Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions.: I.: The case of polyglycine, polyalanine, and poly-α-aminoisobutyric acid in vacuo

Fully quantum mechanical calculations exploiting periodic boundary conditions (PBC) have been applied to the study of four different regular structures (alpha- and 3(10)-helix, fully extended and repeated gamma -turns) of the infinite polypeptides of glycine, alanine, and a-aminoisobutyric acid (Aib) in vacuo. a-Helix is predicted to be the most stable conformer for polyalanine and polyglycine, being stabilized over the 3(10)-helix mainly by more favorable dipole-dipole interactions. Contrary to previous suggestions, steric effects and hydrogen-bond strengths are comparable for both helix structures. 3(10)-Helix is preferred for poly-Aib, since in this case ct-helix is strongly distorted due to unfavorable intrachain repulsions. Extended structures and repeated gamma -turns are much less stable than helix structures for all of the polypeptides examined, mainly due to the absence of favorable long-range interactions. The optimized geometries are in good agreement with the available experimental data and reveal a remarkable dependence on the nature of the residue forming the polypeptides; at the same time the electronic and structural parameters of each residue strongly depend on the secondary structure of the polypeptides.