Three-dimensional, Molecular Structures of Humic Acids and Their Interactions with Water and Dissolved Contaminants

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Abstract
A novel three-dimensional structural concept for humic acids (HAs) in soils and water was developed which was based on comprehensive investigations combining geochemical, wet-chemical, biochemical, spectroscopic, agricultural and ecological data with analytical pyrolysis. Direct, temperature-programmed pyrolysis in the ion-source of the mass spectrometer combined with soft ionization in very high electric fields (Py-FIMS) and Curie-point pyrolysis-gas chromatography/mass spectrometry (Py-GC-MS) were the principal analytical methods for the proposed humic acid monomer. Emphasis was put on molecular modeling and geometry optimization of humic complexes with biological and anthropogenic substances using modern PC software (HyperChem) in order to determine low energy conformations, space requirements, voids, as well as inter and intramolecular hydrogen bonds. Initial simulations of molecular model structures of humic acids for trapping and binding of water molecules and humic-contaminant complexes with pentachlorophenol dissolved in water are illustrated. Molecular mechanics calculations are reported (a) to visualize interactions between humic acid and water as well as humic acid and contaminant; (b) to describe the nanochemistry (e.g. bond distances, angles, torsions, bends, van der Waals forces and inter- and intramolecular hydrogen bonds) of humic acids and their complexes in vacuum and in aqueous solution; and (c) to introduce experiments using periodic boxes containing water molecules with dissolved humic-contaminant complexes.