Simulation of Self-Assembled Monolayers of Polyalanine $α$-Helix Using an Effective Potential

TL;DR

This work develops an atomistic framework to link chiral composition and supramolecular order in self-assembled α-polyalanine monolayers to chiral-induced spin selectivity (CISS). By deriving effective inter-helical potentials from SCC-DFTB (with dispersion) and applying simulated annealing to ensembles of 160 helices, it shows that opposite-handed helices in anti-parallel (OA) and parallel (OP) alignments bind more strongly and pack more densely than equal-handed configurations (EP, EA). Enantiopure films consistently form hexagonal close-packed (hcp) structures, while racemic mixtures favor stripe-like rectangular phases driven by OA/OP stabilization; this also provides a physically plausible explanation for STM height contrasts, attributing them to anti-parallel arrangements and terminal-group electronic differences rather than height offsets. The results offer concrete design rules for peptide-based spintronic materials by linking molecular-scale interactions to macroscopic packing and spin-transport implications, with potential extensions to kinetic models and transport calculations.

Abstract

Self-assembled monolayers of $α$-polyalanine 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 SCC-DFTB derived interaction potentials 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.

Figures (11)

• Figure 1: Schematic representation of an $\alpha$-polyalanine ($\alpha$PA) $\alpha$-helix.
• Figure 2: (a) STM image of a self-assembled film of racemic LD-$\alpha$-polyalanine (LD-PA) on HOPG, showing the hexagonal phase of enantiopure L/D-PA (left) and the dimer phase of LD-PA (right). (b) Height profile taken along the colored lines in (a), showing the regular spacing and equal apparent heights in the hexagonal phase ( blue arrows, left), variations in spacings but equal apperent heights along the parallel row (middel), and regular spacing but differences in apparent height of adjacent rows within the dimer phase (green and black arrows, right).
• Figure 3: Illustration of the $\alpha$-polyalanine ($\alpha$PA) helix, highlighting the periodic repeat unit of 18 alanine residues over five turns. The helical parameters, including the rotation per residue ($\phi_E$) and translation per residue ($L_E$), are indicated.
• Figure 4: Distance-dependent binding energy profiles for representative configurations under fixed orientation parameters ($\varphi_1, \chi, \zeta$). (a) Two cases from the OA class; (b) Two cases from the EP class. Gray curves in the background correspond to all other sampled configurations, illustrating the overall variability across the orientation space. The legends indicate ($\varphi_1$, $\chi$, $\zeta$) values for each highlighted curve. These results demonstrate that opposite-handedness (OA) enables stronger binding and closer contact than same-handedness (EP) arrangements.
• Figure 5: Optimized pair distance $R$ for fixed $\varphi_1$ and $\chi$ as a function of the relative vertical offset $\zeta$ for EP (left) and OA (right) alignment. Each colored circle represents the binding energy for a given $\varphi_1$-$\chi$ combination, with the color scale indicating the magnitude of the interaction energy (blue: stronger binding, red: weaker binding). Triangles indicate the minimal pair distance $R_{\text{best}}$ for each $\zeta$, corresponding to the most favorable angles $\varphi_1$ and $\chi$. The oscillatory dependence on $\zeta$ highlights the critical role of axial registry in achieving optimal interdigitation and binding strength.