In part 1 of this series of papers, the results of electron spray ionization mass spectrometry (ESI-MS) and molecular dynamics (MD) simulation revealed a close relationhsip between nanoaggregation of polyaromatic (PA) compounds and their chemical structures. In this paper, we present the results of investigating the flocculation of fractionated asphaltenes and synthesized PA molecules by dynamic light scattering (DLS). Together, these two papers complement one another and draw a full picture of asphaltene aggregation. Three asphaltene fractions were obtained on the basis of their different adsorption characteristics onto calcium carbonate. The DLS results suggest that the irreversibly adsorbed (Irr-Ads) asphaltenes containing the highest number of polar groups are the fraction of asphaltenes responsible for the observed flocculation in whole asphaltenes. To better understand the aggregation behavior of asphaltenes, flocculation of three synthesized PA compounds, N-(1-hexylhepyl)-N'-(5-carboxypentyl)perylene-3,4,9,10-tetracarboxylic bisimide (C5Pe), N-(1-undecyldodecyl)-N'-(S-carboxypentyl)-perylene-3,4,9,10-tetracarboxylic bisimide ( C5PeC11), and N,N'-bis (1-undecyldodecyl)perylene-3,4,9,10-tctracarb oxylic bisimide (BisAC11), was further studied using DLS. The observed flocculation corresponds well with the results of studying nanoaggregation using ESI-MS. The flocculation of PA compounds was found enhanced with increasing heptane content in the solvent. Among the three synthesized PA compounds studied, C5PeC11 showed flocculation kinetics similar to that of the Irr-Ads asphaltenes. Experiments using mixed PA compounds showed reduced flocculation of C5PeC11 in the presence of CSPe under otherwise identical solution conditions. The presence of polar groups in PA molecules was proven to be critical in accelerating the flocculation of PA compounds beyond the nanoscale. The results from MD simulations showed that pi-pi stacking between polyaromatic cores, hydrogen bonding between polar groups, and tail tail interactions among aliphatic chains all contribute to the observed flocculation of PA compounds.