We aim to get insight into the underlying physics that govern the biological processes by properly taking into account the non covalent interactions in atomistic and coarse-grain modeling of biomolecules. As a first step, we investigate the detail role of hydrogen bonding and its cooperative effect in the thermodynamic stability of alanine and glycine polypeptides in helical conformation. We use density-functional theory to calculate the potential energy surface and the harmonic vibrational spectrum of infinitely long alanine and glycine polypeptides. Studying an infinitely long chain enable us to focus on the properties of the center (bulk) of a long helix, and, to properly describe and analyze the cooperativity of hydrogen bonds. We find that this effect stabilizes the pi-helix, alpha-helix and 3_10-helix to respect to the fully extended structure at 0 K. However this leads to a significant destabilization of the pi-helix with respect to the other helices at room temperature owing to differences in the vibrational-entropy contributions. An analysis of the response of the helix to uniaxial strain and the role of the hydrogen bonds will be presented.
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