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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