The interactions of  soil natural organic matter (NOM) and polycyclic aromatic hydrocarbon (PAH) with biological interfaces studied by MD simulations

Babak Minofar


Faculty of Science, University of South BohemiaBranisovska 31, Ceske Budejovice, Czech Republic

Institute of Nanobiology and Structural Biology of Academy of Sciences of the Czech Republic

E-mail: and


Soil is very complex compound which consists of different components such as mineral surfaces, organic and inorganic ions and natural organic matter thus many factors are important in adsorption and transportation processes in soil. Understanding the interactions of different compounds  of soil not only needed to be addressed experimentally but also theoretically due to the fast growing the speed and capabilities of computers and computational methods. In order words, combined experimental and theoretical methods are more accurate to solve complex problems in soil science. One of most important components of soil, which has strong effect and play important role in the process of adsorption of different elements to the plants and complexation of many metal ions in the environment is natural organic matter (NOM). NOM and in particular humic acids, humates, and fulvic acids derived from dead plant and animal matter by partial decomposition, are present in environments and especially in aquatic environments. They play variety of important roles in soil1-2 and their interactions with metal ions, minerals and organic species are important for environment. 

Humic acids are able to interact with both organic and inorganic substances such as nutrients, metal ions, and hydrophobic organic compounds.3,4 Moreover, the interactions of humic acids with living surfaces have been detected by some experimental methods such as adsorption isotherms, electrophoretic mobility measurements, and transmission electron microscopy.Humic acids and humates have heterogeneous and complex structures with different functional groups such as NH2, COOH, OH, aromatic and aliphatic parts in which the non-covalent intermolecular interactions such van der Waals, charge-transfer, stacking interactions and hydrogen-bonding are the most important interactions.6 Understanding their structure and interactions with ions and hydrophobic organic compounds can give us important information about their biodegradability, toxicity, and transport properties. NOMs are present in soil and water thus they can interact with natural macromolecules such peptide, proteins or enzymes, so that  molecular modeling methods can give useful information about their interactions in molecular level.

In order to understand the solvation structure and interactions of NOMs in aqueous solution we have studied the solvation structure and surface propensity to the air/aqueous solution of building blocks of humic acids and we observed that they have strong surface propensity and decrease of surface tension7 of water which is supported by surface sensitive spectroscopy8 Such as vibrational sum frequency generation spectroscopy.

Garrido et al. studied the structure, conformational changes and aggregation of Temple- Northeastern - Birmingham (TNB)9 model of humic acid which was proposed by Sein et al. by molecular modeling approaches and they revealed water molecules stabilize the system specially when the model has bigger negative charge and in higher concentration of humic acid aqueous solution aggregation takes place10.

High flexibility and presence of different functional groups such as carboxylic acid, alcoholic, phenolic and hydrophobic groups in humic acid make them to be favorable for interaction with metal ions and hydrophobic organic compounds.  Such interactions make humic acids to be involved in metal ion complex formation and aggregation which are studied both theoretically and experimentally. Surface propensity and aggregation to the air/water occur for humates aqueous solutions in which hydrophobic parts of humates were moved towards air/water interface and hydrophilic parts towards the bulk of aqueous solution thus decrease of surface tension of such solution solutions was observed11.

In order to understand the adsorption process of NOM on the surface of living organisms in aquatic  environments we studied the interactions of NOM with  biomembranes which is the crucial as weak interactions such as hydrogen bonding, van der Waals and hydrophobic interactions are the dominant interactions. As studying the interactions of biomembrane of living organisms is very complex  due to the fact that they contain different lipids with different compositions thus study the interaction of  model biomembrane can bring new insights to understand the process of adsorption and influence of the surface of  biomembrane by NOM.

Weak interactions which are involved in the adsorption of NOM on the surface of living organisms can bring information to reveal the role of humic substances on the surface of biomembranes and their key interactions on metal toxicity when binding to the surface of living organisms in aquatic systems take place5. Moreover, studying the interaction of NOM with different biological membrane brings valuable information about the biodegradation process of hydrophobic organic pollutants such as polycyclic aromatic hydrocarbons (PAH) in aqueous environments12.

This study brings new insights  for the adsorption and interaction of different models of NOM with different biomembrane such as, 2-dipalmitoyl-sn-glycero-3-phos- phocholine (DPPC) and 1-palmitoyl -2- oleoyl -sn – glycero -3 - phosphocholine (POPC) as typical components of cell membrane.  As both POPC and DPPC membrane have N(CH3)3+ groups in their structure thus electrostatic interaction between the negatively charged functional groups of the humic substances and the positively charged groups N(CH3)3+ of the biomembranes head groups and hydrophobic interactions between the NOM and membranes bilayer, and hydrogen bonding between the negatively charged functional groups of the NOM and the negatively charged groups of phosphate domain of the head groups are the most important interaction in the process of adsorption of humic substances on the surface of living surfaces.

 To understand such complex phenomena as , we studied the surface propensity and interaction of TNB model of NOM with lipid bilayers such  as both POPC and DPPC as by classical molecular dynamics (MD) simulations and revealed that the hydrophbic interaction between  organic molecules and hydrophobic parts of humic acid is one of the most important factor for interactions and surface propensity to the air/aqueous solution interface.  This study also has characterized the interactions of NOM with biological surfaces in order to understand the role of different functional groups such COOH, OH, aromatic and aliphatic parts of NOM with biologically relevant compounds.


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