Molecular simulations of self-assembly processes in metal-organic frameworks: Model dependence

Theoretical and computational methodologies for understanding coordination self-assembly complexes

This perspective highlights three theoretical and computational methods to capture the coordination self-assembly processes at the molecular level: quantum chemical modeling, molecular dynamics, and reaction network analysis. These methods cover the different scales from the metal-ligand bond to a more global aspect, and approaches that are best suited to understand the coordination self-assembly from different perspectives are introduced. Theoretical and numerical researches based on these methods are not merely ways of interpreting the experimental studies but complementary to them.

Nucleation of zeolitic imidazolate frameworks: from molecules to nanoparticles

We have studied the clusters involved in the initial stages of nucleation of Zeolitic Imidazolate Frameworks, employing a wide range of computational techniques. In the pre-nucleating solution, the prevalent cluster is the ZnIm₄ cluster (formed by a zinc cation, Zn²⁺, and four imidazolate anions, Im^-), although clusters such as ZnIm₃, Zn₂Im₇, Zn₂Im₇, Zn₃Im₉, Zn₃Im₁₀, or Zn₄Im₁₂ have energies that are not much higher, so they would also be present in solution at appreciable quantities. All these species, except ZnIm₃, have a tetrahedrally coordinated Zn²⁺ cation. Small Zn_xIm_y clusters are less stable than the ZnIm₄ cluster. The first cluster that is found to be more stable than ZnIm₄ is the Zn₄₁Im₈₈ cluster, which is a disordered cluster with glassy structure. Bulk-like clusters do not begin to be more stable than glassy clusters until much larger sizes, since the larger cluster we have studied (Zn₁₄₄Im₂₈₈) is still less stable than the glassy Zn₄₁Im₈₈ cluster, suggesting that Ostwald's rule (the less stable polymorph crystallizes first) could be fulfilled, not for kinetic, but for thermodynamic reasons. Our results suggest that the first clusters formed in the nucleation process would be glassy clusters, which then undergo transformation to any of the various crystal structures possible, depending on the kinetic routes provided by the synthesis conditions. Our study helps elucidate the way in which the various species present in solution interact, leading to nucleation and crystal growth.

Early-Stage Formation of the SIFSIX-3-Zn Metal-Organic Framework: An Automated Computational Study

Metal-organic frameworks (MOFs) have attracted significant attention over the past 2 decades due to their wide applicability as functional materials. However, targeted synthesis of novel MOFs remains problematic as their formation mechanisms are poorly understood, which forces us to rely on serendipity in the synthesis of novel MOFs. Here, we demonstrate a workflow employing the artificial force induced reaction (AFIR) method to investigate the self-assembly process of the node of the SIFSIX-3-Zn MOF, [Zn(pyz)₄(SiF₆)₂]^2- (pyz = pyrazine), in an automated manner. The workflow encompassing AFIR calculations, generation of extensive reaction path networks, propagation simulations of intermediates, and further refinements of identified formation pathways showed that the nodal structure can form through multiple competing pathways involving interconvertible intermediates. This finding provides a plausible rationale for the stochastic multistage processes believed to be key in MOF formation. Furthermore, this work represents the first application of an automated reaction mechanism discovery method to a MOF system using a general workflow that is applicable to study the formation of other MOF motifs as well.

Computer simulation of the early stages of self-assembly and thermal decomposition of ZIF-8

We employ all-atom well-tempered metadynamics simulations to study the mechanistic details of both the early stages of nucleation and crystal decomposition for the benchmark metal–organic framework (MOF) ZIF-8. To do so, we developed and validated a force field that reliably models the modes of coordination bonds via a Morse potential functional form and employs cationic and anionic dummy atoms to capture coordination symmetry. We also explored a set of physically relevant collective variables and carefully selected an appropriate subset for our problem at hand. After a rapid increase of the Zn–N connectivity, we observe the evaporation of small clusters in favor of a few large clusters, which leads to the formation of an amorphous highly connected aggregate. [Formula: see text] and [Formula: see text] complexes are observed with lifetimes in the order of a few picoseconds, while larger structures, such as four-, five-, and six-membered rings, have substantially longer lifetimes of a few nanoseconds. The free ligands act as “templating agents” for the formation of sodalite cages. ZIF-8 crystal decomposition results in the formation of a vitreous phase. Our findings contribute to a fundamental understanding of MOF’s synthesis that paves the way to controlling synthesis products. Furthermore, our developed force field and methodology can be applied to model solution processes that require coordination bond reactivity for other ZIFs besides ZIF-8.

Modeling the Layer-by-Layer Growth of HKUST-1 Metal-Organic Framework Thin Films

Metal organic frameworks have emerged as an important new class of materials with many applications, such as sensing, gas separation, drug delivery. In many cases, their performance is limited by structural defects, including vacancies and domain boundaries. In the case of MOF thin films, surface roughness can also have a pronounced influence on MOF-based device properties. Presently, there is little systematic knowledge about optimal growth conditions with regard to optimal morphologies for specific applications. In this work, we simulate the layer-by-layer (LbL) growth of the HKUST-1 MOF as a function of temperature and reactant concentration using a coarse-grained model that permits detailed insights into the growth mechanism. This model helps to understand the morphological features of HKUST-1 grown under different conditions and can be used to predict and optimize the temperature for the purpose of controlling the crystal quality and yield. It was found that reactant concentration affects the mass deposition rate, while its effect on the crystallinity of the generated HKUST-1 film is less pronounced. In addition, the effect of temperature on the surface roughness of the film can be divided into three regimes. Temperatures in the range from 10 to 129 °C allow better control of surface roughness and film thickness, while film growth in the range of 129 to 182 °C is characterized by a lower mass deposition rate per cycle and rougher surfaces. Finally, for T larger than 182 °C, the film grows slower, but in a smooth fashion. Furthermore, the potential effect of temperature on the crystallinity of LbL-grown HKUST-1 was quantified. To obtain high crystallinity, the operating temperature should preferably not exceed 57 °C, with an optimum around 28 °C, which agrees with experimental observations.

A nature-inspired hydrogen-bonded supramolecular complex for selective copper ion removal from water

Herein, we present a scalable approach for the synthesis of a hydrogen-bonded organic–inorganic framework via coordination-driven supramolecular chemistry, for efficient remediation of trace heavy metal ions from water. In particular, using copper as our model ion of interest and inspired by nature’s use of histidine residues within the active sites of various copper binding proteins, we design a framework featuring pendant imidazole rings and copper-chelating salicylaldoxime, known as zinc imidazole salicylaldoxime supramolecule. This material is water-stable and exhibits unprecedented adsorption kinetics, up to 50 times faster than state-of-the-art materials for selective copper ion capture from water. Furthermore, selective copper removal is achieved using this material in a pH range that was proven ineffective with previously reported metal–organic frameworks. Molecular dynamics simulations show that this supramolecule can reversibly breathe water through lattice expansion and contraction, and that water is initially transported into the lattice through hopping between hydrogen-bond sites.

Heavy metals and metalloids pose major threats to health and environmental ecosystems, thus systems for low-cost remediation are needed. Here the authors report the scalable design of a hydrogen-bonded organic–inorganic framework for selective removal of trace heavy metal ions from water.

Understanding Time Dependence on Zinc Metal-Organic Framework Growth Using in Situ Liquid Secondary Ion Mass Spectrometry

The abundance of novel metal-organic framework (MOF) materials continues to increase as more applications are discovered for these highly porous, well-ordered crystalline structures. The simplicity of constituents allows for the design of new MOFs with virtue of functionality and pore topology toward target adsorbates. However, the fundamental understanding of how these frameworks evolve during nucleation and growth is mostly limited to speculation from simulation studies. In this effort, we utilize a unique vacuum compatible system for analysis at the liquid vacuum interface (SALVI) microfluidic interface to analyze the formation and evolution of the benchmark MOF-74 framework using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Principal component analysis of the SIMS mass spectra, together with ex situ electron microscopy, powder X-ray diffractometry, and porosimetry, provides new insights into the structural growth, metal-oxide cluster formation, and aging process of Zn-MOF-74. Samples collected over a range of synthesis times and analyzed closely with in situ ToF-SIMS, transmission electron microscopy, and gas adsorption studies verify the developing pore structure during the aging process.

Ab Initio Flexible Force Field for Metal-Organic Frameworks Using Dummy Model Coordination Bonds

We present force fields developed from periodic density functional theory (DFT) calculations that can be used in classical molecular simulations to model M-MOF-74 (M = Co, Fe, Mg, Mn, Ni, Zn) and its extended linker analogs. Our force fields are based on cationic dummy models (CDMs). These dummy models simplify the methodology required to tune the parameters and improve the accuracy of the force fields. We used our force fields to compare mechanical properties across the M-MOF-74 series and determine that increasing the size of the linker decreases the framework rigidity. In addition, we applied our force fields to an extended linker analog of Mg-MOF-74 and characterized the free energy of a previously reported deformation pattern in which the one-dimensional hexagonal channels of the framework become irregular. The free energy profiles confirm that the deformation is adsorbate induced and impossible to access solely by a pressure stimulus. On the basis of our results, we conclude that the force fields presented here and others that may be developed using our methodology are transferable across metal-organic framework series that share a metal center topology. Finally, we believe that these force fields have the potential to be adapted for the study of complex problems in MOF chemistry, including defects and crystal growth, that have thus far been beyond the scope of classical molecular simulations.

The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation

Metal-organic frameworks (MOFs) are highly tuneable, extended-network, crystalline, nanoporous materials with applications in gas storage, separations, and sensing. We review how molecular models and simulations of gas adsorption in MOFs have informed the discovery of performant MOFs for methane, hydrogen, and oxygen storage, xenon, carbon dioxide, and chemical warfare agent capture, and xylene enrichment. Particularly, we highlight how large, open databases of MOF crystal structures, post-processed to enable molecular simulations, are a platform for computational materials discovery. We discuss how to orient research efforts to routinise the computational discovery of MOFs for adsorption-based engineering applications.