Molecular modelling of sorption processes of a range of diverse small organic molecules in Leonardite humic acid

Abstract

Soil organic matter (SOM) is abundant in the environment and plays an important role in several biogeochemical processes, including microbial activity, soil aggregation, plant growth and carbon storage. One of its key functions is the retention and release of various chemical compounds, primarily governed by the sorption process, which strongly affects the environmental fate of nutrients and pollutants. Sorption largely depends on the composition of SOM, as well as its structure, dynamics and the thermodynamic conditions. Although several approaches are available, experimental characterization of sorption mechanisms is not easy. Computational models for predicting sorption coefficients often require a wealth of experimental data for training and are only applicable to compounds and conditions related to the training dataset. Here, we use molecular dynamics (MD) simulations to study the sorption of a range of small organic compounds. As a model SOM system we use the standard Leonardite humic acid (LHA) sample, which physicochemical properties have recently been characterized computationally in detail. This model allowed us to estimate sorption propensities of the systems at two different hydration levels (water activities close to 0 and 1), showing a remarkable correlation with experimental data. Importantly, this molecular modelling approach based on perturbation free‐energy calculations is rigorously derived from statistical thermodynamics and requires no experimental sorption data for training. It is therefore in principle applicable to any SOM model or thermodynamic condition. Moreover, the power of MD simulations to provide high‐resolution insight into atomistic and molecular interactions was employed to explore how sorbate molecules associate with the LHA matrix and which contacts they form. The heteroatoms of both sorbate and sorbent play an important role and water molecules are identified as further key players in facilitating the sorption process. Highlights Modelling of the sorption processes in soil organic matter at atomistic level. Rigorous, physics‐based approach applicable to a range of SOM systems and conditions. Remarkable level of matching with experimental data with additional insight into the molecular mechanism. Interactions between the sorbate and local environment strongly affects the sorption process.

Exploring the structure and dynamics of proteins in soil organic matter

“…Subsequently, we used SOM models of Leonardite humic acids (LHA) since such models have been shown to yield realistic observations and to reproduce experimental solvation free energies of small compounds. 19 , 20 This study expands our knowledge about protein‐SOM interactions and will facilitate future exploration of SOM molecules with other biomolecules, especially in the context of enzyme engineering for bioremediation, understanding the effect of preservation of toxic proteins in soil as well as understanding the plant rhizosphere.…”

“… 18 Using VSOMM, several recent computational studies were able to reproduce the results of wet‐lab experiments. 19 , 20 , 21 , 22 , 23 Moreover, VSOMM uses the GROMOS 54A7 force field which initially was parameterized for proteins which allows us to accurately describe proteins and SOM molecules in a combined MD simulation. 24 …”

On the Adsorption Mechanism of Humic Substances on Kaolinite and Their Microscopic Structure

“…In this work, the leonardite humic acid model LHA1 developed by Petrov et al [37,38] was used as a representative humic acid (HA) structure to build organo-mineral aggregates using the VSOMM online tool [28,29] (version 2.0, Institute of Molecular Modeling and Simulation -University of Natural Resources and Life Sciences, Vienna, Austria). The VSOMM tool generates condensed phase models of soil organic matter (SOM) based on the concept of building blocks.…”

“…In this work, we focus on the modeling of SOM-clay interactions using models of kaolinite clay mineral that are typical for many and specifically highly weathered soils, as well as the model of the LHA aggregate developed in our previous work [37][38][39]. The LHA model used offers an opportunity to study systematically different types of interactions at the molecular level.…”

Editorial for Soil chemical, physical and biological interfacial reactions (Commission 2.5, WCSS) special section

“…The final two papers use sorption models to simulate and predict the adsorption of organic molecules of differing size and complexity. Petrov, Tunega, Gerzabek and Oostenbrink (2020) use molecular dynamics simulations, based on perturbation free‐energy calculations, to study the adsorption of small organic compounds to well‐characterized humic acid. The ongoing debate on the existence of humic acids is irrelevant to this study.…”