Schaper Larissa, Schmid Rochus
Ruhr-Universität Bochum, Faculty of Chemistry and Biochemistry, Computational Materials Chemistry Group, Universitätsstr. 150, 44801, Bochum, Germany.
Commun Chem. 2023 Oct 28;6(1):233. doi: 10.1038/s42004-023-01025-x.
Flexible metal-organic frameworks (MOFs) can undergo structural transitions with significant pore volume changes upon guest adsorption or other external triggers while maintaining their porosity. In computational studies of this breathing behavior, molecular dynamics (MD) simulations within periodic boundary conditions (PBCs) are commonly performed. However, to account for the finite size and surface effects affecting the phase transition mechanism, the simulation of non-periodic nanocrystallite (NC) models without the constraint of PBCs is an important alternative. In this study, we present an approach allowing the analysis and control of the volume of finite-size structures during MD simulations by a tetrahedral tessellation of the (deformed) NC's volume. The method allows for defining the current NC's volume during the simulation and manipulating it regarding a particular reference volume to compute free energies for the phase transformation via umbrella sampling. The application on differently sized DMOF-1 and DUT-128 NCs reveals flexible pore closing mechanisms without significant biasing of the transition pathway. The concept provides the theoretical foundation for further research on flexible materials regarding targeted initialization of the structural phase behavior to elucidate the underlying mechanism, which can be used to improve the applications of flexible materials by targeted controlling of the phase transition.
柔性金属有机框架材料（MOFs）在客体吸附或其他外部触发因素作用下可发生结构转变，伴随显著的孔体积变化，同时保持其孔隙率。在对这种呼吸行为的计算研究中，通常会在周期性边界条件（PBCs）下进行分子动力学（MD）模拟。然而，为了考虑影响相变机制的有限尺寸和表面效应，模拟不受PBCs约束的非周期性纳米微晶（NC）模型是一种重要的替代方法。在本研究中，我们提出了一种方法，通过对（变形的）NC体积进行四面体镶嵌，在MD模拟过程中分析和控制有限尺寸结构的体积。该方法允许在模拟过程中定义当前NC的体积，并根据特定参考体积对其进行操作，以通过伞形采样计算相变的自由能。在不同尺寸的DMOF-1和DUT-128 NCs上的应用揭示了灵活的孔闭合机制，而不会对转变途径产生显著偏差。该概念为进一步研究柔性材料提供了理论基础，有助于有针对性地初始化结构相行为以阐明潜在机制，从而通过有针对性地控制相变来改善柔性材料的应用。
