Coordination Self-Assembly Processes Revealed by Collaboration of Experiment and Theory: Toward Kinetic Control of Molecular Self-Assembly

Step-by-Step Self-Assembly of a Double-Walled Knotted Cage With Increasing Topological Complexity

The self-assembly process of a double-walled cage formed from a semiflexible tripodal ligand and a Pd(II) 90-degree block was tracked by NMR and x-ray analysis. At least two intermediate structures with distinct topologies were observed prior to the formation of the final double-walled cage. By optimizing the self-assembly conditions (e.g., time, solvent, and concentration), these topological intermediates were successfully isolated and analyzed by x-ray crystallography. They are considered crucial metastable structures that navigate the shortest pathway to the final structure, demonstrating the critical role of molecular topology in guiding and controlling the kinetics of metal-directed self-assembly.

Fine-Tuning of the Sequential Self-Assembly of Entangled Polyhedra by Exploiting the Side-Chain Effect

The control of the sequential self-assembly processes of highly entangled (Ag3L2)n (n=2,4,6,8) and Ag21L12 coordination polyhedra using side-chain effects was studied via the introduction of linear or branched side chains into the tripodal ligands. In addition to changes in the intermediate polyhedral species affording the multi- pathway process, disruption of the kinetic control of the sequential self-assembly was observed, thus demonstrating the utility of steric control for the construction of 3D-entangled molecular materials on the 5 nm scale with high molecular complexity.

Coordination-Induced Emissive Poly-NHC-Derived Metallacage for Pesticide Detection

Developing sensitive, rapid, and convenient methods for the detection of residual toxic pesticides is immensely important to prevent irreversible damage to the human body. Luminescent metal-organic cages and macrocycles have shown great applications, and designing highly emissive supramolecular systems in dilute solution using metal-ligand coordination-driven self-assembly is demanded. In this study, we have demonstrated the development of a silver-carbene bond directed tetranuclear silver(I)-octacarbene metallacage [Ag4(L)2](PF6)4 (1) based on an aggregation-induced emissive (AIE) cored 1,1',1″,1‴-((1,4-phenylenebis(ethene-2,1,1-triyl))tetrakis(benzene-4,1-diyl))tetrakis(3-methyl-1H-imidazol-3-ium) salt (L). A 36-fold enhanced emission was observed after metallacage (1) formation when compared with the ligand (L) in dilute solution due to the restriction of intramolecular motions imparted by metal-ligand coordination. Such an increase in fluorescence made 1 a potential candidate for the detection of a broad-spectrum pesticide, 2,6-dichloro-nitroaniline (DCN). 1 was able to detect DCN efficiently by the fluorescence quenching method with a significant detection limit (1.64 ppm). A combination of static and dynamic quenching was applicable depending on the analyte concentration. The use of silver-carbene bond directed self-assembly to exploit coordination-induced emission as an alternative to AIE in dilute solution and then apply this approach to solve health and safety concerns is noteworthy and carries a lot of potential for future developments.

Pathway selection in the self-assembly of Rh4L4 coordination squares under kinetic control

Pathway selection principles in reversible reaction networks such as molecular self-assembly have not been established yet, because achieving kinetic control in reversible reaction networks is more complicated than in irreversible ones. In this study, we discovered that coordination squares consisting of cis-protected dinuclear rhodium(II) corner complexes and linear ditopic ligands are assembled under kinetic control, perfectly preventing the corresponding triangles, by modulating their energy landscapes with a weak monotopic carboxylate ligand (2,6-dichlorobenzoate: dcb-) as the leaving ligand. Experimental and numerical approaches revealed the self-assembly pathway where the cyclization step to form the triangular complex is blocked by dcb-. It was also found that one of the molecular squares assembled into a dimeric structure owing to the solvophobic effect, which was characterized by nuclear magnetic resonance spectroscopy and single-crystal X-ray analysis.

Rigidification-Induced Emissive Metal-Carbene Complexes for Artificial Light Harvesting

A tetraphenylethylene (TPE)-based flexible imidazolium (L) salt was used to develop a di-nuclear silver(I)-tetracarbene (1) complex. Coordination-induced rigidity upon formation of 1 exhibited a 6-fold increase in emission intensity in acetonitrile compared to starting L. Despite TPE being a well-known aggregation-induced emissive moiety, Ag^I-N-heterocyclic carbene (NHC) complex 1 had a remarkably higher fluorescence emission (4-fold) in dilute solution when compared with L in its aggregated state. Finally, this enhanced emission was used to institute a new platform for an artificial light-harvesting system. 1 acted as an energy donor and efficiently transferred energy to Eosin Y (ESY) with a high saturation at a 67:1 (1/ESY) molar ratio. Use of rigidification-induced emission of the Ag^I-NHC complex to fabricate a light-harvesting scaffold is a new approach and can greatly impact the generation of smart materials.

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.

Mapping the Assembly of Neutral Tetrahedral Cages Tethered by Oximido Linkers and Their Guest Encapsulation Studies

A primary criterion for the design of polyhedral metal-organic cages is the requirement of geometrically matched pairs of metal ions and ligand moieties. However, understanding the pathway it takes to reach the final polyhedral structure can provide more insights into the self-assembly process and improved design strategies. In this regard, we report two neutral tetrahedral cages with the formulas {[Pd₃(NⁱPr)₃PO]₄(L¹)₆} (1-TD) and {[Pd₃(NⁱPr)₃PO]₄(L²)₆} (2-TD) starting from the acetate-bridged cluster {[Pd₃(NⁱPr)₃PO]₂(OAc)₂(OH)}₂·2(CH₃)₂SO (HEXA-Pd) and the respective oxamide precursors (L¹H₂: [C₂(NH₂)₂O₂]) and (L²H₂: (C₂(NHMe)₂O₂]). When subtle variations in the reaction conditions were made, two new tetrameric Pd₁₂ assemblies, {[Pd₃(NⁱPr)₃PO]₄(L¹)₂(OAc)₄(OMe)₄} (1-TM) and {[Pd₃(NⁱPr)₃PO]₄(L²)₂(OAc)₄(OMe)₄} (2-TM), were obtained from the same precursors. Detailed investigations using NMR, mass spectrometry, X-ray crystallography, and computational studies indicate that the macrocyclic complexes 1-TM and 2-TM are the reaction intermediates involved in the formation of the tetrahedral cages 1-TD and 2-TD, respectively. Moreover, the tetrahedral cages 1-TD and 2-TD exhibited intrinsic cavities of volume ∼85 ų. Guest encapsulation studies revealed that the cage 1-TD can encapsulate a wide range of guest molecules such as CH₂Cl₂, CHCl₃, CCl₄, C₆H₆, and C₆H₅F. Interestingly, 1-TD was shown to exhibit a preferential binding of C₆H₅F and C₆H₆ over other halogenated guest molecules, as determined from NMR titrations and computational studies.

Exploiting Supramolecular Interactions to Control Isomer Distributions in Reduced-Symmetry [Pd2L4]4+ Cages

High-symmetry metallosupramolecular architectures (MSAs) have been exploited for a range of applications including molecular recognition, catalysis, and drug delivery. Recently, there have been increasing efforts to enhance those applications by generating reduced-symmetry MSAs. Here we report our attempts to use supramolecular (dispersion and hydrogen-bonding) forces and solvophobic effects to generate isomerically pure [Pd₂(L)₄]⁴⁺ cage architectures from a family of new reduced-symmetry ditopic tripyridyl ligands. The reduced-symmetry tripyridyl ligands featured either solvophilic polyether chains, solvophobic alkyl chains, or amino substituents. We show using NMR spectroscopy, high-performance liquid chromatography, X-ray diffraction data, and density functional theory calculations that the combination of dispersion forces and solvophobic effects does not provide any control of the [Pd₂(L)₄]⁴⁺ isomer distribution with mixtures of all four cage isomers (HHHH, HHHT, cis-HHTT, or trans-HTHT, where H = head and T = tail) obtained in each case. More control was obtained by exploiting hydrogen-bonding interactions between amino units. While the cage assembly with a 3-amino-substituted tripyridyl ligand leads to a mixture of all four possible isomers, the related 2-amino-substituted tripyridyl ligand generated a cis-HHTT cage architecture. Formation of the cis-HHTT [Pd₂(L)₄]⁴⁺ cage was confirmed using NMR studies and X-ray crystallography.

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.

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.

Cyclization or bridging: which occurs faster is the key to the self-assembly mechanism of Pd6L3 coordination prisms

The self-assembly processes of Pd₆L₃ coordination prisms consisting of cis-protected Pd(II) complexes and porphyrin-based tetratopic ligands with four 3-pyridyl or 4-pyridyl groups (L) were investigated by experimental and numerical methods, QASAP (quantitative analysis of self-assembly process) and NASAP (numerical analysis of self-assembly process), respectively. It was found that contrary to common intuition macrocyclization takes place faster than the bridging reaction in the prism assembly and that the bridging reaction occurring before the macrocyclization tends to produce kinetically trapped species. A numerical simulation demonstrates that the relative magnitude of the rate constants between the macrocyclization and the bridging reaction is the key factor that determines whether the self-assembly leads to the thermodynamically most stable prism or to kinetically trapped species. Finding the key elementary reactions that largely affect the selection of the major assembly pathway is helpful to rationally control the products under kinetic control via modulation of the energy landscape.

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.