Comparison of fully optimized alpha- and 3(10)-helices with extended beta-strands. An ONIOM density functional theory study

We compare the structures and energies of beta-strands, alpha-helices, and 3(10)-helices for capped polyalanines, acetyl(ala)(N)()NH(2), for values of N from 2 to 18, using completely optimized mixed DFT/AM1 calculations. Non-pairwise additive cooperativity is manifest from the variation of the relative energies, helical strain, dipole moments, and H-bond lengths of both types of helices, but especially for the alpha-helices. While the gas-phase 3(10)-helices are more stable for small polyalanines, largely due to the additional H-bond, the alpha-helices become relatively more stable as the polyalanines increase in size.