Terahertz Spectra and Normal Mode Analysis of the Crystalline VA Class Dipeptide Nanotubes
David F. Plusquellic, Weimin Zhang, Karen M. Siegrist, Susan K. Gregurick
Terahertz (THz) spectra of the crystalline VA class dipeptide nanotubes were calculated at both the harmonic and Vibrational Self-consistent Field (VSCF) level using the CHARMM22 force field with periodic boundary conditions. Comparison of the calculated THz spectra against the experimental spectra revealed that the VSCF corrections improved the predictions significantly. These improvements were mostly reflected by the overall blueshifts of the VSCF frequencies from the harmonic frequencies, which were attributed to the overall positive coupling strengths in all systems studied. By investigating the normal modes of the most significantly coupled mode pairs, we propose that when two similar sidechain-squeezing modes are coupled, the rapidly increased van der Waals interactions can lead to a stiffening of the effective potential, which eventually causes the blueshifts in the VSCF frequencies. In addition, a normal mode analysis revealed a series of channel-breathing motions in all systems except VA, which is proposed to facilitate the pathway of the guest molecules absorption, substitution and removal in the VA class dipeptide nanotubes.