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

Abstract

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.

A contribution of molecular modeling to supramolecular structures in soil organic matter#

“…Our own previous works aimed at QC modeling of complex HS species using mainly the DFT approach. These studies were focused on typical features of SOM, such as polar functional groups (e.g., carboxyl), nonpolar domains, hydrogen bonding, pH effects, the role of cations and water bridges in the formation of supramolecular structures of SOM, and interactions with small organic molecules such as naphthalene (Aquino et al, 2009(Aquino et al, , 2014Aquino, Tunega, Pasalic et al 2011;Aquino, Tuniga, Schaumann et al, 2011;Kunhi Mouvenchery et al, 2013;Schaumann & Bertmer, 2008;Tunega et al, 2014Tunega et al, , 2020.…”

“…These studies were focused on typical features of SOM, such as polar functional groups (e.g., carboxyl), nonpolar domains, hydrogen bonding, pH effects, the role of cations and water bridges in the formation of supramolecular structures of SOM, and interactions with small organic molecules such as naphthalene (Aquino et al., 2009, 2014; Aquino, Tunega, Pasalic et al. 2011; Aquino, Tuniga, Schaumann et al., 2011; Kunhi Mouvenchery et al., 2013; Schaumann & Bertmer, 2008; Tunega et al., 2014, 2020). The models used in these investigations spanned from small models representing polar functional groups to larger fragment species such as fatty acid chains to model hydrophillic/hydrophobic domains typical for SOM (Figure 2).…”

Detection of terpenoids and steroids in Lindsaea obtusa with thin layer chromatography

“…Compounds can be said to be nonpolar compounds if they have bonds between atoms with an attractive ability to gain electrons together, resulting in a distant state where the electrons are shared equally. Meanwhile, if a compound has one atom capable of attracting electrons stronger than other atoms and the electrons from the bond will not be used together equally, then the compound is called a polar compound (Tunega et al 2020). These results are similar to those of (Azka and Abdullah 2012), who showed that the secondary metabolites of water clover ferns Marsilea crenata most of them also dissolved in polar solvents with the yield of methanol extract of 11.98%, ethyl acetate extract of 1.37%, and chloroform extract of 0.31%.…”

Exploring the structure and dynamics of proteins in soil organic matter

“…Molecular dynamics (MD) simulations allow us to study the dynamics of these models as well as their molecular interactions with proteins. 12 , 13 , 14 , 15 , 16 Computational analysis of such complex systems is opposed by challenges arising from the size of the proteins and the description of their interactions with SOM through force fields. Most proteins active in soil are large, require co‐factors, and/or form complexes with other proteins.…”