A contribution of molecular modeling to supramolecular structures in soil organic matter^#

Abstract

Background Knowledge of the stabilizing mechanisms of soil organic matter (SOM) is extremely important for numerous soil functions. For this, insight into the nature of organic matter through appropriate model concepts are crucial. Aims For several years, a heated debate has emerged on the transformation and stabilization of SOM. In the present work, we try to contribute to this debate using molecular modeling and providing a comprehensive overview of the history of application of molecular modeling tools and developing structural concepts of SOM. Methods Molecular modeling methods based on quantum and/or classical mechanics were used to model SOM and related properties including interactions with reactive surfaces of soil minerals. Results Modeling of SOM aggregates revealed that hydrogen bonds and cation bridges are the main stabilizing factors in soil solution, whereas pH modifies the stability. The modeled supramolecular SOM aggregates exhibit physicochemical properties, similar to those of humic substances (HS) described in literature. The interactions of the HS models with surfaces in kaolinite nanopores led to a partial disintegration of the aggregates into individual molecules and/or smaller subaggregates. Conclusions From the molecular modeling point of view, supramolecular microaggregate models that exhibit the properties of HS are stable in the soil solution. However, their binding to reactive mineral soil constituents can be also in the form of individual molecules or subaggregates. Thus, HS microaggregate stability is relative, depending on the interacting environment. This reconciles two points of view of HS: either as small molecules and/or supramolecular structures.

Organic matter in the pest and plant disease control: a meta-analysis

“…HS was the organic matter source that showed the greatest effectiveness (74.9%) in plants pest and disease control according to model proposed by Sukamto [133], and suggesting their potential role as biotic elicitors in stimulating defense pathways. Humic substances comprise humic and fulvic acids and consist of natural molecules of amphiphilic nature able to generate supramolecular assemblies in solution [134,135]. HS are also widely recognized as biostimulants as they promote plant growthrelated processes, enhance plant nutrient uptake and use efficiency, induce resistance and tolerance to abiotic stress, and improve the quality of crop-derived products when applied in small amounts.…”

Influencing factors and environmental effects of interactions between goethite and organic matter: A critical review

“…The surface properties of OM after adsorption on goethite are influenced by the ionic strength in the solution. Gerzabek et al (2022) proposed a supramolecular view that the screening of HA charge by electrolyte ions or the supramolecular nature of HA promoted different degrees of fractionation or aggregation of HA fractions. It then caused fractionation of HA molecules, and the average molar mass of adsorbed HA increased with ionic strength when the fractionation is fixed.…”

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

“…On an even smaller scale, specific organic matter interactions with mineral surfaces can also be evaluated with the help of molecular modeling, often restricted to simple organic matter fragments as well as short time and length scales (Schaumann & Thiele‐Brun, 2011). Although the full diversity of SOM‐related aggregation is hardly be captured by these methods, the detailed viewpoint by using quantum or classical molecular mechanics has significantly advanced our understanding of the stability of, for example, organic aggregates or of the interactions of organic matter with reactive mineral surfaces (see Gerzabek et al., 2022, for a review).…”