean Weiss, Mikhail Lebyodkin, T.A. Lebedkina, Torbjorn Lamark, František Chmelík, Claude Fressengeas, Yuri Estrin, Laboratoire de physique et mécanique des matériaux (LPMM), Université Paul Verlaine - Metz (UPVM)-Institut National Polytechnique de Lorraine (INPL)-Ecole Nationale d'Ingénieurs de Metz (ENIM)-Centre National de la Recherche Scientifique (CNRS), Institute of Solid State Physics, Russian Academy of Sciences [Moscow] (RAS), Department of Physics of Materials, Charles University [Prague], Bergen Engineering AS, ARC Centre of Excellence for Design in Light Metals, Monash University [Clayton], Department of Materials Engineering, CSIRO Division of Materials Science and Engineering, Laboratoire de glaciologie et géophysique de l'environnement (LGGE), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Research Plan MSM under Grant No. 0021620834 financed by the Ministry of Education, Youth and Sports of the Czech Republic and from the Czech Science Foundation under Grant No. 106/07/0218., Charles University [Prague] (CU), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), and Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)

Subjects
Materials science, Scale (ratio), Acoustics, Flow (psychology), Alloy, plastic flow, 02 engineering and technology, Plasticity, engineering.material, 01 natural sciences, Stress (mechanics), aluminium alloys, 0103 physical sciences, [SDU.STU.GL]Sciences of the Universe [physics]/Earth Sciences/Glaciology, 010306 general physics, Scaling, Condensed matter physics, self-assembly, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Electronic, Optical and Magnetic Materials, Microsecond, Acoustic emission, engineering, 0210 nano-technology, acoustic emission
Abstract

International audience; Scaling behavior is found in acoustic-emission events associated with stress drops observed in velocity-driven plastic deformation of an Al alloy, which exhibits jerky plastic flow. The occurrence of scaling proves that these acoustic-emission events, which are commonly regarded as “elementary” ones, have a small-scale self-organized structure comprising a group of peaks correlated in time. This structure reveals details of the temporal variation in elementary plastic events at a microsecond scale, which are hardly accessible by other measurement techniques.

Published
2009

21. Genetic Analysis of Citrobacter sp.86 Reveals Involvement of Corrinoids in Chlordecone and Lindane Biotransformations

Author

Agnès Barbance, Oriane Della-Negra, Sébastien Chaussonnerie, Valérie Delmas, Delphine Muselet, Edgardo Ugarte, Pierre-Loïc Saaidi, Jean Weissenbach, Cécile Fischer, Denis Le Paslier, and Nuria Fonknechten

Subjects
chlordecone, lindane, dechlorination, corrinoid, cobalamin, Citrobacter, Microbiology, QR1-502
Abstract

Chlordecone (Kepone®) and γ-hexachlorocyclohexane (γ-HCH or lindane) have been used for decades in the French West Indies (FWI) resulting in long-term soil and water pollution. In a previous work, we have identified a new Citrobacter species (sp.86) that is able to transform chlordecone into numerous products under anaerobic conditions. No homologs to known reductive dehalogenases or other candidate genes were found in the genome sequence of Citrobacter sp.86. However, a complete anaerobic pathway for cobalamin biosynthesis was identified. In this study, we investigated whether cobalamin or intermediates of cobalamin biosynthesis was required for chlordecone microbiological transformation. For this purpose, we constructed a set of four Citrobacter sp.86 mutant strains defective in several genes belonging to the anaerobic cobalamin biosynthesis pathway. We monitored chlordecone and its transformation products (TPs) during long-term incubation in liquid cultures under anaerobic conditions. Chlordecone TPs were detected in the case of cobalamin-producing Citrobacter sp.86 wild-type strain but also in the case of mutants able to produce corrinoids devoid of lower ligand. In contrast, mutants unable to insert the cobalt atom in precorrin-2 did not induce any transformation of chlordecone. In addition, it was found that lindane, previously shown to be anaerobically transformed by Citrobacter freundii without evidence of a mechanism, was also degraded in the presence of the wild-type strain of Citrobacter sp.86. The lindane degradation abilities of the various Citrobacter sp.86 mutant strains paralleled chlordecone transformation. The present study shows the involvement of cobalt-containing corrinoids in the microbial degradation of chlorinated compounds with different chemical structures. Their increased production in contaminated environments could accelerate the decontamination processes.

Published
2020
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26. Microbial degradation of a recalcitrant pesticide: chlordecone.

Author

Sébastien Chaussonnerie, Pierre-Loic Saaidi, Edgardo Ugarte, Agnès Barbance, Aurélie Fossey, Valerie Barbe, Gabor Gyapay, Thomas Brüls, Marion Chevallier, Loic Couturat, Stéphanie Fouteau, Delphine Muselet, Emilie Pateau, Georges N Cohen, Nuria Fonknechten, Jean Weissenbach, and Denis Le Paslier

Subjects
Chlordecone, Citrobacter, Metagenomics, Pesticides, Analytical Chemistry, GC-MS, Microbiology, QR1-502
Abstract

Chlordecone (Kepone®) is a synthetic organochlorine insecticide (C10Cl10O) used worldwide mostly during the 1970s and 1980s. Its intensive application in the French West Indies to control the banana black weevil Cosmopolites sordidus led to a massive environmental pollution. Persistence of chlordecone in soils and water for numerous decades even centuries causes global public health and socio-economic concerns. In order to investigate the biodegradability of chlordecone, microbial enrichment cultures from soils contaminated by chlordecone or other organochlorines and from sludge of a wastewater treatment plant have been conducted. Different experimental procedures including original microcosms were carried out anaerobically over long periods of time. GC-MS monitoring resulted in the detection of chlorinated derivatives in several cultures, consistent with chlordecone biotransformation. More interestingly, disappearance of chlordecone (50 µg/mL) in two bacterial consortia was concomitant with the accumulation of a major metabolite of formula C9Cl5H3 (named B1) as well as two minor metabolites C10Cl9HO (named A1) and C9Cl4H4 (named B3). Finally, we report the isolation and the complete genomic sequences of two new Citrobacter isolates, closely related to Citrobacter amalonaticus, and that were capable of reproducing chlordecone transformation. Further characterization of these Citrobacter strains should yield deeper insights into the mechanisms involved in this transformation process.

Published
2016
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27. Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass.

Author

Magali Boutard, Tristan Cerisy, Pierre-Yves Nogue, Adriana Alberti, Jean Weissenbach, Marcel Salanoubat, and Andrew C Tolonen

Subjects
Genetics, QH426-470
Abstract

Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), and anaerobic growth screening. We apply this method to study how the bacterium Clostridium phytofermentans ferments plant biomass components including glucans, mannans, xylans, galactans, pectins, and arabinans. These polysaccharides are fermented with variable efficiencies, and diauxies prioritize metabolism of preferred substrates. Strand-specific RNA-seq reveals how this bacterium responds to polysaccharides by up-regulating specific groups of CAZymes, transporters, and enzymes to metabolize the constituent sugars. Fifty-six up-regulated CAZymes were purified, and their activities show most polysaccharides are degraded by multiple enzymes, often from the same family, but with divergent rates, specificities, and cellular localizations. CAZymes were then tested in combination to identify synergies between enzymes acting on the same substrate with different catalytic mechanisms. We discuss how these results advance our understanding of how microbes degrade and metabolize plant biomass.

Published
2014
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28. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Author

Nikos C Kyrpides, Philip Hugenholtz, Jonathan A Eisen, Tanja Woyke, Markus Göker, Charles T Parker, Rudolf Amann, Brian J Beck, Patrick S G Chain, Jongsik Chun, Rita R Colwell, Antoine Danchin, Peter Dawyndt, Tom Dedeurwaerdere, Edward F DeLong, John C Detter, Paul De Vos, Timothy J Donohue, Xiu-Zhu Dong, Dusko S Ehrlich, Claire Fraser, Richard Gibbs, Jack Gilbert, Paul Gilna, Frank Oliver Glöckner, Janet K Jansson, Jay D Keasling, Rob Knight, David Labeda, Alla Lapidus, Jung-Sook Lee, Wen-Jun Li, Juncai Ma, Victor Markowitz, Edward R B Moore, Mark Morrison, Folker Meyer, Karen E Nelson, Moriya Ohkuma, Christos A Ouzounis, Norman Pace, Julian Parkhill, Nan Qin, Ramon Rossello-Mora, Johannes Sikorski, David Smith, Mitch Sogin, Rick Stevens, Uli Stingl, Ken-Ichiro Suzuki, Dorothea Taylor, Jim M Tiedje, Brian Tindall, Michael Wagner, George Weinstock, Jean Weissenbach, Owen White, Jun Wang, Lixin Zhang, Yu-Guang Zhou, Dawn Field, William B Whitman, George M Garrity, and Hans-Peter Klenk

Subjects
Biology (General), QH301-705.5
Abstract

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

Published
2014
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29. Proteome adaptation to high temperatures in the ectothermic hydrothermal vent Pompeii worm.

Author

Didier Jollivet, Jean Mary, Nicolas Gagnière, Arnaud Tanguy, Eric Fontanillas, Isabelle Boutet, Stéphane Hourdez, Béatrice Segurens, Jean Weissenbach, Olivier Poch, and Odile Lecompte

Subjects
Medicine, Science
Abstract

Taking advantage of the massive genome sequencing effort made on thermophilic prokaryotes, thermal adaptation has been extensively studied by analysing amino acid replacements and codon usage in these unicellular organisms. In most cases, adaptation to thermophily is associated with greater residue hydrophobicity and more charged residues. Both of these characteristics are positively correlated with the optimal growth temperature of prokaryotes. In contrast, little information has been collected on the molecular 'adaptive' strategy of thermophilic eukaryotes. The Pompeii worm A. pompejana, whose transcriptome has recently been sequenced, is currently considered as the most thermotolerant eukaryote on Earth, withstanding the greatest thermal and chemical ranges known. We investigated the amino-acid composition bias of ribosomal proteins in the Pompeii worm when compared to other lophotrochozoans and checked for putative adaptive changes during the course of evolution using codon-based Maximum likelihood analyses. We then provided a comparative analysis of codon usage and amino-acid replacements from a greater set of orthologous genes between the Pompeii worm and Paralvinella grasslei, one of its closest relatives living in a much cooler habitat. Analyses reveal that both species display the same high GC-biased codon usage and amino-acid patterns favoring both positively-charged residues and protein hydrophobicity. These patterns may be indicative of an ancestral adaptation to the deep sea and/or thermophily. In addition, the Pompeii worm displays a set of amino-acid change patterns that may explain its greater thermotolerance, with a significant increase in Tyr, Lys and Ala against Val, Met and Gly. Present results indicate that, together with a high content in charged residues, greater proportion of smaller aliphatic residues, and especially alanine, may be a different path for metazoans to face relatively 'high' temperatures and thus a novelty in thermophilic metazoans.

Published
2012
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30. A holistic approach to marine eco-systems biology.

Author

Eric Karsenti, Silvia G Acinas, Peer Bork, Chris Bowler, Colomban De Vargas, Jeroen Raes, Matthew Sullivan, Detlev Arendt, Francesca Benzoni, Jean-Michel Claverie, Mick Follows, Gaby Gorsky, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels-Lewis, Uros Krzic, Fabrice Not, Hiroyuki Ogata, Stéphane Pesant, Emmanuel Georges Reynaud, Christian Sardet, Michael E Sieracki, Sabrina Speich, Didier Velayoudon, Jean Weissenbach, Patrick Wincker, and Tara Oceans Consortium

Subjects
Biology (General), QH301-705.5
Abstract

The structure, robustness, and dynamics of ocean plankton ecosystems remain poorly understood due to sampling, analysis, and computational limitations. The Tara Oceans consortium organizes expeditions to help fill this gap at the global level.

Published
2011
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31. The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment.

Author

Gilles De Luca, Mohamed Barakat, Philippe Ortet, Sylvain Fochesato, Cécile Jourlin-Castelli, Mireille Ansaldi, Béatrice Py, Gwennaele Fichant, Pedro M Coutinho, Romé Voulhoux, Olivier Bastien, Eric Maréchal, Bernard Henrissat, Yves Quentin, Philippe Noirot, Alain Filloux, Vincent Méjean, Michael S DuBow, Frédéric Barras, Valérie Barbe, Jean Weissenbach, Irina Mihalcescu, André Verméglio, Wafa Achouak, and Thierry Heulin

Subjects
Medicine, Science
Abstract

Ramlibacter tataouinensis TTB310(T) (strain TTB310), a betaproteobacterium isolated from a semi-arid region of South Tunisia (Tataouine), is characterized by the presence of both spherical and rod-shaped cells in pure culture. Cell division of strain TTB310 occurs by the binary fission of spherical "cyst-like" cells ("cyst-cyst" division). The rod-shaped cells formed at the periphery of a colony (consisting mainly of cysts) are highly motile and colonize a new environment, where they form a new colony by reversion to cyst-like cells. This unique cell cycle of strain TTB310, with desiccation tolerant cyst-like cells capable of division and desiccation sensitive motile rods capable of dissemination, appears to be a novel adaptation for life in a hot and dry desert environment. In order to gain insights into strain TTB310's underlying genetic repertoire and possible mechanisms responsible for its unusual lifestyle, the genome of strain TTB310 was completely sequenced and subsequently annotated. The complete genome consists of a single circular chromosome of 4,070,194 bp with an average G+C content of 70.0%, the highest among the Betaproteobacteria sequenced to date, with total of 3,899 predicted coding sequences covering 92% of the genome. We found that strain TTB310 has developed a highly complex network of two-component systems, which may utilize responses to light and perhaps a rudimentary circadian hourglass to anticipate water availability at the dew time in the middle/end of the desert winter nights and thus direct the growth window to cyclic water availability times. Other interesting features of the strain TTB310 genome that appear to be important for desiccation tolerance, including intermediary metabolism compounds such as trehalose or polyhydroxyalkanoate, and signal transduction pathways, are presented and discussed.

Published
2011
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32. A novel acyl-CoA beta-transaminase characterized from a metagenome.

Author

Alain Perret, Christophe Lechaplais, Sabine Tricot, Nadia Perchat, Carine Vergne, Christine Pellé, Karine Bastard, Annett Kreimeyer, David Vallenet, Anne Zaparucha, Jean Weissenbach, and Marcel Salanoubat

Subjects
Medicine, Science
Abstract

BackgroundBacteria are key components in all ecosystems. However, our knowledge of bacterial metabolism is based solely on the study of cultivated organisms which represent just a tiny fraction of microbial diversity. To access new enzymatic reactions and new or alternative pathways, we investigated bacterial metabolism through analyses of uncultivated bacterial consortia.Methodology/principal findingsWe applied the gene context approach to assembled sequences of the metagenome of the anaerobic digester of a municipal wastewater treatment plant, and identified a new gene which may participate in an alternative pathway of lysine fermentation.ConclusionsWe characterized a novel, unique aminotransferase that acts exclusively on Coenzyme A (CoA) esters, and proposed a variant route for lysine fermentation. Results suggest that most of the lysine fermenting organisms use this new pathway in the digester. Its presence in organisms representative of two distinct bacterial divisions indicate that it may also be present in other organisms.

Published
2011
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33. Structure, function, and evolution of the Thiomonas spp. genome.

Author

Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean-Yves Coppée, Michael Chandler, Violaine Bonnefoy, Céline Brochier-Armanet, Mohamed Barakat, Valérie Barbe, Fabienne Battaglia-Brunet, Odile Bruneel, Christopher G Bryan, Jessica Cleiss-Arnold, Stéphane Cruveiller, Mathieu Erhardt, Audrey Heinrich-Salmeron, Florence Hommais, Catherine Joulian, Evelyne Krin, Aurélie Lieutaud, Didier Lièvremont, Caroline Michel, Daniel Muller, Philippe Ortet, Caroline Proux, Patricia Siguier, David Roche, Zoé Rouy, Grégory Salvignol, Djamila Slyemi, Emmanuel Talla, Stéphanie Weiss, Jean Weissenbach, Claudine Médigue, and Philippe N Bertin

Subjects
Genetics, QH426-470
Abstract

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live.

Published
2010
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34. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

Author

Stéphane Vuilleumier, Ludmila Chistoserdova, Ming-Chun Lee, Françoise Bringel, Aurélie Lajus, Yang Zhou, Benjamin Gourion, Valérie Barbe, Jean Chang, Stéphane Cruveiller, Carole Dossat, Will Gillett, Christelle Gruffaz, Eric Haugen, Edith Hourcade, Ruth Levy, Sophie Mangenot, Emilie Muller, Thierry Nadalig, Marco Pagni, Christian Penny, Rémi Peyraud, David G Robinson, David Roche, Zoé Rouy, Channakhone Saenampechek, Grégory Salvignol, David Vallenet, Zaining Wu, Christopher J Marx, Julia A Vorholt, Maynard V Olson, Rajinder Kaul, Jean Weissenbach, Claudine Médigue, and Mary E Lidstrom

Subjects
Medicine, Science
Abstract

BACKGROUND:Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. METHODOLOGY/PRINCIPAL FINDINGS:The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid). CONCLUSION/SIGNIFICANCE:These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.

Published
2009
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35. Comparative analysis of Acinetobacters: three genomes for three lifestyles.

Author

David Vallenet, Patrice Nordmann, Valérie Barbe, Laurent Poirel, Sophie Mangenot, Elodie Bataille, Carole Dossat, Shahinaz Gas, Annett Kreimeyer, Patricia Lenoble, Sophie Oztas, Julie Poulain, Béatrice Segurens, Catherine Robert, Chantal Abergel, Jean-Michel Claverie, Didier Raoult, Claudine Médigue, Jean Weissenbach, and Stéphane Cruveiller

Subjects
Medicine, Science
Abstract

Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.

Published
2008
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36. A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

Author

Daniel Muller, Claudine Médigue, Sandrine Koechler, Valérie Barbe, Mohamed Barakat, Emmanuel Talla, Violaine Bonnefoy, Evelyne Krin, Florence Arsène-Ploetze, Christine Carapito, Michael Chandler, Benoît Cournoyer, Stéphane Cruveiller, Caroline Dossat, Simon Duval, Michael Heymann, Emmanuelle Leize, Aurélie Lieutaud, Didier Lièvremont, Yuko Makita, Sophie Mangenot, Wolfgang Nitschke, Philippe Ortet, Nicolas Perdrial, Barbara Schoepp, Patricia Siguier, Diliana D Simeonova, Zoé Rouy, Béatrice Segurens, Evelyne Turlin, David Vallenet, Alain Van Dorsselaer, Stéphanie Weiss, Jean Weissenbach, Marie-Claire Lett, Antoine Danchin, and Philippe N Bertin

Subjects
Genetics, QH426-470
Abstract

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the beta-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.

Published
2007
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37. Comparative genomics of multidrug resistance in Acinetobacter baumannii.

Author

Pierre-Edouard Fournier, David Vallenet, Valérie Barbe, Stéphane Audic, Hiroyuki Ogata, Laurent Poirel, Hervé Richet, Catherine Robert, Sophie Mangenot, Chantal Abergel, Patrice Nordmann, Jean Weissenbach, Didier Raoult, and Jean-Michel Claverie

Subjects
Genetics, QH426-470
Abstract

Acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. This organism was susceptible to most antibiotics in the 1970s. It has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. Here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resistant A. baumannii strain AYE, which is epidemic in France, as well as to investigate the mechanisms of their acquisition by comparison with the fully susceptible A. baumannii strain SDF, which is associated with human body lice. The assembly of the whole shotgun genome sequences of the strains AYE and SDF gave an estimated size of 3.9 and 3.2 Mb, respectively. A. baumannii strain AYE exhibits an 86-kb genomic region termed a resistance island--the largest identified to date--in which 45 resistance genes are clustered. At the homologous location, the SDF strain exhibits a 20 kb-genomic island flanked by transposases but devoid of resistance markers. Such a switching genomic structure might be a hotspot that could explain the rapid acquisition of resistance markers under antimicrobial pressure. Sequence similarity and phylogenetic analyses confirm that most of the resistance genes found in the A. baumannii strain AYE have been recently acquired from bacteria of the genera Pseudomonas, Salmonella, or Escherichia. This study also resulted in the discovery of 19 new putative resistance genes. Whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance.

Published
2006
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39. Exploring biochemical diversity in bacteria

Author

JEAN WEISSENBACH

Subjects
bacterial metabolism, biochemical function, enzyme discovery, genome annotation, bioremediation, Science
Abstract

Abstract Abstract: The various descriptors of biochemical diversity and an evaluation of its status of knowledge are briefly outlined. Using a few examples from in house research projects, I illustrate strategies used to increase this knowledge. Because bacteria represent an extremely diverse domain of life and carry out the widest known range of biochemical transformations, this mini-review focusses on bacteria.

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