Use of Periodic Boundary Conditions To Calculate Accurate β-Sheet Frequencies Using Density Functional Theory

Calculations of vibrational spectra of peptides that represent the major structural motifs, α-helix, β-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 β-sheet structure is demonstrated in this study using periodic boundary conditions (PBC). A model consisting of four glycines with a pleated parallel β-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 β-sheet and extended conformations, and it is shown that intramolecular hydrogen bonding can be included to quantitatively account for the amide I and amide II spectrum of the β-sheet.