Simulation of Self-Assembled Monolayers of Polyalanine $\alpha$-Helices: Development and Application of an Effective Potential for Film Structure Predictions

Self-assembled monolayers of polyalanine $\alpha$-helices exhibit distinct structural phases with implications for chiral-induced spin selectivity. We combine scanning tunneling microscopy and theoretical modeling to reveal how chiral composition governs supramolecular organization. Enantiopure systems form hexagonal lattices, while racemic mixtures organize into rectangular phases with stripe-like features. Our interaction potentials derived from density-functional based tight binding calculations show that opposite-handed helix pairs exhibit stronger binding and closer packing, explaining the denser racemic structures. Crucially, we demonstrate that the observed STM contrast arises from anti-parallel alignment of opposite-handed helices rather than physical height variations. These findings establish fundamental structure-property relationships for designing peptide-based spintronic materials.