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 nuclear magnetic resonance (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 di-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 di-d-diphenylalanine molecule that is consistent with its equilibrium conformation. The obtained data indicate that there is only one orientation of di-d-diphenylalanine molecules with respect to the nanotube main axis.