Journal of Physical Chemistry A, Vol.107, No.46, 9898-9902, 2003
Use of periodic boundary conditions to calculate accurate beta-sheet frequencies using density functional theory
Calculations of vibrational spectra of peptides that represent the major structural motifs, alpha-helix, beta-sheet, and extended conformations, carried out using density functional theory (DFT) agree only qualitatively with experiment because of the lack of inclusion of intermolecular interactions in the calculated model. One solution to this problem for the parallel beta-sheet structure is demonstrated in this study using periodic boundary conditions (PBC). A model consisting of four glycines with a pleated parallel beta-sheet structure in a box of appropriate dimensions was calculated using DFT methods to obtain accurate frequencies of the amide bands. This model is compared to gas-phase calculation of beta-sheet and extended conformations, and it is shown that intramolecular hydrogen bonding can be included to quantitatively account for the amide I and amide 11 spectrum of the beta-sheet.