Molecules 2007, 12(4), 703-715; doi:10.3390/12040703
Article

Investigation on the Binding of Polycyclic AromaticHydrocarbons with Soil Organic Matter: A Theoretical Approach

1 Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand 2 The Center of Nanoscience KU, Kasetsart University, Bangkok 10900, Thailand 3 Department of Health Science, School of Natural Science, Dongduk Women’s University, Sungbuk-gu, Seoul, 136-714, Korea
* Author to whom correspondence should be addressed.
Received: 26 February 2007; in revised form: 22 March 2007 / Accepted: 23 March 2007 / Published: 5 April 2007
(This article belongs to the Special Issue Heterocycles)
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Abstract: 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 π-π 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 Kow) 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.
Keywords: PAHs; SOM; fulvic acid; humic acid; soil

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MDPI and ACS Style

Saparpakorn, P.; Kim, J.H.; Hannongbua, S. Investigation on the Binding of Polycyclic AromaticHydrocarbons with Soil Organic Matter: A Theoretical Approach. Molecules 2007, 12, 703-715.

AMA Style

Saparpakorn P, Kim JH, Hannongbua S. Investigation on the Binding of Polycyclic AromaticHydrocarbons with Soil Organic Matter: A Theoretical Approach. Molecules. 2007; 12(4):703-715.

Chicago/Turabian Style

Saparpakorn, Patchreenart; Kim, Jae H.; Hannongbua, Supa. 2007. "Investigation on the Binding of Polycyclic AromaticHydrocarbons with Soil Organic Matter: A Theoretical Approach." Molecules 12, no. 4: 703-715.

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