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Exploration of the molecular interaction of a humic acid model with the water by means of molecular dynamics simulations

PUBLISHED March 14, 2023 (DOI: https://doi.org/10.54985/peeref.2303p4473663)



José G. Parra1 , Jesús Roa1 , Arnaldo Armado2
  1. Universidad de Carabobo, Facyt, Dpto. de Química, Bárbula-Venezuela
  2. Universidad de Carabobo, Facyt, Dpto.de Química, Bárbula-Venezuela

Conference / event

LatinXchem 2022, November 2023 (Virtual)

Poster summary

The molecular interaction of molecular structures generated from a humic acid model called TNB with water was explored with MD simulations to explore the affinity and behavior of these species in the aqueous medium. TNB model was described with the all-atom GROMOS53A6 force field. The bonding and non-bonding parameters were obtained from the GROMACS-2019.2 software package. The evaluation was realized for the functional groups −NH2 and -COOH. The spatial conformations of TNB molecules change considerably when evaluating the effect of pH on intermolecular interactions in an aqueous solution. Molecular dynamics calculations showed that the acid sites of the TNB humic acid model to assess molecular interaction have a low affinity for water. Results are consistent with the experimental behavior of humic acids in an aqueous solution, which suggests a low solubility of this specie in an aqueous solution.


Molecular dynamics, Humic acids, Affinity

Research areas

Environmental Sciences, Chemistry


  1. Klučáková, M., & Věžníková, K. (2017). Micro-organization of humic acids in aqueous solutions. Journal of Molecular Structure, 1144, 33-40.
  2. Lan, T., Wu, P., Liu, Z., Stroet, M., Liao, J., Chai, Z., ... & Wang, D. (2022). Understanding the Effect of pH on the Solubility and Aggregation Extent of Humic Acid in Solution by Combining Simulation and the Experiment. Environmental Science & Technology, 56(2), 917-927.
  3. Petrov, D., Tunega, D., Gerzabek, M. H., &Oostenbrink, C. (2017). Molecular dynamics simulations of the standard leonardite humic acid: Microscopic analysis of the structure and dynamics. Environmental Science & Technology, 51(10), 5414-5424.


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Additional information

Competing interests
No competing interests were disclosed.
Data availability statement
The datasets generated during and / or analyzed during the current study are available from the corresponding author on reasonable request.
Creative Commons license
Copyright © 2023 Parra et al. This is an open access work distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Parra, J., Roa, J., Armado, A. Exploration of the molecular interaction of a humic acid model with the water by means of molecular dynamics simulations [not peer reviewed]. Peeref 2023 (poster).
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