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.
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.
Environ Sci Technol. 2017 May 16;51(10):5414-5424. doi: 10.1021/acs.est.7b00266. Epub 2017 May 3.
Humic substances (HS) are abundant in the environment and play an important role in a number of biogeochemical processes including microbial activity, soil aggregation, plant growth, the retention and release of nutrients, the environmental fate of pollutants, and carbon storage. They are flexible, relatively small molecules forming supramolecular structures through weak interactions. Despite the great importance of understanding their behavior at the atomic level, computational modeling, a premier high-resolution technique providing great level of detail, has been surprisingly little-employed to study humic substances. Here, we use the recently developed Vienna Soil Organic-Matter Modeler to create representative models of a real HS sample, the standard Leonardite humic acid. Molecular dynamics simulations were used to probe the structure and dynamics of the system at a range of hydration levels. The studied systems were characterized in terms of their physicochemical properties, including density, dielectric properties, hydrogen bonding, etc. Moreover, the strength of sorption was estimated for three small organic compounds: benzaldehyde, propan-2-ol, and acetone. Strikingly, the HS models were validated against experimental data showing a remarkable agreement with calculated properties. Finally, we make the equilibrated models of the standard Leonardite humic acid, together with corresponding force-field parameters, available at the Vienna Soil Organic-Matter Modeler.
腐殖质（HS）在环境中大量存在，在许多生物地球化学过程中发挥着重要作用，包括微生物活性、土壤团聚、植物生长、养分的保留和释放、污染物的环境归宿以及碳储存。它们是灵活的、相对较小的分子，通过弱相互作用形成超分子结构。尽管在原子水平上理解它们的行为具有重要意义，但计算建模作为一种提供高分辨率细节的首要技术，却出人意料地很少用于研究腐殖质。在这里，我们使用最近开发的维也纳土壤有机质建模器来创建真实 HS 样品（标准莱奥尼丁腐殖酸）的代表性模型。分子动力学模拟用于在一系列水合水平下探测系统的结构和动力学。所研究的系统在物理化学性质方面进行了表征，包括密度、介电性质、氢键等。此外，还估计了三种小分子化合物（苯甲醛、异丙醇和丙酮）的吸附强度。引人注目的是，HS 模型经过验证，与实验数据的吻合度非常高，计算得到的性质与实验值非常吻合。最后，我们在维也纳土壤有机质建模器上提供了标准莱奥尼丁腐殖酸的平衡模型以及相应的力场参数。
