Characterization of low-frequency modes in aqueous peptides using far-infrared spectroscopy and molecular dynamics simulation

Abstract

Far-infrared spectroscopy was used to study the dynamics of three aqueous peptides having varied helicity. Experimental data were compared to the molecular dynamics simulated far-infrared absorbance spectrum derived from the dipole time correlation function. Vibrational density of state (VDOS) simulation was then used to analyze the contribution of different structural elements to the bands. Frozen aqueous peptide samples were studied in the frequency range between 325 and 540 cm-1 where the ice absorbance is low. Three resonances were identified; band I centered at approximately 333 cm-1, band II centered at approximately 380 cm-1, and band III comprising two constituent bands at approximately 519 and 528 cm-1. The peak height and frequency of the maximum absorbance of bands I and II varied depending on the helicity of the peptide. VDOS of the far-infrared absorbance spectrum confirmed that bands I and II were associated with the peptide backbone and that band III had both potential backbone and side chain components.