Computational Design of Functionalized Metal-Organic Framework Nodes for Catalysis

Dialing in Catalytic Sites on Metal Organic Framework Nodes: MIL-53(Al) and MIL-68(Al) Probed with Methanol Dehydration Catalysis

Many metal organic frameworks (MOFs) incorporate metal oxide clusters as nodes. Node sites where linkers are missing can be catalytic sites. We now show how to dial in the number and occupancy of such sites in MIL-53 and MIL-68, which incorporate aluminum-oxide-like nodes. The methods involve modulators used in synthesis and postsynthesis reactions to control the modulator-derived groups on these sites. We illustrate the methods using formic acid as a modulator, giving formate ligands on the sites, and these can be removed to leave μ₂-OH groups and open Lewis acid sites. Methanol dehydration was used as a catalytic reaction to probe these sites, with infrared spectra giving evidence of methoxide ligands as reaction intermediates. Control of node surface chemistry opens the door for placement of a variety of ligands on a wide range of metal oxide cluster nodes for dialing in reactivity and catalytic properties of a potentially immense class of structurally well-defined materials.

Too Many Materials and Too Many Applications: An Experimental Problem Waiting for a Computational Solution

Finding the best material for a specific application is the ultimate goal of materials discovery. However, there is also the reverse problem: when experimental groups discover a new material, they would like to know all the possible applications this material would be promising for. Computational modeling can aim to fulfill this expectation, thanks to the sustained growth of computing power and the collective engagement of the scientific community in developing more efficient and accurate workflows for predicting materials' performances. We discuss the impact that reproducibility and automation of the modeling protocols have on the field of gas adsorption in nanoporous crystals. We envision a platform that combines these tools and enables effective matching between promising materials and industrial applications.

Multiple catalytic sites in MOF-based hybrid catalysts for organic reactions

Hybrid catalysis provides an effective pathway to improve the catalytic efficiency and simplify the synthesis operation, but multiple catalytic sites are required. Catalysts with multiple functions based on/derived from metal-organic frameworks (MOFs) have received growing attention in organic synthesis due to their wide variety and outstanding designability. This review provides an overview of significant advances in the field of organic reactions by MOF-based hybrid catalysts with emphasis on multiple catalytic sites and their synergies, including inherent sites on host frameworks, sites of MOF composites and metal sites in/on MOF-derived hybrid catalysts.

The Surface Chemistry of Metal Oxide Clusters: From Metal-Organic Frameworks to Minerals

Many metal-organic frameworks (MOFs) incorporate nodes that are small metal oxide clusters. Some of these MOFs are stable at high temperatures, offering good prospects as catalysts-prospects that focus attention on their defect sites and reactivities-all part of a broader subject: the surface chemistry of metal oxide clusters, illustrated here for MOF nodes and for polyoxocations and polyoxoanions. Ligands on MOF defect sites form during synthesis and are central to the understanding and control of MOF reactivity. Reactions of alcohols are illustrative probes of Zr₆O₈ node defects in UiO-66, characterized by the interconversions of formate, methoxy, hydroxy, and linker carboxylate ligands and by catalysis of alcohol dehydration reactions. We posit that new reactivities of MOF nodes will emerge from incorporation of a wide range of groups on their surfaces and from targeted substitutions of metals within them.

Standard Practices of Reticular Chemistry

Reticular chemistry is a growing field of science with a multitude of practitioners with diverse frames of thinking, making the need for standard practices and quality indicators ever more compelling.

Sensing mechanism elucidation of a europium(III) metal-organic framework selective to aniline: A theoretical insight by means of multiconfigurational calculations

A theoretical procedure, via quantum chemical computations, to elucidate the detection principle of the turn-off luminescence mechanism of an Eu-based Metal-Organic Framework sensor (Eu-MOF) selective to aniline, is accomplished. The energy transfer channels that take place in the Eu-MOF, as well as understanding the luminescence quenching by aniline, were investigated using the well-known and accurate multiconfigurational ab initio methods along with sTD-DFT. Based on multireference calculations, the sensitization pathway from the ligand (antenna) to the lanthanide was assessed in detail, that is, intersystem crossing (ISC) from the S₁ to the T₁ state of the ligand, with subsequent energy transfer to the ⁵ D₀ state of Eu³⁺ . Finally, emission from the ⁵ D₀ state to the ⁷ F_J state is clearly evidenced. Otherwise, the interaction of Eu-MOF with aniline produces a mixture of the electronic states of both systems, where molecular orbitals on aniline now appear in the active space. Consequently, a stabilization of the T₁ state of the antenna is observed, blocking the energy transfer to the ⁵ D₀ state of Eu³⁺ , leading to a non-emissive deactivation. Finally, in this paper, it was demonstrated that the host-guest interactions, which are not taken frequently into account by previous reports, and the employment of high-level theoretical approaches are imperative to raise new concepts that explain the sensing mechanism associated to chemical sensors.

Electronic Structure Modeling of Metal-Organic Frameworks

Owing to their molecular building blocks, yet highly crystalline nature, metal-organic frameworks (MOFs) sit at the interface between molecule and material. Their diverse structures and compositions enable them to be useful materials as catalysts in heterogeneous reactions, electrical conductors in energy storage and transfer applications, chromophores in photoenabled chemical transformations, and beyond. In all cases, density functional theory (DFT) and higher-level methods for electronic structure determination provide valuable quantitative information about the electronic properties that underpin the functions of these frameworks. However, there are only two general modeling approaches in conventional electronic structure software packages: those that treat materials as extended, periodic solids, and those that treat materials as discrete molecules. Each approach has features and benefits; both have been widely employed to understand the emergent chemistry that arises from the formation of the metal-organic interface. This Review canvases these approaches to date, with emphasis placed on the application of electronic structure theory to explore reactivity and electron transfer using periodic, molecular, and embedded models. This includes (i) computational chemistry considerations such as how functional, k-grid, and other model variables are selected to enable insights into MOF properties, (ii) extended solid models that treat MOFs as materials rather than molecules, (iii) the mechanics of cluster extraction and subsequent chemistry enabled by these molecular models, (iv) catalytic studies using both solids and clusters thereof, and (v) embedded, mixed-method approaches, which simulate a fraction of the material using one level of theory and the remainder of the material using another dissimilar theoretical implementation.

Targeted classification of metal-organic frameworks in the Cambridge structural database (CSD)

Large-scale targeted exploration of metal–organic frameworks (MOFs) with characteristics such as specific surface chemistry or metal-cluster family has not been investigated so far.

Large-scale targeted exploration of metal–organic frameworks (MOFs) with characteristics such as specific surface chemistry or metal-cluster family has not been investigated so far. These definitions are particularly important because they can define the way MOFs interact with specific molecules (e.g. their hydrophilic/phobic character) or their physicochemical stability. We report here the development of algorithms to break down the overarching family of MOFs into a number of subgroups according to some of their key chemical and physical features. Available within the Cambridge Crystallographic Data Centre's (CCDC) software, we introduce new approaches to allow researchers to browse and efficiently look for targeted MOF families based on some of the most well-known secondary building units. We then classify them in terms of their crystalline properties: metal-cluster, network and pore dimensionality, surface chemistry (i.e. functional groups) and chirality. This dynamic database and family of algorithms allow experimentalists and computational users to benefit from the developed criteria to look for specific classes of MOFs but also enable users – and encourage them – to develop additional MOF queries based on desired chemistries. These tools are backed-up by an interactive web-based data explorer containing all the data obtained. We also demonstrate the usefulness of these tools with a high-throughput screening for hydrogen storage at room temperature. This toolbox, integrated in the CCDC software, will guide future exploration of MOFs and similar materials, as well as their design and development for an ever-increasing range of potential applications.

Metal-Organic Framework Nanoparticles Induce Pyroptosis in Cells Controlled by the Extracellular pH

Ion homeostasis is essential for cellular survival, and elevated concentrations of specific ions are used to start distinct forms of programmed cell death. However, investigating the influence of certain ions on cells in a controlled way has been hampered due to the tight regulation of ion import by cells. Here, it is shown that lipid-coated iron-based metal-organic framework nanoparticles are able to deliver and release high amounts of iron ions into cells. While high concentrations of iron often trigger ferroptosis, here, the released iron induces pyroptosis, a form of cell death involving the immune system. The iron release occurs only in slightly acidic extracellular environments restricting cell death to cells in acidic microenvironments and allowing for external control. The release mechanism is based on endocytosis facilitated by the lipid-coating followed by degradation of the nanoparticle in the lysosome via cysteine-mediated reduction, which is enhanced in slightly acidic extracellular environment. Thus, a new functionality of hybrid nanoparticles is demonstrated, which uses their nanoarchitecture to facilitate controlled ion delivery into cells. Based on the selectivity for acidic microenvironments, the described nanoparticles may also be used for immunotherapy: the nanoparticles may directly affect the primary tumor and the induced pyroptosis activates the immune system.

Metal-Organic Framework-Based Catalysts with Single Metal Sites

Metal-organic frameworks (MOFs) are a class of distinctive porous crystalline materials constructed by metal ions/clusters and organic linkers. Owing to their structural diversity, functional adjustability, and high surface area, different types of MOF-based single metal sites are well exploited, including coordinately unsaturated metal sites from metal nodes and metallolinkers, as well as active metal species immobilized to MOFs. Furthermore, controllable thermal transformation of MOFs can upgrade them to nanomaterials functionalized with active single-atom catalysts (SACs). These unique features of MOFs and their derivatives enable them to serve as a highly versatile platform for catalysis, which has actually been becoming a rapidly developing interdisciplinary research area. In this review, we overview the recent developments of catalysis at single metal sites in MOF-based materials with emphasis on their structures and applications for thermocatalysis, electrocatalysis, and photocatalysis. We also compare the results and summarize the major insights gained from the works in this review, providing the challenges and prospects in this emerging field.

Bimetallic metal-organic frameworks and their derivatives

Bimetallic metal-organic frameworks (MOFs) have two different metal ions in the inorganic nodes. According to the metal distribution, the architecture of bimetallic MOFs can be classified into two main categories namely solid solution and core-shell structures. Various strategies have been developed to prepare bimetallic MOFs with controlled compositions and structures. Bimetallic MOFs show a synergistic effect and enhanced properties compared to their monometallic counterparts and have found many applications in the fields of gas adsorption, catalysis, energy storage and conversion, and luminescence sensing. Moreover, bimetallic MOFs can serve as excellent precursors/templates for the synthesis of functional nanomaterials with controlled sizes, compositions, and structures. Bimetallic MOF derivatives show exposed active sites, good stability and conductivity, enabling them to extend their applications to the catalysis of more challenging reactions and electrochemical energy storage and conversion. This review provides an overview of the significant advances in the development of bimetallic MOFs and their derivatives with special emphases on their preparation and applications.

Insights into Catalytic Gas-Phase Hydrolysis of Organophosphate Chemical Warfare Agents by MOF-Supported Bimetallic Metal-Oxo Clusters

Zirconium-based metal-organic frameworks (Zr-MOFs) have been reported to be efficient catalysts for the hydrolysis of organophosphate chemical warfare agents (CWAs) in buffered solutions. However, for the gas-phase reaction, which is more relevant to the situation in a battlefield gas mask application, the kinetics of Zr-MOF catalysts may be severely hindered by strong product inhibition. To improve the catalytic performance, we computationally screened a series of synthetically accessible Zr-MOF-supported bimetallic metal-oxo clusters in which the metal-oxygen-metal active motif is preserved, aiming to find catalysts that have lower binding affinities to the hydrolysis product. For the promising catalyst Al₂O₂(OH)₂@NU-1000 identified from the screening using density functional theory, we mapped out the full reaction pathway of gas-phase dimethyl p-nitrophenolphosphate (DMNP) hydrolysis and analyzed the free energy profile as well as the turnover frequency (TOF). We found that the catalytic mechanism on the new catalyst is slightly different from the one on NU-1000, which also led to a different TOF-limiting step. Additional factors that can affect the overall catalytic performance in practical application, such as the amount of ambient moisture and the existence of acid gases that may poison the catalyst, have also been evaluated.

Improved Predictive Tools for Structural Properties of Metal-Organic Frameworks

The accurate determination of structural parameters is necessary to understand the electronic and magnetic properties of metal-organic frameworks (MOFs) and is a first step toward accurate calculations of electronic structure and function for separations and catalysis. Theoretical structural determination of metal-organic frameworks is particularly challenging because they involve ionic, covalent, and noncovalent interactions, which must be treated in a balanced fashion. Here, we apply a diverse group of local exchange-correlation functionals (PBE, PBEsol, PBE-D2, PBE-D3, vdW-DF2, SOGGA, MN15-L, revM06-L, SCAN, and revTPSS) to a broad test set of MOFs to seek the most accurate functionals to study various structural aspects of porous solids, in particular to study lattice constants, unit cell volume, two types of pore size characteristics, bond lengths, bond angles, and torsional angles). The recently developed meta functionals revM06-L and SCAN, without adding any molecular mechanics terms, are able to predict more accurate structures than previously recommended functionals, both those without molecular mechanics terms (PBE, PBEsol, vdW-DF2, and revTPSS) and those with them (PBE-D2 and PBE-D3). To provide a broader test, these two functionals are also tested for lattice constants and band gaps of unary, binary, and ternary semiconductors.

Hollow waxberry-like cobalt–nickel oxide/S,N-codoped carbon nanospheres as a trifunctional electrocatalyst for OER, ORR, and HER

The catalyst is assembled from small nanoparticles in the shape of a bayberry, and exhibits superior trifunctional electrocatalytic activity.

A new approach to the mechanism for the acetalization of benzaldehyde over MOF catalysts

The benzaldehyde acetalization catalyzed by UiO-66 and UiO-66F, was carried out in a batch-type reactor at room temperature and atmospheric pressure, and the full kinetic study was performed using the Langmuir–Hinshelwood and Eley–Rideal models.

Modeling and Simulation of Crystallization of Metal–Organic Frameworks

Metal–organic frameworks (MOFs) are the porous, crystalline structures made of metal–ligands and organic linkers that have applications in gas storage, gas separation, and catalysis. Several experimental and computational tools have been developed over the past decade to investigate the performance of MOFs for such applications. However, the experimental synthesis of MOFs is still empirical and requires trial and error to produce desired structures, which is due to a limited understanding of the mechanism and factors affecting the crystallization of MOFs. Here, we show for the first time a comprehensive kinetic model coupled with population balance model to elucidate the mechanism of MOF synthesis and to estimate size distribution of MOFs growing in a solution of metal–ligand and organic linker. The oligomerization reactions involving metal–ligand and organic linker produce secondary building units (SBUs), which then aggregate slowly to yield MOFs. The formation of secondary building units (SBUs) and their evolution into MOFs are modeled using detailed kinetic rate equations and population balance equations, respectively. The effect of rate constants, aggregation frequency, the concentration of organic linkers, and concurrent crystallization of organic linkers are studied on the dynamics of SBU and MOF formation. The results qualitatively explain the longer timescales involved in the synthesis of MOF. The fundamental insights gained from modeling and simulation analysis can be used to optimize the operating conditions for a higher yield of MOF crystals.

Multilink F* Method for Combined Quantum Mechanical and Molecular Mechanical Calculations of Complex Systems

Combined quantum mechanical and molecular mechanical (QM/MM) studies on catalysis in metal-organic frameworks (MOFs) are relatively undeveloped in contrast to the wide use of QM/MM for enzyme catalysis. One reason is that the currently available methods for treating QM-MM boundaries are not fully compatible with the combination of features in MOFs, namely, their high connectivity, their polar bonds (e.g., metal-oxygen bonds), and their potential boundary atoms with high partial atomic charges. The treatment of polar bonds can be improved by using tuned link atoms, but both the widely used H link atom method and the F* link atom method provide limited options in placing the QM-MM boundary in MOFs and other covalently bonded solids, which seriously reduces the efficiency of QM/MM calculations. Here, we propose a generalized version of the F* link atom method with greater flexibility for the placement of the QM-MM boundary in MOFs and with a practical scheme for tuning. The new method, called the multilink F* method, allows a large part of an inorganic node of a MOF to be partitioned into the MM subsystem to increase the efficiency. Our validation calculations on dimerization of ethylene to 1-butene by a nickel catalyst supported on a MOF show that the overall performance of QM/MM calculations with the multilink F* method is excellent for energies, geometries, and partial atomic charges.

Selective Methane Oxidation to Methanol on Cu-Oxo Dimers Stabilized by Zirconia Nodes of an NU-1000 Metal-Organic Framework

Mononuclear and dinuclear copper species were synthesized at the nodes of an NU-1000 metal-organic framework (MOF) via cation exchange and subsequent oxidation at 200 °C in oxygen. Copper-exchanged MOFs are active for selectively converting methane to methanol at 150-200 °C. At 150 °C and 1 bar methane, approximately a third of the copper centers are involved in converting methane to methanol. Methanol productivity increased by 3-4-fold and selectivity increased from 70% to 90% by increasing the methane pressure from 1 to 40 bar. Density functional theory showed that reaction pathways on various copper sites are able to convert methane to methanol, the copper oxyl sites with much lower free energies of activation. Combining studies of the stoichiometric activity with characterization by in situ X-ray absorption spectroscopy and density functional theory, we conclude that dehydrated dinuclear copper oxyl sites formed after activation at 200 °C are responsible for the activity.

Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities

Computational chemistry provides a versatile toolbox for studying mechanistic details of catalytic reactions and holds promise to deliver practical strategies to enable the rational in silico catalyst design. The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the standard computational strategies. In this review, we discuss the challenges and capabilities of modern electronic structure methods for studying the reaction mechanisms promoted by 3d transition metal molecular catalysts. Particular focus will be placed on the ways of addressing the multiconfigurational problem in electronic structure calculations and the role of expert bias in the practical utilization of the available methods. The development of density functionals designed to address transition metals is also discussed. Special emphasis is placed on the methods that account for solvation effects and the multicomponent nature of practical catalytic systems. This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals. Cases that involve noninnocent ligands, multicomponent reaction systems, metal-ligand and metal-metal cooperativity, as well as modeling complex catalytic systems such as metal-organic frameworks are presented. Conventionally, computational studies on catalytic mechanisms are heavily dependent on the chemical intuition and expert input of the researcher. Recent developments in advanced automated methods for reaction path analysis hold promise for eliminating such human-bias from computational catalysis studies. A brief overview of these approaches is presented in the final section of the review. The paper is closed with general concluding remarks.

Multiconfigurational Self-Consistent Field Theory with Density Matrix Embedding: The Localized Active Space Self-Consistent Field Method

Density matrix embedding theory (DMET) is a fully quantum-mechanical embedding method which shows great promise as a method of defeating the inherent exponential cost scaling of multiconfigurational wave function-based calculations by breaking large systems into smaller, coupled subsystems. However, we recently [ Pham et al. J. Chem. Theory Comput. 2018 , 14 , 1960 .] encountered evidence that the approximate single-determinantal bath picture inherent to DMET is sometimes problematic when the complete active space self-consistent field (CASSCF) is used as a solver and the method is applied to realistic models of strongly correlated molecules. Here, we show this problem can be defeated by generalizing DMET to use a multiconfigurational wave function as a bath without sacrificing practically attractive features of DMET, such as a second-quantization form of the embedded subsystem Hamiltonian, by dividing the active space into unentangled active subspaces each localized to one fragment. We introduce the term localized active space (LAS) to refer to this kind of wave function. The LAS bath wave function can be obtained by the DMET algorithm itself in a self-consistent manner, and we refer to this approach, introduced here for the first time, as the localized active space self-consistent field (LASSCF) method. LASSCF exploits a modified DMET algorithm, but it is a variational wave function method; it does not require DMET's ambiguous error function minimization, and it reproduces full-molecule CASSCF in cases where comparable DMET calculations fail. Our results for test calculations on the nitrogen double-bond dissociation potential energy curves of several diazene molecules suggest that LASSCF can be an appropriate starting point for a perturbative treatment. Outside of the context of embedding, the LAS wave function is inherently an attractive alternative to a CAS wave function because of its favorable cost scaling, which is exponential only with respect to the size of individual fragment active subspaces, rather than the whole active space of the entire system.

Zirconium-Based Metal-Organic Frameworks for the Removal of Protein-Bound Uremic Toxin from Human Serum Albumin

Uremic toxins often accumulate in patients with compromised kidney function, like those with chronic kidney disease (CKD), leading to major clinical complications including serious illness and death. Sufficient removal of these toxins from the blood increases the efficacy of hemodialysis, as well as the survival rate, in CKD patients. Understanding the interactions between an adsorbent and the uremic toxins is critical for designing effective materials to remove these toxic compounds. Herein, we study the adsorption behavior of the uremic toxins, p-cresyl sulfate, indoxyl sulfate, and hippuric acid, in a series of zirconium-based metal-organic frameworks (MOFs). The pyrene-based MOF, NU-1000, offers the highest toxin removal efficiency of all the MOFs in this study. Other Zr-based MOFs possessing comparable surface areas and pore sizes to NU-1000 while lacking an extended aromatic system have much lower toxin removal efficiency. From single-crystal X-ray diffraction analyses assisted by density functional theory calculations, we determined that the high adsorption capacity of NU-1000 can be attributed to the highly hydrophobic adsorption sites sandwiched by two pyrene linkers and the hydroxyls and water molecules on the Zr₆ nodes, which are capable of hydrogen bonding with polar functional groups of guest molecules. Further, NU-1000 almost completely removes p-cresyl sulfate from human serum albumin, a protein that these uremic toxins bind to in the body. These results offer design principles for potential MOFs candidates for uremic toxin removal.

The effects of active site and support on hydrogen elimination over transition-metal-functionalized yttria-decorated metal–organic frameworks

Transition-metal catalysts supported on a metal–organic framework have been screened computationally to reveal the best catalytic candidates for hydrogen elimination reactions, which are critical in many catalytic cycles.

Mixed-metal metal–organic frameworks

Mixed-metal MOFs contain at least 2 different metal ions presenting promising potential in heterogeneous catalysis, gas sorption/separation, luminescence and sensing.