Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter

Abstract

Dissolved organic matter (DOM) plays a significant role in the transport and transformation of pollutants in the aquatic environment. However, the experimental characterization of DOM has been limited mainly to bulk properties, and the molecular-level interactions among various components of DOM remain to be fully characterized. Here, we use molecular dynamics (MD) simulations to probe the structural properties of model DOM systems at atomic detail. The 200 ns simulations, validated by available experimental data, reveal processes and mechanisms by which chemical species (cations, peptides, lipids, lignin, carbohydrates, and some low-molecular-weight aliphatic and aromatic compounds) aggregate to form complex DOM. The DOM aggregates are dynamic, consisting of a hydrophobic core and amphiphilic exterior. The lipid tails and other hydrophobic fragments form the core, with hydrophilic and amphiphilic groups exposed to water, making DOM accessible to both polar and nonpolar species. Thus, the lipid component acts as a nucleator, whereas cations (especially Ca2+) connect the molecular fragments on the surface by coordinating with the O-containing functional groups of DOM. The structural details revealed here provide new insights including surface accessible atoms, overall assemblage, and interactions among the molecules of DOM for understanding the kinetics and mechanisms through which DOM interacts with metal and other contaminants.

Molecular dynamics simulation of organic contaminant adsorption on organic‐coated smectite clay

“…Combined, these results highlight the complexity of organic contaminant adsorption by organic-coated minerals and soils and suggest that adsorption cannot be estimated by one single property (such as organic C or clay content), especially in high clay-low SOM conditions. A potentially promising avenue for future research may be to examine the coating of clay mineral nanoparticles by the more complex SOM proxies recently proposed by Devarajan et al (2020) or Escalona et al (2021). However, we note that for such complex organic mixtures, the short timescale of typical MD simulations may be insufficient to obtain well equilibrated organic coatings, in which case the use of enhanced sampling techniques, such as replica-exchange MD simulations (Atmani et al, 2020;Vialykh et al, 2020), may be required.…”

“…A potentially promising avenue for future research may be to examine the coating of clay mineral nanoparticles by the more complex SOM proxies recently proposed by Devarajan et al. (2020) or Escalona et al. (2021).…”

“…In studies of SOM, they may prove particularly valuable (Greathouse et al., 2014) as the complexity of SOM binding mechanisms and supra‐molecule structures strongly limits the feasibility of deconvolving experimental data (Kleber et al., 2021). Although significant challenges exist with regard to the examination of SOM and SOM–mineral interactions using atomistic simulations, notably with regard to the definition of SOM proxies and the generation of equilibrium structures for SOM aggregates on the limited timescale of these simulations, previous MD simulation studies have successfully examined the aggregation of various more or less simple or realistic SOM proxies (ranging from single molecules to mixtures of ∼10 compounds) under different aqueous chemistry conditions (Devarajan et al., 2020; Iskrenova‐Tchoukova et al., 2010; Kalinichev, 2012; Loganathan et al., 2020) along with the behavior of these proxies in mesopores (Loganathan et al., 2020), interlayer regions (Kelch et al., 2019; Sutton & Sposito, 2006), and on edge surfaces of smectite clay particles (Y. Zhang et al., 2020).…”

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

“…The effect of different cations on the association of dissolved organic molecules was studied by Devarajan et al (2020). Additionally, the mechanism of adsorption of polycyclic aromatic hydrocarbons (PAHs) on models of the LHA type and the impact of hydration was revealed by classical molecular dynamics (MD) simulations by Zhao et al (2020).…”

Development of the drop Freezing Ice Nuclei Counter (FINC), intercomparison of droplet freezing techniques, and use of soluble lignin as an atmospheric ice nucleation standard

“…It is likely that the material of the tray is contributing to warmer temperatures than expected for homogeneous freezing, but it is difficult to quantify the extent or percentage of this contribution to the overall nonhomogeneous freezing behavior. Imperfections on the surface of each well could also induce nonhomogeneous freezing behavior (Diao et al, 2011), and the use of a larger number of wells could help provide reliable statistics.…”