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Publication Citation: Terahertz Spectra and Normal Mode Analysis of the Crystalline VA Class Dipeptide Nanotubes

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Author(s): David F. Plusquellic; Weimin Zhang; Karen M. Siegrist; Susan K. Gregurick;
Title: Terahertz Spectra and Normal Mode Analysis of the Crystalline VA Class Dipeptide Nanotubes
Published: December 31, 2008
Abstract: 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.
Citation: Journal of the American Chemical Society
Volume: 130
Issue: 52
Pages: pp. 17846 - 17857
Keywords: VSCF, THz Spectroscopy, Nanotubes, Crystalline Dipeptides, CHARMM
Research Areas: Biological Physics
PDF version: PDF Document Click here to retrieve PDF version of paper (2MB)