Abstract:

Structural and spectroscopic features of a model dipeptide, glycine dipeptide (GLYD), were systematically investigated in the gas phase and in aqueous solution. Normal mode analysis was performed on the representative GLYD-D₂O clusters selected from molecular dynamics (MD) trajectory for the vibrational parameters of amide-Ⅰ mode, which is known to be sensitive to the secondary structure of proteins. On this basis, the correlation between the vibrational spectrum and the structural features of specific groups in the polypeptide was constructed. The electrostatic potential from the solvent molecules was calculated and projected onto the backbone of GLYD, and related to the amide-Ⅰ frequency difference for GLYD in gas phase and solution phase. The secondary structure-dependent normal mode amide-Ⅰ frequency database was also introduced for the consideration of the possible vibrational coupling that is intrinsically included in GLYD conformers. An electrostatic frequency map with secondary structural sensitivity was then built for the fast and accurate vibrational frequency prediction of the amide-Ⅰ vibrational band for polypeptides in solution.

Key words: Glycine dipeptide, Amide-Ⅰ band, Vibrational spectrum, Electrostatic frequency map