title: Vienna Soil-Organic-Matter Modeler--Generating condensed-phase models of humic substances.
abstract: 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.
authors.affiliation: Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria.
authors.forename: Axel
authors.initials: A
authors.lastname: Sündermann
authors.affiliation: Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Straße 82, A-1190 Vienna, Austria.
authors.forename: Roland
authors.initials: R
authors.lastname: Solc
authors.affiliation: Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Straße 82, A-1190 Vienna, Austria.
authors.forename: Daniel
authors.initials: D
authors.lastname: Tunega
authors.affiliation: Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Straße 82, A-1190 Vienna, Austria.
authors.forename: Georg
authors.initials: G
authors.lastname: Haberhauer
authors.affiliation: Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Straße 82, A-1190 Vienna, Austria.
authors.forename: Martin H
authors.initials: MH
authors.lastname: Gerzabek
authors.affiliation: Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria. Electronic address: chris.oostenbrink@boku.ac.at.
authors.forename: Chris
authors.initials: C
authors.lastname: Oostenbrink
mesh_terms: D002118:Calcium / Q000737:chemistry; D006812:Humic Substances; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D006812:Humic Substances; D002118:Calcium
keywords: Humic substances; Molecular dynamics simulations; Molecular models; Natural organic matter (NOM); Soil-Organic-Matter (SOM)