Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium

Abstract

One of the most investigated properties of porous crystalline metal-organic frameworks (MOFs) is their potential flexibility to undergo large changes in unit cell size upon guest adsorption or other stimuli, referred to as “breathing”. Computationally, such phase transitions are usually investigated using periodic boundary conditions, where the system’s volume can be controlled directly. However, we have recently shown that important aspects like the formation of a moving interface between the open and the closed pore form or the free energy barrier of the first-order phase transition and its size effects can best be investigated using non-periodic nanocrystallite (NC) models [Keupp et al. (Adv. Theory Simul., 2019, 2, 1900117)]. In this case, the application of pressure is not straightforward, and a distance constraint was used to mimic a mechanical strain enforcing the reaction coordinate. In contrast to this prior work, a mediating particle bath is used here to exert an isotropic hydrostatic pressure on the MOF nanocrystallites. The approach is inspired by the mercury nanoporosimetry used to compress flexible MOF powders. For such a mediating medium, parameters are presented that require a reasonable additional numerical effort and avoid unwanted diffusion of bath particles into the MOF pores. As a proof-of-concept, NCs of pillared-layer MOFs with different linkers and sizes are studied concerning their response to external pressure exerted by the bath. By this approach, an isotropic pressure on the NC can be applied in analogy to corresponding periodic simulations, without any bias for a specific mechanism. This allows a more realistic investigation of the breathing phase transformation of a MOF NC and further bridges the gap between experiment and simulation.

Challenges and Opportunities of Molecular Simulations for Negative Gas Adsorption

“…Importantly, Schmid and co-workers were able to demonstrate that direct molecular simulation of nanoscale discrete crystallites of flexible MOFs is achievable for handful of materials. , They were able to achieve these simulations by removing periodic boundary conditions and free energy sampling employing distance restraints . Moreover, to recreate realistic conditions, without using distance constraints, Schmid et al have also demonstrated an approach to capture the pressure medium . These current simulations do appear to provide a path forward for the simulation of finite-size effects, although the chemical accuracy of the description of the external crystal surface remains an important open question.…”

Crystal Size Dependent Flexibility in ZIF-7: From Macro- to Nanoscale

“…The two orders of magnitude reduction in the crystal size of ZIF-7(18)-STR in comparison to ZIF-7(12) results in a higher surface to volume ratio with a greater number of weaker surface adsorption sites causing a delay for the phase transition. This insight was motivated by the molecular simulation by Zhang et al on ZIF-8 showing that the weaker affinity of surface adsorption sites due to the lack of neighboring groups increases the activation energy barrier to initiate gate opening, requiring a larger adsorbate concentration to trigger dynamic behaviour. − …”

Simulating the Breathing Phase Transitions of Metal-organic Frameworks : Volume Control of Nanocrystallites

“…The volume control method was applied to differently sized DMOF-1 and DUT-128 nanocrystallites to investigate their breathing behavior and compare it to the formerly obtained pressure bath results [18]. For this purpose, MD simulations on the FF level of the structural transition from the open to the closed pore form were performed.…”