Porous Supramolecular Crystalline Probe that Detects Non-Covalent Interactions Involved in Molecular Recognition of Furanic Compounds.

Selective separation and conversion of furan-based biomass-derived compounds, which are closely related to biorefineries, is currently an important issue. To improve their performance, it is important to deepen the understanding of non-covalent interactions that act on the molecular recognition of furanic compounds on separation or catalyst matrices. Here, a new method is reported to comprehensively visualize such intermolecular interactions using a porous supramolecular crystalline probe with polar and non-polar binding sites within a low-symmetric nanochannel consisting of four isomeric PdII 3-macrocycles. Single-crystal X-ray diffraction analysis of the crystals including 5-hydroxymethylfurfural, furfural, furfuryl alcohol, or 2-acetylfuran reveals a variety of interactions involving their furan rings and polar substituents. It is also found that cooperative and competitive effects between guest and solvent molecules significantly change their recognition mode.

Enzymatic synthesis of ligand-bearing oligonucleotides for the development of metal-responsive DNA materials.

Metal-mediated artificial base pairs are some of the most promising building blocks for constructing DNA-based supramolecules and functional materials. These base pairs are formed by coordination bonds between ligand-type nucleobases and a bridging metal ion and have been exploited to develop metal-responsive DNA materials and DNA-templated metal arrays. In this review, we provide an overview of methods for the enzymatic synthesis of DNA strands containing ligand-type artificial nucleotides that form metal-mediated base pairs. Conventionally, ligand-bearing DNA oligomers have been synthesized via solid-phase synthesis using a DNA synthesizer. In recent years, there has been growing interest in enzymatic methods as an alternative approach to synthesize ligand-bearing DNA oligomers, because enzymatic reactions proceed under mild conditions and do not require protecting groups. DNA polymerases are used to incorporate ligand-bearing unnatural nucleotides into DNA, and DNA ligases are used to connect artificial DNA oligomers to natural DNA fragments. Template-independent polymerases are also utilized to post-synthetically append ligand-bearing nucleotides to DNA oligomers. In addition, enzymatic replication of DNA duplexes containing metal-mediated base pairs has been intensively studied. Enzymatic methods facilitate the synthesis of DNA strands containing ligand-bearing nucleotides at both internal and terminal positions. Enzymatically synthesized ligand-bearing DNAs have been applied to metal-dependent self-assembly of DNA structures and the allosteric control of DNAzyme activity through metal-mediated base pairing. Therefore, the enzymatic synthesis of ligand-bearing oligonucleotides holds great potential in advancing the development of various metal-responsive DNA materials, such as molecular sensors and machines, providing a versatile tool for DNA supramolecular chemistry and nanotechnology.

Asymmetric Twisting of C-Centered Octahedral Gold(I) Clusters by Chiral N-Heterocyclic Carbene Ligation.

Asymmetric induction of metal clusters by ligation of chiral ligands is intriguing in terms of the mechanism of chirality transfer and the stability of the resulting chiral structure. Here we report the asymmetric induction of C-centered hexagold(I) CAuI6 clusters into an asymmetrically twisted structure through monodentate, chiral benzimidazolylidene-based N-heterocyclic carbene (NHC) ligands. X-ray diffraction analysis revealed that the NHC-ligated CAuI6 cluster was diastereoselectively twisted with directionally selective, bond length expansion, and contraction of the Au···Au contacts and that the original cluster with high symmetry was transformed into an optically pure, asymmetric CAuI6 cluster with C1 symmetry. Moreover, the circular dichroism spectroscopy and the time-dependent density functional theory calculation confirmed that the asymmetrically twisted CAuI6 structure was maintained even in solution. Such asymmetric induction of configurationally stable metal clusters would greatly expand the molecular design possibilities of asymmetric catalysts and chiroptical materials by utilizing library chiral NHC ligands.

Phase-Dependent Reactivity and Host-Guest Behaviors of a Metallo-Macrocycle in Liquid and Solid-State Photosensitized Oxygenation Reactions.

The photochemical oxygenation reactions of a host-guest complex, pCp⊂[Ag2L0](SbF6)2 (pCp = [2.2]paracyclophane) have been investigated in solution and in the solid state, using the macrocyclic ligand L0 having four anthracene moieties in the framework. As a result, it was found that the reactivity and host-guest functions show remarkable phase dependence. In solution, the photosensitized oxygenation of all the anthracene moieties of L0 resulted in a fully oxygenated macrocycle [Ag2L4](SbF6)2 as the final product, while simultaneously the guest molecule was dissociated from the macrocyclic cavity. On the other hand, in an amorphous solid of pCp⊂[Ag2L0](SbF6)2 prepared by decomposing single crystals through the removal of the crystalline solvent, the oxygenated site of L0 was significantly controlled to provide a site-selectively oxygenated inclusion complex, pCp⊂[Ag2L1](SbF6)2, possessing a mono-oxygenated Cs-symmetrical macrocyclic skeleton.

Multipoint Hydrogen Bonding-Based Molecular Recognition of Amino Acids and Peptide Derivatives in a Porous Metal-Macrocycle Framework: Residue-Specificity, Diastereoselectivity, and Conformational Control.

Porous crystals have great potential to exert space-specific functions such as multipoint molecular recognition. In order to rationally enhance the porous function, it is necessary to precisely control molecular recognition event in the pores. Hydrogen bonding is an effective tool for controlling molecular recognition. However, multiple hydrogen bonds, which are essentially the origin of high complementarity and specificity, remain difficult to innovate in porous crystals in an intelligent way. This paper demonstrates molecular recognition of amino acid and peptide derivatives by multipoint hydrogen bonding in a porous metal-macrocycle framework revealed by single-crystal X-ray diffraction analysis. l-Serine residues are site-selectively and residue-specifically adsorbed on the pore surface via multiple hydrogen bonds. A serine derivative is diastereoselectively recognized on the (P)- or (M)-side of the enantiomeric pore surface. Moreover, the conformation of the peptide is highly regulated, incorporating a poly-l-proline type I helix-like structure into the pore. These findings will bring deep scientific knowledge to the design of new porous crystals and functions.

Novel Porous Crystals with Macrocycle-Based Well-Defined Molecular Recognition Sites.

Molecular recognition is one of the fundamental events in biological systems, as typified by enzymes that enable highly efficient and selective catalytic reactions through precise recognition of substrate(s) and cofactor(s) in the binding pockets. Chemists therefore have long been inspired by such excellent molecular systems to develop various synthetic receptors with well-defined binding sites. Their effort is currently being devoted to the construction of not only molecular receptors but also self-assembled host compounds possessing connected cavities (pores) in the crystalline frameworks to rationally design functional porous materials capable of efficiently adsorbing molecules or ions at binding sites on the pore walls. However, it is still challenging to design multiple distinct binding sites that are precisely arranged in an identical framework, which is currently one of the most important targets in this field to realize elaborate molecular systems beyond natural enzymes.In this Account, we provide an overview of porous crystals with well-defined molecular recognition sites. We first show several strategies for arranging macrocyclic binding sites in crystalline frameworks such as metal-organic frameworks, porous molecular crystals, and covalent organic frameworks. Porous metal-macrocycle frameworks (MMFs) that we have recently developed are then described as a new type of porous crystals with well-defined multiple distinct binding sites. The MMF-1 crystal, which was developed first and is composed of four stereoisomers of helical PdII3-macrocycle complexes, has one-dimensional channels with dimensions of 1.4 nm × 1.9 nm equipped with enantiomeric pairs of five distinct binding sites. This structural feature of MMF-1 therefore allows for site-selective and asymmetric arrangement of not only single but also multiple guest molecules in the crystalline channels based on molecular recognition between the guests and the multiple binding sites. This characteristic was also exploited to develop a heterogeneous catalyst by non-covalently immobilizing an organic acid on the pore surface of MMF-1 to conduct size-specific catalytic reactions. In addition, adsorption of a photoreactive substrate in MMF was found to switch the photoreaction pathway to cause another reaction with the aid of photoactivated PdII centers arranged on the pore walls. Furthermore, the dynamic, transient process of molecular arrangement incorporated in MMF-1 has been successfully visualized by single-crystal X-ray diffraction analysis. The formation of homochiral MMF-2 composed of only (P)- or (M)-helical PdII3-macrocycle complexes is also described. Thus, macrocycle-based porous crystals with a complex structure such as MMFs are expected to serve as novel porous materials that have great potential to mimic or surpass enzymes by utilizing well-defined multiple binding sites capable of spatially arranging a catalyst, substrate, and effector for highly selective and allosterically tunable catalytic reactions, which can be also visualized by crystallographic analysis because of their crystalline nature.

Bipyridine-Modified DNA Three-Way Junctions with Amide Linkers: Metal-Dependent Structure Induction and Self-Sorting.

Invited for the cover of this issue are Yusuke Takezawa, Shiori Sakakibara, and Mitsuhiko Shionoya at The University of Tokyo. The image depicts the formation of stable DNA three-way junction structures crosslinked by an interstrand NiII (bpy)3 complex. Read the full text of the article at 10.1002/chem.202104037.

Bipyridine-Modified DNA Three-Way Junctions with Amide linkers: Metal-Dependent Structure Induction and Self-Sorting.

DNA three-way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)-modified DNA 3WJ by using a newly designed bpy-modified nucleoside, Ubpy -3, in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy-modified 3WJ was greatly enhanced by the formation of an interstrand NiII (bpy)3 complex at the junction core (ΔTm =+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside Ubpy -2, the degree of the NiII -mediated stabilization observed with Ubpy -3 was comparable to that of Ubpy -2. Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of NiII ions. Furthermore, NiII -mediated self-sorting of 3WJs was performed by using the bpy-modified strands and their unmodified counterparts. Both transformations were driven by the formation of NiII (bpy)3 complexes. The structural induction and self-sorting of bpy-modified 3WJs are expected to have many potential applications in the development of metal-responsive DNA materials.

Face-selective adsorption of a prochiral compound on the chiral pore-surface of a metal-macrocycle framework (MMF) directed towards stereoselective reactions.

Molecular adsorption on a surface is a unique way to break the mirror-symmetry of prochiral molecules, and therefore the use of chiral surfaces is an effective strategy for achieving highly selective chiral separation and asymmetric catalytic reactions based on molecular adsorption with high diastereoselectivity. We have previously reported a porous metal-macrocycle framework (MMF) with an enantiomeric pair of chiral pore-surfaces derived from Pd-helical macrocycles as the ingredients of the framework. Aiming at applying the chiral pore-surface of the MMF to asymmetric reactions and chiral separation, herein we propose a strategy to utilize one of the enantiomerically paired pore-surfaces as a homochiral pore-surface with the aid of chiral auxiliaries that can block only one side of the enantiomeric pore-surfaces in a site-selective manner. Single-crystal X-ray diffraction analysis revealed that a chiral auxiliary, (1R)- or (1S)-1-(3-chlorophenyl)ethanol, and a prochiral guest molecule, 2'-hydroxyacetophenone, were cooperatively arranged in each pore unit so that the prochiral guest molecule can face-selectively bind to the homochiral pore-surface.

Multi-Stimuli-Responsive Interconversion between Bowl- and Capsule-Shaped Self-Assembled Zinc(II) Complexes.

Self-assembled metal-organic architectures have great potential to undergo major structural changes into different architectures. Such molecular transformation is widely applicable to responsive systems like drug delivery and allosteric catalysis. A great number of metal-organic architectures responsive to a specific stimulus have been reported so far. However, interconversion between a pair of distinct metal-organic structures in response to multiple stimuli is rarely reported despite its high versatility. Herein we report multi-stimuli-responsive interconversion between a bowl-shaped and a capsule-shaped self-assembled ZnII complexes, [ZnII4L3X6] and [ZnII4L4], respectively, which were found to form in equilibrium from porphyrin-based ligand L and ZnII ions with different stoichiometry. Specifically, this interconversion was induced by four distinct external stimuli: exogenous ligands, Brønsted base/acid, solvents, and guest molecules. The mechanisms of the interconversion system are discussed in detail focusing on the species included in the equilibria. Thus, these findings would provide a helpful clue to design principles for multi-stimuli-responsive systems with functional versatility.

Allosteric Regulation of DNAzyme Activities through Intrastrand Transformation Induced by Cu(II)-Mediated Artificial Base Pairing.

Allosteric regulation is gaining increasing attention as a basis for the production of stimuli-responsive materials in many research areas including DNA nanotechnology. We expected that metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, could serve as allosteric units that regulate the function of DNA molecules. In this study, we established a rational design strategy for developing CuII-responsive allosteric DNAzymes by incorporating artificial hydroxypyridone ligand-type nucleotides (H) that form a CuII-mediated base pair (H-CuII-H). We devised a new enzymatic method using a standard DNA polymerase and a ligase to prepare DNA strands containing H nucleotides. Previously reported DNAzymes were modified by introducing a H-H pair into the stem region, and the stem-loop sequences were altered so that the structure becomes catalytically inactive in the absence of CuII ions. The formation of a H-CuII-H base pair triggers intrastrand transformation from the inactive to the active structure, enabling allosteric regulation of the DNAzyme activity in response to CuII ions. The activity of the H-modified DNAzyme was reversibly switched by the addition and removal of CuII ions under isothermal conditions. Similarly, by incorporating a H-CuII-H pair into an in vitro-selected AgI-dependent DNAzyme, we have developed a DNAzyme that exhibits an AND logic-gate response to CuII and AgI ions. The rational design strategy and the easy enzymatic synthetic method presented here provide a versatile way to develop a variety of metal-responsive allosteric DNA materials, including molecular machines and logic circuits, based on metal-mediated artificial base pairing.

Metal-Dependent DNA Base Pairing of 5-Carboxyuracil with Itself and All Four Canonical Nucleobases.

A 5-carboxyuracil (caU) nucleobase was found to pair not only with A (caU-A) by hydrogen bonding but also with other DNA nucleobases by metal coordination bonding. Metal-dependent formation of caU-CuII-caU, caU-HgII-T, caU-AgI-C, and caU-CuII-G pairs was demonstrated by duplex melting analysis and mass spectrometry. The duplexes containing caU-X (X = caU, T, C, and G) were significantly stabilized in the presence of the corresponding metal ions, while the DNA duplexes containing the caU-A pairs were destabilized by the addition of CuII. These results suggest that the hybridization partner of caU-containing DNA strands can be altered by metal complexation. As a result, this study provides a new direction to integrate caU nucleobases to construct diverse metallo-DNA supramolecules and metal-responsive DNA devices.

Sharp Switching of DNAzyme Activity through the Formation of a CuII -Mediated Carboxyimidazole Base Pair.

DNAzymes are widely used as functional units for creating DNA-based sensors and devices. Switching of DNAzyme activity by external stimuli is of increasing interest. Herein we report a CuII -responsive DNAzyme rationally designed by incorporating one of the most stabilizing artificial metallo-base pairs, a CuII -mediated carboxyimidazole base pair (ImC -CuII -ImC ), into a known RNA-cleaving DNAzyme. Cleavage of the substrate was suppressed without CuII , but the reaction proceeded efficiently in the presence of CuII ions. This is due to the induction of a catalytically active structure by ImC -CuII -ImC pairing. The on/off ratio was as high as 12-fold, which far exceeds that of the previously reported DNAzyme with a CuII -mediated hydroxypyridone base pair. The DNAzyme activity can be regulated specifically in response to CuII ions during the reaction through the addition, removal, or reduction of CuII . This approach should advance the development of stimuli-responsive DNA systems with a well-defined sharp switching function.

Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides.

Metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, have shown promise as functional units to develop stimuli-responsive DNA materials. Although a variety of metal-mediated base pairs have been constructed with artificial ligand-type nucleotides and various metal ions, the application of such metal-mediated base pairs has been relatively poorly explored mainly due to the cumbersome chemical synthesis of artificial DNA strands. Herein we report a facile enzymatic method to synthesize DNA strands containing a ligand-type hydroxypyridone (H) nucleotide, which forms a CuII-mediated base pair (H-CuII-H). A two-step primer extension reaction using two commercially available polymerases enabled the incorporation of a H nucleotide at an internal position of oligonucleotides. The polymerase synthesis was subsequently applied to the development of metal-responsive deoxyribozymes (DNAzymes), whose catalytic activity was regulated by the formation of a single H-CuII-H base pair in its stem region. The DNAzyme activity was reversibly switched by the alternate addition and the removal of CuII ions. Furthermore, metal-dependent orthogonal activation of a CuII-responsive H-DNAzyme and a HgII-responsive T-DNAzyme was experimentally demonstrated by utilizing both H-CuII-H as well as widely explored T-HgII-T base pairs. These results suggest that the incorporation of H-CuII-H base pairs would facilitate the rational design of metal-responsive functional DNAs. Accordingly, the facile enzymatic synthesis of artificial ligand-bearing DNAs developed in this study would significantly expand the toolbox of DNA-based supramolecular chemistry and DNA nanotechnology.

Synthesis of Hetero-multinuclear Metal Complexes by Site-Selective Redox Switching and Transmetalation on a Homo-multinuclear Complex.

Hetero-multinuclear metal complexes are a promising class of compounds applicable to photoluminescence, magnetism, and catalysis. In this work, we have developed a synthetic method for hetero-tetranuclear metal complexes by combining advantages of site-selective redox switching and transmetalation. First, a homo-tetranuclear CoII4 complex was converted to a mixed-valence CoIIICoII3 complex by site-selective oxidation, which was then transmetalated from CoII to NiII to form a heterometallic CoIIINiII3 complex. Finally, a CoIINiII3 complex was synthesized by metal-selective reduction on the CoIII site. The basic structural frameworks of the main products in the whole process starting from the CoII4 complex are isostructural. Notably, the CoIINiII3 complex was not accessible by direct mixing of ligand, CoII, and NiII. This method would provide an alternative strategy for highly selective synthesis of hetero-multinuclear metal complexes.

Preferential Photoreaction in a Porous Crystal, Metal-Macrocycle Framework: PdII-Mediated Olefin Migration over [2+2] Cycloaddition.

A nanosized confined space with well-defined functional surfaces has great potential to control the efficiency and selectivity of catalytic reactions. Herein we report that a 1,6-diene, which normally forms an intramolecular [2+2] cycloadduct under photoirradiation, preferentially undergoes a photoinduced olefin migration in a porous crystal, metal-macrocycle framework (MMF), and alternatively [2+2] cycloaddition is completely inhibited in the confined space. A plausible reaction mechanism for olefin migration triggered by the photoinduced dissociation of the Pd-Cl bond is suggested based on UV-vis diffuse reflectance spectroscopy, single-crystal XRD, and MS-CASPT2 calculation. The substrate scope of the photoinduced olefin migration in MMF was also examined using substituted allylbenzene derivatives.

Chiral metallosupramolecular architectures.

Over the past few decades, supramolecular chirality in discrete metallosupramolecular architectures has received considerable attention. In this review, a comprehensive summary of discrete, chiral coordination-driven structures, including helices, metallacycles, metallocages, etc., is presented. Although chirality can be introduced prior to, during or even after the coordination self-assembly process, this review puts major emphasis on the more recent development of metallosupramolecular architectures from chiral components, where chirality arises from the enantiopure or racemic scaffolds (bridging or auxiliary ligand). Special attention will be paid to homochiral metallo-assemblies using achiral components where chirality is obtained as a consequence of the twisting of the ligands. Additionally, the potential applications of homochiral metallosupramolecular architectures are also discussed. We hope that this review will be of interest to researchers attempting to design new elaborate homochiral metallosupramolecular architectures with even greater complexity and potential for functions such as chiral recognition, enantiomer separation, asymmetric catalysis, nonlinear sensors, and devices.

A Circularly Arranged Sextuple Triptycene Gear Molecule.

Herein we report the synthesis of a circularly arranged sextuple triptycene gear molecule, hexakis(10-dodecyloxy-9-triptycyl)ethynylbenzene, via the trimerization of the corresponding triyne with a cobalt catalyst. The six triptycene gears are closely engaged with each other as confirmed by single crystal X-ray structure analysis, and their motion in solution was established by NMR spectroscopy. Notably, when one bulky RuCp* complex was attached to one triptycene gear, the whole movement of the six gears was highly restricted via their mechanical engagement. Development of such a multigear molecule would provide a structural basis for molecular motion transmission systems with a switching function.

Multifunctional Octamethyltetrasila[2.2]cyclophanes: Conformational Variations, Circularly Polarized Luminescence, and Organic Electroluminescence.

Both symmetrical and unsymmetrical cyclophanes containing disilane units, tetrasila[2.2]cyclophanes 1-9, were synthesized. The syn and anti conformations and the kinetics of inversion between two anti-isomers were investigated by X-ray diffraction and variable-temperature NMR analysis, respectively. The flipping motion of two aromatic rings was affected by the bulkiness of the aromatic moiety (1 vs 6), the phase (solid vs solution), and the inclusion by host molecules (1 vs 1⊂[Ag2L]2+). The photophysical, electrochemical, and structural properties of the compounds were thoroughly investigated. Unsymmetrical tetrasila[2.2]cyclophanes 5-8 displayed blue-green emission arising from intramolecular charge transfer. Compound 6 emitted a brilliant green light in the solid state under 365 nm irradiation and showed a higher fluorescence quantum yield in the solid state (Φ = 0.49) than in solution (Φ = 0.05). We also obtained planar chiral tetrasila[2.2]cyclophane 9, which showed interesting chiroptical properties, such as a circularly polarized luminescence (CPL) with a dissymmetry factor of |glum| = ca. 2 × 10-3 at 500 nm. Moreover, an organic green light-emitting diode that showed a maximum external quantum efficiency (ηext) of ca. 0.4% was fabricated by doping 4,4'-bis(2,2'-diphenylvinyl)-1,1'-biphenyl with 6.

Rotational Control of a Dirhodium-Centered Supramolecular Four-Gear System by Ligand Exchange.

Self-assembled molecular machines have great potential to enable noncovalent regulation of a coupled motion of the building blocks. Herein we report the synthesis and the rotational control of a lantern-type dirhodium complex with circularly arranged four 2,3,6,7,14,15-hexamethyltriptycene carboxylates as gears and two axial ligands as the rate control elements. The rotating rates in solution were markedly affected by the coordination ability and the bulkiness of axial ligands. Notably, the rate changes were closely correlated with the changes in the electronic states of the dirhodium center. Such ligand exchange-based control of rotational motions with color changes would advance stimulus-responsive metallo-molecular multirotors.