<p>Two poly(phenylene ethynylene) derivatives were characterized by spectroscopic and computational means. These polymers are distinguished as having alkyl and alkoxy solvating side chains, respectively. It was found that both polymers exhibit tendencies to aggregate in polar solvents as indicated by bathochromic shifts in electronic spectra and accompanied by the emergence of sharp absorption bands associated with ordered aggregates. These findings were confirmed by direct measurement of particle size by dynamic light scattering. In contrast, the results of fluorescence lifetime measurements and quantum yield determination indicate that the nature of the aggregates is distinct for alkyl-linked polymers compared to those with alkoxy linkages. Additional solvent dependency studies showed that alkoxy-linked polymers show a greater propensity to form more compact aggregates in poor solvent and disaggregate less readily upon addition of good solvent. The results of molecular dynamics simulations corroborate these findings. It is concluded that the electron-donating oxygen atoms play a critical role in the aggregation behavior of conjugated polymers.</p>