Projet ANR-11-NS08-0001 – SPIONCLUS : Structure, Dynamique et Spectroscopie de Clusters Ioniques. Synergie entre expériences IR-PD et simulations DFT-MD.
Programme : Blanc International I - SIMI 8 - Chimie du solide, colloïdes, physicochimie (Blanc Inter I SIMI 8)
Année de financement : 2011
Coordinateur du projet : Madame Marie-Pierre GAIGEOT (CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE - DELEGATION REGIONALE ILE-DE-FRANCE SECTEUR EST)
Partenaires : Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement; School of Chemical Sciences
Montant : 328641.0 euros
Date de début : 2012
Durée : 36 mois
Résumé : SPIONCLUS Structure, Dynamique et Spectroscopie de Clusters Ioniques. Synergie entre expériences IR-PD et simulations DFT-MD.Structure, Dynamique et Spectroscopie de Clusters Ioniques. Synergie entre expériences IR-PD et simulations DFT-MD.
Enjeux et objectifsThe proposed research is an effort to understand the role of non-covalent interactions in formation of secondary structures in biological systems, and the selective sequestration of ions. The focus will be on understanding how intermediate configurations, of higher energy, ultimately reach the ground state configuration, a process analogous to protein folding, going from a collapsed and/or denatured state to the native structure. This will be accomplished through by a combined experimental and theoretical investigation of ion-molecule complexes, partially hydrated, that exhibit a variety of structural conformers. Newly developed experimental methods, combining mass spectrometry and infrared laser spectroscopy, will be used to identify and characterize the molecular configurations of these systems. State-of-the-art theoretical methods, density functional theory combined with molecular dynamics (DFT-MD), will be applied to these systems to characterize the energy barriers between different configurations and the pathways over these barriers connecting them. Anharmonic vibrational spectra will be obtained from DFT-MD, compared to the experiments, and the band assignments will provide a detailed microscopic interpretation of the experimental features, and will provide final assessments of conformations experimentally probed.
MéthodesThe experiment developed in the Lisy group is unique and brings a new possibility of detailed conformational mapping of clusters’s conformers and energy barriers, within the gas-phase community. By combining mass spectrometric methods with infrared laser spectroscopy, Prof. Lisy helped pioneer the field of ion cluster spectroscopy. Prof. Lisy’s insistence that cluster internal energy (or effective cluster temperature) is crucial to understanding cluster structure and conformation has changed the way the others in the field now approach these systems. The Gaigeot group brings originality in the emerging field of DFT-MD to the experimental facets of the research that desperately need accurate anharmonic vibrational frequencies, potential energy barrier heights and vibrational energy relaxation. The expertise of the group in theoretical spectroscopy using MD simulations and its coupling to action spectroscopy experiments is unique in Europe. The association between the two groups will bring novelty and excellence to the domain of vibrational spectroscopy of strongly anharmonic molecular ions.
Résumé de la soumission : The proposed research is an effort to understand the role of non-covalent interactions in formation of secondary structures in biological systems, and the selective sequestration of ions. The focus will be on understanding how intermediate configurations, of higher energy, ultimately reach the ground state configuration, a process analogous to protein folding, going from a collapsed and/or denatured state to the native structure. This will be accomplished through by a combined experimental and theoretical investigation of ion-molecule complexes, partially hydrated, that exhibit a variety of structural conformers. Newly developed experimental methods, combining mass spectrometry and infrared laser spectroscopy, will be used to identify and characterize the molecular configurations of these systems. State-of-the-art theoretical methods, density functional theory combined with molecular dynamics (DFT-MD), will be applied to these systems to characterize the energy barriers between different configurations and the pathways over these barriers connecting them. Anharmonic vibrational spectra will be obtained from DFT-MD, compared to the experiments, and the band assignments will provide a detailed microscopic interpretation of the experimental features, and will provide final assessments of conformations experimentally probed. Initial studies will target solvated cations and anions in order to map out potential energy surfaces and to develop/refine the combined experimental/theoretical approach. Next, specific molecules of biological interest: n-methyl acetamide (a model for the protein backbone), amino-phenyl ethanol (a model neurotransmitter), and serotonin (a neurotransmitter) will be investigated. The selective sequestering of mono and divalent ions of biological interest, Na+, K+, Mg2+, and Ca2+, as well as environmental interest, Cs+, I-, and Sr2+, with specific ionophores in a hydrated environment will also be studied. More broadly, mono and divalent ions are ubiquitous in biological systems, they are involved in wide range of functions and play important roles in the structure of proteins, RNA and DNA. Environmental remediation is also of particular interest in light of safety concerns associated with nuclear facilities, world-wide. The experiment developed in the Lisy group is unique and brings a new possibility of detailed conformational mapping of clusters’s conformers and energy barriers, within the gas-phase community. By combining mass spectrometric methods with infrared laser spectroscopy, Prof. Lisy helped pioneer the field of ion cluster spectroscopy. Prof. Lisy’s insistence that cluster internal energy (or effective cluster temperature) is crucial to understanding cluster structure and conformation has changed the way the others in the field now approach these systems. The Gaigeot group brings originality in the emerging field of DFT-MD to the experimental facets of the research that desperately need accurate anharmonic vibrational frequencies, potential energy barrier heights and vibrational energy relaxation. The expertise of the group in theoretical spectroscopy using MD simulations and its coupling to action spectroscopy experiments is unique in Europe. The association between the two groups will bring novelty and excellence to the domain of vibrational spectroscopy of strongly anharmonic molecular ions. This proposal aims to develop a new cadre of young scientists, with the knowledge of experimental methods to probe fundamental issues in biological and environmental issues, and equipped with modern theoretical approaches that go beyond implementing computational software packages. The collaboration and exchange between the groups at the University of Illinois and the University of Evry will make this possible.
Résultats : Major results obtained over the first 18 months of SPIONCLUS : 
The structures of Cl--(Methanol)1-2 clusters have been unraveled combining Infrared Predissociation (IR-PD) experiments and DFT-based molecular dynamics simulations (DFT-MD) at 100K . The dynamical IR spectra extracted from DFT-MD provide the initial 600 cm-1 large anharmonic red-shift of the O-H stretch from uncomplexed methanol (3682 cm-1) to Cl--(Methanol)1 complex (3085 cm-1) as observed in the IR-PD experiment, as well as the subtle supplementary blue- and red- shifts of the O-H stretch in Cl--(Methanol)2 depending on the structure.
[Paper In Press, 2013, Spectro. Chimica Acta A: Molecular and Biomolecular Spectroscopy, http://dx.doi.org/10.1016/j.saa.2013.05.073] : 
IRPD spectra of Cl (NMA)1(H2O)0 2Ar2 combined with BOMD dynamical IR spectra clearly show that the chloride ion is bound to the amine hydrogen, forming a strong ionic hydrogen bond.  The dynamical spectra of Cl (NMA)1(H2O)0 2 complexes show that the interpretation of the IR-PD spectra can be achieved unambiguously, as these theoretical spectra naturally provide the initial 500-600 cm-1 red-shift of the NH stretch from NMA to NMA complexed with Cl-, and the subsequent supplementary 100 cm-1 red-shifts when adding water molecules. This is achieved without any rescaling factors.
[Paper In Press, 2013, Phys. Chem. Chem. Phys., DOI:10.1039/C3CP52418C ] : 
We have developped experimental and theoretical tools to follow the formation of high energy conformers of clusters, including a full comprehension of the processes occuring during their formation. This has been demonstrated on Li+(H2O)3-4 clusters. The synergy is made between IR-PD experiments [Prof Lisy’s group, USA] and DFT-MD trajectories [Prof Gaigeot’s group, France] simulating the collisions between the metal ion and the water clusters (4 ps timescale) complemented with RRKM calculations (microseconds timescale). 
[Paper In preparation]
Perspectives : We continue our project following the outlines described above for biologically relevant systems of interest.
Publications et brevets : Publications about the project during the first 18 months by the french team of ANR SPIONCLUS (international peer reviewed journals) : 
O-H anharmonic vibrational motions  in Cl-(CH3OH)1-2 ionic clusters. Combined IRPD experiments and AIMD simulations.
J.P. Beck, A. Cimas, J.M. Lisy, M.P. Gaigeot
2013, In Press, Spectro. Chimica Acta A: Molecular and Biomolecular Spectroscopy, 
DOI: http://dx.doi.org/10.1016/j.saa.2013.05.073
Anharmonic vibrations from the Chloride...Amide ionic hydrogen bonds in Cl-(N-methylacetamide)1(H2O)0-2Ar2 cluster ions. Combined IRPD experiments and AIMD simulations.
J.P. Beck, M.P. Gaigeot, J.M. Lisy
2013, In Press,  Phys. Chem. Chem. Phys., 
DOI:10.1039/C3CP52418C
Results presented in 6 international conferences + 3 national conferences