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Humic substances are ubiquitous in the environment and have manifold functions. While their composition is well known, information on the chemical structure and three-dimensional conformation is scarce. Here we describe the Vienna Soil-Organic-Matter Modeler, which is an online tool to generate condensed phase computer models of humic substances (http://somm.boku.ac.at). Many different models can be created that reflect the diversity in composition and conformations of the constituting molecules. To exemplify the modeler, 18 different models are generated based on two experimentally determined compositions, to explicitly study the effect of varying e.g. the amount of water molecules in the models or the pH. Molecular dynamics simulations were performed on the models, which were subsequently analyzed in terms of structure, interactions and dynamics, linking macroscopic observables to the microscopic composition of the systems. We are convinced that this new tool opens the way for a wide range of in silico studies on soil organic matter.

Organoclays are sorbent materials prepared from clays by exchanging inorganic with organic cations. Their properties depend on the loading and conformational structure of the organic cations, but little information is available about the surface structures of organoclays. In this work, X-ray photoelectron spectroscopy (XPS) and classical molecular dynamics (MD) simulations are combined to characterize the external interface of an organoclay prepared from hexadecylpyridinium (HDPy+) and bentonite. The XPS survey spectra show well the varying elemental composition of the surface with increasing amount of surfactant, showing a decreasing contribution of clay-derived elements with increasing organic coverage. The high-resolution C 1s XPS spectra depict sensitively the surface arrangement of the surfactant. In combination with MD simulations, the results implied a monolayer coating for low surfactant coverage and a disordered bilayer arrangement at high surfactant uptakes. Molecular dynamics simulations showed that for very high cation uptake a quasi-paraffin-like configuration is also possible. The combination of experimental and modelling methods yielded congruent information on the molecular-scale arrangement of organic cations at the organoclay surfaces and the controlling mechanisms.

A systematic study on the structural properties of para-phenylene oligomers based on the self-consistent charge density-functional tight binding approach (SCC-DFTB) and its time-dependent (TD) version is presented. Our goal is to investigate the applicability of DFTB for the present class of compounds and to use its computational efficiency for on-the-fly dynamics calculations and to perform in this way simulations of absorption and fluorescence spectra. For this purpose geometry optimizations have been performed for the ground state and for the electronically lowest excited state of oligomers containing two to seven aromatic rings. The torsional potential curves have been computed for para-biphenyl and para-terphenyl in the ground and lowest excited state. Agreement with previously computed DFT results is quite encouraging and DFTB seems to be well suited for the treatment of the class of conjugated pi systems investigated in this work. The intrachain vibrational broadening of absorption and emission spectra computed from dynamics simulations are presented and compared with experimental spectra.