Unbiased structure assignment of peptide conformers: application of similarity scores to Ace-AA-O-Bzl vibrational spectra

Vibrational spectroscopy is a valuable tool for elucidating the structure and interaction of polypeptides at atomistic level. Although the atomistic structure is assigned by comparing experimental spectra with computed spectra of candidate conformers, the comparison performed with visual inspection becomes a challenge, requiring much knowledge and experience on spectral assignments. To overcome this issue, we have recently proposed an efficient conformational search scheme along with similarity scores, which quantify a spectral agreement [H. Otaki et al., Phys. Chem. Chem. Phys. 26 (2024) 9906–9914]. In this study, we apply the method to a capped dipeptide, N -acetyl-(Ala) 2 -O-benzyl. The present calculation has identified two conformers, whose structures are consistent with the previous experimental work [E. Gloaguen et al., J. Am. Chem. Soc. 132 (2010) 11860–11863]. This study demonstrates the utility of our conformational search scheme and similarity scores in facilitating the assignment of atomistic structures, while reducing reliance on purely subjective visual inspection.