Designing Processive Catalytic Systems. Threading Polymers through a Flexible Macrocycle Ring

Formation of Direction-Controllable Pseudorotaxane and Catenane Using Chemically Cyclized Oligodeoxynucleotides and Their Noncovalent RNA Labeling

The formation of interlocked structures, such as rotaxane and catenane, enables noncovalent conjugations. We previously confirmed that the chemically cyclized pseudorotaxane-forming oligodeoxynucleotides (prfODNs) with double-tailed parts formed a pseudorotaxane structure with the target DNA and RNA via the slipping process. Here, we report the one-step synthesis of cyclized prfODNs from alkyne-modified ODNs, after which we investigated the properties and mechanism of the slipping process and performed noncovalent RNA labeling with prfODNs. Additionally, the catenane structure was formed by the combination of pseudorotaxane formation with a 5'-end-phosphorylated RNA and enzymatic ligation. The newly synthesized prfODN represents a new tool for achieving the noncovalent conjugation of various functional moieties to RNAs.

Paramagnetic relaxation enhancement NMR as a tool to probe guest binding and exchange in metallohosts

Paramagnetic metallohost systems can bind guest molecules and find application as biomimetic catalysts. Due to the presence of the paramagnetic metal center, rigorous characterization of these systems by NMR spectroscopy can be very difficult. We report here that metallohost-guest systems can be studied by using the paramagnetic relaxation enhancement (PRE) effect. Manganese(III) porphyrin cage compounds are shown through their PRE to thread and bind viologen guests, including a polymeric one. The binding constants and dethreading activation parameters are lower than those of the metal-free porphyrin cage compounds, which is proposed to be a result of charge repulsion of the trivalent metal center and dicationic viologen guest. The threading rate of the manganese(III) porphyrin cage onto the polymer is more than 10 times faster than that of the non-metallated one, which is ascribed to initial binding of the cage to the polymer chain prior to threading, and to an entron effect.

Paramagnetic metallohost systems are difficult to characterize. Here the authors report that the paramagnetic relaxation enhancement effect can be used to prove by nuclear magnetic resonance experiments that Mn(III) porphyrin cage compounds can bind and thread low molecular weight and polymeric guests.

Macrocycles in Bioinspired Catalysis: From Molecules to Materials

Macrocyclic compounds have been studied extensively as the host molecules in supramolecular chemistry. Their structural characteristics make macrocycles desirable in the field of molecular recognition, which is the key to high catalytic efficiencies of natural enzymes. Therefore, macrocycles are ideal building blocks for the design of bioinspired catalysts. This mini review highlights recent advances ranging from single-molecule to metal-organic framework materials, exhibiting multilevel macrocycle catalysts with unique catalytic centers and substrate-binding affinities.

Size-selective Catalytic Polymer Acylation with a Molecular Tetrahedron

Selective catalysis at the molecular level represents a cornerstone of chemical synthesis. However, it still remains an open question how to elevate tunable catalysis to larger length scales to functionalize whole polymer chains in a selective manner. We now report a hydrazone-linked tetrahedron with wide openings, which acts as a catalyst to size-selectively functionalize polydisperse polymer mixtures. Our experimental and computational evidence supports a dual role of the hydrazone-linked tetrahedron. To accelerate functionalization of the polymer substrates, the tetrahedron (i) unfolds the polymer substrates and/or breaks the polymer aggregates as well as (ii) enables target sites (amino groups) on the polymers to coordinate with catalytic units (triglyme) attached to the tetrahedron. With the tetrahedron as the catalyst, we find that the reactivity of the shorter polymers increases selectively. Our findings enable the possibility to engineer hydrolytically stable molecular polyhedra as organocatalysts for size-selective polymer modification.

Porphyrin cage compounds based on glycoluril – from enzyme mimics to functional molecular machines

This Feature Article gives an overview of the application of glycoluril-based porphyrin cage compounds in host–guest chemistry, allosterically controlled self-assembly, biomimetic catalysis, and polymer encoding.

Acyclic Cucurbit[n]uril-type Receptors: Preparation, Molecular Recognition Properties and Biological Applications

This article traces the development of acyclic cucurbit[n]uril-type receptors with a focus on work from the Isaacs group. First, we describe the synthesis of methylene bridged glycoluril dimers capped with aromatic sidewalls which allowed us to probe the interconversion of the S- and C-shaped dimers which is a fundamental step in CB[n] formation. The C-shaped compounds were found to undergo discrete self-assembly (dimerization) in both water and organic solvents which lead us to investigate multicomponent self-sorting systems. We supressed the self-association of 8 by electrostatic repulsion in the putative dimer which allowed expression of its innate molecular recognition properties toward methylene blue and related planar cationic dyes. Longer glycoluril oligomers (trimer - hexamer, acyclic decamer) were prepared by starving the CB[n]-forming reaction of formaldehyde. The longer oligomers (e.g. 15 and 16) bind to alkylammonium ions in water ≈ 100-fold weaker than macrocyclic CB[n] highlighting the high preorganization of the acyclic but polycyclic framework. We prepared a wide variety of acyclic CB[n] compounds (wall variants, solubilizing group variants, linker variants) based on glycoluril trimer and tetramer. In particular, 26 and 27 have been shown to possess a wide variety of chemically and biologically interesting functions. For example, 26 was used to formulate the insoluble drug Albendazole and treat mice bearing SK-OV-3 xenograft tumors. Compound 27 binds tightly to the neuromuscular blocking agents rocuronium, vecuronium, and cisatracurium and acts as an in vivo reversal agent for these compounds in anesthetized rats. Container 27 was also found to modulate the hyperlocomotive effect of rats that had been treated with methamphetamine. Finally, 38 has been used as a cross reactive component of sensor arrays that are capable of classifying and quantifying cancer related nitroamines and a range of over the counter drugs. Overall, the work demonstrates that acyclic CB[n]-type compounds are nicely pre-organized and therefore retain the essential aspects of the recognition properties of macrocyclic CB[n] but allow for more straightforward tailoring of structure and solubility that enables a variety of chemically and biologically important applications.

Spacer Length-Independent Shuttling of the Pillar[5]arene Ring in Neutral [2]Rotaxanes

For a series of neutral [2]rotaxanes consisting of a pillar[5]arene ring and axles possessing two stations separated by flexible spacers of different lengths, the free energies of activation for the ring shuttling between the stations were found to be independent of the spacer length. The constitution of the spacer affects the activation energies: replacement of CH₂ groups by repulsive oxygen atoms in the axle increases the barrier. The explanation for the observed length‐independence lies in the presence of a barrier for re‐forming the stable co‐conformation, which makes the ring travel back and forth along the thread in an intermediate state.

Flexible, Linear Chains Act as Baffles To Inhibit the Intramolecular Rotation of Molecular Turnstiles

In artificial molecular devices, flexible, linear chains typically exhibit very weak capability in inhibiting molecular motion. Herein, we describe the dynamic properties of a series of molecular turnstiles consisting of a rigid frame and a phenyl rotator flanked with linear alkoxymethyl substituents. The long, flexible substituents act as elastic baffles to inhibit the rotations of the rotator at medium to fast speeds on the NMR time scale. When the rotator moves slowly, the substituents become more relaxed, thus obtaining an opportunity to completely thread through the cavity of the turnstiles. These findings reveal a basic but missing correlation between steric hindrance and speed of motion for flexible, linear chains in dynamic molecular devices, thus opening up a new direction toward molecular machines with more elaborate dynamic functions.

Self-Assembly of a [2]Pseudorotaxane by an Inchworm-Motion Mechanism

The threading of biomolecules through pores or channels in membranes is important to validate the physiological activities of cells. To aid understanding of the controlling factors required for the translocation in space with confined size and distorted conformation, it is desirable to identify experimental systems with minimized complexity. We demonstrate the mechanism of a linear guest L1 threading into a tris(crown ether) host TC with a combinational distorted cavity to form a triply interlocked [2]pseudorotaxane 3in-[L1⊂TC]. An inchworm-motion mechanism is proposed for the process. For the forward-threading steps that lead to the formation of higher-order interlocked species, guest L1 must adopt a bent conformation to find the next crown ether cavity. Two simplified models are applied to investigate the self-assembly dynamic of 3in-[L1⊂TC]. Kinetic NMR spectroscopic and molecular dynamics (MD) studies show that formation of the singly penetrated species is fast, whereas formation of the doubly and triply threaded species is several orders of magnitude slower. During threading the freedom of both the guest L1 and host TC gradually decrease due to their interactions. This results in a significant entropy effect for the threading dynamic, which is also observed for the threading of a biomolecular chain through a channel.

Catalysts Encapsulated in Molecular Machines

Smart catalysts offer the control of chemical processes and sequences of transformations, and catalysts with unique catalytic behavior can afford chiral products or promote successive polymerization. To meet advanced demands, the key to constructing smart catalysts is to incorporate traditional catalytic functional groups with trigger-induced factors. Molecular machines with dynamic properties and particular topological structures have typical stimulus-responsive features. In recent years, scientists have made efforts to utilize molecular machines (molecular switches, rotaxanes, motors, etc.) as scaffolds to develop smart catalysts. This Minireview focuses on the achievements of developing catalysts encapsulated in molecular machines and their remarkable specialties. This strategy is believed to provide more potential applications in switchable reactions, asymmetric synthesis, and processive catalysis.

Selective complexation of di-n-hexylammonium salts by tailed porphyrin host

A di-n-hexylammonium ion was selectively encapsulated in the cavity of tailed porphyrins due to induced fit and lipophilic interactions.

Sensitive Structural Control of Macrocycle Threading by a Fluorescent Squaraine Dye Flanked by Polymer Chains

A macrocyclic tetralactam is threaded by a complementary squaraine dye that is flanked by two polyethylene glycol chains to produce a pseudorotaxane complex with favorable near-infrared fluorescence properties. The association thermodynamics and kinetics were measured for a homologous series of squaraines with different N-alkyl substituents at both ends of the dye. The results show that subtle changes in substituent steric size have profound effects on threading kinetics without greatly altering the very high association constant.

Rapid Macrocycle Threading by a Fluorescent Dye-Polymer Conjugate in Water with Nanomolar Affinity

A macrocyclic tetralactam host is threaded by a highly fluorescent squaraine dye that is flanked by two polyethylene glycol (PEG) chains with nanomolar dissociation constants in water. Furthermore, the rates of bimolecular association are very fast with k(on) ≈ 10(6)-10(7) M(-1) s(-1). The association is effective under cell culture conditions and produces large changes in dye optical properties including turn-on near-infrared fluorescence that can be imaged using cell microscopy. Association constants in water are ∼1000 times higher than those in organic solvents and strongly enthalpically favored at 27 °C. The threading rate is hardly affected by the length of the PEG chains that flank the squaraine dye. For example, macrocycle threading by a dye conjugate with two appended PEG2000 chains is only three times slower than threading by a conjugate with triethylene glycol chains that are 20 times shorter. The results are a promising advance toward synthetic mimics of streptavidin/biotin.