Coarse-grained molecular dynamics simulations of nanoplastics interacting with a hydrophobic environment in aqueous solution

Dettmann, Lorenz F.; Kühn, Oliver; Ahmed, Ashour A.

doi:10.1039/d1ra04439g

Cited by 6 publications

(2 citation statements)

References 87 publications

(96 reference statements)

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“…It is of major interest to better understand sorption processes with SOM. For instance, interactions between carbon nanotubes and nanoplastic particles were previously investigated by our group, using the Martini force field 15 . Among other aspects, this allowed the cavity and trapping effects to be investigated, which are similar to the adsorption processes that occur in SOM.…”

Section: Introductionmentioning

confidence: 99%

A Martini-based coarse-grained soil organic matter model derived from atomistic simulations

Dettmann,

Kuehn,

Ahmed

2024

Preprint

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The significance of soil organic matter (SOM) in environmental contexts, particularly its role in pollutant adsorption, has prompted increased utilization of molecular simulations to understand microscopic interactions. This study introduces a coarse-grained SOM model, parametrized within the framework of the versatile Martini 3 force field. Utilizing systems generated by the Vienna Soil Organic Matter Modeler 2, which constructs humic substance systems from a fragment database, we employed Swarm-CG to parametrize the fragments and subsequently assembled them into macromolecules. Direct Boltzmann Inversion (DBI) facilitated the determination of bonded parameters between fragments. The parametrization yielded favorable agreement in the radius of gyration and solvent-accessible surface area. Transfer free energies exhibited a strong correlation with hexadecane-water and chloroformwater values, albeit deviations were noted for octanol-water values. Comparing densities of modeled Leonardite Humic Acid (LHA) systems at coarse-grained and atomistic levels revealed promising agreement, particularly at higher water concentrations. The DBI approach effectively reproduced average values of bonded interactions between fragments. Radial distribution functions between carboxylate groups and calcium ions partially concurred, yet limitations arose in reproducing certain peaks due to fixed bead sizes. Detailed analysis of atomistic systems elucidated different configurations between groups, further explaining discrepancies. The present contribution provides a comprehensive insight into the properties, strengths, and weaknesses of the coarse-grained SOM model, serving as a foundation for future investigations encompassing pollutant interactions and varied SOM compositions.

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Section: Introductionmentioning

confidence: 99%

A Martini-based coarse-grained soil organic matter model derived from atomistic simulations

Dettmann,

Kuehn,

Ahmed

2024

Preprint

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show abstract

“…It is of major interest to better understand sorption processes with SOM. For instance, interactions between carbon nanotubes and nanoplastic particles were previously investigated by our group using the Martini force field . Among other aspects, this allowed the cavity and trapping effects to be investigated, which are similar to the adsorption processes that occur in SOM.…”

Section: Introductionmentioning

confidence: 99%

Martini-Based Coarse-Grained Soil Organic Matter Model Derived from Atomistic Simulations

Dettmann,

Kühn,

Ahmed

2024

J. Chem. Theory Comput.

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The significance of soil organic matter (SOM) in environmental contexts, particularly its role in pollutant adsorption, has prompted an increased utilization of molecular simulations to understand microscopic interactions. This study introduces a coarse-grained SOM model, parametrized within the framework of the versatile Martini 3 force field. Utilizing models generated by the Vienna Soil Organic Matter Modeler 2, which constructs humic substance systems from a fragment database, we employed Swarm-CG to parametrize the fragments and subsequently assembled them into macromolecules. Direct Boltzmann inversion (DBI) facilitated the determination of bonded parameters between fragments. The parametrization yielded favorable agreement in the radius of gyration and solvent-accessible surface area. Transfer free energies exhibited a strong correlation with hexadecane−water and chloroform−water values, albeit deviations were noted for octanol−water values. Comparing densities of modeled Leonardite humic acid systems at coarse-grained and atomistic levels revealed promising agreement, particularly at higher water concentrations. The DBI approach effectively reproduced average values of bonded interactions between fragments. Radial distribution functions between carboxylate groups and calcium ions showed partial agreement, however, reproducing certain peaks was challenging due to fixed bead sizes. Detailed analysis of atomistic systems revealed different configurations between the groups, explaining discrepancies. The present contribution provides a comprehensive insight into the properties, strengths, and weaknesses of the coarse-grained SOM model, serving as a foundation for future investigations encompassing pollutant interactions and varied SOM compositions.

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Recent advances on nanotechnology-driven strategies for remediation of microplastics and nanoplastics from aqueous environments

Ouda

Banat

Hasan

et al. 2023

Journal of Water Process Engineering

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Coarse-grained molecular dynamics simulations of nanoplastics interacting with a hydrophobic environment in aqueous solution

Abstract: The binding mechanisms of nanoplastics (NPs) to carbon nanotubes as hydrophobic environmental systems have been explored by coarse-grained MD simulations. The results could be closely connected to fate of NPs in soil and water treatment technologies.

Cited by 6 publications

References 87 publications

A Martini-based coarse-grained soil organic matter model derived from atomistic simulations

A Martini-based coarse-grained soil organic matter model derived from atomistic simulations

Martini-Based Coarse-Grained Soil Organic Matter Model Derived from Atomistic Simulations

Recent advances on nanotechnology-driven strategies for remediation of microplastics and nanoplastics from aqueous environments

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