Department of Chemistry, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada.
J Chem Phys. 2017 Jul 28;147(4):044702. doi: 10.1063/1.4994700.
Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.
分子模拟是研究各种化学系统微观行为的有力工具，在该领域中，成功再现感兴趣的实际系统的结构和动态特性的关键是使用合适的模型。在这种情况下，对金属-有机骨架（MOF）自组装过程的分子动力学模拟研究具有一定的挑战性，因为预期需要合理准确地表示金属-配体相互作用。在当前的研究中，我们不仅研究了一些现有模型的性能，还引入和测试了新模型，以帮助探索典型 Zn-羧酸酯 MOF 体系的自组装过程。为此，我们检查并验证了六种不同的 Zn 离子模型、三种溶剂模型和两种配体模型的行为，以与关键实验结构参数相对应。为了通过显式溶剂模拟探索 MOF 自组装过程中的更长时间尺度有序事件，有必要确定代表金属离子、有机配体和溶剂分子的简化模型组件的合适组合。结果表明，与全原子羧酸配体模型和简单偶极溶剂模型结合使用的扩展阳离子虚拟原子（ECDA）Zn 离子模型可以再现典型 MOF 系统的特征实验结构。这些模型在大量分子模拟中的成功应用，为理解该典型 MOF 系统在自组装早期阶段的自组装机制提供了关键的见解，这一成果最近已被报道。
