Application of a Novel Coarse-Grained Soil Organic Matter Model in the Environment

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

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.

Multiscale computational simulation of pollutant behavior at water interfaces

The investigation of pollutant behavior at water interfaces is critical to understand pollution in aquatic systems. Computational methods allow us to overcome the limitations of experimental analysis, delivering valuable insights into the chemical mechanisms and structural characteristics of pollutant behavior at interfaces across a range of scales, from microscopic to mesoscopic. Quantum mechanics, all-atom molecular dynamics simulations, coarse-grained molecular dynamics simulations, and dissipative particle dynamics simulations represent diverse molecular interaction calculation methods that can effectively model pollutant behavior at environmental interfaces from atomic to mesoscopic scales. These methods provide a rich variety of information on pollutant interactions with water surfaces. This review synthesizes the advancements in applying typical computational methods to the formation, adsorption, binding, and catalytic conversion of pollutants at water interfaces. By drawing on recent advancements, we critically examine the current challenges and offer our perspective on future directions. This review seeks to advance our understanding of computational techniques for elucidating pollutant behavior at water interfaces, a critical aspect of water research.

Dynamic Behavior and Interaction Mechanism of Soil Organic Matter in Water Systems: A Coarse-Grained Molecular Dynamics Study

Investigating soil organic matter's (SOM) microscale assembly and functionality is challenging due to its complexity. This study constructs comparatively realistic SOM models, including diverse components such as Leonardite humic acid (LHA), lipids, peptides, carbohydrates, and lignin, to unveil their spontaneous self-assembly behavior at the mesoscopic scale through microsecond coarse-grained molecular dynamics simulations. We discovered an ordered SOM aggregation creating a layered phase from its hydrophobic core to the aqueous phase, resulting in an increasing O/C ratio and declining structural amphiphilicity. Notably, the amphiphilic lipids formed a bilayer membrane, partnering with lignin to constitute SOM's hydrophobic core. LHA, despite forming a layer, was embedded within this structure. The formation of such complex architectures was driven by nonbonded interactions between components. Our analysis revealed component-dependent diffusion effects within the SOM system. Lipids, peptides, and lignin showed inhibitory effects on self-diffusion, while carbohydrates facilitated diffusion. This study offers novel insights into the dynamic behavior and assembly of SOM components, introducing an effective approach for studying dynamic SOM mechanisms in aquatic environments.

Quantitative assessment of the contribution of soil organic matter functional groups and heteroatoms to PAHs adsorption based on the COSMO-RS model

Soil organic matter (SOM) is considered as a pivotal factor influencing the adsorption of pollutants. However, few prior quantitative investigations of the SOM functional group distribution to the contaminants' fate have been conducted. In this paper, the SOM cluster method based on COSMO-RS theory has been conducted to illustrate the chemical composition variables of SOM that affect the polycyclic aromatic hydrocarbons (PAHs) fate in quantitative terms. In the theoretical simulations, the contributions of carbonyl, carboxyl, aromatic, oxyalkyl and aliphatic groups in SOM to phenanthrene (Phe) and pyrene (Pyr) adsorption are evaluated by calculating the partition coefficients (LogP). The results show that the increase in oxyalkyl content leads to a decrease in LogP. Inversely, carbonyl and carboxyl groups of SOMs positively associated with Phe adsorption. The changes in aromatic and alkyl components have a similar magnitude of influence on LogP. Moreover, the effect of non-carbon-based functional groups in SOM on the Phe partitioning has been examined for the first time. The increase of sulfur and nitrogen content in SOM hinder Phe adsorption, while the rise of phosphorus content promotes the adsorption. In soil adsorption experiments, four natural soils, characterized by X-ray photoelectron spectroscopy (XPS) and Diffuse reflectance infrared Fourier transform (DRIFT), are selected to verify the influence of SOM functional group distribution. Comparing the experimental SOM-water partition coefficient (LogK_oc) with the simulation predicted LogP suggests that the COSMO-RS based SOM cluster method can predict PAHs adsorption ability in SOM.

Occurrence, profiles, and ecotoxicity of poly- and perfluoroalkyl substances and their alternatives in global apex predators: A critical review

Certain poly- and perfluoroalkyl substances (PFASs) exhibit significant bioaccumulation/biomagnification behaviors in ecosystems. PFASs, such as perfluorooctane sulfonate (PFOS), perfluorooctanoic acid (PFOA), perfluorohexanesulfonic acid (PFHxS) and related precursors, have elicited attention from both public and national regulatory agencies, which has resulted in worldwide restrictions on their production and use. Apex predators occupy the top trophic positions in ecosystems and are most affected by the biomagnification behavior of PFASs. Meanwhile, the long lifespans of apex predators also lead to the high body burden of PFASs. The high body burden of PFASs might be linked to adverse health effects and even pose a potential threat to their reproduction. As seen in previous reviews of PFASs, knowledge is lacking between the current stage of the PFAS body burden and related effects in apex predators. This review summarized PFAS occurrence in global apex predators, including information on the geographic distribution, levels, profiles, and tissue distribution, and discussed the trophic transfer and ecotoxicity of PFASs. In the case where legacy PFASs were restricted under international convention, the occurrence of novel PFASs, such as 6:2 chlorinated polyfluorinated ether sulfonate (6:2 Cl-PFESA) and perfluoroethylcyclohexane sulfonate (PFECHS), in apex predators arose as an emerging issue. Future studies should develop an effective analytical method and focus on the toxicity and trophic transfer behavior of novel PFASs.

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

Nanoplastics (NPs) are emerging threats for marine and terrestrial ecosystems, but little is known about their fate in the environment at the molecular scale. In this work, coarse-grained molecular dynamics simulations were performed to investigate nature and strength of the interaction between NPs and hydrophobic environments. Specifically, NPs were simulated with different hydrophobic and hydrophilic polymers while carbon nanotubes (CNTs) were used to mimic surface and confinement effects of hydrophobic building blocks occurring in a soil environment. The hydrophobicity of CNTs was modified by introducing different hydrophobic and hydrophilic functional groups at their inner surfaces. The results show that hydrophobic polymers have a strong affinity to adsorb at the outer surface and to be captured inside the CNT. The accumulation within the CNT is even increased in presence of hydrophobic functional groups. This contribution is a first step towards a mechanistic understanding of a variety of processes connected to interaction of nanoscale material with environmental systems. Regarding the fate of NPs in soil, the results point to the critical role of the hydrophobicity of NPs and soil organic matter (SOM) as well as of the chemical nature of functionalized SOM cavities/voids in controlling the accumulation of NPs in soil. Moreover, the results can be related to water treatment technologies as it is shown that the hydrophobicity of CNTs and functionalization of their surfaces may play a crucial role in enhancing the adsorption capacity of CNTs with respect to organic compounds and thus their removal efficiency from wastewater.

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.

First insights into the formation and long-term dynamic behaviors of nonextractable perfluorooctanesulfonate and its alternative 6:2 chlorinated polyfluorinated ether sulfonate residues in a silty clay soil

Per- and polyfluoroalkyl substances (PFAS) are persistent and toxic contaminants that are ubiquitous in the environment. They can incorporate into soil as nonextractable residues (NER) which are not detectable with conventional analytical protocols but are still possible to remobilize with changes of surrounding conditions, and thus will be bioavailable again. Therefore, there is a need to investigate thoroughly the long-term fate of NER-PFAS. In this study, a 240-day incubation of perfluorooctanesulfonate (PFOS) and its alternative 6:2 chlorinated polyfluorinated ether sulfonate (F-53B) in a silty clay topsoil was carried out. Solvent extraction, alkaline hydrolysis and sequential chemical degradation were applied on periodically sampled soil to obtain extractable, moderately bound and deeply bound PFAS, respectively. The results confirmed the formation of NER of both compounds but with different preferences of incorporating mechanisms. NER-PFOS was formed predominantly by covalent binding (via head group) and strong adsorption (via tail group). The formation of NER-F-53B was mainly driven by physical entrapment. Both bound compounds within the incubation period showed three-stage behaviors including an initial period with slight release followed by a (re) incorporating stage and a subsequent remobilizing stage. This work provides some first insights on the long-term dynamic behaviors of nonextractable PFAS and will be conducive to their risk assessment and remediation (e.g. estimating potential NER-PFAS level based on their free extractable level, and selecting remediation methods according to their prevailing binding mechanisms).

Exploring the structure and dynamics of proteins in soil organic matter

Alongside inorganic materials, water, and air, soil organic matter (SOM) is one of the major components of soil and has tremendous influence on the environment given its vital role in the carbon cycle. Many soil dwelling organisms like plants, fungi and bacteria excrete proteins, whose interaction with SOM is poorly understood on an atomistic level. In this study, molecular dynamics simulations were used to investigate selected proteins in soil models of different complexity from simple co-solvent molecules to Leonardite humic acids (LHA). We analyzed the proteins in terms of their structural stability, the nature and strength of the interactions with their surroundings, as well as their aggregation behavior. Upon insertion of proteins in complex SOM models, their structural stability decreased, although no unfolding or disruption of secondary structure was observed. The interactions of proteins and SOM were primarily governed by electrostatic forces, often in form of hydrogen bonds. However, also weaker van der Waals forces made a significant contribution to the total interaction energies. Moreover, we showed that even though the molecular structure and size of SOM molecules varied, the functional groups of SOM ordered around the protein in a similar pattern. Finally, the number of aggregates formed by proteins and SOM molecules was shown to be primarily proportional to the size of the latter. Strikingly, for varying protein net charges no changes in the formation of aggregates with the strongly negatively charged LHA were observed.

Computational Assessment of the Three-Dimensional Configuration of Dissolved Organic Matter Chromophores and Influence on Absorption Spectra

The three-dimensional configuration of dissolved organic matter (DOM) is an important factor in determining the role of DOM in natural and engineered systems, yet there is still considerable uncertainty regarding the formation and potential stability of molecular aggregates within DOM. In this paper, we describe a computational assessment of the three-dimensional configuration of DOM. Specifically, we were interested in evaluating the hypothesis that DOM forms thermodynamically stable molecular aggregates that as a result were potentially shielded from water solvent molecules. Molecular dynamics simulations of DOM model compounds carefully selected based on ultrahigh-resolution mass spectrometry data revealed that, while DOM does indeed form molecular aggregates, the large majority of molecules (especially, O-atom bearing molecules) are solvent accessible. Additionally, these computations revealed that molecular aggregates are weak and dissociate when placed in organic solvents (tetrahydrofuran, methyl tert-butyl ether). Time-dependent density functional theory calculations demonstrated long-wavelength absorbance for both model DOM chromophores and their molecular aggregates. This study has important implications for determining the origin of DOM optical properties and for enhancing our collective understanding of DOM three-dimensional structures.

Molecular dynamics simulation of the interaction of water and humic acid in the adsorption of polycyclic aromatic hydrocarbons

Humic acid (HA) and water play an important role in polycyclic aromatic hydrocarbons (PAHs) adsorption and biodegradation in soil. In this work, molecular dynamics (MD) and electrostatic potential surfaces (EPSs) simulations are conducted to research the contribution of quartz surface, leonardite humic acid (LHA), and water to PAH adsorption. The adsorption energies between PAHs and LHA are much higher than that between PAHs and quartz. Simulation shows that the hydroxyl and carboxyl groups' attraction by LHA is the main adsorption force between PAHs and LHA. The π-π interaction between PAHs and LHA also contributes to the adsorption process. In addition, the mobility of water on quartz surface is much higher than that of LHA. Water should be regarded as an adsorbate in the system as well as PAHs. However, the presence of water has a remarkable negative effect on the adsorption of PAHs on LHA and quartz. The bridging effect of water could only enhance the stability of the aggregation system. The adsorption contribution of quartz and LHA to PAHs in the soil model tends to 0 if the water layer reaches 2.0 nm. Graphical abstract.

A review of sources, environmental occurrences and human exposure risks of hexachlorobutadiene and its association with some other chlorinated organics

Research on hexachlorobutadiene (HCBD) has increased since its listing in the Stockholm Convention on Persistent Organic Pollutants in 2011. However, thorough reports on recent data regarding this topic are lacking. Moreover, potential associations between HCBD and some chlorinated organics have usually been ignored in previous research. In this review, possible formation pathways and sources, current environmental occurrences and human exposure risks of HCBD are discussed, as well as the association with several organochlorine compounds. The results reveal that unintentional production and emission from industrial activities and waste treatments are the main sources of HCBD. Similar precursors are found for HCBD and chlorobenzenes, indicating the presence of common sources. Although recent data indicates that levels of HCBD in the environment are generally low, risks from human exposure to HCBD, together with other pollutants, may be high. More attention in the future needs to be paid to the mixed contamination of HCBD and other pollutants from common sources.