Molecular Docking as a Tool to Examine Organic Cation Sorption to Organic Matter

Abstract

Molecular docking simulations were performed to examine the structural effects of organic cations on their sorption to organic matter. A set of benzylamine compounds was used to assess the sorption trends arising from the systematic structural differences between ring or nitrogen substituents. Binding simulations were performed using AutoDock 4.2 with Schulten’s proposed soil organic matter as a representative organic matter structure. The calculated binding energies for the sorbate compounds correlated strongly with the measured sorption energies for Pahokee peat, indicating that the simulated binding energies and their associated sorbate orientations were representative of the experimental conditions. Graphical docking orientations showed primary, secondary, and tertiary aminium compounds to form hydrogen-bond interactions with deprotonated carboxylic acid groups in a pocket of the organic matter structure. Quaternary ammonium compounds formed pi–pi or cation–pi interactions with the aromatic groups elsewhere in the same organic matter pocket. Ring substituents showed no clear trends in sorption energies with the substituent group type for primary aminium compounds. Rather, substituent groups altered the simulated van der Waals, electrostatic, hydrogen-bond, and desolvation energy contributions to the overall sorption energies, in part because of the variations in docking orientations between compounds. Increasing methyl substitution of the aminium nitrogen group was associated with an increase in van der Waals energy contributions and a decrease in electrostatic energy contributions to the overall compound sorption energies because of aminium charge delocalization into methyl substituents and steric hindrance from methyl substituents to form specific interactions. The findings illustrate how molecular docking can be used to explore the effects of organic cation structure on sorption interactions with organic matter.

Molecular Dynamics Simulation Prediction of the Partitioning Constants (KH, Kiw, Kia) of 82 Legacy and Emerging Organic Contaminants at the Water–Air Interface

“…To facilitate such studies, we provide a library of MD simulation input files for the compounds examined here []. We encourage efforts to expand this database; to refine it in the case of compounds identified as outliers, for example, using DFT simulations; , to use it to evaluate the affinity of OCs for other phases and interfaces; ,, to evaluate its performance against quantum mechanical approaches; to evaluate the importance of solvent effects in molecular docking simulations; ,,, and to apply machine learning approaches to identify clusters and trends within our compound library. , …”

Structure–Thermodynamic Relationship of a Polysaccharide Gel (Alginate) as a Function of Water Content and Counterion Type (Na vs Ca)

“…Computational sampling techniques aim to overcome the challenge outlined above by using either coarse-grained representations of the simulated systems , or, alternatively, approaches that accelerate the exploration of the energetic landscape of the system. , The replica exchange molecular dynamics (REMD) technique, also known as parallel tempering, has emerged as one of the primary methods used by computational biologists to ascertain the equilibrium conformations of biopolymers and biopolymer aggregates at the atomistic level. ,− In REMD, multiple simulations of identical systems are run concurrently at a range of temperatures and allowed to exchange with neighboring systems based on the Metropolis criterion; the technique can be thought of as a random walk in temperature space . This effectively allows for stable configurations discovered by higher temperature replicas to “trickle down” to the lowest temperature replica, which enables the discovery of stable configurations even in systems characterized by inherently slow configurational rearrangement.…”

Nanoscale Interactions of Humic Acid and Minerals Reveal Mechanisms of Carbon Protection in Soil

“…10,11 Since HA typically contains aliphatic and aromatic moieties with numerous functional groups (such as −OH and −COOH), it can bind to soil minerals through various interaction mechanisms. 12,13 Currently, it is well accepted that the prolonged residence periods of HA are generally related to the sorption of organic species to the surfaces of minerals, particularly clay-sized particles, which offer reactive sites for physical and chemical stabilization that limit NOM release and degradation. 14−16 It is widely recognized that a significant determinant of the quantity of carbon retained in the soil and the rate of carbon released is the abundance of certain clay minerals, particularly montmorillonite (Mt).…”

“…Humic acid (HA), a major DOM class, is present widely in soil and aquatic ecosystems as heterogeneous and macromolecular mixtures. , Since HA typically contains aliphatic and aromatic moieties with numerous functional groups (such as −OH and −COOH), it can bind to soil minerals through various interaction mechanisms. , Currently, it is well accepted that the prolonged residence periods of HA are generally related to the sorption of organic species to the surfaces of minerals, particularly clay-sized particles, which offer reactive sites for physical and chemical stabilization that limit NOM release and degradation. − It is widely recognized that a significant determinant of the quantity of carbon retained in the soil and the rate of carbon released is the abundance of certain clay minerals, particularly montmorillonite (Mt). , However, the detailed processes of carbon sequestration by clay minerals remain unclear. In particular, evidence shows that carbon associated with clay is labile and can be released relatively quickly, perhaps due to the complex environmental properties of soils .…”