Molecular Docking Simulations to Determine Organic Cation Sorption to Organic Matter

Scott, S.E.; Hadad, Christopher M.; Fernandez, Joseph; MacKay, Allison A.

doi:10.46427/gold2020.2327

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Section: Resultsmentioning

confidence: 99%

“…To take full advantage of the possible applications of molecular docking in environmental sorption applications, there is a need for further method refinement to improve the calculations of total sorption energies to achieve 1:1 correlations between the measured and calculated binding energies. 65 First, weighting factors in the binding scoring functions of the existing software tools were determined experimentally for protein−ligand interactions, and they are not directly translatable to calculate the accurate absolute interaction energies for organic matter. There is a need to determine the interaction energy weighting factors for the docking scoring functions to improve the search for low-energy binding orientations and to standardize the calculated total sorption energies that presently appear to overestimate sorption energies.…”

Section: ■ Introductionmentioning

confidence: 99%

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

Scott

Fernandez

Hadad

et al. 2022

Environ. Sci. Technol.

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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.

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Section: Resultsmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%