title: Interpretation of Raman and Raman optical activity spectra of a flexible sugar derivative, the gluconic acid anion.
abstract: Raman scattering and its polarized extension, Raman optical activity (ROA), are commonly used for monitoring of molecular conformational equilibria in solutions. This is complicated for saccharides due to extensive motions of the hydroxyl groups and other molecular parts. Standard interpretation procedures involving ab initio spectral simulations for a limited set of conformers are not adequate. In this study, a more general approach is proposed for the gluconic acid anion taken as a model compound, where quantum simulations of the spectra are directly coupled with molecular dynamics (MD) techniques. Such a multiscale approach reveals how the structural information is encoded in the broadened spectral lines. The spectra were simulated for solvent-solute clusters generated by MD. Conformational averaging was enabled by a limited library of conformers for which the spectral parameters could be calculated ab initio and moved on the MD geometries by Cartesian coordinate tensor transfer techniques. The B3LYP/CPCM/6-31+G** approximation was used as a default for computation of the source force fields and polarizability derivatives. The spectra thus obtained relatively faithfully reproduced most of the experimental features. The Amber and polarizable Amoeba MD force fields produced similar results; application of the latter, however, was limited by the long time necessary to achieve a converged conformational equilibrium. Both MD simulation and spectral averaging suggest that the hydroxyl groups as well as the backbone C-C bonds rotate relatively freely, with some restrictions in the vicinity of the carboxyl group. In spite of the averaging, spectral response of characteristic vibrational normal mode families, such as CH and OH bending, can clearly be identified in the spectra. The simulations thus confirm the experimental fact that flexible saccharides exhibit significant vibrational activity that reveals precious information about molecular structure and dynamics encoded in the Raman and ROA spectral shapes.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic. kaminskj@gmail.com
authors.forename: Jakub
authors.initials: J
authors.lastname: Kaminský
authors.forename: Josef
authors.initials: J
authors.lastname: Kapitán
authors.forename: Vladimír
authors.initials: V
authors.lastname: Baumruk
authors.forename: Lucie
authors.initials: L
authors.lastname: Bednárová
authors.forename: Petr
authors.initials: P
authors.lastname: Bour
mesh_terms: D003198:Computer Simulation; D005240:Feasibility Studies; D005942:Gluconates / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D012997:Solvents / Q000737:chemistry; D013059:Spectrum Analysis, Raman; D014732:Vibration
chemical_list: D005942:Gluconates; D012997:Solvents; C030691:gluconic acid