Abstract In this study, clay-soil organic matters (SOMs) interactions were investigated by combining first principles molecular dynamics (FPMD) and classical molecular dynamics (CMD) techniques. FPMD was employed to quantify the binding mechanisms of reactive SOMs groups on clay surfaces and to derive parameters for the bonding of the reactive groups on edge surfaces. By integrating the derived parameters with CVFF–CLAYFF force fields, CMD simulations were carried out to investigate the structures of large models of clay-SOMs associations. All possible reactive SOMs groups, including carboxylate, phosphate, quinone species and ammonium groups were taken into account. FPMD results showed that all these groups are important to the complexation of SOMs on clay surfaces under dry conditions but only chemical bonding of carboxylate and phosphate and cation bridging are of significance under wet conditions. pH dependence of carboxylate and phosphate and Eh-pH dependence of quinone species are presented. CMD simulations showed that SOMs bound on clay surfaces via direct bonding of carboxylate and Ca2+ bridging and revealed the effect of water on structures of the clay-SOMs association. Based on the computational results, a procedure was proposed for constructing realistic molecular models for soils. Possible applications and further improvements of these models are discussed.

中文翻译：

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黏土-土壤有机质 (SOM) 相互作用的第一性原理与经典分子动力学相结合的研究

摘要 在本研究中，结合第一性原理分子动力学（FPMD）和经典分子动力学（CMD）技术，研究了粘土-土壤有机质（SOMs）相互作用。FPMD 用于量化粘土表面上反应性 SOM 基团的结合机制，并推导出边缘表面上反应性基团的结合参数。通过将导出的参数与 CVFF-CLAYFF 力场相结合，进行了 CMD 模拟以研究粘土-SOM 关联的大型模型的结构。所有可能的反应性 SOM 基团，包括羧酸盐、磷酸盐、醌类和铵基团都被考虑在内。FPMD 结果表明，所有这些基团对干燥条件下粘土表面上 SOM 的络合都很重要，但只有羧酸盐和磷酸盐的化学键合以及阳离子桥接在潮湿条件下才有意义。介绍了羧酸盐和磷酸盐的 pH 值依赖性以及醌类物质的 Eh-pH 值依赖性。CMD 模拟表明，SOM 通过羧酸盐和 Ca2+ 桥接的直接键合与粘土表面结合，并揭示了水对粘土-SOM 缔合结构的影响。根据计算结果，提出了一种构建现实土壤分子模型的程序。讨论了这些模型的可能应用和进一步改进。介绍了羧酸盐和磷酸盐的 pH 值依赖性以及醌类物质的 Eh-pH 值依赖性。CMD 模拟表明，SOM 通过羧酸盐和 Ca2+ 桥接的直接键合与粘土表面结合，并揭示了水对粘土-SOM 缔合结构的影响。根据计算结果，提出了一种构建现实土壤分子模型的程序。讨论了这些模型的可能应用和进一步改进。介绍了羧酸盐和磷酸盐的 pH 值依赖性以及醌类物质的 Eh-pH 值依赖性。CMD 模拟表明，SOM 通过羧酸盐和 Ca2+ 桥接的直接键合与粘土表面结合，并揭示了水对粘土-SOM 缔合结构的影响。根据计算结果，提出了一种构建现实土壤分子模型的程序。讨论了这些模型的可能应用和进一步改进。