Multiscale Model for a Metal–Organic Framework: High-Spin Rebound Mechanism in the Reaction of the Oxoiron(IV) Species of Fe-MOF-74

Controlled Growth and Self-Assembly of Multiscale Organic Semiconductor

Currently, organic semiconductors (OSs) are widely used as active components in practical devices related to energy storage and conversion, optoelectronics, catalysis, and biological sensors, etc. To satisfy the actual requirements of different types of devices, chemical structure design and self-assembly process control have been synergistically performed. The morphology and other basic properties of multiscale OS components are governed on a broad scale from nanometers to macroscopic micrometers. Herein, the up-to-date design strategies for fabricating multiscale OSs are comprehensively reviewed. Related representative works are introduced, applications in practical devices are discussed, and future research directions are presented. Design strategies combining the advances in organic synthetic chemistry and supramolecular assembly technology perform an integral role in the development of a new generation of multiscale OSs.

Exploring mechanistic routes for light alkane oxidation with an iron-triazolate metal-organic framework

In this work, we computationally explore the formation and subsequent reactivity of various iron-oxo species in the iron-triazolate framework Fe₂(μ-OH)₂(bbta) (H₂bbta = 1H,5H-benzo(1,2-d:4,5-d')bistriazole) for the catalytic activation of strong C-H bonds. With the direct conversion of methane to methanol as the probe reaction of interest, we use density functional theory (DFT) calculations to evaluate multiple mechanistic pathways in the presence of either N₂O or H₂O₂ oxidants. These calculations reveal that a wide range of transition metal-oxo sites - both terminal and bridging - are plausible in this family of metal-organic frameworks, making it a unique platform for comparing the electronic structure and reactivity of different proposed active site motifs. Based on the DFT calculations, we predict that Fe₂(μ-OH)₂(bbta) would exhibit a relatively low barrier for N₂O activation and energetically favorable formation of an [Fe(O)]²⁺ species that is capable of oxidizing C-H bonds. In contrast, the use of H₂O₂ as the oxidant is predicted to yield an assortment of bridging iron-oxo sites that are less reactive. We also find that abstracting oxo ligands can exhibit a complex mixture of both positive and negative spin density, which may have broader implications for relating the degree of radical character to catalytic activity. In general, we consider the coordinatively unsaturated iron sites to be promising for oxidation catalysis, and we provide several recommendations on how to further tune the catalytic properties of this family of metal-triazolate frameworks.

Efficiently Computing Excitations of Complex Systems: Linear-Scaling Time-Dependent Embedded Mean-Field Theory in Implicit Solvent

Quantum embedding schemes have the potential to significantly reduce the computational cost of first-principles calculations while maintaining accuracy, particularly for calculations of electronic excitations in complex systems. In this work, I combine time-dependent embedded mean field theory (TD-EMFT) with linear-scaling density functional theory and implicit solvation models, extending previous work within the ONETEP code. This provides a way to perform multilevel calculations of electronic excitations on very large systems, where long-range environmental effects, both quantum and classical in nature, are important. I demonstrate the power of this method by performing simulations on a variety of systems, including a molecular dimer, a chromophore in solution, and a doped molecular crystal. This work paves the way for high accuracy calculations to be performed on large-scale systems that were previously beyond the reach of quantum embedding schemes.

Catalytic properties of the ferryl ion in the solid state: a computational review

This review summarises the last findings in the emerging field of heterogeneous catalytic oxidation of light alkanes by ferryl species supported on solid-state systems such as the conversion of methane into methanol by FeO-MOF74.

Performance of GFN1-xTB for periodic optimization of Metal Organic Frameworks

Tight-binding approaches bridge the gap between force field methods and Density Functional Theory (DFT). Density Functional Tight Binding (DFTB) has been employed for a wide range of systems containing up...

Importance of Lattice Constants in QM/MM Calculations on Metal-Organic Frameworks

Metal-organic frameworks (MOFs) are crystalline materials with novel physical and chemical properties. Computational simulations have become powerful complements to experiment for understanding catalysis in MOFs and developing new MOFs and their applications. However, due to their relatively large and complex structures, MOFs can be burdensome for fully quantum mechanical calculations. A combined quantum mechanical and molecular mechanical (QM/MM) method that combines the accuracy of fully quantum mechanical methods and the efficiency of MM methods is therefore attractive. In this study, we employ a QM/MM method for the study of two classes of chemical process in a MOF: the conversion of reaction intermediates in an Ir-containing borylation catalyst supported on MOF UiO-67 and the diffusion of a diborylated methane molecule in the pristine UiO-67 framework. We compare the QM/MM results with full-quantum mechanical results on large systems to validate the accuracy of the applied QM/MM method. In the first case, we consider a model of the entire system by partitioning it into subsystems that interact covalently, and in the second case the subsystem interaction is mainly steric. We observe that the QM/MM results agree with the full-quantum mechanical results within an average of 4 kcal/mol in the first case with strong electronic interactions and within an average of 3 kcal/mol in the case with only noncovalent interactions. An important lesson learned from the present study is that the quantitative results are very sensitive to the lattice constants predicted by the MM method used in the QM/MM calculations.

Quantum Mechanical Calculations for Biomass Valorization over Metal-Organic Frameworks (MOFs)

Metal-organic framework (MOF) in biomass valorization is a promising technology developed in recent decades. By tailoring both the metal nodes and organic ligands, MOFs exhibit multiple functionalities, which not only extend their applicability in biomass conversion but also increase the complexity of material designs. To address this issue, quantum mechanical simulations have been used to provide mechanistic insights into the catalysis of biomass-derived molecules, which could potentially facilitate the development of novel MOF-based materials for biomass valorization. The aim of this review is to survey recent quantum mechanical simulations on biomass reactions occurring in MOF catalysts, with the emphasis on the studies of the catalytic activity of active sites and the effects of organic ligand and porous structures on the kinetics. Moreover, different model systems and computational methods used for MOF simulations are also surveyed and discussed in this review.

On the limit of proton-coupled electronic doping in a Ti(iv)-containing MOF

Ti^IV-containing metal–organic frameworks are known to accumulate electrons in their conduction bands, accompanied by protons, when irradiated in the presence of alcohols. The archetypal system, MIL-125, was recently shown to reach a limit of 2e⁻ per Ti₈ octomeric node. However, the origin of this limit and the broader applicability of this unique chemistry relies not only on the presence of Ti^IV, but also access to inorganic inner-sphere Lewis basic anions in the MOF nodes. Here, we study the loading of protons and electrons in MIL-125, and assess the thermodynamic limit of doping these materials. We find that the limit is determined by the reduction potential of protons: in high charging regimes the MOF exceeds the H⁺/H₂ potential. Generally, we offer the design principle that inorganic anions in MOF nodes can host adatomic protons, which may stabilize meta-stable low valent transition metals. This approach highlights the unique chemistry afforded by MOFs built from inorganic clusters, and provides one avenue to developing novel catalytic scaffolds for hydrogen evolution and transfer hydrogenation.

Photo-promoted doping of MIL-125 is limited by the potential of MOF-bound protons exceeding the hydrogen evolution reaction.

Unveiling the catalytic potential of the Fe(iv)oxo species for the oxidation of hydrocarbons in the solid state

We have investigated the three steps in the conversion of methane into methanol by Fe(iv)Ooxo species supported in MOF-74. We use ab initio MD and static approximations to predict the reaction barriers using enthalpy ΔH and free energy ΔG.

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.

Application of computational chemistry for adsorption studies on metal–organic frameworks used for carbon capture

Computational chemistry is invaluable in calculating macroscopic and microscopic details of systems application in chemical industries which are involved in carbon capture through precombustion, post-combustion and oxy combustion technologies. This review discusses the role of computational chemistry for adsorption studies of metal–organic frameworks (MOFs) which can be utilized for carbon capture. Principles of quantum mechanics–molecular mechanics are used to devise the electrostatic charges and isotherm parameters on the MOFs. MOFs for carbon capture which can be compatible and which can withstand the severity in chemical industries can be effectively studied using grand canonical Monte Carlo simulation by selecting appropriate force fields. Since flue gases contain a host of other gases in addition to oxides of carbon, capture by MOFs has to be carefully modelled and the software useful for this study are mentioned in this review. The simulated adsorption isotherms should be compared with experimental adsorption isotherms to validate the study. The adsorption model for carbon dioxide adsorption on MOFs is generally reported to be type I reversible isotherm and the kinetics is in good agreement with pseudo-second-order kinetics.

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BN-Doped Graphene and Single-Walled Carbon Nanotubes for the Catalysis of SN2 Reactions: Insights from Density Functional Theory Modeling

The inner space of carbon nanotubes has already been proven to provide a type of confinement, which can dramatically alter the energetics of chemical reactions when compared to the gas phase. Moreover, BN doping can be used to fine-tune electronic properties, which might influence the enthalpy and activation energy of chemical reactions that take place inside their inner space. The energy profile of the prototype Menshutkin S_N2 reaction between ammonia and chloromethane has been analyzed in a variety of carbon-based materials at the DFT (density functional theory) level. Pristine zigzag (9,0) and (12,0) single-walled carbon nanotubes and graphene sheets have been doped with boron and nitrogen at different stoichiometries, namely, BN, BNC, BNC₂, and BNC₄, that resulted in remarkable variations of their catalytic effects. Graphene has revealed to be the support material, which depends less on doping in terms of enthalpy and energy barrier of the reaction. However, when graphene is rolled up into tubular forms, the influence of doping becomes increasingly stronger as the nanotube radius decreases. In the case of BNC₄ doping of (9,0) nanotubes, the activation energy drops 10 kcal/mol when compared to the pristine case, and the reaction became even exothermic by more than 15 kcal/mol.

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.

Electronic structure and reactivity of Fe(iv)oxo species in metal-organic frameworks

We investigate the potential use of Fe(iv)oxo species supported on a metal-organic framework in the catalytic hydroxylation of methane to produce methanol. We use periodic density-functional theory calculations at the 6-31G**/B3LYP level of theory to study the electronic structure and chemical reactivity in the hydrogen abstraction reaction from methane in the presence of Fe(iv)O(oxo) supported on MOF-74. Our results indicate that the Fe(iv)O moiety in MOF-74 is characterised by a highly reactive (quintet) ground-state, with a distance between Fe(iv) and O(oxo) of 1.601 Å, consistent with other high-spin Fe(iv)O inorganic complexes in the gas phase and in aqueous solution. Similar to the latter systems, the highly electrophilic character (and thus the reactivity) of Fe(iv)O in MOF-74 is determined by the presence of a low-lying anti-bonding virtual orbital (3σ*), which acts as an electron acceptor in the early stages of the hydrogen atom abstraction from methane. We estimate an energy barrier for hydrogen abstraction of 50.77 kJ mol-1, which is comparable to the values estimated in other gas-phase and hydrated Fe(iv)O-based complexes with the ability to oxidise methane. Our findings therefore suggest that metal-organic frameworks can provide suitable supports to develop new solid-state catalysts for organic oxidation reactions.

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.

Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms

Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM−MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM−MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM−MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

Computational Design of Functionalized Metal-Organic Framework Nodes for Catalysis

Recent progress in the synthesis and characterization of metal-organic frameworks (MOFs) has opened the door to an increasing number of possible catalytic applications. The great versatility of MOFs creates a large chemical space, whose thorough experimental examination becomes practically impossible. Therefore, computational modeling is a key tool to support, rationalize, and guide experimental efforts. In this outlook we survey the main methodologies employed to model MOFs for catalysis, and we review selected recent studies on the functionalization of their nodes. We pay special attention to catalytic applications involving natural gas conversion.

Combined quantum mechanical and molecular mechanical method for metal–organic frameworks: proton topologies of NU-1000

A force field is presented for NU-1000 and tested by electronically embedded QM/MM calculations, which yield accurate structures and relative energies for various proton topologies.

Ligand field effects on the ground and excited states of reactive FeO2+ species

Multiconfigurational quantum chemical calculations on bare and representative ligated iron oxide dicationic species suggest that weak ligand fields promote more reactive channels, whereas strong ligand fields stabilize the less reactive iron-oxo structure.

Insights into the unprecedented epoxidation mechanism of fumitremorgin B endoperoxidase (FtmOx1) from Aspergillus fumigatus by QM/MM calculations

QM/MM calculations indicate that the quintet of the Fe^IVO complex firstly abstracts the hydrogen from Tyr228 to initiate the reaction, then the generated Tyr228 radical extracts the hydrogen from C₂₁ to form the C₂₁ radical, which binds the second dioxygen to complete the epoxidation.

Ethane C–H bond activation on the Fe(iv)–oxo species in a Zn-based cluster of metal–organic frameworks: a density functional theory study

The generation of a Fe(iv)–oxo complex and its reactivity for C–H bond activation of ethane have been theoretically unraveled.

The mechanism of an asymmetric ring-opening reaction of epoxide with amine catalyzed by a metal–organic framework: insights from combined quantum mechanics and molecular mechanics calculations

QM/MM computations suggest that the asymmetric ring-opening reaction of epoxide with amine is controlled by CH–π interactions between aniline and a naphthol moiety.

Dioxygen binding to Fe-MOF-74: microscopic insights from periodic QM/MM calculations

Accurate MOF-FF parameter sets were determined for the ferrous and ferric forms of an iron-based metal–organic framework (MOF) called Fe-MOF-74. For this purpose, density functional theory (DFT) calculations were applied to truncated cluster models of Fe-MOF-74, and the DFT-calculated geometries and energy derivatives were used for the force-field parameterization. The resultant parameter sets performed remarkably well in reproducing the experimentally determined structure of the MOF. We also performed periodic quantum mechanics (QM) / molecular mechanics (MM) calculations employing a subtractive scheme called ONIOM, with the optimized MOF-FF parameters used for the MM calculations, in an attempt to evaluate the binding energies between O2 and several Fe-MOF-74 variants. The calculated binding energy for Fe-MOF-74 agreed very well with the experimental value, and QM/MM geometry optimization calculations confirmed that the O2-bound complex has a side-on geometry. Our calculations also predicted that, when the two neighboring iron ions around the O2-binding site are replaced with other metal ions (Mg2+, Ni2+, Zn2+, Co2+, or Mn2+), there are noticeable variations in the binding energy, indicating that these substituted metal ions affect the O2 binding indirectly.

How PBDEs Are Transformed into Dihydroxylated and Dioxin Metabolites Catalyzed by the Active Center of Cytochrome P450s: A DFT Study

Predicting metabolism of chemicals and potential toxicities of relevant metabolites remains a vital and difficult task in risk assessment. Recent findings suggested that polybrominated diphenyl ethers (PBDEs) can be transformed into dihydroxylated and dioxin metabolites catalyzed by cytochrome P450 enzymes (CYPs), whereas the mechanisms pertinent to these transformations remain largely unknown. Here, by means of density functional theory (DFT) calculations, we probed the metabolic pathways of 2,2',4,4'-tetraBDE (BDE-47) using the active center model of CYPs (Compound I). Results show that BDE-47 is first oxidized to monohydroxylated products (HO-BDEs), wherein a keto-enol tautomerism is identified for rearrangement of the cyclohexenone intermediate. Dihydroxylation with HO-BDEs as precursors, has a unique phenolic H-abstraction and hydroxyl rebound pathway that is distinct from that for monohydroxylation, which accounts for the absence of epoxides in in vitro studies. Furthermore, we found only dihydroxylated PBDEs with heterophenyl -OH substituents ortho- and meta- to the ether bond serve as precursors for dioxins, which are evolved from aryl biradical coupling of diketone intermediates that are produced from dehydrogenation of the dihydroxylated PBDEs by Compound I. This study may enlighten the development of computational models that afford mechanism-based prediction of the xenobiotic biotransformation catalyzed by CYPs.

Toward the synthesis of more reactive S = 2 non-heme oxoiron(IV) complexes

2003 marked a banner year in the bioinorganic chemistry of mononuclear non-heme iron enzymes. The first non-heme oxoiron(IV) intermediate (called J) was trapped and characterized by Bollinger and Krebs in the catalytic cycle of taurine dioxygenase (TauD), and the first crystal structure of a synthetic non-heme oxoiron(IV) complex was reported by Münck, Nam, and Que. These results stimulated inorganic chemists to synthesize related oxoiron(IV) complexes to shed light on the electronic structures and spectroscopic properties of these novel intermediates and gain mechanistic insights into their function in biology. All of the biological oxoiron(IV) intermediates discovered since 2003 have an S = 2 ground spin state, while over 90% of the 60 or so synthetic oxoiron(IV) complexes reported to date have an S = 1 ground spin state. This difference in electronic structure has fueled an interest to more accurately model these enzymatic intermediates and synthesize S = 2 oxoiron(IV) complexes.

This Account follows up on a previous Account (Acc. Chem. Res. 2007, 40, 493) that provided a perspective on the early developments in this field up to 2007 and details our group’s efforts in the development of synthetic strategies to obtain oxoiron(IV) complexes with an S = 2 ground state. Upon inspection of a qualitative d-orbital splitting diagram for a d⁴ metal–oxo center, it becomes evident that the key to achieving an S = 2 ground state is to decrease the energy gap between the d_x²–y² and d_xy orbitals. Described below are two different synthetic strategies we used to accomplish this goal.

The first strategy took advantage of the realization that the d_x²–y² and d_xy orbitals become degenerate in a C₃-symmetric ligand environment. Thus, by employing bulky tripodal ligands, trigonal-bipyramidal S = 2 oxoiron(IV) complexes were obtained. However, substrate access to the oxoiron(IV) center was hindered by the bulky ligands, and the complexes showed limited ability to cleave substrate C–H bonds. The second strategy entailed introducing weaker-field equatorial ligands in six-coordinate oxoiron(IV) complexes to decrease the d_x²–y²/d_xy energy gap to the point where the S = 2 ground state is favored. These pseudo-octahedral S = 2 oxoiron(IV) complexes exhibit high H-atom transfer reactivity relative to their S = 1 counterparts and shed light on the role that the spin state may play in these reactions. Among these complexes is a highly reactive species that to date represents the closest electronic and functional model of the enzymatic intermediate, TauD-J.

A modelling approach for MOF-encapsulated metal catalysts and application to n-butane oxidation

A surrogate pore mimics the steric constraints provided by a MOF on n-butane in a MOF-encapsulated metal catalyst.