Role of dipole cooperativity and polarization frustration in the conformation distribution of hydrated peptides

by Wang, Feng

The phys. driving forces for secondary structure preferences of hydrated alanine peptide are investigated with B3LYP-D3(BJ) and the adaptive force matching method. Our results show a dominant role of polarization in secondary structural preferences. While the a helix is stabilized by solvent polarization due to dipole cooperativity, the two adjacent amide groups in the ß strand forms a nearly planar trapezoid that is not much larger than the size of water mols. Our results show that water is having trouble to properly solvate such a ß trapezoid leading to destablization due to polarization frustration. Although the PP-II conformation is very close to the ß strand, the small twist in the backbone angles allowed much improved polarization stabilization. The improved polarization when combined with favorable intrapeptide interactions lead to the PP-II to be lowest in free energy. The effects of other factors, such as the entropy and the F,? coupling are also studied and are found to be less important in determining peptide conformations.