Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous contaminants of the terrestrial environment that have been designated as Environmental Protection Agency (EPA) Priority Pollutants. In this study, molecular modeling was used to examine the physical and chemical characteristics of soil organic matter (SOM), fulvic acid (FA) and humic acid (HA), as well as their binding interactions with PAHs. The molecular structures of 18 PAHs were built by using the SYBYL 7.0 program and then fully optimized by a semiempirical (AM1) method. A molecular docking program, AutoDock 3.05, was used to calculate the binding interactions between the PAHs, and three molecular structure models including FA (Buffle's model), HA (Stevenson's model) and SOM (Schulten and Schnitzer's model). The pi-pi interactions and H-bonding interactions were found to play an important role in the intermolecular bonding of the SOM/PAHs complexes. In addition, significant correlations between two chemical properties, boiling point (bp) and octanol/water partition coefficient (Log K(ow)) and final docking energies were observed. The preliminary docking results provided knowledge of the important binding modes to FA, HA and SOM, and thereby to predict the sorption behavior of PAHs and other pollutants.