Molecular dynamics simulations of dissolved humic substances: can small molecules maintain stable large associates?

Molecular modeling and molecular dynamics (MD) simulations are capable of improving our molecular-level understanding of natural organic matter (NOM) by providing new alternatives such as virtual experiments that may be difficult (or even impossible) to perform in real tests. The fine control of molecular structure required in molecular simulations is highly valuable and significant due to the fact that neither the structure nor (often) detailed composition of real NOM is known. The control of molecular structure and its educated variation guided by experimental data on ¹³C NMR-derived composition may be performed using Vienna Soil Organic Matter Modeller (VSOMM) [1], which allows accounting for the simultaneous presence of multiple NOM molecules of different structures. This work exploring the VSOMM is focused on examining how and whether the humic substances (HS) models representing Leonardite humic acid (LHA) can maintain stable associates in water. In this approach, the stability of HS aggregates was elucidated in the 100 ns MD simulations by varying amounts of water in a broad range, from representing "water solution in NOM" to aqueous dissolved NOM, and modifying molecular size and extent of ionization of HS models, and the type of counter-ions (Na⁺ vs Ca²⁺). Multiple properties characterizing HS-water systems have been calculated, e.g., cumulative coordination numbers, numbers of HS-HS and HS-water contacts and H-bonds at short-range distances, number and size of formed clusters as well as energies of Coulomb and Lennard-Jones interactions of HS with ions (Na⁺ or Ca²⁺), HS and water. One outcome of this modeling work is that it shows how HS dilution leads to the decomposition of HS aggregates which occurs, in particular in the presence of the Na+ counter ion, gradually. The results of this work are placed into the context of experimental data and discussion on whether the detected large HS sizes can be assigned to the presence of large aggregates and the formation of supramolecular structures [2]. Although strong interactions between HS molecules may lead to small stable aggregates (e.g., dimers) persisting during dilution, the modeling suggests that the formation and decomposition of HS associates is "a step-wise" process, and, together with experimental data on LHA dialysis proposes that large-size HS molecules (aggregated or not) may need to be taken into account while examining HS properties in aqueous solutions.

[1] Escalona, Y., Petrov, D., & Oostenbrink, C. (2021). Vienna soil organic matter modeler 2 (VSOMM2). Journal of Molecular Graphics and Modelling, 103, 107817.

[2] Borisover, M., Petrov, D., Oostenbrink, C., & Galicia-Andrés, E. (2025). Diluting humic substances in water in molecular dynamics simulations: Are aggregates stable? Colloids and Surfaces A: Physicochemical and Engineering Aspects, 704, 135507.