title: Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field.
abstract: The 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-NH2 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.
authors.affiliation: Laboratoire de Chimie Moléculaire, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France. carine.clavaguera@polytechnique.edu.
authors.forename: Florian
authors.initials: F
authors.lastname: Thaunay
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Dognon
authors.forename: Gilles
authors.initials: G
authors.lastname: Ohanessian
authors.forename: Carine
authors.initials: C
authors.lastname: Clavaguéra
mesh_terms: D004151:Dipeptides / Q000737:chemistry*; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D013055:Spectrophotometry, Infrared / Q000379:methods*; D013696:Temperature
chemical_list: D004151:Dipeptides; C039552:phenylalanylalanine