The performance of donor-acceptor type conjugated polymers in photovoltaic devices is strongly dependent on the morphology of the thin film, which can be controlled by the substitution of various side groups on to the conjugated backbone. We investigate the effects of fluorination of the acceptor unit, and differences in the symmetry of alkyl side chain branching on the resulting photovoltaic device efficiency. Chemical variants of the donor-acceptor copolymerUsing Raman spectroscopy we find that the benzodithiophenethiophene (BDT-T) inter-unit bond dihedral torsion is minimized by using a symmetrically branched alkyl side chain on the benzotriazole (BTz) unit. This leads to an increased quality of molecular packing, resulting in the highest hole mobility (~3.8 × 10 -3 cm 2 /Vs) and overall device efficiency (~5.5 %). By contrast, fluorination of the BTz unit is detrimental to device performance. In this case, whilst the BTz-T inter-unit bond dihedral angle is reduced, the neighboring BDT-T inter-unit bond dihedral is increased, and the π-π packing distance is increased (from 4.05 to 4.60 Å) in the neat film. We conclude that, whilst the fluorination tends to planarize the polymer backbone, it also introduces repulsive fluorinehydrocarbon interactions, which oppose close molecular packing, and hinder efficient charge generation in the photovoltaic blend.