Large-Scale Molecular Dynamics Simulations Reveal New Insights Into the Phase Transition Mechanisms in MIL-53(Al)

Abstract

Soft porous crystals have the ability to undergo large structural transformations upon exposure to external stimuli while maintaining their long-range structural order, and the size of the crystal plays an important role in this flexible behavior. Computational modeling has the potential to unravel mechanistic details of these phase transitions, provided that the models are representative for experimental crystal sizes and allow for spatially disordered phenomena to occur. Here, we take a major step forward and enable simulations of metal-organic frameworks containing more than a million atoms. This is achieved by exploiting the massive parallelism of state-of-the-art GPUs using the OpenMM software package, for which we developed a new pressure control algorithm that allows for fully anisotropic unit cell fluctuations. As a proof of concept, we study the transition mechanism in MIL-53(Al) under various external pressures. In the lower pressure regime, a layer-by-layer mechanism is observed, while at higher pressures, the transition is initiated at discrete nucleation points and temporarily induces various domains in both the open and closed pore phases. The presented workflow opens the possibility to deduce transition mechanism diagrams for soft porous crystals in terms of the crystal size and the strength of the external stimulus.

The importance of crystal size for breathing kinetics in MIL-53(Al)

“…34 Finally, Speybroeck and co-workers simulated the phase transition in MIL-53(Al) using crystal-size dependent molecular dynamics simulations showing two different types of transition: layer-by-layer transition at low-pressure and formation of np (np – narrow pore phase) and lp (lp – large pore phase) domains at higher pressure. 35 In addition, a three orders of magnitude slower transition was observed for a 37 × 10 × 37 system as compared to a 1 × 2 × 1 cell (∼10 ns versus ∼10 ps).…”

“…We analyse the kinetics of reopening to get insights into activation barriers and mechanisms of guest-stimulated switching and prove the theoretical calculations, suggesting faster switching kinetics for smaller crystallites. 35 Three different samples were synthesized: (a) MIL-53(Al)-1 (average crystal size 28AE18 mm); (b) MIL-53(Al)-2 (average crystal size 1.2AE0.5 mm); (c) MIL-3(Al)-3 (average crystal size 0.6AE0.1 mm) (for characterization details see Fig. 1 and Fig.…”

“…We analyse the kinetics of reopening to get insights into activation barriers and mechanisms of guest-stimulated switching and prove the theoretical calculations, suggesting faster switching kinetics for smaller crystallites. 35…”

Molecular Dynamics of Solids at Constant Pressure and Stress Using Anisotropic Stochastic Cell Rescaling

“…The cell is, thus, provided with an inertia, and its acceleration is controlled by the difference between the internal pressure and the external stress, resulting in a second-order differential equation for the components of the lattice vectors. Monte Carlo algorithms can also be used to sample cell deformations [5,6], although their application has been limited. A number of variants of the original Parrinello-Rahman method has been published [7][8][9][10][11][12], all of them based on a second-order differential equation.…”

Machine Learning Potentials for Metal-Organic Frameworks using an Incremental Learning Approach

“…Classical force fields have become tractable within the MOF field as they are now starting to bridge the length scale gap towards experimentally observed MOF crystallites. 17,18 However, they are less accurate than DFT-based methods and exhibit only limited transferability; force fields derived under certain thermodynamic conditions are not necessarily applicable to other operating conditions. In addition, they are generally unable to describe bond formation or breakage.…”