Carine Clavaguéra

Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies

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 −1,638xa0kcal/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.

IRMPD Spectroscopy of a Protonated, Phosphorylated Dipeptide†

The protonated, phosphorylated dipeptide [GpY+H](+) is characterized by mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free-electron laser. The IRMPD spectra are recorded in the 900-1730 cm(-1) range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP-D and coupled cluster, is carried out to obtain reliable relative energies of the low-energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P=O group in all low-energy structures. This leads to a P=O stretching frequency for [GpY+H](+) that is closer to that of [pS+H](+) than to that of [pY+H](+) and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.

Structure of Sodiated Polyglycines

The intrinsic folding of peptides about a sodium ion has been investigated in detail by using infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD spectroscopy was carried out on sodiated polyglycines G(n)-Na(+) (n=2-8), in both the fingerprint and N-H/O-H stretching regions. Interplay between experimental and computational approaches (classical and quantum) enables us to decipher most structural details. The most stable structures of the small peptides up to G(6)-Na(+) maximize metal-peptide interactions with all peptidic C=O groups bound to sodium. In addition, direct interactions between peptide termini are possible for G(6)-Na(+) and larger polyglycines. The increased flexibility of larger peptides leads to more complex folding and internal peptide structuration through γ or β turns. A structural transition is found to occur between G(6)-Na(+) and G(7)-Na(+), leading to a structure with sodium coordination that becomes tri-dimensional for the latter. This transition was confirmed by H/D exchange experiments on G(n)-Na(+) (n=3-8). The most favorable hydrogen-bonding pattern in G(8)-Na(+) involves direct interactions between the peptide termini and opens the way to salt-bridge formation; however, there is only good agreement between experimental and computational data over the entire spectral range for the charge solvation isomer.

A new, centered 32-electron system: the predicted [U@Si20]6−-like isoelectronic series

In addition to Lewis octets and Langmuirs 18-electron principle, 32-electron centered systems are possible. We now propose a new, third example on 32e-bonding between a central metal atom and a ligand cage. Moreover, these actinide-filled Si20 clusters could lead to novel silicon nanostructures.

Hydration gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics

AbstractThe hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. Parameters for the metal cations are derived from an ab initio bottom-up strategy. MD simulations of six cations solvated in bulk water are subsequently performed with the AMOEBA polarizable force field. The calculated first-and second shell hydration numbers, water residence times, and free energies of hydration are consistent with experimental/theoretical values leading to a predictive modeling of f-elements compounds.n Graphical AbstractSolvation free energy of the actinide (III) and lanthanide (III) cations in water: AMOEBA vs. reference data

Structural, energetic and dynamical properties of sodiated oligoglycines: relevance of a polarizable force field.

Oligoglycine peptides (from two to ten residues) complexed to the sodium ion were studied by quantum chemical and molecular mechanics calculations to understand their structural and energetic properties. Modeling such systems required the use of a polarizable force field and AMOEBA, as developed by Ren and Ponder [J. Comput. Chem., 2002, 23, 1497], was chosen. Some electrostatic and torsional parameters were re-optimized using a rigorous procedure and validated against both geometric and energetic ab initio data in the gas phase. Molecular dynamics simulations were performed on seven sodiated octa-glycine (G(8)) structures. Structural transitions were generally observed (with the notable exception of the a-helix), leading to new structures that were further proved by ab initio calculations to be of low energies. The main result is that for G(8)-Na(+), there is a compromise between sodium peptide interactions and multiple hydrogen bonding. The accuracy achieved with AMOEBA demonstrates the potential of this force field for the realistic modeling of gaseous peptides.

Ultraviolet degradation of procymidone – structural characterization by gas chromatography coupled with mass spectrometry and potential toxicity of photoproducts using in silico tests

RATIONALEnProcymidone is a dicarboximide fungicide mainly used for vineyard protection but also for different crops. The structural elucidation of by-products arising from the UV-visible photodegradation of procymidone has been investigated by gas chromatography coupled with mass spectrometry. The potential toxicities of photoproducts were estimated by in silico tests.nnnMETHODSnAqueous solutions of procymidone were irradiated for up to 90 min in a self-made reactor equipped with a mercury lamp. Analyses were carried out on a gas chromatograph coupled with an ion trap mass spectrometer operated in electron ionization and methanol positive chemical ionization. Multistage collision-induced dissociation (CID) experiments were performed to establish dissociation pathways of ions. Toxicities of byproducts were estimated using the QSAR T.E.S.T. program.nnnRESULTSnSixteen photoproducts were investigated. Chemical structures were proposed mainly based on the interpretation of multistage CID experiments, but also on their relative retention times and kinetics data. These structures enabled photodegradation pathways to be suggested. Only three photoproducts remain present after 90 min of irradiation. Among them, 3,5-dichloroaniline presents a predicted rat LD50 toxicity about ten times greater than that of procymidone.nnnCONCLUSIONSn3,5-Dichloroaniline is the only photoproduct reported in previous articles. Eight by-products among the sixteen characterized might be as toxic, if not more, than procymidone itself considering the QSAR-predicted rat LD50.

Accuracy of density functionals in the description of dispersion interactions and IR spectra of phosphates and phosphorylated compounds

The performances of quantum chemistry methods (i.e., DFT and ab initio) in calculating the structural and vibrational properties of phosphates and phosphorylated compounds have been evaluated. Diethyl-phosphate, phosphonic acid, dihydrogen phosphate anion, phosphoric acid dimer and protonated glycylphosphotyrosine dipeptide were selected for our study. Geometry and harmonic frequency deviations were investigated, pointing out the contribution of dispersion interactions on diethyl-phosphate, [Gly-pTyr+H]+ and the phosphoric acid dimer. The B3LYP-D functional, followed by CC2 and MP2 methods, revealed significant accuracy for frequency calculations of the majority of the phosphorylated compounds in comparison with available experimental data. These investigations provide a guide to the accurate computation of phosphorylated biological compounds.

The shape of gaseous n-butylbenzene: assessment of computational methods and comparison with experiments.

Conformational landscape of neutral and ionized n‐butylbenzene has been examined. Geometries have been optimized at the B3LYP/6‐31G(d), B3LYP/6‐31+G(d,p), B3LYP‐D/6‐31+G(d,p), B2PLYP/6‐31+G(d,p), B2PLYP‐D/6‐31+G(d,p), B97‐D/6‐31+G(d,p), and M06‐2X/6‐31+G(d,p) levels. This study is complemented by energy computations using 6‐311++G(3df,2p) basis set and CBS‐QB3 and G3MP2B3 composite methods to obtain accurate relative enthalpies. Five distinguishable conformers have been identified for both the neutral and ionized systems. Comparison with experimentally determined rotational constants shows that the best geometrical parameters are provided by B3LYP‐D and M06‐2X functionals, which include an explicit treatment of dispersion effects. Composite G3MP2B3 and CBS‐QB3 methods, and B2PLYP‐D, B3LYP‐D, B97‐D, and M06‐2X functionals, provide comparable relative energies for the two sets of neutral and ionized conformers of butyl benzene. An exception is noted however for conformer V+ the stability of which being overestimated by the B3LYP‐D and B97‐D functionals. The better stability of neutral conformers I, III, and IV, and of cation I+, demonstrated by our computations, is in perfect agreement with conclusions based on micro wave, fluorescence, and multiphoton ionization experiments.

UV-visible degradation of boscalid – structural characterization of photoproducts and potential toxicity using in silico tests

RATIONALEnBoscalid is a carboximide fungicide mainly used for vineyard protection as well as for tomato, apple, blueberry and various ornamental cultivations. The structural elucidation of by-products arising from the UV-visible photodegradation of boscalid has been investigated by gas chromatography/multi-stage mass spectrometry (GC/MS(n) ) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) couplings. The potential toxicities of transformation products were estimated by in silico calculations.nnnMETHODSnAqueous solutions of boscalid were irradiated up to 150u2009min in a self-made reactor equipped with a mercury lamp. Analyses were carried out using a gas chromatograph coupled with an ion trap mass spectrometer operated in both electron ionization (EI) and chemical ionization (CI) modes and a liquid chromatograph coupled with a quadrupole time-of-flight (Q-TOF) mass spectrometer operated in electrospray ionization (ESI) mode. Multiple-stage collision-induced dissociation (CID) experiments were performed to establish dissociation pathways of ions. The QSAR (Quantitative Structure-Activity Relationship) T.E.S.T. program allowed the estimation of the toxicities of the by-products.nnnRESULTSnEight photoproducts were investigated. Chemical structures were proposed not only on the interpretation of multi-stage CID experiments, but also on kinetics data. These structures led us to suggest photodegradation pathways. Three photoproducts were finally detected in Lebanon in a real sample of grape leaves for which routine analysis had led to the detection of boscalid at 4u2009mgu2009kg(-1).nnnCONCLUSIONSnWith one exception, the structures proposed for the photoproducts on the basis of mass spectra interpretation have not been reported in previous studies. In silico toxicity predictions showed that two photoproducts are potentially more toxic than the parent compound considering oral rat LD50 while five photoproducts may induce mutagenic toxicity. With the exception of one compound, all photoproducts may potentially induce developmental toxicity.