We study the molecular origin of a prepeak (PP) observed at low q values in the structure factors of three oligomers in a bulk (poly(mercaptopropyl)methylsiloxane, PMMS, poly(methylmercaptopropyl)-grafted-hexylmethacrylate, PMMS-g-HMA, and poly(methylphenyl)siloxane, PMPS) in order to understand the lowering of the PP intensity detected for oligomers confined in cylindrical pores with low diameter. For this purpose, we use a combination of X-ray diffraction measurements and coarse-grained bead-spring molecular dynamics simulations. Our molecular modelling demonstrated that the planarity of the pendant groups triggers the self-association of oligomers into nanoaggregates. However, the formation of oligomeric nanodomains is not sufficient for building-up the PP. The latter requires spatial disturbance in the arrangement of the side groups of oligomers within clusters. Importantly, our numerical analysis revealed that the increasing degree of the confinement of oligomers limits their aggregation and consequently lowers the amplitude of the PP observed in the experimental data.