Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid state packing and polymer-electrolyte interactions being poorly understood. Presented here is a Molecular Dynamics (MD) force field for modelling alkoxylated and glycolated polythiophenes. The force field is validated against known packing motifs for their monomer crystals. MD simulations, coupled with X-ray Diffraction (XRD), show that alkoxylated polythiophenes will pack with a 'tilted stack' and straight interdigitating side chains, whilst their glycolated counterpart will pack with a 'deflected stack' and an s-bend side chain configuration. MD simulations reveal water penetration pathways into the alkoxylated and glycolated crystals - through the π-stack and through the lamellar stack respectively. Finally, the two distinct ways tri-ethylene glycol polymers can bind to cations are revealed, showing the formation of a meta-stable single bound state, or an energetically deep double bound state, both with a strong side chain length dependance. The minimum energy pathways for the formation of the chelates are identified, showing the physical process through which cations can bind to one or two side chains of a glycolated polythiophene, with consequences for ion transport in bithiophene semiconductors. This article is protected by copyright. All rights reserved.