Simulation of Metal–Ligand Self-Assembly into Spherical Complex M6L8

Picking the lock of coordination cage catalysis

The design principles of metallo-organic assembly reactions have facilitated access to hundreds of coordination cages of varying size and shape. Many of these assemblies possess a well-defined cavity capable of hosting a guest, pictorially mimicking the action of a substrate binding to the active site of an enzyme. While there are now a growing collection of coordination cages that show highly proficient catalysis, exhibiting both excellent activity and efficient turnover, this number is still small compared to the vast library of metal-organic structures that are known. In this review, we will attempt to unpick and discuss the key features that make an effective coordination cage catalyst, linking structure to activity (and selectivity) using lessons learnt from both experimental and computational analysis of the most notable exemplars. We will also provide an outlook for this area, reasoning why coordination cages have the potential to become the gold-standard in (synthetic) non-covalent catalysis.

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.

Design of self-assembling mesoscopic Goldberg polyhedra

Palladium ions complexed with nonlinear bidentate ligands have been shown to form hollow, spherical shells with high symmetries. We show that such structures can be reproduced using model anisotropic mesoscale building blocks featuring excluded volume and long-range ionic interactions. A linear building block with a central charged particle, in combination with a bent 'ligand' particle with opposite charges at the ends is sufficient to drive the system towards planar coordination, and the charge ratio determines the coordination number. Similar to the molecular systems, the bend in the 'ligand' particle determines the curvature of the shells that these building blocks prefer. Besides reproducing exotic structures such as M₃₀L₆₀ and M₄₈L₉₆ tetravalent Goldberg polyhedra, we identify highly cooperative single transition state rearrangements between low-energy competing structures as well, corresponding to rotatory motions of a planar subunit within the spherical shell.

Computational Modeling of Supramolecular Metallo-organic Cages-Challenges and Opportunities

Self-assembled metallo-organic cages have emerged as promising biomimetic platforms that can encapsulate whole substrates akin to an enzyme active site. Extensive experimental work has enabled access to a variety of structures, with a few notable examples showing catalytic behavior. However, computational investigations of metallo-organic cages are scarce, not least due to the challenges associated with their modeling and the lack of accurate and efficient protocols to evaluate these systems. In this review, we discuss key molecular principles governing the design of functional metallo-organic cages, from the assembly of building blocks through binding and catalysis. For each of these processes, computational protocols will be reviewed, considering their inherent strengths and weaknesses. We will demonstrate that while each approach may have its own specific pitfalls, they can be a powerful tool for rationalizing experimental observables and to guide synthetic efforts. To illustrate this point, we present several examples where modeling has helped to elucidate fundamental principles behind molecular recognition and reactivity. We highlight the importance of combining computational and experimental efforts to speed up supramolecular catalyst design while reducing time and resources.

Conformation-Selective Self-Assembly of Pd6 Trifacial Molecular Barrels Using a Tetrapyridyl Ligand

A conformationally flexible tetrapyridyl ligand L was assembled separately with three cis-blocked 90° Pd^II acceptors (M1, M2, and M3) containing different blocking diamines. Surprisingly, different conformations of the donor L were arrested by the acceptors depending on the nature of the blocking amine, leading to the formation of isomeric Pd₆ barrels (B1, B2, and B3). B2 and B3 with larger windows have been used to encapsulate polyaromatic hydrocarbons.

Unlocking the computational design of metal-organic cages

Metal-organic cages are macrocyclic structures that can possess an intrinsic void that can hold molecules for encapsulation, adsorption, sensing, and catalysis applications. As metal-organic cages may be comprised from nearly any combination of organic and metal-containing components, cages can form with diverse shapes and sizes, allowing for tuning toward targeted properties. Therefore, their near-infinite design space is almost impossible to explore through experimentation alone and computational design can play a crucial role in exploring new systems. Although high-throughput computational design and screening workflows have long been known as powerful tools in drug and materials discovery, their application in exploring metal-organic cages is more recent. We show examples of structure prediction and host-guest/catalytic property evaluation of metal-organic cages. These examples are facilitated by advances in methods that handle metal-containing systems with improved accuracy and are the beginning of the development of automated cage design workflows. We finally outline a scope for how high-throughput computational methods can assist and drive experimental decisions as the field pushes toward functional and complex metal-organic cages. In particular, we highlight the importance of considering realistic, flexible systems.

Improved Recovery and Selectivity of Lanthanide-Ion-Binding Cyclic Peptide Hosts by Changing the Position of Acidic Amino Acids

The development of an effective host molecule to separate lanthanide (Ln) ions and a method for predicting its guest recognition/self-assembly behavior based on primary chemical structures are highly sought after in both academia and industry. Herein, we report the improvement of one-pot Ln ion recovery and a performance prediction method for four new cyclic peptide hosts that differ in the position of acidic amino acids. These cyclic peptide hosts could recognize Ln3+ directly through a 1:1 complexation–precipitation process and exhibited high Lu3+ selectivity in spite of similar ion size and electronegativity when the positions of the acidic amino acids were changed. This unpredictable selectivity was explained by considering the dipole moment, lowest unoccupied molecular orbital, and cohesion energy. In addition, a semi-empirical function using these parameters was proposed for screening the sequence and estimating the isolated yields without long-time molecular dynamics calculations. The insights obtained from this study can be employed for the development of high-performance peptides for the selective recovery of Ln and other metal ions, as well as for the construction of diverse supramolecular recognition systems.

Surface Functionality-Regulated and Entropy-Driven Thermodynamics of the Formation of Coordination Nanocages

Coordination nanocages (CNCs) are under intense research in nanoscience and supramolecular chemistry for their enriched surface functionalities and micro-porosity; however, the understanding of their formation mechanism is still poor due to the difficulty in probing their solution structures. Herein, the CNC formation process from the coordination complexation of the macromolecular isophthalic acid (IPA) ligand and Cu²⁺ is studied via isothermal titration calorimetry, and its entropy-driven feature is revealed to be originated from the collapse of solvation layers of the assembly units. The CNC formation is thermodynamically less favored with smaller binding constants when the sizes of macromolecular IPA ligands are larger, which originated from the space crowding of macromolecules of the ligands on CNC surfaces and the resulting entropy loss of polymer chain conformations. Meanwhile, the chemical equilibrium of CNC formation can be tuned upon altering the Cu²⁺/IPA ratio, and the yield of CNCs, suggested from size exclusion chromatography studies, decreases when excessive Cu²⁺ is applied, providing guidelines for CNC design and synthesis.

Unexpected Self-Assembly Pathway to a Pd(II) Coordination Square-Based Pyramid and Its Preferential Formation beyond the Boltzmann Distribution

Experimental and theoretical investigations of the self-assembly process of a Pd(II) coordination M₆L₄ square-based pyramid (SP) were conducted. It was found that the probable self-assembly pathway, in which the dimerization of M₂L₂ with two M leads to SP, expected from the connectivity of the building blocks is not a major self-assembly pathway to the M₆L₄ SP. Whether the M₆L₄ SP is assembled or M₂L₂ is trapped is determined by an inter- or intramolecular reaction in a chain-like M₂L₂X, where X is a leaving ligand. The kinetically trapped state where the M₆L₄ SP is produced from M₂L₂ beyond the Boltzmann distribution was realized by a concentration-induced process and was kept for at least 2 months at 298 K.

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.

Unique Dynamics of Hierarchical Constrained Macromolecular Ligands on Coordination Nanocage Surface Promotes Facile and Precise Assembly of Polymers

With access to the solution structures of nanocomposites of coordination nanocages (CNCs) via scattering and chromatography techniques, their mysterious solution dynamics have been, for the first time, resolved, and interestingly, the surface macromolecules can be substituted by extra free macromolecules in solutions. Obvious exchange of macromolecules can be observed in the solution mixtures of CNC nanocomposites at high temperatures, revising the understanding of the dynamics of CNC nanocomposites. Being distinct from nanocomposites of a simple coordination complex, the quantified solution dynamics of CNC nanocomposites indicates a typical logarithmic time dependence with the dissociation of surface macromolecules as the thermodynamically limiting step, suggesting strongly coupled and hierarchically constrained dynamics among the surface macromolecules. Their dynamics can be activated only upon application of high temperature or selected solvents, and therefore, the rational design of polymer assemblies, for example, hybrid-arm star polymers with precisely controlled compositions and reprocessable, robust CNC-cross-linked supramolecular polymer networks, is facilitated.

Revealing Thermodynamics and Kinetics of Lipid Self-Assembly by Markov State Model Analysis

Self-assembly is ubiquitous in the realm of biology and has become an elegant bottom-up approach to fabricate new materials. Although molecular dynamics (MD) simulations can complement experiments by providing the missing atomic details, it still remains a grand challenge to reveal the thermodynamic and kinetic information on a self-assembly system. In this work, we demonstrate for the first time that the Markov state model analysis can be used to delineate the variation of free energy during the self-assembly process of a typical amphiphilic lipid dipalmitoyl-phosphatidylcholine (DPPC). Free energy profiles against the solvent-accessible surface area and the root-mean-square deviation have been derived from extensive MD results of more than five hundred trajectories, which identified a metastable crossing-cylinder (CC) state and a transition state of the distorted bilayer with a free energy barrier of ∼0.02 kJ mol^-1 per DPPC lipid, clarifying a long-standing speculation for 20 years that there exists a free energy barrier during lipid self-assembly. Our simulations also unearth two mesophase structures at the early stage of self-assembly, discovering two assembling pathways to the CC state that have never been reported before. Further thermodynamic analysis derives the contributions from the enthalpy and the entropy terms to the free energy, demonstrating the critical role played by the enthalpy-entropy compensation. Our strategy opens the door to quantitatively understand the self-assembly processes in general and provides new opportunities for identifying common thermodynamic and kinetic patterns in different self-assembly systems and inspiring new ideas for experiments. It may also contribute to the refinement of force field parameters of various self-assembly systems.

Topological prediction of palladium coordination cages

The preparation of functionalized, heteroleptic Pd_xL_2x coordination cages is desirable for catalytic and optoelectronic applications. Current rational design of these cages uses the angle between metal-binding (∠B) sites of the di(pyridyl)arene linker to predict the topology of homoleptic cages obtained via non-covalent chemistry. However, this model neglects the contributions of steric bulk between the pyridyl residues—a prerequisite for endohedrally functionalized cages, and fails to rationalize heteroleptic cages. We describe a classical mechanics (CM) approach to predict the topological outcomes of Pd_xL_2x coordination cage formation with arbitrary linker combinations, accounting for the electronic effects of coordination and steric effects of linker structure. Initial validation of our CM method with reported homoleptic Pd₁₂LFu₂₄ (LFu = 2,5-bis(pyridyl)furan) assembly suggested the formation of a minor topology Pd₁₅LFu₃₀, identified experimentally by mass spectrometry. Application to heteroleptic cage systems employing mixtures of LFu (∠B = 127°) and its thiophene congener LTh (∠B = 149° ∠B_exp = 152.4°) enabled prediction of Pd₁₂L₂₄ and Pd₂₄L₄₈ coordination cages formation, reliably emulating experimental data. Finally, the topological outcome for exohedrally (LEx) and endohedrally (LEn) functionalized heteroleptic Pd_xL_2x coordination cages were predicted to assess the effect of steric bulk on both topological outcomes and coordination cage yields, with comparisons drawn to experimental data.

A molecular mechanics approach enables the accurate prediction of polyhedral topology for homoleptic and heteroleptic palladium M_xL_2x coordination cages, allowing for new insight and design when considering endo- and exo-hedral functionalization.

Improved Description of a Coordinate Bond in the ReaxFF Reactive Force Field

To improve the description of a coordinate bond of the reactive force field (ReaxFF), we have developed ReaxFF_coord by explicitly incorporating the coordinate bond contribution, E_coord, into the original ReaxFF ( Chenoweth et al. J. Phys. Chem. A 2008 , 112 , 1040 - 1053 ), in which the auxiliary functions are newly suggested to describe the plug-in behavior of lone-pair electrons from a donor atom to a vacant orbital of an acceptor atom. To validate the developed ReaxFF_coord, we tested it in various systems, including a representative coordinate bond-containing molecule, namely, carbon monoxide or ammonia borane. Although the fitting abilities of the ReaxFF_coord and original ReaxFF are similar, their molecular dynamics (MD) simulations are significantly different, where MD simulations employing ReaxFF_coord provide more realistic dynamic behaviors of atoms. It is expected that the ReaxFF_coord will significantly help ReaxFF to successfully extend its applicability to the material and biological systems, including coordinate bonds in organometallic systems.

Early stages of phase selection in MOF formation observed in molecular Monte Carlo simulations

Metal–organic frameworks (MOF) comprising metal nodes bridged by organic linkers show great promise because of their guest-specific gas sorption, separation, drug-delivery, and catalytic properties. The selection of metal node, organic linker, and synthesis conditions in principle offers engineered control over both structure and function. For MOFs to realise their potential and to become more than just promising materials, a degree of predictability in the synthesis and a better understanding of the self-assembly or initial growth processes is of paramount importance. Using cobalt succinate, a MOF that exhibits a variety of phases depending on synthesis temperature and ligand to metal ratio, as proof of concept, we present a molecular Monte Carlo approach that allows us to simulate the early stage of MOF assembly. We introduce a new Contact Cluster Monte Carlo (CCMC) algorithm which uses a system of overlapping “virtual sites” to represent the coordination environment of the cobalt and both metal–metal and metal–ligand associations. Our simulations capture the experimentally observed synthesis phase distinction in cobalt succinate at 348 K. To the best of our knowledge this is the first case in which the formation of different MOF phases as a function of composition is captured by unbiased molecular simulations. The CCMC algorithm is equally applicable to any system in which short-range attractive interactions are a dominant feature, including hydrogen-bonding networks, metal–ligand coordination networks, or the assembly of particles with “sticky” patches, such as colloidal systems or the formation of protein complexes.

Clusters produced in simulations of MOF assembly at metal : ligand ratios of (a) 5 : 1 and (b) 1 : 1 with identical interaction potentials.

A kinetics study of ligand substitution reaction on dinuclear platinum complexes: Stochastic versus deterministic approach

The kinetics on a basic ligand substitution reaction on dinuclear platinum complexes [Pt(PEt₃ )₂ PhPt(PEt₃ )₂ ]²⁺ and [Pt(PEt₃ )₂ PhCOPhPt(PEt₃ )₂ ]²⁺ , with the ligands pyridine and 3-chloropyridine, is studied. This is a fundamental step in a self-assembly, and the time evolution has been observed with a new experimental technique, QASAP (quantitative analysis of self-assembly process), which is recently developed by Hiraoka's group. As a result of numerical calculations based on master equation, we succeed in specifying the reaction rate constants with a simple reaction model. In addition, the time evolutions of all the intermediate components produced and consumed in chemical reaction are revealed, including those unobserved in the experiments. The convergence behavior of the existence ratios of specific chemical species calculated with the stochastic algorithm method is compared with those obtained from deterministic formalism based on rate equations, revealing a clear dependence on the number of constituent molecules. © 2018 Wiley Periodicals, Inc.

Recent developments in the construction of metallacycle/metallacage-cored supramolecular polymers via hierarchical self-assembly

Supramolecular polymers have received considerable attention during the last few decades due to their scientific value in polymer chemistry and profound implications for future developments of advanced materials. Discrete supramolecular coordination complexes (SCCs) with well-defined size, shape, and geometry have been widely employed to construct hierarchical systems by coordination-driven self-assembly with the spontaneous formation of metal-ligand bonds, which results in the formation of well-defined two-dimensional (2D) metallacycles or three-dimensional (3D) metallacages with high functionalities. The incorporation of discrete SCCs into supramolecular polymers by the orthogonal combination of metal-ligand coordination and other noncovalent interactions or covalent bonding could further facilitate the construction of novel supramolecular polymers with hierarchical architectures and multiple functions including controllable uptake and release of guest molecules, providing a flexible platform for the development of smart materials. In this review, the recent progress in metallacycle/metallacage-cored supramolecular polymers that were constructed by the combination of metal-ligand interactions and other orthogonal interactions (including hydrophobic or hydrophilic interactions, hydrogen bonding, van der Waals forces, π-π stacking, electrostatic interactions, host-guest interactions and covalent bonding) has been discussed. In addition, the potential applications of metallacycle/metallacage-cored supramolecular polymers in the areas of light emitting, sensing, bio-imaging, delivery and release, etc., are also presented.

Self-Assembly of Nanocubic Molecular Capsules via Solvent-Guided Formation of Rectangular Blocks

We investigate the mechanism underlying the self-assembly of gear-shaped amphiphilic molecules into a highly ordered nanocubic capsule ("nanocube") in aqueous methanol. Simulation results show that the solvent molecules play a significant role in the assembly process by directing the primitive intermediates to orthogonal/rectangular shapes, thus creating appropriate building blocks for cubic assembly while avoiding off-pathway stacked aggregates. Free-energy analyses reveal that the interplay of the direct intermonomer interaction and the solvent-mediated repulsion between large aromatic cores (via preferential solvation of methanol on hydrophobic surfaces) leads to the strong trend for perpendicular binding of monomers and hence the solvent-guided formation of rectangular blocks. Furthermore, we report the self-assembly simulation of the nanocube using replica exchange with solute tempering and demonstrate that the simulation can predict a highly ordered nanocapsule structure, assembly intermediates, and encapsulated molecules, which helps promote computer-aided design of functional molecular self-assemblies in explicit solvent.

A Rotaxane-like Cage-in-Ring Structural Motif for a Metallosupramolecular Pd6 L12 Aggregate

A BODIPY-based bis(3-pyridyl) ligand undergoes self-assembly upon coordination to tetravalent palladium(II) cations to form a Pd₆ L₁₂ metallosupramolecular assembly with an unprecedented structural motif that resembles a rotaxane-like cage-in-ring arrangement. In this assembly the ligand adopts two different conformations-a C-shaped one to form a Pd₂ L₄ cage which is located in the center of a Pd₄ L₈ ring consisting of ligands in a W-shaped conformation. This assembly is not mechanically interlocked in the sense of catenation but it is stabilized only by attractive π-stacking between the peripheral BODIPY chromophores and the ligands' skeleton as well as attractive van der Waals interactions between the long alkoxy chains. As a result, the co-arrangement of the two components leads to a very efficient space filling. The overall structure can be described as a rotaxane-like assembly with a metallosupramolecular cage forming the axle in a metallosupramolecular ring. This unique structural motif could be characterized via ESI mass spectrometry, NMR spectroscopy, and X-ray crystallography.

Self-Assembly in Polyoxometalate and Metal Coordination-Based Systems: Synthetic Approaches and Developments

Utilizing new experimental approaches and gradual understanding of the underlying chemical processes has led to advances in the self-assembly of inorganic and metal–organic compounds at a very fast pace over the last decades. Exploitation of unveiled information originating from initial experimental observations has sparked the development of new families of compounds with unique structural characteristics and functionalities. The main source of inspiration for numerous research groups originated from the implementation of the design element along with the discovery of new chemical components which can self-assemble into complex structures with wide range of sizes, topologies and functionalities. Not only do self-assembled inorganic and metal–organic chemical systems belong to families of compounds with configurable structures, but also have a vast array of physical properties which reflect the chemical information stored in the various “modular” molecular subunits. The purpose of this short review article is not the exhaustive discussion of the broad field of inorganic and metal–organic chemical systems, but the discussion of some representative examples from each category which demonstrate the implementation of new synthetic approaches and design principles.

Harnessing complexity in molecular self-assembly using computer simulations

In molecular self-assembly, hundreds of thousands of freely-diffusing molecules associate to form ordered and functional architectures in the absence of an actuator. This intriguing phenomenon plays a critical role in biology and has become a powerful tool for the fabrication of advanced nanomaterials. Due to the limited spatial and temporal resolutions of current experimental techniques, computer simulations offer a complementary strategy to explore self-assembly with atomic resolution. Here, we review recent computational studies focusing on both thermodynamic and kinetic aspects. As we shall see, thermodynamic approaches based on modeling and statistical mechanics offer initial guidelines to design nanostructures with modest computational effort. Computationally more intensive analyses based on molecular dynamics simulations and kinetic network models (KNMs) reach beyond it, opening the door to the rational design of self-assembly pathways. Current limitations of these methodologies are discussed. We anticipate that the synergistic use of thermodynamic and kinetic analyses based on computer simulations will provide an important contribution to the de novo design of self-assembly.

Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study

Self-organization processes of a gear-shaped amphiphile molecule (1) to form a hexameric structure (nanocube,1₆) were inferred from sequential dissociation processes by using molecular dynamics (MD) simulations.

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

Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.

Modeling Coordination-Directed Self-Assembly of M2L4 Nanocapsule Featuring Competitive Guest Encapsulation

Exploring the mechanism of self-assembly and guest encapsulation of nanocapsules is highly imperative for the design of sophisticated molecular containers and multistimuli-responsive functional materials. Here we present a molecular dynamics simulation protocol with implicit solvent and simulated annealing techniques to investigate the self-assembly and competitive guest (C₆₀ and C₇₀ fullerenes) encapsulation of a M₂L₄ nanocapsule that is self-assembled by the coordination of mercury cations and bent bidentate ligands. Stepwise formation of the nanocapsule and competitive fullerene encapsulation during dynamic structural changes in the self-assembly were detected successfully. Such processes were driven by coordination bonding and π-π stacking and obey the minimum total potential energy principle. Potential of mean force calculations for guest binding to the M₂L₄ nanocapsule explained the mechanism underlying the competitive encapsulations of C₆₀ and C₇₀. This work helps design new functional nanomaterials capable of guest encapsulation and release.

Coding the Assembly of Polyoxotungstates with a Programmable Reaction System

Chemical transformations are normally conducted in batch or flow mode, thereby allowing the chemistry to be temporally or spatially controlled, but these approaches are not normally combined dynamically. However, the investigation of the underlying chemistry masked by the self-assembly processes that often occur in one-pot reactions and exploitation of the potential of complex chemical systems requires control in both time and space. Additionally, maintaining the intermediate constituents of a self-assembled system “off equilibrium” and utilizing them dynamically at specific time intervals provide access to building blocks that cannot coexist under one-pot conditions and ultimately to the formation of new clusters. Herein, we implement the concept of a programmable networked reaction system, allowing us to connect discrete “one-pot” reactions that produce the building block{W₁₁O₃₈} ≡ {W₁₁} under different conditions and control, in real time, the assembly of a series of polyoxometalate clusters {W₁₂O₄₂} ≡ {W₁₂}, {W₂₂O₇₄} ≡ {W₂₂} 1a, {W₃₄O₁₁₆} ≡ {W₃₄} 2a, and {W₃₆O₁₂₀} ≡ {W₃₆} 3a, using pH and ultraviolet–visible monitoring. The programmable networked reaction system reveals that is possible to assemble a range of different clusters using {W₁₁}-based building blocks, demonstrating the relationship between the clusters within the family of iso-polyoxotungstates, with the final structural motif being entirely dependent on the building block libraries generated in each separate reaction space within the network. In total, this approach led to the isolation of five distinct inorganic clusters using a “fixed” set of reagents and using a fully automated sequence code, rather than five entirely different reaction protocols. As such, this approach allows us to discover, record, and implement complex one-pot reaction syntheses in a more general way, increasing the yield and reproducibility and potentially giving access to nonspecialists.

Here we describe a programmable networked reaction system connecting reactors that produce the building block{W₁₁O₃₈} ≡ {W₁₁} under different conditions and control the assembly of a series of polyoxometalate clusters {W₁₂O₄₂} ≡ {W₁₂}, {W₂₂O₇₄} ≡ {W₂₂} 1a, {W₃₄O₁₁₆} ≡ {W₃₄} 2a, and {W₃₆O₁₂₀} ≡ {W₃₆} 3a, using pH and ultraviolet−visible monitoring. This approach led to the isolation of five clusters using a fully automated sequence code, rather than five entirely different reaction protocols.

Probing Molecular Mechanisms of Self-Assembly in Metal-Organic Frameworks

Metal-organic framework materials (MOFs) are a class of nanoporous materials, important to many applications (e.g., gas storage, separation), and their synthesis has received considerable attention. Yet, very little is known about the mechanisms of self-assembly of MOFs. Here, we provide molecular-level insights into the previously unexplored behavior of the self-assembly process, through molecular dynamics simulations, for an archetypal Zn-carboxylate MOF system exhibiting complex vertex topologies (e.g., paddle-wheel clusters). A key finding of this study is the characterization of a stochastic and multistage ordering process intrinsic to self-assembly of the Zn-carboxylate MOF system. A variety of transient intermediate structures consisting of various types of Zn-ion clusters and carboxylate-ligand coordination, and featuring a range of geometric arrangements, are observed during structural evolution. The general features deduced here for the mechanism of the self-assembly of this archetypal MOF system expose the complexities of the various molecular-level events that can occur during the early stages of this process spanning time scales of nano- to microseconds. More generally, we provide fundamental insights that elucidate key aspects of the early stages of the self-assembly mechanism for an important class of nanoporous materials, and of experimental studies exploring nucleation and growth processes in such materials.

A reaction model on the self-assembly process of octahedron-shaped coordination capsules

Master equation was utilized to track the time evolution in a self-assembly process.

Elucidating dominant pathways of the nano-particle self-assembly process

Self-assembly processes play a key role in the fabrication of functional nano-structures with wide application in drug delivery and micro-reactors.

Highly branched and loop-rich gels via formation of metal-organic cages linked by polymers

Gels formed via metal-ligand coordination typically have very low branch functionality, f, as they consist of ∼2-3 polymer chains linked to single metal ions that serve as junctions. Thus, these materials are very soft and unable to withstand network defects such as dangling ends and loops. We report here a new class of gels assembled from polymeric ligands and metal-organic cages (MOCs) as junctions. The resulting 'polyMOC' gels are precisely tunable and may feature increased branch functionality. We show two examples of such polyMOCs: a gel with a low f based on a M2L4 paddlewheel cluster junction and a compositionally isomeric one of higher f based on a M12L24 cage. The latter features large shear moduli, but also a very large number of elastically inactive loop defects that we subsequently exchanged for functional ligands, with no impact on the gel's shear modulus. Such a ligand substitution is not possible in gels of low f, including the M2L4-based polyMOC.

Recent advances in the construction of fluorescent metallocycles and metallocages via coordination-driven self-assembly

During the last few years, the construction of fluorescent metallocycles and metallocages has attracted considerable attention because of their wide applications in fluorescence detection of metal ions, anions, or small molecules, mimicking complicated natural photo-processes, and preparing photoelectric devices, etc. This perspective focuses on the recent advances in the construction of a variety of fluorescent metallocycles and metallocages via coordination-driven self-assembly. In addition, the fluorescence properties and the applications of these organometallic architectures have also been discussed.

Conformation-selective coordination-driven self-assembly of a ditopic donor with PdII acceptors

Different binding conformations of 3-(5-(pyridin-3-yl)-1H-1,2,4-triazol-3-yl)pyridine (L) yielded a self-assembled 3D cube and 2D macrocycles selectively depending on the nature of acceptors. Selection of a particular conformation of the donor L by a specific metal acceptor during self-assembly was corroborated well by a theoretical study.

Simulation of metal–organic framework self-assembly

Spontaneous growth of metal–organic frameworks (MOFs) composed of metal ions and 4,4′-bipyridine ligands was successfully demonstrated by molecular dynamics simulations, starting from a random initial placement of the metals and the ligands.