Modelling of interactions of polar and nonpolar pollutants with soil minerals and soil organic matter

Environmental pollution of soils by organic contaminants such as pesticides is one of the serious problems of our civilization. Contaminants can undergo various physical, chemical and biological transformation processes in soils governing behaviour, distribution, and fate of organic species in environment and subsequent environmental risks. Mechanistic understanding of molecular interactions of organic pollutants with main soil components represents a key factor for estimating the behaviour of contaminants in soils. Molecular modelling offers an opportunity to investigate and characterize various details of these interactions at molecular level providing specifications, which are difficult to obtain at the experimental level. This work represents a comprehensive overview of our investigations of the molecular interactions of organic contaminants with selected soil components. Particularly, we focused on the characterization of the structure and the surface complexation of the phenoxyacetic acid derivatives (herbicides MCPA and 2,4-D) and typical soil minerals such as clay minerals (kaolinite and montmorillonite) and iron oxyhydroxides (goethite and lepidocrocite). Further, interactions of several representative nonpolar polycyclic aromatic hydrocarbons (e.g. naphthalene, anthracene, pyrene, and phenanthrene) with iron oxyhydroxides were modelled, as well. It was found that in case of polar species, hydrogen bonds and electrostatic interactions play an important role in the formation of the surface complexes. In case of nonpolar PAHs, dispersion forces dominate in the planar stacking of the PAHs molecules on mineral surfaces. Another study focused at a complex 3D model representing humic substances firstly, featuring polar hydrophilic and nonpolar hydrophobic domains and also a nanopore SOM structure. This model was taken to simulate trapping and interactions of MCPA (polar) and naphthalene (nonpolar) species inside of the nanopore. It was found that MCPA is preferentially stabilized close to polar functional groups (carboxyl) whereas naphthalene interacts mostly with nonpolar aliphatic chains through dispersion interactions

Structures and properties of bioorgano-clays

Interactions between microbial matter and clays are a common interfacial phenomenon in soil and sediment environments. However, fundamental mechanisms governing the formation and interactions of clay minerals with microbial-derived organic substances are still poorly understood. Therefore, our central aim was to study the formation of bioorgano-clay composites and their specific material properties and compare these properties with those of well-studied organo-clays. Pure organic cations (e.g., alkylammonium homologues) and complex microbial biomass (e.g., fungal biomass from Aphanocladium sp.) were used to prepare organo- and bioorgano-clays by varying the amount of clay (montmorillonite) and organic materials used. Interaction mechanisms between organic materials and clay and the resulting structure and physicochemical properties were explored by multiple experimental methods (e.g. IR spectroscopy, contact angle, zeta potential, X-ray photoelectron spectroscopy, transmission electron microscopy) in a combination with molecular modelling to determine the structure, composition, and properties of the prepared bioorgano-clays. Depending on origin, type, and size of the organic material and the clay, two basic types of bioorgano-clays were found: (i) bioorgano-clays having their clay particles coated by bioorganic matter with only limited or no penetration into interlayer galleries and (ii) bioorgano-clays having bioorganic matter distributed in the interlayer galleries and/or on the external surfaces of clay particles. Both types show heterogeneous arrangements of the amended organic matter inducing differences in shape and size of organo-clay particles. Consequently, changes in pore volumes, stability, and elemental interface properties can be verified. Compared to organo-clays, bioorgano-clays provided e.g. a higher adsorption capacity for uranyl, suggesting that modification of clays by rather unspecific microbial compounds significantly enhanced the number of exchange sites. Bioorganic-clays, although being less specific in nature, might therefore be applied more broadly in situations where a high sorption capacity, e.g., for contaminants, is required

Structure of hydrated calcium carbonates: A first-principles study

The structures of both ikaite (CaCO3·6H2O) and monohydrocalcite (CaCO3·H2O) were computed at the PBE0 level of theory, using all electron Gaussian type basis sets. Correction for the long-range dispersion contribution was included for the oxygen–oxygen interactions by using an additive pairwise term with the atomic coefficients fitted against the calcite vs aragonite enthalpy difference. The potential chirality of monohydrocalcite is discussed, as well as the helical motifs created by the three-fold rototranslational axes parallel to the [001] direction. These elements represent a significant link between monohydrocalcite and vaterite, both appearing as intermediate species during CaCO3 crystallization from amorphous calcium carbonate. The hydrogen bond pattern, never fully discussed for monohydrocalcite, is here described and compared to the available experimental data. Both phases are characterized by the presence of hydrogen bonds of moderate to high strength. Water molecules in monohydrocalcite interact quite strongly with 2 View the MathML source units through such hydrogen bonds, whereas their interaction with each other is minor. On the contrary, water molecules in ikaite create a complex network of hydrogen bonds, where each water molecule is strongly hydrogen bonded to one View the MathML source anion and to one or two other water molecules

Bonds, bands and elasticity of smithsonite rock

The objective here is to spread out in detail the various fundamental state properties of smithsonite rock (ZnCO3) for which the most intrinsic quantities remain still unknown. First-principles electronic structure calculations based on the density functional theory with the pseudopotential method were performed using diverse functionals. A number of mechanical quantities were evaluated such as bulk modulus, elastic constants, Young’s and shear moduli, and transversal and longitudinal sound velocities (VS and VP). Fitting the compression data of smithsonite to the third-order Birch–Murnaghan equation of state gives a bulk modulus of 124.17 GPa, which reflects an important rigidity compared to the other carbonates. The analysis of the band structure reveals a band-gap energy of 3.36 eV that is close enough to some semiconductors rather than insulators. Finally the chemical bonding was analyzed through the electronic charge density of the total contributions of the valence bands. A pronounced charge transfer was observed towards the carbonate ion, indicating thereby the ionic character of ZnCO3

Response of sorption processes of MCPA to the amount and origin of organic matter in a long-term field experiment

Changes in farming practices over long times can affect the sorption behaviour of MCPA ((4-chloro-2- methylphenoxy)acetic acid). We studied the adsorption±desorption mechanisms of MCPA on soil with varied amounts and origins of soil organic matter obtained from a long-term field experiment with various organic amendments. The origin of the soil organic matter seems to be crucial for the sorption behaviour of MCPA. Samples of soil amended with sewage sludge sorbed MCPA more strongly than the soil under any other treatment. Peat-amended soil was second followed by soil receiving animal manure, green manure, mineral fertilizer without N and the fallowed soil. Both the carbon content and the origin of the organic matter are important for the sorption. A decrease of carbon content of a soil does not necessarily imply a reduction of sorption capacity for polar organic acids such as MCPA. Nevertheless, our adsorption±desorption experiments suggest that with decreasing carbon content the role of mineral sorption mechanisms could become more pronounced. Our results showed that interactions of soil organic matter and soil minerals distinctly influence adsorption properties for MCPA