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Lebel M, Very T, Gloaguen E, Tardivel B, Mons M, Brenner V. Excited States Computation of Models of Phenylalanine Protein Chains: TD-DFT and Composite CC2/TD-DFT Protocols. Int J Mol Sci 2022; 23:621. [PMID: 35054802 PMCID: PMC8776158 DOI: 10.3390/ijms23020621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 11/16/2022] Open
Abstract
The present benchmark calculations testify to the validity of time-dependent density functional theory (TD-DFT) when exploring the low-lying excited states potential energy surfaces of models of phenylalanine protein chains. Among three functionals suitable for systems exhibiting charge-transfer excited states, LC-ωPBE, CAM-B3LYP, and ωB97X-D, which were tested on a reference peptide system, we selected the ωB97X-D functional, which gave the best results compared to the approximate coupled-cluster singles and doubles (CC2) method. A quantitative agreement for both the geometrical parameters and the vibrational frequencies was obtained for the lowest singlet excited state (a ππ* state) of the series of capped peptides. In contrast, only a qualitative agreement was met for the corresponding adiabatic zero-point vibrational energy (ZPVE)-corrected excitation energies. Two composite protocols combining CC2 and DFT/TD-DFT methods were then developed to improve these calculations. Both protocols substantially reduced the error compared to CC2 and experiment, and the best of both even led to results of CC2 quality at a lower cost, thus providing a reliable alternative to this method for very large systems.
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Affiliation(s)
| | | | | | | | | | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (M.L.); (T.V.); (E.G.); (B.T.); (M.M.)
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2
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Hernandez-Castillo AO, Bischoff J, Lee JH, Langenhan J, Karra M, Meijer G, Eibenberger-Arias S. High-resolution UV spectroscopy of 1-indanol. Phys Chem Chem Phys 2021; 23:7048-7056. [PMID: 33625420 DOI: 10.1039/d0cp06170k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report on rotationally resolved laser induced fluorescence (LIF) and vibrationally resolved resonance-enhanced multiphoton ionization (REMPI) spectroscopy of the chiral molecule 1-indanol. Spectra of the S1← S0 electronic transition are recorded in a jet-cooled, pulsed molecular beam. Using two time-delayed pulsed lasers, the lifetimes of the S1 state of the two most stable conformers, referred to as eq1 and ax2, have been determined. The S1← S0 origin bands of these conformers as well as the transition to a vibrationally excited level in the S1 state of eq1 are recorded with full rotational resolution (25 MHz observed linewidth) by measuring the LIF intensity following excitation with a tuneable, narrowband cw laser. On selected rotationally resolved electronic transitions, Lamb-dips are measured to confirm the Lorentzian lifetime-contribution to the observed lineshapes. The rotationally resolved S1← S0 origin band of a neon-complex of eq1 is measured via LIF as well. The fit of the rotationally resolved LIF spectra of the origin bands to those of an asymmetric rotor yields a standard deviation of about 6 MHz. The resulting spectroscopic parameters are tabulated and compared to the outcome of ab initio calculations. For both conformers as well as for the Ne-eq1 complex, the geometric structures in the S0 and S1 states are discussed. For all systems, the transition dipole moment is mainly along the a-axis, the contributions along the b- and c-axes being about one order of magnitude smaller.
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Affiliation(s)
- A O Hernandez-Castillo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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3
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Goldsztejn G, Mundlapati VR, Donon J, Tardivel B, Gloaguen E, Brenner V, Mons M. An intraresidue H-bonding motif in selenocysteine and cysteine, revealed by gas phase laser spectroscopy and quantum chemistry calculations. Phys Chem Chem Phys 2021; 22:20409-20420. [PMID: 32914809 DOI: 10.1039/d0cp02825h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Models of protein chains containing a seleno-cysteine (Sec) residue have been investigated by gas phase laser spectroscopy in order to document the effect of the H-bonding properties of the SeH group in the folding of the Sec side chain, by comparison with recent data on Ser- and Cys-containing sequences. Experimental data, complemented by quantum chemistry calculations and natural bonding orbital (NBO) analyses, are interpreted in terms of the formation of a so-called 5γ intra-residue motif, which bridges the acceptor chalcogen atom of the side chain to the NH bond of the same residue. This local structure, in which the O/S/Se atom is close to the plane of the N-terminal side amide, is constrained by local backbone-side chain hyperconjugation effects involving the S and Se atoms. Theoretical investigations of the Cys/Sec side chain show that (i) this 5γ motif is an intrinsic feature of these residues, (ii) the corresponding H-bond is strongly non-linear and intrinsically weak, (iii) but enhanced by γ- and β-turn secondary structures, which promote a more favorable 5γ H-bonding approach and distance. The resulting H-bonds are slightly stronger in selenocysteine than in cysteine, but nearly inexistent in serine, whose side chain in contrast behaves as a H-bonding donor. The modest spectral shifts of the Cys/Sec NH stretches measured experimentally reflect the moderate strength of the 5γ H-bonding, in agreement with the correlation obtained with a NBO-based H-bond strength indicator. The evolution along the Ser, Cys and Sec series emphasizes the compromise between the several factors that control the H-bonding in a hyperconjugation-constrained geometry, among them the chalcogen van der Waals and covalent radii. It also illustrates the 5γ H-bond enhancements with the Sec and Cys residues favoured by the constraints imposed by the γ- and β-turn structures of the peptide chain.
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Affiliation(s)
- Gildas Goldsztejn
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | | | - Jérémy Donon
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | - Benjamin Tardivel
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | - Eric Gloaguen
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | - Valérie Brenner
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
| | - Michel Mons
- Laboratoire Interactions Dynamiques et Lasers (LIDYL), Université Paris-Saclay, Paris, France.
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4
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Alauddin M, Roy M, Nam SH, Song JK, Park SM. Structure of
Mono‐Hydrated
Aniline Dimer Cation. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mohammad Alauddin
- Department of Theoretical and Computational Chemistry University of Dhaka Dhaka Bangladesh
| | - Madhusudan Roy
- Department of Chemistry Kyung Hee University Seoul 02447 Republic of Korea
| | - Sang Hwan Nam
- Department of Chemistry Kyung Hee University Seoul 02447 Republic of Korea
| | - Jae Kyu Song
- Department of Chemistry Kyung Hee University Seoul 02447 Republic of Korea
| | - Seung Min Park
- Department of Chemistry Kyung Hee University Seoul 02447 Republic of Korea
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5
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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6
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Soorkia S, Jouvet C, Grégoire G. UV Photoinduced Dynamics of Conformer-Resolved Aromatic Peptides. Chem Rev 2019; 120:3296-3327. [DOI: 10.1021/acs.chemrev.9b00316] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satchin Soorkia
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Christophe Jouvet
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
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7
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Scutelnic V, Prlj A, Zabuga A, Corminboeuf C, Rizzo TR. Infrared Spectroscopy as a Probe of Electronic Energy Transfer. J Phys Chem Lett 2018; 9:3217-3223. [PMID: 29847947 DOI: 10.1021/acs.jpclett.8b01216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have combined electronic and vibrational spectroscopy in a cryogenic ion trap to produce highly resolved, conformer-selective spectra for the ground and excited states of a peptide containing two chromophores. These spectra permit us to determine the precise three-dimensional structure of the peptide and give insight into the migration of the electronic excitation from phenylalanine to tyrosine because changes in the excited-state infrared spectra are sensitive to localization of the electronic energy in each chromophore. The well-controlled experimental conditions make this result a stringent test for theoretical methods dealing with electronic energy transfer.
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Affiliation(s)
- Valeriu Scutelnic
- Laboratory of Molecular Physical Chemistry , Ecole Polytechnique Fédérale de Lausanne , Station 6 , CH-1015 Lausanne , Switzerland
| | - Antonio Prlj
- Laboratory for Computational Molecular Design , Ecole Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Aleksandra Zabuga
- Laboratory of Molecular Physical Chemistry , Ecole Polytechnique Fédérale de Lausanne , Station 6 , CH-1015 Lausanne , Switzerland
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design , Ecole Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Thomas R Rizzo
- Laboratory of Molecular Physical Chemistry , Ecole Polytechnique Fédérale de Lausanne , Station 6 , CH-1015 Lausanne , Switzerland
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8
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Mališ M, Došlić N. Nonradiative Relaxation Mechanisms of UV Excited Phenylalanine Residues: A Comparative Computational Study. Molecules 2017; 22:E493. [PMID: 28335582 PMCID: PMC6155328 DOI: 10.3390/molecules22030493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/09/2017] [Accepted: 03/16/2017] [Indexed: 11/17/2022] Open
Abstract
The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory. The work emphasizes the role that excitation transfer from the phenylππ*to amidenπ*state plays in the deactivation of the three systems and shows how the ease of out-of-plane distortions of the amide group determines the rate of population transfer between the two electronic states. The subsequent dynamics on thenπ*state is barrierless along several pathways and leads to fast deactivation to the ground electronic state.
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Affiliation(s)
- Momir Mališ
- Ruđer Bošković Institute, HR-10000 Zagreb, Croatia.
- Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Nađa Došlić
- Ruđer Bošković Institute, HR-10000 Zagreb, Croatia.
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9
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Kopysov V, Makarov A, Boyarkin OV. Nonstatistical UV Fragmentation of Gas-Phase Peptides Reveals Conformers and Their Structural Features. J Phys Chem Lett 2016; 7:1067-1071. [PMID: 26950179 DOI: 10.1021/acs.jpclett.6b00292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Solving the 3D structure of a biomolecule requires recognition of its conformers and measurements of their individual structural identities, which can be compared with calculations. We employ the phenomenon of nonstatistical photofragmentation, detected by a combination of UV cold ion spectroscopy and high-resolution mass spectrometry, to identify the main conformers of gas-phase peptides and to recover individual UV absorption and mass spectra of all of these conformers in a single laser scan. We first validate this approach with a benchmark dipeptide, Tyr-Ala, and then apply it to a decapeptide, gramicidin S. The revealed characteristic structural difference between the conformers of the latter identifies some of the previously calculated structures of gramicidin S as the most likely geometries of its remaining unsolved conformer.
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Affiliation(s)
- Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , Station-6, 1015 Lausanne, Switzerland
| | - Alexander Makarov
- Thermo Fisher Scientific , Hanna-Kunath Str. 11, 28199 Bremen, Germany
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , Station-6, 1015 Lausanne, Switzerland
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10
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Sohn WY, Brenner V, Gloaguen E, Mons M. Local NH–π interactions involving aromatic residues of proteins: influence of backbone conformation and ππ* excitation on the π H-bond strength, as revealed from studies of isolated model peptides. Phys Chem Chem Phys 2016; 18:29969-29978. [DOI: 10.1039/c6cp04109d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gas phase conformer-selective IR spectroscopy combined and relevant quantum chemistry methods document the NH–π interactions in Phe residues.
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Affiliation(s)
| | | | - Eric Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
| | - Michel Mons
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
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11
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Alauddin M, Gloaguen E, Brenner V, Tardivel B, Mons M, Zehnacker‐Rentien A, Declerck V, Aitken DJ. Intrinsic Folding Proclivities in Cyclic β‐Peptide Building Blocks: Configuration and Heteroatom Effects Analyzed by Conformer‐Selective Spectroscopy and Quantum Chemistry. Chemistry 2015; 21:16479-93. [DOI: 10.1002/chem.201501794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Mohammad Alauddin
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
- Current address: Department of Chemistry, University of Dhaka, Dhaka‐1000 (Bangladesh)
| | - Eric Gloaguen
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Valérie Brenner
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Benjamin Tardivel
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Michel Mons
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | | | - Valérie Declerck
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
| | - David J. Aitken
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
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12
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Loquais Y, Gloaguen E, Habka S, Vaquero-Vara V, Brenner V, Tardivel B, Mons M. Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry. J Phys Chem A 2014; 119:5932-41. [DOI: 10.1021/jp509494c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yohan Loquais
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Sana Habka
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Vanesa Vaquero-Vara
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA,
IRAMIS, Laboratoire
Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France
- CNRS, INP, Laboratoire
Francis Perrin, URA 2453, CEA Saclay,
Bât 522, 91191 Gif-sur-Yvette, France
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