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1. Three-Dimensional-Printed Device for In Situ Monitoring of an Organic Redox-Flow Battery via NMR/MRI

Author: Borja Caja-Munoz, Kévin Chighine, Jean-Pierre Dognon, Lionel Dubois, and Patrick Berthault
Subjects: Analytical Chemistry
Published: 2023
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2. Determining nuclear quadrupole moments of Bi and Sb from molecular data

Author: Jean-Pierre Dognon and Pekka Pyykkö
Subjects: General Physics and Astronomy, Physical and Theoretical Chemistry
Abstract: An independent value of −422(3) millibarn (mb) is obtained for the nuclear quadrupole moment Q(209Bi) using experimental coupling constants for diatomic BiN, BiP, BiF, BiCl, and BiI, combined with full-Dirac CCSD-T calculations of the field gradient q.
Published: 2023
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3. New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: From ab initio to molecular dynamics.

Author: Jean-Francois Fuchs, Hristo Nedev, David Poger, Michel Ferrand, Valérie Brenner, Jean-Pierre Dognon, and Serge Crouzy
Published: 2006
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4. Can we understand the different coordinations and structures of closed-shell metal cation-water clusters?

Author: A.-L. Derepas, J.-M. Soudan, Valérie Brenner, Jean-Pierre Dognon, and Ph. Millié
Published: 2002
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5. Large shape staggering in neutron-deficient Bi isotopes

Author: A.V. Oleynichenko, Julian C. Berengut, Mark Bissell, Jean-Pierre Dognon, K. Chrysalidis, R. F. Garcia Ruiz, V. N. Fedosseev, B. Andel, Sacha Schiffmann, V. Panteleev, C. Raison, B. A. Marsh, C. Seiffert, G. J. Farooq-Smith, Magdalena Elantkowska, D. V. Fedorov, J. Karls, Thomas Elias Cocolios, Ephraim Eliav, Andréi Zaitsevskii, Sebastian Rothe, M. D. Seliverstov, Dominik Studer, M. Huyse, M. Al Monthery, Kara Marie Lynch, P. Mosat, K. Rezynkina, P. Van Duppen, P. Molkanov, L. V. Skripnikov, M. L. Reitsma, Ralf Erik Rossel, A. Barzakh, M. Stryjczyk, S. Péru, S. Sels, S. Hilaire, C. Granados, R. D. Harding, P. Larmonier, R. Heinke, J. G. Li (李冀光), S. Goriely, Anastasia Borschevsky, L. P. Gaffney, Jacek Bieron, Andrei Andreyev, T. Day Goodacre, Jarosław Ruczkowski, Michel Godefroid, M. Verlinde, Sebastian Wilman, S. Antalic, D. E. Maison, J. G. Cubiss, Pekka Pyykkö, National Research Centre 'Kurchatov Institute': Petersburg Nuclear Physics Institute, Department of Physics, University of York, Heslington, York YO10 5DD, United Kingdom, Advanced Science Research Center and Nuclear Science Research Institute, Japan Atomic Energy Agency, Japan Atomic Energy Agency, Instituut voor Kern- en Stralingsfysica (K.U. LEUVEN), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Laboratoire Matière sous Conditions Extrêmes (LMCE), DAM Île-de-France (DAM/DIF), Direction des Applications Militaires (DAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction des Applications Militaires (DAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut d'Astronomie et d'Astrophysique [Bruxelles] (IAA), Université libre de Bruxelles (ULB), Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, School of Physics, University of New South Wales [Canberra Campus] (UNSW), Instytut Fizyki Teoretycznej, Uniwersytet Warszawski, School of Physics and Astronomy [Manchester], University of Manchester [Manchester], Van Swinderen Institute, University of Groningen [Groningen], European Organization for Nuclear Research (CERN), Institut für Physik Johannes Gutenberg Universität, Johannes Gutenberg - Universität Mainz (JGU), TRIUMF [Vancouver], Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), 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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Poznan University of Technology (PUT), School of Chemistry, Tel Aviv University [Tel Aviv], School of Computing and Engineering [London] (https://www.uwl.ac.uk/academic-schools/computing), University of West London, Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), CERC - Centre d'Études et de Recherches Comparatistes - EA 172 (CERC), Université Sorbonne Nouvelle - Paris 3, Department of Physics [Gothenburg], University of Gothenburg (GU), Institute of Applied Physics and Computational Mathematics [Beijing] (IAPCM), China Academy of Engineering Physics (CAEP), Saint Petersburg State University (SPBU), Department of Chemistry, Lomonosov Moscow State University, Lomonosov Moscow State University (MSU), Department of Chemistry [Helsinki], Falculty of Science [Helsinki], University of Helsinki-University of Helsinki, University of Jyväskylä (JYU), National Natural Science Foundation of China under Grant No. 11874090, Fonds de la Recherche Scientifique (F. R. S.-FNRS) and the Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO) under the EOS Project No. O022818F, by GOA/2015/010 (BOF KU Leuven), U.K. Science and Technology Facilities Council, Slovak Research and Development Agency (Contract No. APVV-18-0268), the Slovak grant agency VEGA (Contract No. 1/0651/21), RFBR according to the research projects N 19-02-00005 and N 20-32-70177, the Russian Science Foundation (Grant No. 19-72-10019), The foundation for the advancement of theoretical physics and mathematics 'BASIS' grant according to Projects No. 21-1-2-47-1 and No. 20-1-5-76-1, European Project: 771036,MAIDEN, European Project: 654002,H2020,H2020-INFRAIA-2014-2015,ENSAR2(2016), Comenius University in Bratislava, Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), 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), Tel Aviv University (TAU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Precision Frontier, and Department of Chemistry
Subjects: Physics, Magnetic moment, 010308 nuclear & particles physics, 116 Chemical sciences, General Physics and Astronomy, [CHIM.MATE]Chemical Sciences/Material chemistry, 01 natural sciences, Physique atomique et nucléaire, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Charge radius, Neutron number, 0103 physical sciences, Quadrupole, Nuclear Physics - Experiment, Neutron, Atomic physics, 010306 general physics, Spin (physics), Ground state, Magnetic dipole
Abstract: The changes in the mean-square charge radius (relative to 209Bi), magnetic dipole, and electric quadrupole moments of 187,188,189,191Bi were measured using the in-source resonance-ionization spectroscopy technique at ISOLDE (CERN). A large staggering in radii was found in 187,188,189Big, manifested by a sharp radius increase for the ground state of 188Bi relative to the neighboring 187,189Big. A large isomer shift was also observed for 188Bim. Both effects happen at the same neutron number, N=105, where the shape staggering and a similar isomer shift were observed in the mercury isotopes. Experimental results are reproduced by mean-field calculations where the ground or isomeric states were identified by the blocked quasiparticle configuration compatible with the observed spin, parity, and magnetic moment. ispartof: Physical Review Letters vol:127 issue:9 ispartof: location:United States status: published
Published: 2021
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6. Reaction Mechanisms of the Degradation of Fluoroethylene Carbonate, an Additive of Lithium-Ion Batteries, Unraveled by Radiation Chemistry

Author: Sergey A. Denisov, Viacheslav Shcherbakov, Philippe Moreau, Marin Puget, Sophie Le Caër, Jean-Pierre Dognon, and Mehran Mostafavi
Subjects: Reaction mechanism, 010405 organic chemistry, Organic Chemistry, Solvation, chemistry.chemical_element, General Chemistry, Electrolyte, Radiation chemistry, 010402 general chemistry, Photochemistry, 01 natural sciences, Catalysis, 0104 chemical sciences, Ion, chemistry, Radiolysis, Oxidizing agent, Lithium
Abstract: Numerous additives are used in the electrolytes of lithium-ion batteries, especially for the formation of an efficient solid electrolyte interphase at the surface of the electrodes. Understanding the degradation processes of these compounds is thus important; they can be seen through radiolysis. In the case of fluoroethylene carbonate (FEC), picosecond pulse radiolysis experiments evidenced the formation of FEC.- . This radical is stabilized in neat FEC, whereas the ring opens to form more stable radical anions when FEC is a solute in other solvents, as confirmed by quantum chemistry calculations. In neat FEC, pre-solvated electrons primarily undergo attachment rather than solvation. On long timescales, the gases produced (H2 , CO, and CO2 ) were quantified. A reaction scheme for both the oxidizing and reducing pathways at stake in irradiated FEC is proposed. This work shows that the nature of the primary species formed in FEC depends on the amount of FEC in the solution.
Published: 2021

7. Reaction Mechanisms of Fluoroethylene Carbonate Degradation, an Additive of Lithium-Ion Batteries, Unraveled by Radiation Chemistry

Author: Marin Puget, Viacheslav Shcherbakov, Sergey Denisov, Moreau, P., Jean-Pierre Dognon, Mehran Mostafavi, Sophie Le Caer, Laboratoire Interdisciplinaire sur l'Organisation Nanométrique et Supramoléculaire (LIONS), 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), Institut de Chimie Physique (ICP), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), 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), 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), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN), Fondation Maison de la Chimie, French EMIR&A network, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - Ecole Polytechnique de l'Université de Nantes (Nantes Univ - EPUN), and Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)
Subjects: [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry
Abstract: International audience; Numerous additives are used in electrolytes of lithium-ion batteries, especially for the formation of efficient solid electrolyteinterphase at the surface of the electrodes. It is, therefore, necessary to elucidate the degradation processes of these compoundssince it directly affects the lifetime of the battery. These mechanisms can be obtained through radiolysis. In this work, weinvestigated the degradation mechanisms induced by irradiation in fluoroethylene carbonate (FEC), a cyclic carbonate, whichis an additive commonly used in lithium-ion batteries. The first reaction steps were studied by pulse radiolysis. At longtimescales, the radiolytic yields of produced gases (H$_2$, CO, and CO$_2$) were quantified. Pulse radiolysis experimentsevidenced the formation of the FEC$^{●-}$ radical anion, characterized by an absorption band centered ca. 430 nm. The radicalanion is not detected when FEC is solubilized in other solvents: ethanol, diethylcarbonate, etc. This radical is indeed stabilizedin neat FEC, whereas the ring opens to form more stable radical anions when FEC is a solute in other solvents, as confirmedby calculations. A multi-species deconvolution of the spectrum measured in pure FEC revealed a small absorption bandcentered around 560 nm, attributed to the solvated electron, decaying in ca. 100 ps. In neat FEC, excess electrons primarilyundergo attachment compared to solvation. Together with gas chromatography coupled to mass spectrometry measurements,all these observations have allowed us to propose a reaction scheme for both the oxidizing and reducing pathways at stake inirradiated FEC. This work gives clues for the reaction mechanisms undergone by FEC present in electrolytes of lithium-ionbatteries and evidences that the nature of the primary species formed in FEC depends on the amount of FEC in the solution
Published: 2021
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8. Maximizing Chiral Perturbation on Thermally Activated Delayed Fluorescence Emitters and Elaboration of the First Top‐Emission Circularly Polarized OLED

Author: Sylvia Meunier-Della-Gatta, Pierre Thuéry, Alaric Desmarchelier, Ludovic Favereau, Benoit Racine, Gilles Muller, Romain Plais, Etienne Quesnel, Lucas Frédéric, Jeanne Crassous, Leonid Lavnevich, Cassie Villafuerte, Jean-Pierre Dognon, Grégory Pieters, Gilles Clavier, Service de Chimie Bio-Organique et de Marquage (SCBM), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Chemistry [San José], San Jose State University [San José] (SJSU), Photophysique et Photochimie Supramoléculaires et Macromoléculaires (PPSM), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), 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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire de Chimie Moléculaire et de Catalyse pour l'Energie (ex LCCEF) (LCMCE), 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), 'Programme Transverse de Compétences du CEA' (POLEM project), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-19-CE07-0040,iChiralight,Molécules Chirales Innovantes pour la Construction de Dispositifs Emetteurs de Lumière Circulairement Polarisée Performants(2019), San Jose State University [San Jose] (SJSU), 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), 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: Materials science, Perturbation (astronomy), 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Article, law.invention, Biomaterials, chemistry.chemical_compound, law, Electrochemistry, OLED, Aggregation-induced emission, Common emitter, Carbazole, business.industry, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Fluorescence, Circularly Polarized Luminescence, Aggregation induced emission, 0104 chemical sciences, Electronic, Optical and Magnetic Materials, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry, Optoelectronics, 0210 nano-technology, Luminescence, business, Thermally Activated Delayed Fluorescence, Light-emitting diode
Abstract: International audience; Molecular designs merging circularly polarized luminescence (CPL) and thermally activated delayed fluorescence (CP-TADF) using the concept of chiral perturbation appeared recently as a cornerstone for the development of efficient CP-organic light emitting diodes (CP-OLED). Such devices could strongly increase the energy efficiency and performances of conventional OLED displays, in which 50% of the emitted light is often lost due to the use of antiglare filters. In this context, herein, ten couples of enantiomers derived from novel chiral emitter designs are reported, exhibiting CPL, TADF, and aggregation induced enhancement emission properties (AIEE). Representing the first structure properties relationship investigation for CP-TADF materials, this thorough experimental and theoretical work brings crucial findings on the key structural and electronic parameters (isomerism, nature of the carbazole substituents) governing the synergy between CPL and TADF properties. To conclude this study, the first top emission CP-OLED is elaborated as a new approach of generating CP light in comparison with classical bottom-emission CP-OLED architecture. Indeed, the top-emission configuration represents the only relevant device architecture for future microdisplay applications. Thereby, in addition to offer molecular guidelines to combine efficiently TADF and CPL properties, this study opens new avenues toward practical applications for CP-OLEDs.
Published: 2020
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9. Functionalization of Bambusurils by a Thiol-Ene Click Reaction and a Facile Method for the Preparation of Anion-Free Bambus[6]urils

Author: Pierre Thuéry, Jean-Pierre Dognon, Marie-Pierre Heck, Gaspard Huber, Julie Rivollier, Marine Lafosse, Michel Meyer, Djamille Azazna, Jialan Wang, Imen Ben Cheikh, Service de Chimie Bio-Organique et de Marquage (SCBM), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Chimie Moléculaire et de Catalyse pour l'Energie (ex LCCEF) (LCMCE), 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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), NEEDS program (project BambiDetex), 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), and 'NEEDS BLanc' program (project BambiDetex)
Subjects: chemistry.chemical_classification, [CHIM.ORGA]Chemical Sciences/Organic chemistry, 010405 organic chemistry, Organic Chemistry, Iodide, General Chemistry, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, 01 natural sciences, Medicinal chemistry, Quantum chemistry, Catalysis, Coupling reaction, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry.chemical_compound, chemistry, Bromide, [CHIM.CRIS]Chemical Sciences/Cristallography, Click chemistry, Reactivity (chemistry), Ene reaction
Abstract: Sulfide-functionalized bambus[4]urils ((RS)8 BU[4]) and bambus[6]urils ((RS)12 BU[6]) were synthesized through thiol-ene click coupling reactions (TEC) of allylbambus[n]urils. Thiosugars were grafted to BU[4] and BU[6]. Synthesis of BU[6] derivatives always requires the use of a template anion (iodide, chloride, or bromide), which is enclosed in the cavity of BU[6]. We show that this anion influences the reactivity of bambus[6]urils. An encapsulated iodide makes allyl functions of allyl12 BU[6] less reactive towards TEC and hydrogenation reactions in comparison to the corresponding chloride or bromide inclusion complexes. This is critical for the chemical reactivity of BU[6] and even more to determine their anion-binding properties. We report a new, facile and fast method using AgSbF6 to prepare anion-free BU[6]. NMR spectroscopic methods were used to estimate association constants of these new empty BU[6] with different anions. Quantum chemical calculations were employed to rationalize the observed results. These new functionalized bambusuril scaffolds in alternate conformations could find applications as multivalent binders.
Published: 2018
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10. Accurate pH Sensing using Hyperpolarized 129 Xe NMR Spectroscopy

Author: Jean-Pierre Dognon, Patrick Berthault, Delphine Pitrat, Thierry Brotin, Estelle Léonce, and Jean-Christophe Mulatier
Subjects: 010405 organic chemistry, Chemistry, Chemical shift, Organic Chemistry, Analytical chemistry, General Chemistry, Nuclear magnetic resonance spectroscopy, Ph measurement, 010402 general chemistry, 01 natural sciences, Quantum chemistry, Catalysis, Cryptophane, 3. Good health, 0104 chemical sciences, Hyperpolarized xenon, Ph sensing
Abstract: In the search for powerful non-invasive methods for pH measurement, NMR usually suffers from biases, especially for heterogeneous samples or tissues. In this Communication, using the signals of hyperpolarized $^{129}$Xe encapsulated in a pair of water-soluble cryptophanes, we show that a differential pH measurement can be achieved, free from most of these biases, by monitoring the difference between their chemical shifts.
Published: 2018
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11. Accurate pH Sensing using Hyperpolarized

Author: Estelle, Léonce, Jean-Pierre, Dognon, Delphine, Pitrat, Jean-Christophe, Mulatier, Thierry, Brotin, and Patrick, Berthault
Abstract: In the search for powerful non-invasive methods for pH measurement, NMR usually suffers from biases, especially for heterogeneous samples or tissues. In this Communication, using the signals of hyperpolarized
Published: 2018

12. Understanding a Host-Guest Model System through129Xe NMR Spectroscopic Experiments and Theoretical Studies

Author: Jean-Pierre Dognon, Estelle Léonce, Bernard Rousseau, Yves Boulard, Christophe Dugave, Céline Boutin, Patrick Berthault, Emmanuelle Dubost, Gaëlle Milanole, Service de Chimie Bio-Organique et de Marquage (SCBM), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Chimie Moléculaire et de Catalyse pour l'Energie (ex LCCEF) (LCMCE), 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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), 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), 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-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010405 organic chemistry, Chemistry, Supramolecular chemistry, Analytical chemistry, chemistry.chemical_element, Model system, General Medicine, General Chemistry, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, 01 natural sciences, Quantum chemistry, Catalysis, Cryptophane, Spectral line, 0104 chemical sciences, symbols.namesake, Xenon, Chemical physics, Physics::Atomic and Molecular Clusters, symbols, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], van der Waals force
Abstract: International audience; Gaining an understanding of the nature of host–guest interactions in supramolecular complexes involving heavy atoms is a difficult task. Described herein is a robust simulation method applied to complexes between xenon and members of a cryptophane family. The calculated chemical shift of xenon caged in a H2O2 probe, as modeled by quantum chemistry with complementary-orbital, topological, and energy-decomposition analyses, is in excellent agreement with that observed in hyperpolarized 129Xe NMR spectra. This approach can be extended to other van der Waals complexes involving heavy atoms.
Published: 2014
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13. Synthesis of Cucurbit[6]uril Derivatives and Insights into Their Solubility in Water

Author: Sylvie Coudert, Gaspard Huber, Hana Kouřilová, Marie-Pierre Heck, François-Xavier Legrand, Delphine Baumann, Jean-Pierre Dognon, Bernard Rousseau, Patrick Berthault, Julie Rivollier, David-Alexandre Buisson, and Véronique Lewin
Subjects: Cyclohexane, Chemistry, Hydrogen bond, Organic Chemistry, Intermolecular force, Limiting, Nuclear magnetic resonance spectroscopy, Medicinal chemistry, chemistry.chemical_compound, Molecular geometry, Cucurbituril, Organic chemistry, Physical and Theoretical Chemistry, Solubility
Abstract: Four new cucurbiturils CynCB[6] containing n (n = 1, 2, 4, 5) cyclohexyl equatorial units have been synthesized to complete the family of known Cy3CB[6] and Cy6CB[6] derivatives. A new CB[6] member bearing a propanediurea unit has also been prepared. The CB[6] derivatives show better solubility in pure water than native CB[6]. One cyclohexyl unit is sufficient to enhance the solubility in water by a factor of 170 with respect to CB[6], and Cy6CB[6] is around 30 times more soluble than Cy1CB[6]. The cyclohexane moieties, by limiting or impeding the formation of intermolecular C–H···O hydrogen bonds, may explain this increase in solubility. The effect of modification of the molecular shape on the solubility was assessed by liquid-state NMR spectroscopy and DFT calculations.
Published: 2013
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14. Towards energy decomposition analysis for open and closed shell f-elements mono aqua complexes

Author: Jean-Philip Piquemal, Christophe Gourlaouen, Carine Clavaguéra, Jean-Pierre Dognon, Aude Marjolin, Laboratoire de Chimie de Coordination des Eléments f (LCF) (LCCEf), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie théorique (LCT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie Quantique, Centre National de la Recherche Scientifique (CNRS), Laboratoire des mécanismes réactionnels (DCMR), and École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Lanthanide, Work (thermodynamics), 010304 chemical physics, Chemistry, Ab initio, General Physics and Astronomy, Actinide, 010402 general chemistry, Polarization (waves), 01 natural sciences, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Unpaired electron, Polarizability, 0103 physical sciences, Physics::Atomic and Molecular Clusters, Physical and Theoretical Chemistry, Atomic physics, Open shell
Abstract: International audience; We propose an energy decomposition analysis of mono aqua systems of both open and closed shell lanthanide and actinide cations using the CSOV scheme. We compared the values obtained with either large f-in-core or small core quasi relativistic pseudopotentials and computed the unpaired electrons contribution to the polarization energy component. Through a quasi-systematic approach on a number of chosen f-element cations, we quantified the different trends across both series for each contribution. This work is an important preliminary step for the acquisition of reference ab initio data for further parameterization of polarizable force fields for lanthanides and actinides. (Cop) 2013 Elsevier B. V. All rights reserved.
Published: 2013
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15. Chemistry of the 5g Elements: Relativistic Calculations on Hexafluorides

Author: Pekka Pyykkö, Jean-Pierre Dognon, Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), 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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire de Chimie Moléculaire et de Catalyse pour l'Energie (ex LCCEF) (LCMCE), Department of Chemistry [Helsinki], University of Helsinki, 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), and Helsingin yliopisto = Helsingfors universitet = University of Helsinki
Subjects: Periodic system, 010304 chemical physics, Stereochemistry, Periodic table (large cells), Chemistry, Ionic bonding, General Medicine, [CHIM.MATE]Chemical Sciences/Material chemistry, 02 engineering and technology, General Chemistry, Basis (universal algebra), 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Catalysis, 0104 chemical sciences, 0103 physical sciences, Atomic physics, 0210 nano-technology
Abstract: International audience; A Periodic System was proposed for the elements 1-172 by Pyykkö (Phys. Chem. Chem. Phys. 2011, 13, 161) on the basis of atomic and ionic calculations. In it, the elements 121-138 were nominally assigned to a 5g row. We now perform molecular, relativistic four-component DFT calculations and find that the hexafluorides of the elements 125-129 indeed enjoy occupied 5g states.
Published: 2017
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16. Electronic structure theory to decipher the chemical bonding in actinide systems

Author: Jean-Pierre Dognon, Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), 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), 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: f-elements, Orbital overlap, Electronic structure, 010402 general chemistry, 01 natural sciences, energy decomposition analysis, Inorganic Chemistry, Theoretical physics, bonding analysis, Atomic orbital, Computational chemistry, 0103 physical sciences, Materials Chemistry, actinide complexes, Physical and Theoretical Chemistry, Topology (chemistry), 010304 chemical physics, Chemistry, Charge (physics), Actinide, [CHIM.MATE]Chemical Sciences/Material chemistry, molecular wave function analysis, Bond order, 0104 chemical sciences, Chemical bond, quantum chemical topology
Abstract: International audience; The chemical bonding in actinide compounds is usually analysed by inspecting the shape and the occupation of the orbitals or by calculating bond orders which are based on orbital overlap and occupation numbers. However, this may not give a definite answer because the choice of the partitioning method may strongly influence the result possibly leading to qualitatively different answers. In this review, we summarized the state-of-the-art of methods dedicated to the theoretical characterisation of bonding including charge, orbital, quantum chemical topology and energy decomposition analyses. This review is not exhaustive but aims to highlight some of the ways opened up by recent methodological developments. Various examples have been chosen to illustrate this progress.
Published: 2017
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17. Interactions within the alcohol dehydrogenase Zn(II)-metalloenzyme active site: Interplay between subvalence, electron correlation/dispersion, and charge transfer/induction effects

Author: Benoit de Courcy, Carine Clavaguéra, Jean-Pierre Dognon, Nohad Gresh, and Jean-Philip Piquemal
Subjects: 010304 chemical physics, Electronic correlation, biology, Chemistry, Atoms in molecules, Active site, Charge (physics), 010402 general chemistry, Condensed Matter Physics, 01 natural sciences, Quantum chemistry, Atomic and Molecular Physics, and Optics, Electron localization function, 0104 chemical sciences, Chemical physics, Computational chemistry, 0103 physical sciences, biology.protein, Density functional theory, Physical and Theoretical Chemistry, Binding site
Abstract: Following our preceding works (de Courcy et al. J Chem Theo Comput 2008, 4, 1659; de Courcy, et al. Interdiscip Sci Comput Life Sci 2009, 1, 55), we have studied by quantum chemistry a model of the alcohol dehydrogenase Zn-metalloenzyme (ADH) binding site. Using several interpretative techniques such as the topological analysis of the electron localization function (ELF) and quantum theory of atoms in molecules combined with energy decomposition analysis schemes, we have analyzed the physical origin of the interactions occurring in this site, which is stabilized by an indirect cation-π interaction. While polarization effects are important for the metal, which is able to adapt its outer-shell density (the so-called subvalence domains) to its ligands, they do not play a key role in the overall interaction of the system that is dominated by dispersion. The ELF analysis shows that only minor charge transfer phenomena are observed between the constitutive fragments of the system. From a methodological standpoint, density functional theory functionals appear unable to handle the system whereas dispersion-corrected methods (DFT-D) perform significantly better, giving reasonable answers as compared with post-Hartree-Fock methods. The stabilization energy brought by the presence of Phe93 to the active binding site of ADH is about −3 kcal/mol. The importance of accounting for basis set superposition error is also emphasized. © 2010 Wiley Periodicals, Inc.
Published: 2010
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18. Chemical properties of the predicted 32-electron systems Pu@Sn12 and Pu@Pb12

Author: Carine Clavaguéra, Pekka Pyykkö, Jean-Pierre Dognon, Laboratoire de Chimie de Coordination des Eléments f (LCF) (LCCEf), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des mécanismes réactionnels (DCMR), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Department of Chemistry
Subjects: Actinide chemistry, Icosahedral symmetry, Chemistry, General Chemical Engineering, 02 engineering and technology, General Chemistry, Electron, Electronic structure, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, Ion, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Atom, Physics::Atomic and Molecular Clusters, Physical chemistry, Density functional theory, 0210 nano-technology
Abstract: International audience; The electronic structures, as well as spectroscopic and thermodynamic properties of the title Pu@M12 clusters, are considered at the density functional theory level. In both cases, a Pu2+ ion is encapsulated in an icosahedral, stanna-or plumbaspherene M2-12 cage. As suggested before forM= Pb, both systems are reported to follow a 32-electron principle for the central atom. © 2010 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.
Published: 2010
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19. An Isolated CO2 Adduct of a Nitrogen Base: Crystal and Electronic Structures

Author: Rodolphe Pollet, Claude Villiers, Jean-Pierre Dognon, Michel Ephritikhine, and Pierre Thuéry
Subjects: chemistry.chemical_classification, Crystal, chemistry.chemical_compound, Crystallography, chemistry, Base (chemistry), Inorganic chemistry, chemistry.chemical_element, General Chemistry, Guanidine, Nitrogen, Catalysis, Adduct
Published: 2010
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20. An Isolated CO2Adduct of a Nitrogen Base: Crystal and Electronic Structures

Author: Claude Villiers, Jean-Pierre Dognon, Rodolphe Pollet, Pierre Thuéry, and Michel Ephritikhine
Subjects: General Medicine
Published: 2010
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21. Toward the Limits of Sandwich Immunoassay of Very Low Molecular Weight Molecules

Author: Hervé Volland, Marie-Claire Nevers, Lise Charruault, Christophe Créminon, Jean-Pierre Dognon, Frédéric Taran, and Julia Quinton
Subjects: Immunoassay, Molecular mass, Chemistry, Stereochemistry, Model study, Antibodies, Monoclonal, Homovanillic Acid, Combinatorial chemistry, Small molecule, Epitope, Analytical Chemistry, Molecular Weight, Epitopes, Molecule, Histidine, Sandwich immunoassay
Abstract: A model study aiming at exploring the limits of sandwich immunoassays of very small molecules is described. Combinatorial association of antibody couples to detect small molecules constituted by two small epitopes connected via different linear spacers was used to investigate the minimum size of compounds susceptible to be simultaneously bound by two distinct antibodies. The results clearly indicated that despite the fact that below 10 carbon atoms unfavorable interactions between antibodies took place, molecules bearing two epitopes separated by only 5 carbon atoms might be directly detected by sandwich immunoassays.
Published: 2010
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22. Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations

Author: David Semrouni, Jean-Pierre Dognon, Carine Clavaguéra, Ashwani Sharma, Gilles Ohanessian, Laboratoire de chimie moléculaire (LCM), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie Moléculaire et de Catalyse pour l'Energie (ex LCCEF) (LCMCE), 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), 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-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: chemistry.chemical_classification, 010304 chemical physics, Chemistry, Hydrogen bond, Biomolecule, Infrared spectroscopy, 010402 general chemistry, Polarization (waves), 01 natural sciences, Spectral line, 0104 chemical sciences, Computer Science Applications, Molecular dynamics, Chemical physics, Polarizability, 0103 physical sciences, Molecule, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Physical and Theoretical Chemistry, Atomic physics
Abstract: International audience; Infrared spectra of biomolecules are obtained from molecular dynamics simulations at finite temperature using the AMOEBA force field. Diverse examples are presented such as N-methylacetamide and its derivatives and a helical peptide. The computed spectra from polarizable molecular dynamics are compared in each case to experimental ones at various temperatures. The role of high-level electrostatic treatment and explicit polarization, including parameters improvements, is highlighted for obtaining spectral sensitivity to the environment including hydrogen bonds and water molecules and a better understanding of the observed experimental bands
Published: 2015
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23. Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field

Author: Jean-Pierre Dognon, Gilles Ohanessian, Carine Clavaguéra, Florian Thaunay, Laboratoire de chimie moléculaire (LCM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Laboratoire de Chimie Moléculaire et de Catalyse pour l'Energie (ex LCCEF) (LCMCE), 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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-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-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), and Laboratoire des mécanismes réactionnels (DCMR)
Subjects: Quantitative Biology::Biomolecules, Spectrophotometry, Infrared, Chemistry, Anharmonicity, Molecular Conformation, Temperature, General Physics and Astronomy, Infrared spectroscopy, [CHIM.MATE]Chemical Sciences/Material chemistry, Dipeptides, Molecular Dynamics Simulation, Molecular physics, Molecular conformation, Force field (chemistry), [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Molecular dynamics, Polarizability, Computational chemistry, Molecular vibration, Physics::Chemical Physics, Physical and Theoretical Chemistry
Abstract: International audience; The calculation of infrared spectra by molecular dynamics simulations based on the AMOEBA polarizable force field has recently been demonstrated [Semrouni et al., J. Chem. Theory Comput., 2014, 10, 3190]. While this approach allows access to temperature and anharmonicity effects, band assignment requires additional tools, which we describe in this paper. The Driven Molecular Dynamics approach, originally developed by Bowman, Kaledin et al. [Bowman et al. J. Chem. Phys., 2003, 119, 646, Kaledin et al. J. Chem. Phys., 2004, 121, 5646] has been adapted and associated with AMOEBA. Its advantages and limitations are described. The IR spectrum of the Ac-Phe-Ala-NH 2 model peptide is analyzed in detail. In addition to differentiation of conformations by reproducing frequency shifts due to non-covalent interactions, DMD allows visualizing the temperature-dependent vibrational modes.
Published: 2015
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24. Calculated lanthanide contractions for molecular trihalides and fully hydrated ions: The contributions from relativity and 4f-shell hybridization

Author: Jean-Pierre Dognon, Carine Clavaguéra, and Pekka Pyykkö
Subjects: Lanthanide contraction, Lanthanide, Coupling constant, Chemistry, Shell (structure), General Physics and Astronomy, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, Ion, Theory of relativity, Quadrupole, Physical and Theoretical Chemistry, Atomic physics, 0210 nano-technology, Relativistic quantum chemistry
Abstract: The calculated lanthanide contraction in the title systems is typically 18–21 pm of which about 9–23% comes from relativistic effects. A pronounced 4f hybridization is found for LuF 3 using three different relativistic methods of calculation. Large lanthanide nuclear quadrupole coupling constants are predicted for the molecular trihalides.
Published: 2006
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25. Intrinsic Folding of Small Peptide Chains: Spectroscopic Evidence for the Formation of β-Turns in the Gas Phase

Author: Jean-Pierre Dognon, Wutharath Chin, Benjamin Tardivel, Iliana Dimicoli, Michel Mons, François Piuzzi, Laboratoire Francis PERRIN (LFP - URA 2453), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Protein Folding, spectroscopy, Spectrophotometry, Infrared, Stereochemistry, Phenylalanine, Glycine, Infrared spectroscopy, Peptide, Sequence (biology), 010402 general chemistry, 01 natural sciences, Biochemistry, Protein Structure, Secondary, Catalysis, Residue (chemistry), Colloid and Surface Chemistry, 0103 physical sciences, beta-turn UV, Spectroscopy, Protein secondary structure, chemistry.chemical_classification, 010304 chemical physics, spectroscopy IR, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Chemistry, Protected peptide, Dipeptides, General Chemistry, 0104 chemical sciences, Folding (chemistry), Crystallography, Potential energy surface, Spectrophotometry, Ultraviolet, Gases
Abstract: Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.
Published: 2004
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26. The 32-Electron Principle

Author: Jean-Pierre Dognon, Pekka Pyykkö, Carine Clavaguéra, Department of Chemistry, Laboratoire de chimie moléculaire (LCM), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), 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), Dolg, Michael, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), 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: 010405 organic chemistry, Chemistry, Inorganic chemistry, Radiochemistry, Thorium, chemistry.chemical_element, [CHIM.MATE]Chemical Sciences/Material chemistry, Actinide, Electron, 010402 general chemistry, 01 natural sciences, ComputingMilieux_MISCELLANEOUS, 0104 chemical sciences
Abstract: International audience
Published: 2015
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27. Design and Synthesis of New Cryptophanes with Intermediate Cavity Sizes

Author: Bernard Rousseau, David-Alexandre Buisson, Jean-Pierre Dognon, Ténin Traoré, Léa Delacour, Naoko Kotera, Nawal Tassali, and Patrick Berthault
Subjects: Alkane, chemistry.chemical_classification, Chemistry, Organic Chemistry, Hyperpolarized xenon, Alkoxy group, Nanotechnology, Physical and Theoretical Chemistry, Molecular imaging, Biochemistry, Combinatorial chemistry, Biosensor, Cryptophane
Abstract: The development of molecular imaging using hyperpolarized xenon MRI needs highly optimized biosensors. Cryptophane-111 and cryptophane-222 are promising candidates that show complementary encapsulation properties although they only differ by the length of the three alkane linkers joining two cyclotriphenolene units. Cryptophanes containing both methoxy and ethoxy linkers have never been synthesized. Here we synthesize two new cages with intermediate internal volumes, in two steps from cyclotriphenolene.
Published: 2011
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28. Understanding a host-guest model system through ¹²⁹Xe NMR spectroscopic experiments and theoretical studies

Author: Emmanuelle, Dubost, Jean-Pierre, Dognon, Bernard, Rousseau, Gaëlle, Milanole, Christophe, Dugave, Yves, Boulard, Estelle, Léonce, Céline, Boutin, and Patrick, Berthault
Subjects: Magnetic Resonance Spectroscopy, Xenon, Molecular Structure, Polycyclic Compounds, Models, Biological
Abstract: Gaining an understanding of the nature of host-guest interactions in supramolecular complexes involving heavy atoms is a difficult task. Described herein is a robust simulation method applied to complexes between xenon and members of a cryptophane family. The calculated chemical shift of xenon caged in a H2O2 probe, as modeled by quantum chemistry with complementary-orbital, topological, and energy-decomposition analyses, is in excellent agreement with that observed in hyperpolarized (129)Xe NMR spectra. This approach can be extended to other van der Waals complexes involving heavy atoms.
Published: 2014

29. Complexation of lanthanum(III) nitrate by N,N′,N,N′-tetraethylmalonamide

Author: Pierre Thuéry, Jean-Pierre Dognon, Christophe Den Auwer, Marie-Christine Charbonnel, and Martine Nierlich
Subjects: Phase transition, chemistry.chemical_element, Crystal structure, Triclinic crystal system, Inorganic Chemistry, Turn (biochemistry), chemistry.chemical_compound, Nuclear reprocessing, Crystallography, Nitrate, chemistry, Materials Chemistry, Lanthanum, Physical and Theoretical Chemistry, Monoclinic crystal system
Abstract: A monoclinic form of the complex between lanthanum(III) nitrate and tetraethylmalonamide (TEMA), La(NO3)3(TEMA)2, 1, differing from the triclinic form 2 previously reported, is described. 1 undergoes an evolution with time which leads to the form 2, which in its turn undergoes a temperature-driven phase transition previously unreported, leading to the formation of 3.
Published: 1999
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30. Theoretical insights into the chemical bonding in actinide complexes

Author: Jean-Pierre Dognon, Laboratoire de Chimie Moléculaire et de Catalyse pour l'Energie (ex LCCEF) (LCMCE), 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), 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-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Actinide chemistry, f-Elements Actinide complexes Molecular wavefunction analysis Quantum chemical topology Energy decomposition analysis Bonding analysis, 010405 organic chemistry, Chemistry, Bent molecular geometry, Charge (physics), Orbital overlap, 010402 general chemistry, 01 natural sciences, Bond order, 0104 chemical sciences, Inorganic Chemistry, Chemical bond, Atomic orbital, Chemical physics, Materials Chemistry, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Physical and Theoretical Chemistry, Atomic physics, Topology (chemistry)
Abstract: International audience; Abstract The chemical bonding in actinide compounds is usually analyzed by inspecting the shape and the occupation of the orbitals or by calculating bond orders which are based on orbital overlap and occupation numbers. However, this may not give a definite answer because the choice of the partitioning method may strongly influence the result leading sometimes to qualitatively different answers. This review highlights that the joint and complementary tools such as charge, orbital, quantum chemical topology and energy decomposition analyses are very powerful to understand chemical bonding in the field of actinide chemistry. However, understanding the actinide–ligand bond is not straightforward and requires caution in the use of these methods. This review is illustrated through applications to newly discovered bent actinocene compounds and actinide endohedral clusters fulfilling a 32-electron rule.
Published: 2014
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31. Infrared absorption spectra of polymers from classical molecular simulation

Author: Armand Soldera and Jean-Pierre Dognon
Subjects: chemistry.chemical_classification, Polymers and Plastics, Infrared, Chemistry, Organic Chemistry, Analytical chemistry, Infrared spectroscopy, Molecular simulation, Polymer, Condensed Matter Physics, Molecular physics, Spectral line, Amorphous solid, Middle infrared, Materials Chemistry, Absorption (electromagnetic radiation)
Abstract: A method is proposed to predict the infrared spectra of amorphous polymers. Based on classical molecular simulation and Kramers-Kronig relations, it allows the computations of absorption and transmittance spectra of polymer films in near and middle infrared domains with good agreement with experimental data.
Published: 1997
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32. Molecular Dynamics Study of the Hydration of Lanthanum(III) and Europium(III) Including Many-Body Effects

Author: Rodolphe Pollet, Carine Clavaguéra, Jean-Pierre Dognon, J. M. Soudan, Valérie Brenner, Laboratoire Francis PERRIN (LFP - URA 2453), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Lanthanide, Ligand, Inorganic chemistry, chemistry.chemical_element, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, Surfaces, Coatings and Films, Ion, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Solvent, chemistry.chemical_compound, Molecular dynamics, chemistry, Computational chemistry, Materials Chemistry, Lanthanum, Organic synthesis, Physical and Theoretical Chemistry, 0210 nano-technology, Europium
Abstract: Lanthanides complexes are widely used as contrast agents in magnetic resonance imaging (MRI) and are involved in many fields such as organic synthesis, catalysis, and nuclear waste management. The complexation of the ion by the solvent or an organic ligand and the resulting properties (for example the relaxivity in MRI) are mainly governed by the structure and dynamics of the coordination shells. All of the MD approaches already carried out for the lanthanide(III) hydration failed due to the lack of accurate representation of many-body effects. We present the first molecular dynamics simulation including these effects that accounts for the experimental results from a structural and dynamic (water exchange rate) point of view.
Published: 2005
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33. Revisiting the chemistry of the actinocenes [(η8-C8H8)2An] (An = U, Th) with neutral Lewis bases. Access to the bent sandwich complexes [(η8-C8H8)2An(L)] with thorium (L = py, 4,4'-bipy, tBuNC, R4phen)

Author: Jean-Claude, Berthet, Pierre, Thuéry, Nicolas, Garin, Jean-Pierre, Dognon, Thibault, Cantat, and Michel, Ephritikhine
Subjects: Lewis Bases, Thorium, Organometallic Compounds, Quantum Theory, Uranium
Abstract: In stark contrast to uranocene, (Cot)2Th reacts with neutral mono- or bidentate Lewis bases to give the bent sandwich complexes (Cot)2Th(L) (L = py, 4,4'-bipy, tBuNC, phen, Me4phen). DFT calculations in the gas phase show that, for both U and Th, formation of the bent compound (Cot)2An(L) should be facile, the linear and bent forms being close in energy.
Published: 2013

34. Understanding the structure and electronic properties of Th4+-water complexes

Author: Carine Clavaguéra, Jean-Philip Piquemal, Jean-Pierre Dognon, Aude Marjolin, Christophe Gourlaouen, Laboratoire de Chimie Quantique, Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie de Coordination des Eléments f (LCF) (LCCEf), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des mécanismes réactionnels (DCMR), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie théorique (LCT), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 010304 chemical physics, Chemistry, 0103 physical sciences, Organic Chemistry, Physical chemistry, General Chemistry, 010402 general chemistry, 01 natural sciences, Catalysis, 0104 chemical sciences, Electronic properties
Abstract: International audience; Le présent article a pour but de présenter une étude de chimie quantique systématique des complexes [Th(H2O)n]4+ (n = 1 à 10) réalisée en vue de comprendre leur structure électronique et leurs propriétés : l'effet de la distribution du ligand sur les couches de valence de l'ion thorium(IV) est étudié par une analyse topologique de la fonction de localisation électronique (ELF). Une attention particulière est accordée à l'étude du complexe monoaqua dans sa géométrie d'équilibre en utilisant divers outils, tels des analyses de décomposition de l'énergie d'interaction (EDA), ainsi que le long de son chemin de dissociation. En effet, comme plusieurs états électroniques croisent l'état fondamental Th4+-H2O0 le long du chemin d'énergie minimale, nous démontrons que la représentation diabatique implémentée dans MOLPRO est capable de générer les surfaces d'énergie potentielle de référence qui mènerons à l'évaluation des courbes de dissociation diabatique. La courbe d'énergie d'interaction diabatique calculée permettra de procéder à une paramétrisation cohérente des champs de forces de nouvelle génération consacrés aux métaux lourds en se basant sur la chimie quantique. [Traduit par la Rédaction]
Published: 2013
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35. Ab Initio Extension of the AMOEBA Polarizable Force Field to Fe2+

Author: Laura Gagliardi, Carine Clavaguéra, Jean Pierre Dognon, William C. Isley, Christopher J. Cramer, David Semrouni, Laboratoire des mécanismes réactionnels (DCMR), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie de Coordination des Eléments f (LCF) (LCCEf), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010304 chemical physics, Spin states, Chemistry, Ab initio, Interaction energy, 010402 general chemistry, 7. Clean energy, 01 natural sciences, Molecular physics, 0104 chemical sciences, Computer Science Applications, Molecular dynamics, Polarizability, 0103 physical sciences, Condensed Matter::Strongly Correlated Electrons, Singlet state, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Physical and Theoretical Chemistry, Atomic physics, Physics::Chemical Physics, Ground state, Mechanical energy
Abstract: International audience; We extend the AMOEBA polarizable molecular mechanics force field to the Fe2+ cation in its singlet, triplet, and quintet spin states. Required parameters are obtained either directly from first principles calculations or optimized so as to reproduce corresponding interaction energy components in a hexaaquo environment derived from quantum mechanical energy decomposition analyses. We assess the importance of the damping of point-dipole polarization at short distance as well as the influence of charge-transfer for metal-water interactions in hydrated Fe2+; this analysis informs the selection of model systems employed for parametrization. We validate our final Fe2+ model through comparison of molecular dynamics (MD) simulations to available experimental data for aqueous ferrous ion in its quintet electronic ground state.
Published: 2013
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36. Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies

Author: Aude Marjolin, Christophe Gourlaouen, Carine Clavaguéra, Pengyu Y. Ren, Johnny C. Wu, Nohad Gresh, Jean-Pierre Dognon, and Jean-Philip Piquemal
Published: 2012
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37. Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: From gas-phase energetics to hydration free energies

Author: Jean-Philip Piquemal, Jean Pierre Dognon, Johnny Wu, Nohad Gresh, Aude Marjolin, Christophe Gourlaouen, Pengyu Ren, Carine Clavaguéra, Lab Chim Coordinat Elements F, Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie théorique (LCT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des mécanismes réactionnels (DCMR), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Biomedical Engineering, affiliation inconnue, 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), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de chimie théorique ( LCT ), Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ), Laboratoire des mécanismes réactionnels ( DCMR ), École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), 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 ), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), and Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Lanthanide, 010304 chemical physics, Chemistry, Coordination number, Solvation, Ab initio, Thermodynamics, Actinide, 010402 general chemistry, 01 natural sciences, Force field (chemistry), 0104 chemical sciences, Molecular dynamics, Polarizability, 0103 physical sciences, Physics::Atomic and Molecular Clusters, Physical and Theoretical Chemistry, Atomic physics, Physics::Chemical Physics
Abstract: International audience; In this contribution, we focused on the use of polarizable force fields to model the structural, energetic, and thermodynamical properties of lanthanides and actinides in water. In a first part, we chose the particular case of the Th(IV) cation to demonstrate the capabilities of the AMOEBA polarizable force field to reproduce both reference ab initio gas-phase energetics and experimental data including coordination numbers and radial distribution functions. Using such model, we predicted the first polarizable force field estimate of Th(IV) solvation free energy, which accounts for -1,638 kcal/mol. In addition, we proposed in a second part of this work a full extension of the SIBFA (Sum of Interaction Between Fragments Ab initio computed) polarizable potential to lanthanides (La(III) and Lu(III)) and to actinides (Th(IV)) in water. We demonstrate its capabilities to reproduce all ab initio contributions as extracted from energy decomposition analysis computations, including many-body charge transfer and discussed its applicability to extended molecular dynamics and its parametrization on high-level post-Hartree-Fock data. © 2012 Springer-Verlag.
Published: 2012
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38. Theoretical study of the bent U(η8-C8H8)2(CN)- complex

Author: Carine Clavaguéra, Jean-Pierre Dognon, Laboratoire des mécanismes réactionnels (DCMR), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Lab Chim Coordinat Elements F, and Centre National de la Recherche Scientifique (CNRS)
Subjects: Actinide chemistry, 010405 organic chemistry, Infrared, Chemistry, Bent molecular geometry, Electronic structure, 010402 general chemistry, 01 natural sciences, Molecular physics, 0104 chemical sciences, chemistry.chemical_compound, Uranocene, Density functional theory, Symmetry breaking, Physical and Theoretical Chemistry, Atomic physics, Relativistic quantum chemistry
Abstract: International audience; The ground-state electronic structure of the cyanido complex [U(η8-C8H8)2(CN)]− as well as the thermodynamic properties and infrared spectrum are investigated using density functional theory including scalar relativistic effects. The complex is compared with the well-known uranocene U(η8-C8H8)2. Despite the broken symmetry, the gain in electrostatic interaction and a significant uranium-CN− orbital interaction is sufficient to stabilize the bent CN− complex with respect to uranocene. The formation of the CN− complex is exothermic justifying the recently experimentally reported compound.. © 2011 Springer-Verlag.
Published: 2011
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39. Assessment of density functionals for predicting the infrared spectrum of sodiated octa-glycine

Author: Gilles Ohanessian, Carine Clavaguéra, David Semrouni, Jean-Pierre Dognon, Laboratoire des mécanismes réactionnels (DCMR), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie de Coordination des Eléments f (LCF) (LCCEf), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010304 chemical physics, Chemistry, Hydrogen bond, Infrared, Ab initio, Infrared spectroscopy, Electronic structure, 010402 general chemistry, Condensed Matter Physics, 01 natural sciences, Dissociation (chemistry), 0104 chemical sciences, Computational chemistry, 0103 physical sciences, Density functional theory, Infrared multiphoton dissociation, Physical and Theoretical Chemistry, Instrumentation, Spectroscopy
Abstract: International audience; The sodiated peptide GGGGGGGG-Na+ or G8-Na+ has a remarkable structure with a highly coordinated sodium ion and an acidic OH that is strongly hydrogen-bound with the N-terminus. The presence of the sodium ion makes this hydrogen bond unusually strong and makes proton transfer easy, leading to an equally stable, salt bridge isomer. The performances of a variety of density functionals in describing the geometries, energetics and infrared spectra of these two isomers were investigated. Usual density functionals were tested and moreover, more recent functionals such as dispersion-corrected ones and Truhlar's M06 series were also considered. The computed infrared spectra are compared with ab initio results and InfraRed Multiple Photon Dissociation (IRMPD) experiments. Two functionals in the M06 series have been proved to be quite efficient. A large number of functionals seems to be inadequate to compute infrared spectra for peptide in the amide N-H stretching region. In addition, a detailed analysis of the sodium-peptide interaction and of the hydrogen bond between the two peptide terminations points out a distinct electronic structure for the two isomers. © 2010 Elsevier B.V.
Published: 2010
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40. A predicted organometallic series following a 32-electron principle: An@C28 (An = Th, Pa+, U2+, Pu4+)

Author: Pekka Pyykkö, Jean-Pierre Dognon, Carine Clavaguéra, Service de Chimie Moléculaire (SCM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des mécanismes réactionnels (DCMR), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Department of Chemistry
Subjects: Valence (chemistry), Chemistry, 02 engineering and technology, General Chemistry, Actinide, Electron, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Biochemistry, Catalysis, 0104 chemical sciences, Metal, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Colloid and Surface Chemistry, Atomic orbital, Computational chemistry, visual_art, visual_art.visual_art_medium, Molecule, Physical chemistry, Density functional theory, Molecular orbital, 0210 nano-technology
Abstract: International audience; The spectroscopic and thermodynamic properties of the molecules M@C28 (M = Ce, Th, Pa+, U2+, Pu4+) are calculated using density functional theory. The systems have considerable energetic stability. It is shown that the actinide cases can be classified as "32-electron" systems, using the bonding s-, p-, d-, and f-type orbitals of the central metal. The rest of the valence molecular orbitals have purely carbon character.
Published: 2009
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41. Electronic Spectrum of Tryptophan-Phenylalanine. A Correlated Ab Initio and Time-Dependent Density Functional Theory Study

Author: Jean-Pierre Dognon, François Piuzzi, Carine Clavaguéra, Laboratoire des mécanismes réactionnels (DCMR), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Francis PERRIN (LFP - URA 2453), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Claude Fréjacques (LCF - URA 331), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Time Factors, Phenylalanine, Ab initio, Electrons, 010402 general chemistry, 01 natural sciences, chemistry.chemical_compound, 0103 physical sciences, Materials Chemistry, Complete active space, Physical and Theoretical Chemistry, Perturbation theory, Quantitative Biology::Biomolecules, Dipeptide, 010304 chemical physics, Tryptophan, Dipeptides, State (functional analysis), Time-dependent density functional theory, Quantitative Biology::Genomics, 0104 chemical sciences, Surfaces, Coatings and Films, chemistry, Excited state, Density functional theory, Atomic physics
Abstract: International audience; The theoretical electronic spectrum of the tryptophan-phenylalanine bichromophoric dipeptide was obtained for one of the lowest-energy conformer by various high-level computational methods such as complete active space with second order perturbation theory, second-order approximate coupled-cluster theory, and time-dependent density functional theory. The results show that the first excited state is located on the tryptophan residue and called Lb state in the amino-acid. The second and third excited states correspond respectively to the La state of Trp and the excited state in the Phe residue. Time-dependent density functional methods appeared to be not efficient to calculate the excited states of such a peptide (except the first one) due to the inclusion of charge transfer states.
Published: 2009
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42. In silico prediction of atomic static electric-dipole polarizabilities of the early tetravalent actinide ions:Th4+(5f0),Pa4+(5f1), andU4+(5f2)

Author: Jean-Pierre Dognon, Florent Réal, Valérie Vallet, and Carine Clavaguéra
Subjects: Physics, 010304 chemical physics, Basis (linear algebra), Ab initio, Actinide, 010402 general chemistry, 01 natural sciences, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Ion, Dipole, Polarizability, 0103 physical sciences, Atomic physics, Hyperfine structure, Basis set
Abstract: The dipole polarizability tensor components of the tetravalent actinide ions ${\mathrm{Th}}^{4+}$, ${\mathrm{Pa}}^{4+}$, and ${\mathrm{U}}^{4+}$ are computed using the numerical finite-field technique. Four-component correlated calculations have been performed to serve as a reference for establishing the accuracy of two- and one-component relativistic methods. A good agreement within all methods is achieved provided that extended basis sets are used to reach the complete basis set limit. The four-component correlated polarizabilities represent a database of reference values of the dipole polarizability for the early tetravalent actinide ions.
Published: 2008
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43. Sterically congested uranyl complexes with seven-coordination of the UO2 unit: the peculiar ligation mode of nitrate in [UO2(NO3)2(Rbtp)] complexes

Author: Denis Guillaneux, Michel Ephritikhine, Pierre Thuéry, Jean-Claude Berthet, and Jean-Pierre Dognon
Subjects: Denticity, Chemistry, Stereochemistry, Coordination number, Crystal structure, Uranyl, Inorganic Chemistry, chemistry.chemical_compound, Crystallography, Bipyridine, Pyridine, Physical and Theoretical Chemistry, Terpyridine, Coordination geometry
Abstract: Addition of 1 or 2 molar equiv of Rbtp [Rbtp = 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine; R = Me, Pr ( n )] to UO 2(OTf) 2 in anhydrous acetonitrile gave the neutral compounds [UO 2(OTf) 2(Rbtp)] [R = Me ( 1), ( n )Pr ( 2)] and the cationic complexes [UO 2(Rbtp) 2][OTf] 2 [R = Me ( 3), Pr ( n ) ( 4)], respectively. No equilibrium between the mono and bis(Rbtp) complexes or between [UO 2(Rbtp) 2][OTf] 2 and free Rbtp in acetonitrile was detected by NMR spectroscopy. The crystal structures of 1 and 3 resemble those of their terpyridine analogues, and 3 is another example of a uranyl complex with the uranium atom in the unusual rhombohedral environment. In the presence of 1 molar equiv of Rbtp in acetonitrile, UO 2(NO 3) 2 was in equilibrium with [UO 2(NO 3) 2(Rbtp)] and the formation of the bis adduct was not observed, even with an excess of Rbtp. The X-ray crystal structures of [UO 2(NO 3) 2(Rbtp)] [R = Me ( 5), Pr ( n ) ( 6)] reveal a particular coordination geometry with seven coordinating atoms around the UO 2 fragment. The large steric crowding in the equatorial girdle forces the bidentate nitrate ligands to be almost perpendicular to the mean equatorial plane, inducing bending of the UO 2 fragment. The dinuclear oxo compound [U(CyMe 4btbp) 2(mu-O)UO 2(NO 3) 3][OTf] ( 7), which was obtained fortuitously from a 1:2:1 mixture of U(OTf) 4, CyMe 4btbp, and UO 2(NO 3) 2 [CyMe 4btbp = 6,6'-bis-(3,3,6,6-tetramethyl-cyclohexane-1,2,4-triazin-3-yl)-2,2'-bipyridine] is a very rare example of a mixed valence complex involving covalently bound U (IV) and U (VI) ions; its crystal structure also exhibits a seven coordinate uranyl moiety, with one bidentate nitrate group almost parallel to the UO 2 fragment. The distinct structural features of [UO 2(kappa (2)-NO 3) 2(Mebtp)], with its high coordination number and a noticeable bending of the UO 2 fragment, and of [UO 2(kappa (2)-NO 3)(kappa (1)-NO 3)(terpy)], which displays a classical geometry, were analyzed by Density Functional Theory, considering the bonding energy components and the molecular orbitals involved in the interaction between the uranyl, nitrate, and Mebtp or terpy moieties. The unusual geometry of the Mebtp derivative with the seven coordinating atoms around the UO 2 fragment was found very stable. In both the Mebtp and terpy complexes, the origin of the interaction appears to be primarily steric (Pauli repulsion and electrostatic); this term represents 62-63% of the total bonding energy while the orbital term contributes to about 37-38%.
Published: 2008

44. Towards a 32-electron principle : Pu@Pb12 and related systems

Author: Jean-Pierre Dognon, Pekka Pyykkoe, Carine Clavaguéra, Laboratoire de Chimie de Coordination des Eléments f (LCF) (LCCEf), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des mécanismes réactionnels (DCMR), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry [Helsinki], University of Helsinki, and Helsingin yliopisto = Helsingfors universitet = University of Helsinki
Subjects: Ytterbium, 010405 organic chemistry, Radiochemistry, Inorganic chemistry, chemistry.chemical_element, General Medicine, General Chemistry, Electron, Actinide, 010402 general chemistry, 01 natural sciences, Catalysis, 0104 chemical sciences, Lead (geology), chemistry, Chemical physics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2007
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45. Ultrasoft pseudopotentials for lanthanide solvation complexes: Core or valence character of the 4f electrons

Author: Rodolphe Pollet, Jean-Pierre Dognon, Carine Clavaguéra, Laboratoire Francis PERRIN (LFP - URA 2453), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 73.20.At, 73.20.Fz, 71.15.Dx, 71.70.Gm, 71.15.Ap, 72.25.-b, Core charge, General Physics and Astronomy, gadolinium compounds, 02 engineering and technology, Electron, 01 natural sciences, core levels, Pseudopotential, Core electron, 0103 physical sciences, Physical and Theoretical Chemistry, 010306 general physics, BASIS-SETS, electron spin polarisation, Valence (chemistry), Spin polarization, Chemistry, pseudopotential methods, valence bands, exchange interactions (electron), Solvation, 021001 nanoscience & nanotechnology, charge exchange, GD(III), [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, MOLECULAR-DYNAMICS, Atomic physics, solvation, 0210 nano-technology, Valence electron
Abstract: International audience; The 4f electrons of lanthanides, because of their strong localization in the region around the nucleus, are traditionally included in a pseudopotential core. This approximation is scrutinized by optimizing the structures and calculating the interaction energies of Gd3+(H2O) and Gd3+(NH3) microsolvation complexes within plane wave Perdew-Burke-Ernzerhof calculations using ultrasoft pseudopotentials where the 4f electrons are included either in the core or in the valence space. Upon comparison to quantum chemical MP2 and CCSD(T) reference calculations it is found that the explicit treatment of the 4f electrons in the valence shell yields quite accurate results including the required small spin polarization due to ligand charge transfer with only modest computational overhead.
Published: 2006
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46. Gd(III) polyaminocarboxylate chelate: realistic manybody molecular dynamics simulations for molecular imaging applications

Author: Jean-Pierre Dognon, Florent Calvo, Emmanuelle Sansot, Carine Clavaguéra, Laboratoire Francis PERRIN (LFP - URA 2453), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Quantique (LPQ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)
Subjects: 010405 organic chemistry, Ligand, Gadolinium, Coordination number, Ab initio, chemistry.chemical_element, Charge (physics), 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Surfaces, Coatings and Films, Ion, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Molecular dynamics, chemistry, Computational chemistry, Chemical physics, Materials Chemistry, Physical and Theoretical Chemistry, Molecular imaging
Abstract: Realistic molecular dynamics simulations of polyaminocarboxylate complexes of gadolinium (III) ion in water are performed, providing coordination numbers and average residence times in quantitative agreement with available experimental data. A theoretical analysis, based on fitting a fluctuating charges model on ab initio data, also indicates that charge transfer between the ion and the ligand is significant.
Published: 2006
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47. Theoretical study of the hydrated Gd3+ ion: Structure, dynamics, and charge transfer

Author: Jean-Pierre Dognon, Carine Clavaguéra, Florent Calvo, Laboratoire Francis PERRIN (LFP - URA 2453), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Quantique (LPQ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)
Subjects: POLARIZATION, Gadolinium, POTENTIALS, General Physics and Astronomy, chemistry.chemical_element, 010402 general chemistry, 01 natural sciences, Force field (chemistry), Ion, Molecular dynamics, Ab initio quantum chemistry methods, 61.20.Ja, 61.25.Em, 71.15.-m, 0103 physical sciences, Molecule, WATER, Water cluster, EQUALIZATION, Physical and Theoretical Chemistry, LANTHANIDE IONS, 010304 chemical physics, SIMULATIONS, 0104 chemical sciences, Solvent, MODEL, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry, Chemical physics, MOLECULAR-DYNAMICS, MECHANICS, FORCE-FIELD, Atomic physics
Abstract: International audience; The dynamical processes taking place in the first coordination shells of the gadolinium (III) ion are important for improving the contrast agent efficiency in magnetic-resonance imaging. An extensive study of the gadolinium (III) ion solvated by a water cluster is reported, based on molecular dynamics simulations. The AMOEBA force field [P. Y. Ren and J. W. Ponder, J. Phys. Chem. B 107, 5933 (2003)] that includes many-body polarization effects is used to describe the interactions among water molecules, and is extended here to treat the interactions between them and the gadolinium ion. In this purpose accurate ab initio calculations have been performed on Gd3+-H2O for extracting the relevant parameters. Structural data of the first two coordination shells and some dynamical properties such as the water exchange rate between the first and second coordination shells are compared to available experimental results. We also investigate the charge transfer processes between the ion and its solvent, using a fluctuating charges model fitted to reproduce electronic structure calculations on [Gd(H2O)(n)](3+) complexes, with n ranging from 1 to 8. Charge transfer is seen to be significant (about one electron) and correlated with the instantaneous coordination of the ion.
Published: 2006
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48. New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: From ab initio to molecular dynamics

Author: Serge Crouzy, Jean-Pierre Dognon, Jean-Francois Fuchs, Hristo Nedev, Michel Ferrand, Valérie Brenner, David Poger, Laboratoire de biophysique moléculaire et cellulaire (LBMC), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Francis PERRIN (LFP - URA 2453), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Claude Fréjacques (LCF - URA 331), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: MESH: Databases, Protein, fit from ab initio potential, MESH: Ions, metalloproteins, Static Electricity, Ab initio, chemistry.chemical_element, 010402 general chemistry, Models, Biological, 01 natural sciences, Force field (chemistry), Metal, 03 medical and health sciences, Molecular dynamics, MESH: Computer Simulation, Computational chemistry, MESH: Water, Computer Simulation, MESH: Proteins, MESH: Mercury, Databases, Protein, MESH: Static Electricity, 030304 developmental biology, Ions, 0303 health sciences, Chemistry, Ligand, Anharmonicity, MESH: Models, Biological, Proteins, Water, Mercury, General Chemistry, Copper, 0104 chemical sciences, MESH: Copper, MESH: Sulfur, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Bond length, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Computational Mathematics, molecular dynamics simulation, visual_art, visual_art.visual_art_medium, Cu(I), Hg(II), CHARMM force field, Sulfur
Abstract: We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water. (Brooks BR et al. J Comput Chem 1983, 4, 1987.[1]) © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 837-856, 2006
Published: 2006
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49. Accurate static electric dipole polarizability calculation of +3 charged lanthanide ions

Author: Carine Clavaguéra, Jean-Pierre Dognon, Laboratoire Francis PERRIN (LFP - URA 2453), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Lanthanide, 010304 chemical physics, Chemistry, Scalar (mathematics), General Physics and Astronomy, 010402 general chemistry, Polarization (waves), 01 natural sciences, 0104 chemical sciences, Ion, Pseudopotential, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Dipole, Polarizability, 0103 physical sciences, Physics::Atomic and Molecular Clusters, Physics::Atomic Physics, Physical and Theoretical Chemistry, Atomic physics, Relativistic quantum chemistry
Abstract: An accurate determination of the heavy element static atomic dipole polarizability is a challenge for theoretical methods. We present in this paper computed values of the dipole polarizability of the lanthanide ions from La3+ to Lu3+. The results were obtained by performing fully relativistic and pseudopotential calculations including the treatment of open-shell systems. We have shown that, in order to obtain accurate results, it is essential to take into account scalar relativistic effects, core polarization and flexibility of the basis sets. Finally, we present a database of reference values of dipole polarizability for the Ln3+ ions.
Published: 2005
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50. Secondary structures of short peptide chains in the gas phase: double resonance spectroscopy of protected dipeptides

Author: François Piuzzi, Gert von Helden, Isabelle Compagnon, Jean-Pierre Dognon, Wutharath Chin, Gerard Meijer, Clélia Canuel, Iliana Dimicoli, Michel Mons, Laboratoire Francis PERRIN (LFP - URA 2453), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), FOM Institute for Plasma Physics : Rijnhuizen, Foundation for Fundamental Research on Matter, Fritz-Haber-Institut der Max-Planck-Gesellschaft (FHI), and Max Planck Society
Subjects: Protein Conformation, Stereochemistry, Population, Ribbon diagram, infrared spectra, General Physics and Astronomy, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Protein structure, Side chain, molecular biophysics, macromolecules, Amino Acids, Physical and Theoretical Chemistry, education, Conformational isomerism, Protein secondary structure, education.field_of_study, Chemistry, Lasers, Spectrum Analysis, Hydrogen Bonding, Dipeptides, ultraviolet spectra, 021001 nanoscience & nanotechnology, proteins, 0104 chemical sciences, Folding (chemistry), [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 36.20.Fz, 36.20.Hb, 87.15.By, 87.15.Cc, 87.15.He, 33.40.+f, 33.20.Ea, 33.20.Lg, optical double resonance, hydrogen bonds, Gases, 0210 nano-technology, Alpha helix
Abstract: The conformational structure of short peptide chains in the gas phase is studied by laser spectroscopy of a series of protected dipeptides, Ac-Xxx-Phe-NH(2), Xxx=Gly, Ala, and Val. The combination of laser desorption with supersonic expansion enables us to vaporize the peptide molecules and cool them internally; IR/UV double resonance spectroscopy in comparison to density functional theory calculations on Ac-Gly-Phe-NH(2) permits us to identify and characterize the conformers populated in the supersonic expansion. Two main conformations, corresponding to secondary structures of proteins, are found to compete in the present experiments. One is composed of a doubly gamma-fold corresponding to the 2(7) ribbon structure. Topologically, this motif is very close to a beta-strand backbone conformation. The second conformation observed is the beta-turn, responsible for the chain reversal in proteins. It is characterized by a relatively weak hydrogen bond linking remote NH and CO groups of the molecule and leading to a ten-membered ring. The present gas phase experiment illustrates the intrinsic folding properties of the peptide chain and the robustness of the beta-turn structure, even in the absence of a solvent. The beta-turn population is found to vary significantly with the residues within the sequence; the Ac-Val-Phe-NH(2) peptide, with its two bulky side chains, exhibits the largest beta-turn population. This suggests that the intrinsic stabilities of the 2(7) ribbon and the beta-turn are very similar and that weakly polar interactions occurring between side chains can be a decisive factor capable of controlling the secondary structure.
Published: 2005
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