Porphyrin Macrocyclic Catalysts for the Processive Oxidation of Polymer Substrates

Gene Editing with Artificial DNA Scissors

Artificial metallo-nucleases (AMNs) are small molecule DNA cleavage agents, also known as DNA molecular scissors, and represent an important class of chemotherapeutic with high clinical potential. This review provides a primary level of exploration on the concepts key to this area including an introduction to DNA structure, function, recognition, along with damage and repair mechanisms. Building on this foundation, we describe hybrid molecules where AMNs are covalently attached to directing groups that provide molecular scissors with enhanced or sequence specific DNA damaging capabilities. As this research field continues to evolve, understanding the applications of AMNs along with synthetic conjugation strategies can provide the basis for future innovations, particularly for designing new artificial gene editing systems.

Mechanistic Studies on the Epoxidation of Alkenes by Macrocyclic Manganese Porphyrin Catalysts

Macrocyclic metal porphyrin complexes can act as shape-selective catalysts mimicking the action of enzymes. To achieve enzyme-like reactivity, a mechanistic understanding of the reaction at the molecular level is needed. We report a mechanistic study of alkene epoxidation by the oxidant iodosylbenzene, mediated by an achiral and a chiral manganese(V)oxo porphyrin cage complex. Both complexes convert a great variety of alkenes into epoxides in yields varying between 20-88 %. We monitored the process of the formation of the manganese(V)oxo complexes by oxygen transfer from iodosylbenzene to manganese(III) complexes and their reactivity by ion mobility mass spectrometry. The results show that in the case of the achiral cage complex the initial iodosylbenzene adduct is formed on the inside of the cage and in the case of the chiral one on the outside of the cage. Its decomposition leads to a manganese complex with the oxo ligand on either the inside or outside of the cage. These experimental results are confirmed by DFT calculations. The oxo ligand on the outside of the cage reacts faster with a substrate molecule than the oxo ligand on the inside. The results indicate how the catalytic activity of the macrocyclic porphyrin complex can be tuned and explain why the chiral porphyrin complex does not catalyze the enantioselective epoxidation of alkenes.

Robotic end-to-end fusion of microtubules powered by kinesin

The active assembly of molecules by nanorobots has advanced greatly since “molecular manufacturing”—that is, the use of nanoscale tools to build molecular structures—was proposed. In contrast to a catalyst, which accelerates a reaction by smoothing the potential energy surface along the reaction coordinate, molecular machines expend energy to accelerate a reaction relative to the baseline provided by thermal motion and forces. Here, we design a nanorobotics system to accelerate end-to-end microtubule assembly by using kinesin motors and a circular confining chamber. We show that the mechanical interaction of kinesin-propelled microtubules gliding on a surface with the walls of the confining chamber results in a nonequilibrium distribution of microtubules, which increases the number of end-to-end microtubule fusion events 20-fold compared with microtubules gliding on a plane. In contrast to earlier nanorobots, where a nonequilibrium distribution was built into the initial state and drove the process, our nanorobotic system creates and actively maintains the building blocks in the concentrated state responsible for accelerated assembly through the adenosine triphosphate–fueled generation of force by kinesin-1 motor proteins. This approach can be used in the future to develop biohybrid or bioinspired nanorobots that use molecular machines to access nonequilibrium states and accelerate nanoscale assembly.

New horizons for catalysis disclosed by supramolecular chemistry

The adoption of a supramolecular approach in catalysis promises to address a number of unmet challenges, ranging from activity (unlocking of novel reaction pathways) to selectivity (alteration of the innate selectivity of a reaction, e.g. selective functionalization of C-H bonds) and regulation (switch ON/OFF, sequential catalysis, etc.). Supramolecular tools such as reversible association and recognition, pre-organization of reactants and stabilization of transition states upon binding offer a unique chance to achieve the above goals disclosing new horizons whose potential is being increasingly recognized and used, sometimes reaching the degree of ripeness for practical use. This review summarizes the main developments that have opened such new frontiers, with the aim of providing a guide to researchers approaching the field. We focus on artificial supramolecular catalysts of defined stoichiometry which, under homogeneous conditions, unlock outcomes that are highly difficult if not impossible to attain otherwise, namely unnatural reactivity or selectivity and catalysis regulation. The different strategies recently explored in supramolecular catalysis are concisely presented, and, for each one, a single or very few examples is/are described (mainly last 10 years, with only milestone older works discussed). The subject is divided into four sections in light of the key design principle: (i) nanoconfinement of reactants, (ii) recognition-driven catalysis, (iii) catalysis regulation by molecular machines and (iv) processive catalysis.

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.

Allosteric Guest Binding in Chiral Zirconium(IV) Double Decker Porphyrin Cages

Chiral zirconium(IV) double cage sandwich complex Zr(1)2 has been synthesized in one step from porphyrin cage H21. Zr(1)2 was obtained as a racemate, which was resolved by HPLC and the enantiomers were isolated in >99.5 % ee. Their absolute configurations were assigned on the basis of X-ray crystallography and circular dichroism spectroscopy. Vibrational circular dichroism (VCD) experiments on the enantiomers of Zr(1)2 revealed that the chirality around the zirconium center is propagated throughout the whole cage structure. The axial conformational chirality of the double cage complex displayed a VCD fingerprint similar to the one observed previously for a related chiral cage compound with planar and point chirality. Zr(1)2 shows fluorescence, which is quenched when viologen guests bind in its cavities. The binding of viologen and dihydroxybenzene derivatives in the two cavities of Zr(1)2 occurs with negative allostery, the cooperativity factors α (=4 K2/K1) being as low as 0.0076 for the binding of N,N'-dimethylviologen. These allosteric effects are attributed to a pinching of the second cavity as a result of guest binding in the first cavity.

Functional Rotaxanes in Catalysis

Mechanically interlocked molecules (MIMs) have gained attention in the field of catalysis due to their unique molecular properties. Central to MIMs, rotaxanes are highly promising and attractive supramolecular catalysts due to their unique three-dimensional structures and the flexibility of their subcomponents. This Minireview discusses the use of rotaxanes in organocatalysis and transition-metal catalysis.

Double Porphyrin Cage Compounds

The synthesis and characterization of double porphyrin cage compounds are described. They consist of two porphyrins that are each attached to a diphenylglycoluril-based clip molecule via four ethyleneoxy spacers, and are linked together by a single alkyl chain using "click"-chemistry. Following a newly developed multistep synthesis procedure we report three of these double porphyrin cages, linked by spacers of different lengths, i.e. 3, 5, and 11 carbon atoms. The structures of the double porphyrin cages were fully characterized by NMR, which revealed that they consist of mixtures of two diastereoisomers. Their zinc derivatives are capable of forming sandwich-like complexes with the ditopic ligand 1,4-diazabicyclo[2,2,2]octane (dabco).

Cyclodextrin Rotaxanes of Pt Complexes and Their Conversion to Pt Nanoparticles

The cationic Pt complex (Pt(NC₆H₄-C₆H₄N-(CH₂)₁₀-O(C₆H₃-3,5-(OMe)₂)(MeN-(CH₂CH₂NMe₂)₂))⁺ was prepared by the reaction of alkylbipyridinium ligand with a nitrateplatinum(II) complex. Mixing the complex and α- and β-cyclodextrins in aqueous media produced the corresponding [2]rotaxanes with 1:1 stoichiometry. γ-Cyclodextrin and the Pt complex formed a rotaxane having components in a 1:1 or 2:1 molar ratio. The results of mass and nuclear magnetic resonance (NMR) measurements confirmed the rotaxane structures of the Pt complexes. Transmission electron microscopy (TEM) and atomic force microscope (AFM) analyses revealed the formation of micelles or vesicles. The addition of NaBH₄ to the rotaxanes in aqueous media formed Pt nanoparticles with diameters of 1.3-2.8 nm, as characterized by TEM. The aggregated size of the nanoparticles formed from the rotaxane did not change even at 70 °C, and they showed higher thermal stability than those obtained from the reduction of the cyclodextrin-free Pt complex.

Self-Assembly of Covalently Linked Porphyrin Dimers at the Solid-Liquid Interface

The synthesis and surface self-assembly behavior of two types of metal-porphyrin dimers is described. The first dimer type consists of two porphyrins linked via a rigid conjugated spacer, and the second type has an alkyne linker, which allows rotation of the porphyrin moieties with respect to each other. The conjugated dimers were equipped with two copper or two manganese centers, while the flexible dimers allowed a modular built-up that also made the incorporation of two different metal centers possible. The self-assembly of the new porphyrin dimers at a solid-liquid interface was investigated at the single-molecule scale using scanning tunneling microscopy (STM). All dimers formed monolayers, of which the stability and the internal degree of ordering of the molecules depended on the metal centers in the porphyrins. While in all monolayers the dimers were oriented coplanar with respect to the underlying surface ('face-on'), the flexible dimer containing a manganese and a copper center could be induced, via the application of a voltage pulse in the STM setup, to self-assemble into monolayers in which the porphyrin dimers adopted a non-common perpendicular ('edge-on') geometry with respect to the surface.

Effect of Chirality on the Binding of Viologen Guests in Porphyrin Macrocycles

As part of a project aimed at the development of chiral processive catalysts that can write information on a polymer chain we describe the synthesis of two optically active porphyrin macrocycles, which are prepared in 3 steps from an achiral precursor compound. Fluorescence and 1H-NMR studies show that one of the macrocycles displays selectivity in the binding of chiral viologen guest molecules.

Aerobic Epoxidation of Low-Molecular-Weight and Polymeric Olefins by a Supramolecular Manganese Porphyrin Catalyst

We report on the highly efficient epoxidation of low-molecular-weight and polymeric olefins catalyzed by a supramolecular manganese porphyrin complex using molecular oxygen as an oxidant and an aldehyde as a co-reductant. At ambient temperature and under optimized reaction conditions, the catalyst showed high activity and stereoselectivity. The efficiency of the supramolecular manganese porphyrin was higher than that of a reference porphyrin catalyst, possibly because it was more stable under the applied reaction conditions. Mechanistic studies suggest that a manganese oxo porphyrin complex may be an intermediate in the epoxidation reaction.

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.

Directional threading of a chiral porphyrin cage compound onto viologen guests

We report the face-selective threading of a chiral porphyrin cage compound onto viologen guests that are provided on both ends with substituents of different sizes. Depending on the types of terminal groups on the guest the cage compound orients itself in one of two possible directions.

Direct Synthesis of Chiral Porphyrin Macrocyclic Receptors via Regioselective Nitration

Nitration of tetraphenylporphyrin cage compound 1, at -40 °C, leads to the regioselective formation of the chiral mononitro compound 2 (75% isolated yield) and, at -30 °C, to the achiral syn-dinitro-derivative 3 and the chiral anti-dinitro derivative 4 in a diastereomeric ratio of 5:2, which were separated by chromatography (46 and 20% yields, respectively). The structures of the compounds were confirmed by X-ray crystallography.

Synthetic polymers as substrates for a DNA-sliding clamp protein

The clamp protein (gp45) of the DNA polymerase III of the bacteriophage T4 is known to bind to DNA and stay attached to it in order to facilitate the process of DNA copying by the polymerase. As part of a project aimed at developing new biomimetic data-encoding systems we have investigated the binding of gp45 to synthetic polymers, that is, rigid, helical polyisocyanopeptides. Molecular modelling studies suggest that the clamp protein may interact with the latter polymers. Experiments aimed at verifying these interactions are presented and discussed.

A manganese porphyrin–α-cyclodextrin conjugate as an artificial enzyme for the catalytic epoxidation of polybutadiene

A manganese porphyrin–α-cyclodextrin conjugate was designed as an artificial clamp-like enzyme to catalyze the epoxidation of cis-polybutadiene with trans-epoxide preference.

Mimicking the Regulation Step of Fe-Monooxygenases: Allosteric Modulation of FeIV -Oxo Formation by Guest Binding in a Dinuclear ZnII -FeII Calix[6]arene-Based Funnel Complex

A heteroditopic ligand associated with a calix[6]arene scaffold bearing a tris(imidazole) coordinating site at its small rim and an amine/pyridine ligand at its large rim has been prepared, and its regioselective coordination to Zn^II at the small rim and Fe^II in the amine/pyridine ligand has been achieved. The heterodinuclear complex obtained displays an overall cone conformation capped by the tris(imidazole)Zn^II moiety and bears a non-heme Fe^II complex at its base. Each of the metal centers exhibits one labile position, allowing the coordination inside the cavity of a guest alkylamine at Zn^II and the generation of reaction intermediates (Fe^III (OOH) and Fe^IV O) at the large rim. A dependence between the chain length of the encapsulated alkylamine and the distribution of Fe^III (OOH) intermediates and Fe^III (OMe) is observed. In addition, it is shown that the generation of the Fe^IV O intermediate is enhanced by addition of the alkylamine guest. Hence, this supramolecular system gathers the three levels of reactivity control encountered in oxidoreductases: i) control of the Fe^II redox properties through its first coordination sphere, allowing us to generate high valent reactive species; ii) control of guest binding through a hydrophobic funnel that drives its alkyl chain next to the reactive iron complex, thus mimicking the binding pocket of natural systems; iii) guest-modulated reactivity of the Fe^II center towards oxidants.

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.

Wholly Synthetic Molecular Machines

The past quarter of a century has witnessed an increasing engagement on the part of physicists and chemists in the design and synthesis of molecular machines de novo. This minireview traces the development of artificial molecular machines from their prototypes in the form of shuttles and switches to their emergence as motors and pumps where supplies of energy in the form of chemical fuel, electrochemical potential and light activation become a minimum requirement for them to function away from equilibrium. The challenge facing this rapidly growing community of scientists and engineers today is one of putting wholly synthetic molecules to work, both individually and as collections. Here, we highlight some of the recent conceptual and practical advances relating to the operation of wholly synthetic rotary and linear motors.

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.

Transition metal catalysis in confined spaces

Transition metal catalysis plays an important role in both industry and in academia where selectivity, activity and stability are crucial parameters to control. Next to changing the structure of the ligand, introducing a confined space as a second coordination sphere around a metal catalyst has recently been shown to be a viable method to induce new selectivity and activity in transition metal catalysis. In this review we focus on supramolecular strategies to encapsulate transition metal complexes with the aim of controlling the selectivity via the second coordination sphere. As we will discuss, catalyst confinement can result in selective processes that are impossible or difficult to achieve by traditional methods. We will describe the template-ligand approach as well as the host-guest approach to arrive at such supramolecular systems and discuss how the performance of the catalyst is enhanced by confining it in a molecular container.

Molecular computing: paths to chemical Turing machines

In this perspective, we highlight some of the recent advances in the development of molecular and biomolecular systems for performing logic operations and computing. We also present a blueprint of a chemical Turing machine using a processive catalytic approach.

To comply with the rapidly increasing demand of information storage and processing, new strategies for computing are needed. The idea of molecular computing, where basic computations occur through molecular, supramolecular, or biomolecular approaches, rather than electronically, has long captivated researchers. The prospects of using molecules and (bio)macromolecules for computing is not without precedent. Nature is replete with examples where the handling and storing of data occurs with high efficiencies, low energy costs, and high-density information encoding. The design and assembly of computers that function according to the universal approaches of computing, such as those in a Turing machine, might be realized in a chemical way in the future; this is both fascinating and extremely challenging. In this perspective, we highlight molecular and (bio)macromolecular systems that have been designed and synthesized so far with the objective of using them for computing purposes. We also present a blueprint of a molecular Turing machine, which is based on a catalytic device that glides along a polymer tape and, while moving, prints binary information on this tape in the form of oxygen atoms.

Hexaethylsubporphyrins: β-alkyl analogues in the subporphyrin family

Two new subporphyrins were synthesized for the first time from a β-substituted pyrrole i.e. 3,4-diethylpyrrole via pyridine-tri-N-(3,4-diethylpyrrolyl)borane as building blocks.

Biomimetic cavity-based metal complexes

The biomimetic association of a metal ion with a cavity allows selective recognition, unusual redox properties and new reactivity patterns.

Slippage of a porphyrin macrocycle over threads of varying bulkiness: implications for the mechanism of threading polymers through a macrocyclic ring

Threading of a polymer through a macrocyclic ring may occur directly, that is, by finding the end of the polymer chain, or by a process in which the polymer chain first folds and then threads through the macrocyclic ring in a hairpin-like conformation. We present kinetic and thermodynamic studies on the threading of a macrocyclic porphyrin receptor (H2 1) onto molecular threads that are blocked on one side and are open on the other side. The open side is modified by groups that vary in ease of folding and in bulkiness. Additionally, the threads contain a viologen binding site for the macrocyclic receptor, which is located close to the blocking group. The rates of threading of H2 1 were measured under various conditions, by recording as a function of time the quenching of the fluorescence of the porphyrin, which occurs when receptor H2 1 reaches the viologen binding site. The kinetic data suggest that threading is impossible if the receptor encounters an open side that is sterically encumbered in a similar way as a folded polymer chain. This indicates that threading of polymers through macrocyclic compounds through a folded chain mechanism is unlikely.

Control of reaction pathways in the photochemical reaction of a quinone with tetramethylethylene by metal binding

The present study reports a novel supramolecular photochemical reaction that focuses on the direct electronic interactions between a host reaction substrate and guest metal salts. The reaction pathways in the photochemical reactions of quinone derivatives bearing a methoxy group and a long oligoether sidearm QEn (n = 0 and 3) with tetramethylethylene (TME) are changed upon noncovalent complexations of the host reactant with alkali and alkaline earth metal ions and a transition metal salt. The photochemical reaction of QEn with TME provides a mixture of [2 + 2] cycloadducts 1aEn and 1bEn, hydroquinone H2QEn, and monoallyl ether adducts of hydroquinones 2aEn and 2bEn. The photochemical reaction proceeds by the photoinduced electron transfer mechanism, where photoirradiation brings about formation of a radical ion pair [QEn˙(-), TME˙(+)] as the primary intermediate. We found that the yields and selectivity of these photoproducts are changed upon electronic interactions of QEn˙(-) with the metal salts. The photochemical reaction in the absence of metal salts provides H2QEn as its major product, whereas QE3, having the long sidearm, dominantly produces 2aE3 at the expense of 1aE3, 1bE3, and H2QE3 when it forms a size-favorable host-guest complex with divalent Ca(2+). In contrast, QEn selectively provides oxetanes 1aEn and 1bEn in the presence of Pd(OAc)2, which can form complexes with the quinone through metal-olefin and coordination interactions in the ground and photoexcited states of the quinone.

Processive catalysis

Nature's enzymes are an ongoing source of inspiration for scientists. The complex processes behind their selectivity and efficiency is slowly being unraveled, and these findings have spawned many biomimetic catalysts. However, nearly all focus on the conversion of small molecular substrates. Nature itself is replete with inventive catalytic systems which modify, replicate, or decompose entire polymers, often in a processive fashion. Such processivity can, for example, enhance the rate of catalysis by clamping to the polymer substrate, which imparts a large effective molarity. Reviewed herein are the various strategies for processivity in nature's arsenal and their properties. An overview of what has been achieved by chemists aiming to mimic one of nature's greatest tricks is also included.