title: The Raman optical activity of β-D-xylose: where experiment and computation meet.
abstract: Besides its applications in bioenergy and biosynthesis, β-d-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, and benefits much from theoretical support for interpretation. Our simulation approach combines density functional theory (DFT) and molecular dynamics (MD) in order to efficiently account for the crucial hydration effects in the simulation of carbohydrates and their spectroscopic response predictions. Excellent agreement between the simulated spectrum and the experiment was obtained with a solvation radius of 10 Å. Vibrational bands have been resolved from the computed ROA data, and compared with previous results on different monosaccharides in order to identify specific structure-spectrum relationships and to investigate the effect of the solvation environment on the conformational dynamics of small sugars. From the comparison with ROA analytical results, a shortcoming of the classical force field used for the MD simulations has been identified and overcome, again highlighting the complementary role of experiment and theory in the structural characterisation of complex biomolecules. Indeed, due to unphysical puckering, a spurious ring conformation initially led to erroneous conformer ratios, which are used as weights for the averaging of the spectral average, and only by removing this contribution was near perfect comparison between theory and experiment achieved.
authors.affiliation: Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. pla@manchester.ac.uk.
authors.forename: François
authors.initials: F
authors.lastname: Zielinski
authors.forename: Shaun T
authors.initials: ST
authors.lastname: Mutter
authors.forename: Christian
authors.initials: C
authors.lastname: Johannessen
authors.forename: Ewan W
authors.initials: EW
authors.lastname: Blanch
authors.forename: Paul L A
authors.initials: PL
authors.lastname: Popelier
mesh_terms: D002236:Carbohydrate Conformation; D056004:Molecular Dynamics Simulation; D013059:Spectrum Analysis, Raman; D014994:Xylose / Q000737:chemistry*
chemical_list: D014994:Xylose