Role of Side-Chain Length and Counterion Mediation on Dimerization of Rigid Sphere-Rod Amphiphiles: A Molecular Dynamics Investigation.

Rigid sphere-rod amphiphiles (RSRAs) comprising a Keggin polyoxometalate (POM) headgroup and an oligofluorene rod with different side chain lengths (C2, C6, C10, C16, are the number of carbon atoms per side chain) were probed by all-atom molecular dynamics in THF/water mixtures (15 and 33 vol % THF) with tetrabutylammonium (TBA+) counterions to elucidate the molecular origins of dimerization. Despite strong Keggin-Keggin electrostatic repulsion, stable dimers form through a synergy of (i) hydrophobic rod/side-chain interaction that strengthens with side-chain length and (ii) counterion-mediated attraction by TBA+, which localizes near the Keggins to screen electrostatic repulsion. Packing evolves from near-parallel rods for short chains to interdigitated, tilted arrangements for long chains, while solvent reorganizes cooperatively. Water is depleted from the inter-rod gap, while tetrahydrofuran (THF) accumulates on exterior hydrophobic surfaces as a loose solvation shell. Around Keggins, terminal and bridging oxygens sustain a structured hydration layer with long water residence time. Dynamically, single-molecule root-mean-square deviation (RMSD) increases with side-chain length while dimer self-diffusion decreases modestly. Trends are consistent across solvent fractions, with expected shifts in magnitudes. These results provide an atomistic framework linking side-chain architecture, counterion screening, and solvent organization to the thermodynamic stabilization and dynamic behaviors of RSRA dimers, clarifying early events that preceded higher-order self-assembled structures.