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Chahkandi B, Chahkandi M. An accurate DFT study within conformational survey of the D-form serine-alanine protected dipeptide. BMC Chem 2023; 17:138. [PMID: 37828563 PMCID: PMC10571400 DOI: 10.1186/s13065-023-01051-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
The conformational analysis of N-formyl-D-serine-D-alanine-NH2 dipeptide was studied using density functional theory methods at B3LYP, B3LYP‒D3, and M06‒2X levels using 6‒311 + G (d,p) basis set in the gas and water phases. 87 conformers of 243 stable ones were located and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model bears serine in βL, γD, γL and the alanine in γL and γD configurations. The investigation of side‒chain‒backbone interactions revealed that the most stable conformer, γD-γL, is in the β‒turn region of Ramachandran map; therefore, serine-alanine dipeptide model should be adopted with a β‒turn conformation. Intramolecular hydrogen bonding in β‒turns consideration by QTAIM disclosed γD-γL includes three hydrogen bonds. The computed UV‒Vis spectrum alongside of NBO calculation showed the five main electronic transition bands derived of n → n* of intra‒ligand alanine moiety of dipeptide structure.
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Affiliation(s)
- Behzad Chahkandi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
| | - Mohammad Chahkandi
- Department of Chemistry, Hakim Sabzevari University, Sabzevar, 96179-76487, Iran
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2
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Le Barbu-Debus K, Pérez-Mellor A, Lepère V, Zehnacker A. How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer. Phys Chem Chem Phys 2022; 24:19783-19791. [PMID: 35969161 DOI: 10.1039/d2cp03110h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.
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Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
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Kumar S, Borish K, Dey S, Nagesh J, Das A. Sequence dependent folding motifs of the secondary structures of Gly-Pro and Pro-Gly containing oligopeptides. Phys Chem Chem Phys 2022; 24:18408-18418. [PMID: 35880873 DOI: 10.1039/d2cp01306a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Folding motifs of the secondary structures of peptides and proteins are primarily based on the hydrogen bonding interactions in the backbone as well as the sequence of the amino acid residues present. For instance, the β-turn structure directed by the Pro-Gly sequence is the key to the β-hairpin structure of peptides/proteins as well as a selective site for the enzymatic hydroxylation of pro-collagen. Herein, we have investigated the sequence dependent folding motifs of end-protected Gly-Pro and Pro-Gly dipeptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). All three observed conformers of the Gly-Pro peptide in the gas phase have been found to have extended β-strand or polyproline-II (PP-II) structures with C5-C7 hydrogen bonding interactions, which correlates well with the structure obtained from solution phase spectroscopy and XRD. On the other hand, we have found that the Pro-Gly peptide has a C10/β-turn structure in the solution phase in contrast to the C7-C7 (i.e. 27-ribbon) structure observed in the gas phase. Although the lowest energy structure in the gas phase is not C10, we find that C7-C7 is an abundantly found structural motif of Pro-Gly containing peptides in the Cambridge Structural Database, indicating that the gas phase conformers are not sampling any unusual forms. We surmise that the role of the solvent could be crucial in dictating the preferential stabilization of the C10 structure in the solution phase. The present investigation provides a comprehensive picture of the folding motifs of the Gly-Pro and Pro-Gly peptides observed in the gas phase and condensed phase weaving a fine interplay of the intrinsic conformational properties, solvation, and crystal packing of the peptides.
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Affiliation(s)
- Satish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
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Gaigeot MP. Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119864. [PMID: 34052762 DOI: 10.1016/j.saa.2021.119864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France.
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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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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M, Cabezas C, León I, Alonso JL. Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group. Phys Chem Chem Phys 2021; 22:20284-20294. [PMID: 32966425 DOI: 10.1039/d0cp03136d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field. These structural and spectroscopic results, complemented by a theoretical Natural Bond Orbital analysis, enabled us to document the capacity of the weakly polar -CH2-SH side chain of Cys to adapt itself to the intrinsic local preferences of the peptide backbone, i.e., a γ-turn or a β-sheet extended secondary structure. The corresponding local H-bonding bridges the side chain acceptor S atom to the backbone NH donor site of the same or the next residue along the chain, through a 5- or a 6-membered ring respectively.
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Affiliation(s)
- Gildas Goldsztejn
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | | | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Carlos Cabezas
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - José Luis Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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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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Dupuy MS, Gloaguen E, Tardivel B, Mons M, Brenner V. CC2 Benchmark for Models of Phenylalanine Protein Chains: 0–0 Transition Energies and IR Signatures of the ππ* Excited State. J Chem Theory Comput 2019; 16:601-611. [DOI: 10.1021/acs.jctc.9b00923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mi-Song Dupuy
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
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9
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Li H, Wang Z, Jiang J, Luo Y. Competition between dispersion interactions and conventional hydrogen bonding: insights from a theoretical study on Z-Arg-OH. Phys Chem Chem Phys 2019; 21:17893-17900. [PMID: 31380529 DOI: 10.1039/c9cp03130h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dispersion interaction was reported to play a critical role in the stabilization of model dipeptide Z-Arg-OH, even greater than the conventional hydrogen bond (HB), which is opposite to the traditional opinion. Here the conformation of Z-Arg-OH has been systematically searched by the effective fragment based step-by-step strategy. All the newly-found low-energy conformers determined at the advanced DSD-PBEP86-D3(BJ)/aug-cc-pVTZ level are clearly in the stretched form with strong conventional HBs, rather than the reported folded structures with emphasis on the dispersion interactions. The simulated IR spectra of the stretched conformers fit better than those of the folded ones compared with the previous experimental observations. Near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges have also been simulated to unambiguously identify different isomers. This work thus provides valuable insight into the competitions between the conventional HB and the dispersion interactions and demonstrates that the conventional hydrogen bonding is still more important for such small peptides.
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Affiliation(s)
- Hongbao Li
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui University, Hefei, Anhui 230601, China
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Galimberti DR, Bougueroua S, Mahé J, Tommasini M, Rijs AM, Gaigeot MP. Conformational assignment of gas phase peptides and their H-bonded complexes using far-IR/THz: IR-UV ion dip experiment, DFT-MD spectroscopy, and graph theory for mode assignment. Faraday Discuss 2019; 217:67-97. [DOI: 10.1039/c8fd00211h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Graph theory based vibrational modes as new entities for vibrational THz spectroscopy.
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Affiliation(s)
| | | | - Jérôme Mahé
- LAMBE UMR8587
- Univ Evry
- Université Paris-Saclay
- CNRS
- 91025 Evry
| | - Matteo Tommasini
- Department of Chemistry, Materials, Chemical Engineering “G. Natta” Politecnico di Milano
- 20133 Milano
- Italy
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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Habka S, Sohn WY, Vaquero-Vara V, Géléoc M, Tardivel B, Brenner V, Gloaguen E, Mons M. On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins. Phys Chem Chem Phys 2018; 20:3411-3423. [DOI: 10.1039/c7cp07605c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The anchoring properties of an asparagine (Asn) residue to its local backbone environment in turn model peptides is characterized using gas phase laser spectroscopy and compared to crystallized protein structures.
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Affiliation(s)
- S. Habka
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - W. Y. Sohn
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | | | - M. Géléoc
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - B. Tardivel
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - V. Brenner
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - E. Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - M. Mons
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
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