Polarized Raman Spectroscopy for Determining the Orientation of di-D-phenylalanine Molecules in a Nanotube

Self-assembly of short peptides into nanostructures has become an important strategy for the bottom-up fabrication of nanomaterials. Significant interest to such peptide-based building blocks is due to the opportunity to control the structure and properties of well-structured nanotubes, nanofibrils, and hydrogels. X-ray crystallography and solution NMR, two major tools of structural biology, have significant limitations when applied to peptide nanotubes because of their non-crystalline structure and large weight. Polarized Raman spectroscopy was utilized for structural characterization of well-aligned D-Diphenylalanine nanotubes. The orientation of selected chemical groups relative to the main axis of the nanotube was determined. Specifically, the C-N bond of CNH₃⁺groups is oriented parallel to the nanotube axis, the peptides' carbonyl groups are tilted at approximately 54° from the axis and the COO^- groups run perpendicular to the axis. The determined orientation of chemical groups allowed the understanding of the orientation of D-diphenylalanine molecule that is consistent with its equilibrium conformation. The obtained data indicate that there is only one orientation of D-diphenylalanine molecules with respect to the nanotube main axis.