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Classical mechanical simulations of layer- and tunnel-structured manganese oxide minerals
Geochimica et Cosmochimica Acta ( IF 4.5 ) Pub Date : 2020-12-01 , DOI: 10.1016/j.gca.2020.04.034
Aric G. Newton , Kideok D. Kwon

Abstract Tecto- and phyllo-manganate minerals serve as important controls in the geochemical cycle of many elements in soils and sediments due to their high surface areas and chemical reactivity. These nanoscale Mn oxides are mainly composed of Mn octahedra in edge- and corner-sharing configurations that produce a range of tunnel and layer structures. Some fundamental aspects of their atomic structures, however, are difficult to characterize unambiguously because of dynamic structural transformations and a wide range of the structural and chemical compositions. Molecular dynamics (MD) simulations based on interatomic pair potentials provide a perspective on nanoscale Mn-oxides that can be inaccessible to experiment or density functional theory (DFT) calculations. We recently introduced a set of interatomic potentials for the atomistic simulation of Mn-oxides (MnFn) that reproduced many of the subtle phyllomanganate structural variations associated with pH, vacancy content, and Mn oxidation state. In this manuscript, we expand the roster of simulated Mn-oxide minerals to include hydrous and anhydrous tunnel structures and δ-MnO2 with octahedral vacancy contents up to 20%. The MnFn potentials reproduced the experimental tectomanganate lattice parameters and interatomic distances to within 5% and the relative energetics of tectomanganates as predicted by a recent DFT study. We also provide new insights into the Mg site occupancy in todorokite and the Zn coordination in vernadite through large-scale atomistic simulations with MnFn that are challenging to simulate with DFT. In the 3 × 3 tunnel structures of todorokite, the central tunnel site is the predominant site for fully-hydrated Mg2+·6H2O with a minority of partially-hydrated Mg2+ cations binding to corner sites at decreased water/cation ratios. The occurrence of tetrahedral Zn complexes is dependent upon not only the Mn(IV) vacancy content but also the layer spacing and sheet registry. These atomistic simulation results demonstrate the ability of the MnFn potentials to reproduce the basic structures of nanophase Mn-oxides and the capability to perform large-scale modeling that is required to address the subtle structural variations associated with changes in environmental conditions.

中文翻译:

层状和隧道结构氧化锰矿物的经典力学模拟

摘要 构造和叶状锰酸盐矿物由于其高表面积和化学反应性,在土壤和沉积物中许多元素的地球化学循环中起着重要的控制作用。这些纳米级 Mn 氧化物主要由边缘和角共享配置的 Mn 八面体组成,可产生一系列隧道和层结构。然而,由于动态结构转变和广泛的结构和化学成分,它们的原子结构的一些基本方面难以明确表征。基于原子间对势的分子动力学 (MD) 模拟提供了对纳米级 Mn 氧化物的看法,而这些氧化物在实验或密度泛函理论 (DFT) 计算中是无法获得的。我们最近引入了一组用于 Mn 氧化物 (MnFn) 原子模拟的原子间势,这些势能再现许多与 pH、空位含量和 Mn 氧化态相关的微妙叶锰酸盐结构变化。在这份手稿中,我们扩展了模拟锰氧化物矿物的名单,包括含水和无水隧道结构以及八面体空位含量高达 20% 的 δ-MnO2。MnFn 电位将实验的 tectomanganate 晶格参数和原子间距离复制到 5% 以内,以及最近的 DFT 研究预测的 tectomanganates 的相对能量学。我们还通过 MnFn 的大规模原子模拟,提供了对 todorokite 中 Mg 位点占有率和 vernadite 中 Zn 配位的新见解,这些模拟很难用 DFT 模拟。在 todorokite 的 3 × 3 隧道结构中,中央隧道位置是完全水合 Mg2+·6H2O 的主要位置,少数部分水合的 Mg2+ 阳离子以降低的水/阳离子比结合到角落位置。四面体锌配合物的出现不仅取决于 Mn(IV) 空位含量,还取决于层间距和片材注册。这些原子模拟结果证明了 MnFn 电位具有重现纳米相 Mn 氧化物基本结构的能力,以及执行大规模建模的能力,这是解决与环境条件变化相关的细微结构变化所需的。中央隧道位置是完全水合的 Mg2+·6H2O 的主要位置,少数部分水合的 Mg2+ 阳离子以降低的水/阳离子比结合到角落位置。四面体锌配合物的出现不仅取决于 Mn(IV) 空位含量,还取决于层间距和片材注册。这些原子模拟结果证明了 MnFn 电位具有重现纳米相 Mn 氧化物基本结构的能力,以及进行大规模建模的能力,这是解决与环境条件变化相关的细微结构变化所必需的。中央隧道位置是完全水合的 Mg2+·6H2O 的主要位置,少数部分水合的 Mg2+ 阳离子以降低的水/阳离子比结合到角落位置。四面体锌配合物的出现不仅取决于 Mn(IV) 空位含量,还取决于层间距和片材注册。这些原子模拟结果证明了 MnFn 电位具有重现纳米相 Mn 氧化物基本结构的能力,以及进行大规模建模的能力,这是解决与环境条件变化相关的细微结构变化所必需的。
更新日期:2020-12-01
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