Adsorption process of polar and nonpolar compounds in a nanopore model of humic substances


Humic substances (HSs) as a major part of soil organic matter (SOM) are complex combinations of natural organic matter, which are ubiquitous in the environment and occur predominantly in soils, residues and natural water. They play a crucial role in the fate and behaviour of contaminants in the environment. In this work, an HS nanopore model was based on a structural motif containing polar and nonpolar domains. The polar domain was represented by the carboxyl groups that predominate in the composition of HSs, whereas the nonpolar domain was constructed by aliphatic chains. The effect of hydrophobic/hydrophilic interactions on sorption in HSs was analysed by the inclusion of the nonpolar polycyclic aromatic hydrocarbon naphthalene and the polar herbicide 2-methyl-4-chlorophenoxyacetic acid (MCPA) in the nanopore. Water cluster was also included to allow the formation of the water molecular bridges (WaMB), which stabilized the whole system. Thermodynamic potential-of-mean-force (PMF) calculations by means of classical molecular dynamics simulations were performed to investigate the effect of polar and nonpolar domains in the adsorption mechanism. The polar MCPA molecule was stabilized at the hydrophilic water–HS interface, whereas nonpolar naphthalene was stabilized inside of the hydrophobic nanovoid of the HS nanopore model. The obtained results demonstrated that the adsorption strength of HSs regarding polar and nonpolar species is similar, but the adsorption mechanisms differ. Highlights: The work elucidates the adsorption mechanism of polar and nonpolar species in SOM at the molecular scale. The derived HS model was suitable to describe and explain the adsorption properties of SOM by means of constrained molecular dynamics simulations. Adsorption mechanisms for polar and nonpolar species in SOM differ. Polar molecules prefer the water–SOM interface, whereas nonpolar molecules are trapped in hydrophobic nanovoids of SOM. Molecular dynamics simulation is an effective method providing a detailed description of the adsorption processes in SOM.


© 2019 The Authors. European Journal of Soil Science published by John Wiley & Sons Ltd on behalf of British Society of Soil Science. cc-by


adsorption, constrained molecular dynamics, humic substances model, hydrophilic/hydrophobic domains, MCPA, naphthalene, potential of mean force


Tunega, D., Gerzabek, M.H., Haberhauer, G., Lischka, H., Solc, R., & Aquino, A.J.A.. 2020. Adsorption process of polar and nonpolar compounds in a nanopore model of humic substances. European Journal of Soil Science, 71(5).