Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field †

International audienceThe 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

Développement de champs de forces polarisables et applications à la spectroscopie vibrationnelle

Spectroscopy dissociation by absorption of infrared photons (IRPD) provides vibrational signatures of charged species in the gas phase, such as small peptides or hydrated ions in water clusters. The vibrational normal modes assignment to establish a relationship between the experimental spectrum and molecular structure is a delicate task and requires the use of molecular modeling.This manuscript presents a set of theoretical tools for calculation and assignment of vibrational spectra, based mainly on classical molecular dynamics and polarizable AMOEBA force field, and its application to gaseous ions of various sizes. Hydrated ions in water clusters M(H2O)n (n in 6-100 range) are characterized by a dynamic behavior, and their experimental spectrum can not be described by a single structure. The signature of peptides changes with temperature and dynamic anharmonicity effects. They can also be the site of proton transfer mechanisms, with a very characteristic vibrational signature.The potential energy surface of these systems is explored by classical molecular dynamics in individual trajectories or replica exchange to generate energetically stable structures. For smaller systems, quantum methods, as DFT and post-HF, are used to confirm the lowest energy structures, calculate their static IR and propose normal modes assignments. For larger systems, i.e ions in water drops of several tens of molecules, the simulation of IR spectra at finite temperature is based on the Fourier transform of the autocorrelation function of the dipole moment (DACF), calculated during a classical molecular dynamics trajectory. As this method does not allow direct access to the vibrational normal modes, we implemented a method of dynamic assigments, based on the Driven Molecular Dynamics (DMD) and coupled to the DACF. The combination AMOEBA /DACF / DMD was used to reproduce and assign the spectrum of the dipeptide Ace-Phe-Ala-NH2, and those of hydrated ions in water clusters.Finally, the vibrational signature of a proton transfer can not be described by quantum static methods or by classical dynamics. Its modeling required the development of a two states Empirical Valence Bond Model (EVB), coupled with AMOEBA polarizable force field. The two states EVB model was implemented in the software TINKER. It can reproduce the dynamic behavior of proton transfer in small peptides and deprotonated acids, as well as the spectroscopic signatures observed experimentally.An important part of the applications of these developments relates simple hydrated ions in nano-droplets, and in particular the sulfate ion of great environmental importance. We were able to reproduce satisfactorily, for the first time, the spectra of clusters containing up to 100 water molecules. The main contributor to this experimental spectroscopy is the team of E. Williams from the University of California of Berkeley. We have established cooperation with them to complete this work by modeling the IR spectra of hydrated sulfates ions [SO4(H2O) n=9-36]2-, for which they obtained experimental signatures.La spectroscopie de dissociation par absorption de photons infrarouges (IRPD) permet d’obtenir les signatures vibrationnelles d’espèces chargées en phase gazeuse, telles que de petits peptides ou des ions hydratés dans des agrégats d’eau. L’attribution des modes de vibration pour établir une relation entre le spectre expérimental et une structure moléculaire est une tâche délicate et nécessite le recours à la modélisation moléculaire.Ce manuscrit présente un ensemble d’outils théoriques pour le calcul et l’attribution de spectres vibrationnels, basée principalement sur la dynamique moléculaire classique et le champ de forces polarisable AMOEBA, ainsi que son application à des ions gazeux de tailles diverses. Les ions hydratés dans des agrégats d’eau M(H2O)n (n allant de 6 à 100) sont caractérisés par une dynamique importante, et leur spectre expérimental ne peut pas être décrit par une seule structure. La signature des peptides évolue avec la température et les effets d’anharmonicité dynamique. Ils peuvent également être le siège de mécanismes de transfert de proton, présentant une signature vibrationnelle très caractéristique.La surface d’énergie potentielle de ces systèmes est explorée par la dynamique moléculaire classique en trajectoires individuelles ou avec échange de répliques, afin d’engendrer des structures énergétiquement stables. Pour les plus petits systèmes, les méthodes quantiques DFT et post-HF sont utilisées pour confirmer les structures de plus basse énergie, calculer leurs spectres IR statiques et proposer des attributions des modes de vibration. Pour les plus systèmes de plus grandes tailles, c’est-à-dire les ions dans des gouttes d’eau de plusieurs dizaines de molécules, la simulation des spectres IR à température finie est basée sur la transformée de Fourier de la fonction d’autocorrélation du moment dipolaire (DACF), calculée pour une trajectoire de dynamique moléculaire classique. Cette méthode n’offrant pas d’accès direct aux modes normaux de vibration, nous avons implémenté une méthode d’attribution dynamique, basée sur la Driven Molecular Dynamics (DMD) et couplée au DACF. La combinaison AMOEBA/DACF/DMD a été utilisée pour reproduire et attribuer le spectre du dipeptide Ace-Phe-Ala-NH2, et ceux d’ions hydratés dans des agrégats d’eau.Enfin, la signature vibrationnelle d’un transfert de proton ne peut être décrite, ni par des méthodes statiques quantiques, ni par la dynamique classique. Sa modélisation a nécessité le développement d’un modèle Empirical Valence Bond (EVB) à deux états, couplé au champ de forces polarisable AMOEBA. Le modèle EVB a été implémenté dans la suite logicielle Tinker. Il permet de reproduire le comportement dynamique du transfert de proton au sein de petits peptides et de diacides déprotonés, ainsi que la signature spectroscopique observée expérimentalement.Une partie importante des applications de ces développements concerne des ions simples hydratés dans des nano-gouttelettes, et en particulier l’ion sulfate de grande importance environnementale. Nous avons pu reproduire de façon satisfaisante, pour la première fois, les spectres d’agrégats contenant jusqu’à 100 molécules d’eau. Le principal contributeur à cette spectroscopie expérimentale est l’équipe d’E. Williams à l’université de Californie à Berkeley. Nous avons établi avec eux une collaboration pour compléter ce travail en modélisant les spectres IR d’ions sulfates hydratés [SO4(H2O)n=9-36]2-, dont ils ont obtenu les signatures expérimentales

Development of polarizable force fields and applications in vibrational spectroscpy

La spectroscopie de dissociation par absorption de photons infrarouges (IRPD) permet d’obtenir les signatures vibrationnelles d’espèces chargées en phase gazeuse, telles que de petits peptides ou des ions hydratés dans des agrégats d’eau. L’attribution des modes de vibration pour établir une relation entre le spectre expérimental et une structure moléculaire est une tâche délicate et nécessite le recours à la modélisation moléculaire.Ce manuscrit présente un ensemble d’outils théoriques pour le calcul et l’attribution de spectres vibrationnels, basée principalement sur la dynamique moléculaire classique et le champ de forces polarisable AMOEBA, ainsi que son application à des ions gazeux de tailles diverses. Les ions hydratés dans des agrégats d’eau M(H2O)n (n allant de 6 à 100) sont caractérisés par une dynamique importante, et leur spectre expérimental ne peut pas être décrit par une seule structure. La signature des peptides évolue avec la température et les effets d’anharmonicité dynamique. Ils peuvent également être le siège de mécanismes de transfert de proton, présentant une signature vibrationnelle très caractéristique.La surface d’énergie potentielle de ces systèmes est explorée par la dynamique moléculaire classique en trajectoires individuelles ou avec échange de répliques, afin d’engendrer des structures énergétiquement stables. Pour les plus petits systèmes, les méthodes quantiques DFT et post-HF sont utilisées pour confirmer les structures de plus basse énergie, calculer leurs spectres IR statiques et proposer des attributions des modes de vibration. Pour les plus systèmes de plus grandes tailles, c’est-à-dire les ions dans des gouttes d’eau de plusieurs dizaines de molécules, la simulation des spectres IR à température finie est basée sur la transformée de Fourier de la fonction d’autocorrélation du moment dipolaire (DACF), calculée pour une trajectoire de dynamique moléculaire classique. Cette méthode n’offrant pas d’accès direct aux modes normaux de vibration, nous avons implémenté une méthode d’attribution dynamique, basée sur la Driven Molecular Dynamics (DMD) et couplée au DACF. La combinaison AMOEBA/DACF/DMD a été utilisée pour reproduire et attribuer le spectre du dipeptide Ace-Phe-Ala-NH2, et ceux d’ions hydratés dans des agrégats d’eau.Enfin, la signature vibrationnelle d’un transfert de proton ne peut être décrite, ni par des méthodes statiques quantiques, ni par la dynamique classique. Sa modélisation a nécessité le développement d’un modèle Empirical Valence Bond (EVB) à deux états, couplé au champ de forces polarisable AMOEBA. Le modèle EVB a été implémenté dans la suite logicielle Tinker. Il permet de reproduire le comportement dynamique du transfert de proton au sein de petits peptides et de diacides déprotonés, ainsi que la signature spectroscopique observée expérimentalement.Une partie importante des applications de ces développements concerne des ions simples hydratés dans des nano-gouttelettes, et en particulier l’ion sulfate de grande importance environnementale. Nous avons pu reproduire de façon satisfaisante, pour la première fois, les spectres d’agrégats contenant jusqu’à 100 molécules d’eau. Le principal contributeur à cette spectroscopie expérimentale est l’équipe d’E. Williams à l’université de Californie à Berkeley. Nous avons établi avec eux une collaboration pour compléter ce travail en modélisant les spectres IR d’ions sulfates hydratés [SO4(H2O)n=9-36]2-, dont ils ont obtenu les signatures expérimentales.Spectroscopy dissociation by absorption of infrared photons (IRPD) provides vibrational signatures of charged species in the gas phase, such as small peptides or hydrated ions in water clusters. The vibrational normal modes assignment to establish a relationship between the experimental spectrum and molecular structure is a delicate task and requires the use of molecular modeling.This manuscript presents a set of theoretical tools for calculation and assignment of vibrational spectra, based mainly on classical molecular dynamics and polarizable AMOEBA force field, and its application to gaseous ions of various sizes. Hydrated ions in water clusters M(H2O)n (n in 6-100 range) are characterized by a dynamic behavior, and their experimental spectrum can not be described by a single structure. The signature of peptides changes with temperature and dynamic anharmonicity effects. They can also be the site of proton transfer mechanisms, with a very characteristic vibrational signature.The potential energy surface of these systems is explored by classical molecular dynamics in individual trajectories or replica exchange to generate energetically stable structures. For smaller systems, quantum methods, as DFT and post-HF, are used to confirm the lowest energy structures, calculate their static IR and propose normal modes assignments. For larger systems, i.e ions in water drops of several tens of molecules, the simulation of IR spectra at finite temperature is based on the Fourier transform of the autocorrelation function of the dipole moment (DACF), calculated during a classical molecular dynamics trajectory. As this method does not allow direct access to the vibrational normal modes, we implemented a method of dynamic assigments, based on the Driven Molecular Dynamics (DMD) and coupled to the DACF. The combination AMOEBA /DACF / DMD was used to reproduce and assign the spectrum of the dipeptide Ace-Phe-Ala-NH2, and those of hydrated ions in water clusters.Finally, the vibrational signature of a proton transfer can not be described by quantum static methods or by classical dynamics. Its modeling required the development of a two states Empirical Valence Bond Model (EVB), coupled with AMOEBA polarizable force field. The two states EVB model was implemented in the software TINKER. It can reproduce the dynamic behavior of proton transfer in small peptides and deprotonated acids, as well as the spectroscopic signatures observed experimentally.An important part of the applications of these developments relates simple hydrated ions in nano-droplets, and in particular the sulfate ion of great environmental importance. We were able to reproduce satisfactorily, for the first time, the spectra of clusters containing up to 100 water molecules. The main contributor to this experimental spectroscopy is the team of E. Williams from the University of California of Berkeley. We have established cooperation with them to complete this work by modeling the IR spectra of hydrated sulfates ions [SO4(H2O) n=9-36]2-, for which they obtained experimental signatures

Dynamics of ions in a water drop using the AMOEBA polarizable force field

International audienceVarious ions carrying a charge from À2 to +3 were confined in a drop of 100 water molecules as a way to model coordination properties inside the cluster and at the interface. The behavior of the ions has been followed by molecular dynamics with the AMOEBA polarizable force field. Multiply charged ions and small singly charged ions are found to lie inside the droplet, while bigger monovalent ions sit near the surface. The results provide a coherent picture of average structural properties as well as residence times for which a general trend is proposed, especially for the anions

Hydration of the sulfate dianion in cold nanodroplets: SO 4 2− (H 2 O) 12 and SO 4 2− (H 2 O) 13

International audienceThe structures, energetics and infrared spectra of SO 4 2À (H 2 O) 12 and SO 4 2À (H 2 O) 13 have been investigated by a combination of classical polarizable molecular dynamics and static quantum chemical calculations. Snapshots extracted from MD trajectories were used as inputs for local DFT optimization. Energies of the most stable structures were further refined at the ab initio level. A number of new low energy structures have thus been identified. The most stable structures of SO 4 2À (H 2 O) 12 have the sulfate on the surface of the water cluster, while it may be slightly more burried in SO 4 2À (H 2 O) 13 , however still with an incomplete first hydration shell. Differences in the infrared spectra arise in part from mixing of sulfate stretching and water librational modes in the 900-1100 cm À1 region, leading to some sensitivity of the IR spectrum to the structure. Second shell water molecules however do not generate signatures that are specific enough to relate spectra to structures straightforwardly, at least in this frequency range. Thus the emergence of a new band at 970 cm À1 in the SO 4 2À (H 2 O) 13 spectrum cannot be taken as a clue as to the number of water molecules which is necessary for a cluster to close the first hydration shell of sulfate. This number is at least 14 and possibly larger. However the density of low energy isomers is large enough that individual structures may loose meaning at all but the lowest temperatures

Manifolds of low energy structures for a magic number of hydrated sulfate : SO 4 2− (H 2 O) 24

International audienceLow energy structures of SO 2− 4 (H 2 O) 24 have been obtained using a combination of classical molecular dynamics simulations and refinement of structures and energies by quantum chemical calculations. Extensive exploration of the potential energy surface led to a number of low-energy structures, confirmed by accurate calibration calculations. An overall analysis of this large set was made after devising appropriate structural descriptors such as the numbers of cycles and their combinations. Low energy structures bear common motifs, the most prominent being fused cycles involving alternatively four and six water molecules. The latter adopt specific conformations which ensure the appropriate surface curvature to form a closed cage without dangling O-H bonds and at the same time provide 12-coordination of the sulfate ion. A prominent feature to take into account is isomerism via inversion of hydrogen bond orientations along cycles. This generates large families of ca. 100 isomers for this cluster size, spanning energy windows of 10-30 kJ.mol −1. This relatively ignored isomerism must be taken into account to identify reliably the lowest energy minima. The overall picture is that the magic number cluster SO 2− 4 (H 2 O) 24 does not correspond to formation of a single, remarkable structure, but rather to a manifold of structural families with similar stabilities. Extensive calculations on isomerization mechanisms within a family indicate that large barriers are associated to direct inversion of hydrogen bond networks. Possible implications of these results for magic number clusters of other anions are discussed

Strategy for Modeling the Infrared Spectra of Ion-Containing Water Drops

International audienceHydrated ions are ubiquitous in environmental and biological media. Understanding the perturbation exerted by an ion on the water hydrogen bond network is possible in the nanodrop regime by recording vibrational spectra in the O−H bond stretching region. This has been achieved experimentally in recent years by forming gaseous ions containing tens to hundreds of water molecules and recording their infrared photodissociation spectra. In this paper, we demonstrate the capabilities of a modeling strategy based on an extension of the AMOEBA polarizable force field to implement water atomic charge fluctuations along with those of intramolecular structure along the dynamics. This supplementary flexibility of nonbonded interactions improves the description of the hydrogen bond network and, therefore, the spectroscopic response. Finite temperature IR spectra are obtained from molecular dynamics simulations by computing the Fourier transform of the dipole moment autocorrelation function. Simulations of 1−2 ns are required for extensive sampling in order to reproduce the experimental spectra. Furthermore, bands are assigned with the driven molecular dynamics approach. This method package is shown to compare successfully with experimental spectra for 11 ions in water drops containing 36−100 water molecules. In particular, band frequency shifts of the free O−H stretching modes at the cluster surface are well reproduced as a function of both ion charge and drop size

Infrared Spectra of Deprotonated Dicarboxylic Acids: IRMPD Spectroscopy and Empirical Valence‐Bond Modeling

International audienceExperimental infrared multiple-photon dissociation (IRMPD) spectra recorded for a series of deprotonated dicarboxylic acids, HO 2 (CH 2) n CO À 2 (n = 2-4), are interpreted using a variety of computational methods. The broad bands centered near 1600 cm À 1 can be reproduced neither by static vibrational calculations based on quantum chemistry nor by a dynamical description of individual structures using the many-body polar-izable AMOEBA force field, strongly suggesting that these molecules experience dynamical proton sharing between the two carboxylic ends. To confirm this assumption, AMOEBA was combined with a two-state empirical valence-bond (EVB) model to allow for proton transfer in classical molecular dynamics simulations. Upon suitable parametrization based on ab initio reference data, the EVB-AMOEBA model satisfactorily reproduces the experimental infrared spectra, and the finite temperature dynamics reveals a significant amount of proton sharing in such systems

Hydration of the sulfate dianion in size-selected water clusters: From SO42−(H2O)9 to SO42−(H2O)13

International audienceIn celebration of Jose Riveros' many essential contributions to gas phase ion chemistry. Keywords: Hydrated sulfate IRPD spectroscopy AMOEBA polarizable force field Second hydration shell Mixed quantum classical modelling O H stretching frequency a b s t r a c t Infrared photodissociation (IRPD) spectra of SO 4 2− (H 2 O) n , n = 9-13, recorded in the cooled cell of a Fourier-transform ion cyclotron resonance mass spectrometer, between 2900 and 3800 cm −1 , are reported. The structures, energetics and infrared spectra of n = 9 and 11-13 were investigated by a combination of classical polarizable molecular dynamics and static quantum chemical calculations. Low-energy structures are mainly determined by the strong structuring effect of the sulfate ion, however, the highest cohesion is achieved when strong water-water interactions are present as well. As a result, the sulfate ion in the most stable structures for n = 9, 11 and 12 is on the surface of the water cluster. While SO 4 2− (H 2 O) 9 involves a mixture of isomers, the other sizes are found to be described by a single structural family, with the most stable structures of SO 4 2− (H 2 O) 11 and SO 4 2− (H 2 O) 13 deriving from that of SO 4 2− (H 2 O) 12 by removal and addition of a water molecule, respectively, without substantial reorganization. An important feature of these structures is that the number of water molecules in the second solvation sphere increases with cluster size, up to 3 for n = 12 and 4 for n = 13. This is directly reflected in the IRPD spectra. All spectra display two main features in the 3150-3350 and 3350-3650 cm −1 range, plus a small band near 3100 cm −1. The 3350-3650 cm −1 massif, which includes most bands arising from second sphere molecules, acquires larger intensity relative to that at 3150-3350 cm −1 which is mainly composed of stretches in first sphere molecules. Whereas most water molecules have ADD coordination (where A stands for acceptor and D stands for donor of a hydrogen bond), special cases, including DD and AADD account for bands at the red and blue ends of the spectra. Computed IR spectra are able to account for most experimental features, especially when anharmonicities are taken into account for the largest red shifts. Finally, the higher abundance of n = 12 relative to other sizes is related to a lower water evaporation rate constant, in good agreement with the water binding energy which is computed to be larger for n = 12 than for 13