Accurate static electric dipole polarizability calculation of +3 charged lanthanide ions

An accurate determination of the heavy element static atomic dipole polarizability is a challenge for theoretical methods. We present in this paper computed values of the dipole polarizability of the lanthanide ions from La3+ to Lu3+. The results were obtained by performing fully relativistic and pseudopotential calculations including the treatment of open-shell systems. We have shown that, in order to obtain accurate results, it is essential to take into account scalar relativistic effects, core polarization and flexibility of the basis sets. Finally, we present a database of reference values of dipole polarizability for the Ln3+ ions

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

Theoretical study of the hydrated Gd3+ ion: Structure, dynamics, and charge transfer

The dynamical processes taking place in the first coordination shells of the gadolinium (III) ion are important for improving the contrast agent efficiency in magnetic-resonance imaging. An extensive study of the gadolinium (III) ion solvated by a water cluster is reported, based on molecular dynamics simulations. The AMOEBA force field [P. Y. Ren and J. W. Ponder, J. Phys. Chem. B 107, 5933 (2003)] that includes many-body polarization effects is used to describe the interactions among water molecules, and is extended here to treat the interactions between them and the gadolinium ion. In this purpose accurate ab initio calculations have been performed on Gd3+-H2O for extracting the relevant parameters. Structural data of the first two coordination shells and some dynamical properties such as the water exchange rate between the first and second coordination shells are compared to available experimental results. We also investigate the charge transfer processes between the ion and its solvent, using a fluctuating charges model fitted to reproduce electronic structure calculations on [Gd(H2O)n]3+ complexes, with n ranging from 1 to 8. Charge transfer is seen to be significant (about one electron) and correlated with the instantaneous coordination of the ion

Theoretical study of the bent U(η8-C8H8)2(CN)- complex

International audienceThe ground-state electronic structure of the cyanido complex [U(η8-C8H8)2(CN)]− as well as the thermodynamic properties and infrared spectrum are investigated using density functional theory including scalar relativistic effects. The complex is compared with the well-known uranocene U(η8-C8H8)2. Despite the broken symmetry, the gain in electrostatic interaction and a significant uranium-CN− orbital interaction is sufficient to stabilize the bent CN− complex with respect to uranocene. The formation of the CN− complex is exothermic justifying the recently experimentally reported compound.. © 2011 Springer-Verlag

Vibrational spectroscopy of deprotonated peptides containing an acidic side chain

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

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

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

International audienceOligoglycine 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