Metal ion binding by humic substances as emergent functions of labile supramolecular assemblies

Abstract

Environmental contextThe fundamental basis for the high flexibility of humic substances is still unclear, though it is crucial for the understanding of metal bioavailability and toxicity in soil and aqueous environments. We show at the molecular level how characteristics of organic matter affect metal binding depending on the environmental conditions. Such understanding will help in the modulation of metal availability in soil and water in changing environmental situations. AbstractIn this work, we explore the hypothesis that humic substances (HS) can be perceived as labile supramolecular assemblages, the functioning of which is mainly determined by chemical composition and characteristics, the size of molecular units and weak intermolecular forces, rather than the exact primary structure of molecular moieties and their spatial configuration. To test the hypothesis, 72 computational models of three different organic mixtures were composed. The formation of inner and outer sphere metal–ligand complexes, metal binding sites, complex configurations, binding energies and aggregation/dissolution as emergent properties of HS were determined under various conditions. The results of computational modelling revealed that: (i) the highest Cu2+ binding (55.6%) was by the SRFA-22 organic model, which represents low-molecular-weight fulvic acids. In contrast, the highest amount of inner-sphere Mg–organic matter complex (63.4%) was formed in SRHA-6, which has higher-molecular-weight constituents. Therefore, a correlation between the type of cation, the system aromaticity and the extent of metal complexation is proposed. (ii) Increase of metal ion concentration and decrease of water content resulted in an increase in the number of hydrogen bonds and more compact and stable aggregates with lower hydrophilic and higher hydrophobic surface areas in SRFA-22. However, in SRHA-6, the results varied owing to the competition between metal binding, H-bonding and non-polar interactions in the structural arrangement of the aggregates. In general, the aggregation process, driven by metal complexation and water removal, resulted in the formation of more stable conformers, with lower potential energy, with the only exception of SRHA-6–Cu.

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

“…In this work, five models representing Suwannee River fulvic acid (SRFA) were developed. The models were created on the basis of SRFA chemical characteristics using principles proposed by Vialykh et al , The following algorithm of fragment selection from FTICR-MS data was implemented: (1) three chromophores identified in DOM , were selected; (2) three molecules with the highest intensity in SRFA FTICR-MS data were added to the previous molecules; (3) average parameters (see Screening Criteria below) for selected molecules were calculated; and (4) 2 to 15 molecules from FTICR-MS data were added to previously selected ones such that the average chemical characteristics described in Screening Criteria of each model were in agreement with experimental data for SRFA, and the number of atoms ranged between 450 and 500. Structural formula for fragments with molecular sizes between 100 and 450 Da was selected from structures presented in PubChem for a particular empirical formula.…”

The Effect of Supramolecular Humic Acids on the Diffusivity of Metal Ions in Agarose Hydrogel

“…The most important binding sites in humic molecules are carboxylic and phenolic functional groups [ 1 , 2 , 3 , 4 , 5 , 6 , 22 , 32 , 39 , 40 ]. Their different combinations can result in a large number of different coordination (chelation) sites that are able to bind metal ions by attractive interactions of different strengths.…”

“…Nowadays, the concept of humic acids having a supramolecular structure is widely accepted. This concept presumes that humic substances are associations of small molecules self-assembled by weak forces and hydrogen bonds [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. Humic associations are formed by the self-organization of hydrophobic and amphiphilic compounds whereby hydrophilic structures are formed mainly by carbohydrate chains and aromatic rings, amphiphilic by ionizable functional groups [ 14 , 15 ].…”

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

“…One of the main pitfalls of classical FFMD simulations is the impossibility to simulate chemical processes such as bond breaking/forming by using standard types of force fields. In recent publications, the stability of HAs aggregates with varying chemical composition and size has been described (Vialykh, Salahub, Achari et al., 2019; Vialykh, Salahub, Achari, Cook et al., 2019) by using the ReaxFF force field (van Duin et al., 2001), which is able to model, within some limits, chemical processes as well. Another direction in simulation of the SOM is application of so‐called coarse‐grained (CG) force field approach, in which groups of atoms or entire molecules are replaced by individual beads (pseudo‐particles) and interactions between them are described by a specific form of interaction potentials.…”