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Updated: Jun 24, 2025

Combined Size and Density Fractionation of Soils for Investigations of Organo-Mineral Interactions
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Martini-Based Coarse-Grained Soil Organic Matter Model Derived from Atomistic Simulations.

Lorenz F Dettmann1, Oliver Kühn1,2, Ashour A Ahmed2

  • 1Institute of Physics, University of Rostock, Albert-Einstein-Street 23-24, Rostock D-18059, Germany.

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|June 4, 2024
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Summary

This study developed a coarse-grained soil organic matter (SOM) model using the Martini 3 force field. The model shows promise for simulating pollutant interactions and understanding SOM behavior.

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Area of Science:

  • Environmental Science
  • Computational Chemistry
  • Materials Science

Background:

  • Soil organic matter (SOM) is crucial for environmental processes, including pollutant adsorption.
  • Molecular simulations are increasingly used to investigate microscopic interactions within SOM.
  • Understanding SOM at a molecular level is essential for environmental remediation and management.

Purpose of the Study:

  • To develop and validate a coarse-grained model for soil organic matter (SOM) using the Martini 3 force field.
  • To assess the model's ability to reproduce key structural and thermodynamic properties of humic substances.
  • To lay the groundwork for future studies on pollutant interactions with SOM.

Main Methods:

  • Generation of humic substance models using the Vienna Soil Organic Matter Modeler 2.
  • Coarse-graining of molecular models with Swarm-CG and parametrization using the Martini 3 force field.
  • Determination of bonded parameters via Direct Boltzmann Inversion (DBI).
  • Validation through comparison of radius of gyration, solvent-accessible surface area, transfer free energies, and radial distribution functions.

Main Results:

  • The coarse-grained SOM model demonstrated favorable agreement in radius of gyration and solvent-accessible surface area.
  • Transfer free energies correlated well with hexadecane-water and chloroform-water values, with minor deviations for octanol-water.
  • Density comparisons between coarse-grained and atomistic models showed good agreement, especially at higher water concentrations.
  • DBI effectively reproduced average bonded interactions, though challenges remained in reproducing specific peaks in radial distribution functions due to fixed bead sizes.

Conclusions:

  • The developed coarse-grained SOM model provides valuable insights into SOM properties and interactions.
  • The model shows potential for simulating pollutant adsorption and diverse SOM compositions.
  • Further refinement is needed to address limitations in reproducing specific molecular interactions, particularly involving charged species.