Artificial Processive Catalytic Systems

Processive catalysts remain attached to a substrate and perform multiple rounds of catalysis. They are abundant in nature. This review highlights artificial processive catalytic systems, which can be divided into (A) catalytic rings that move along a polymer chain, (B) catalytic pores that hold polymer chains and decompose them, (C) catalysts that remain attached to and move around a cyclic substrate via supramolecular interactions, and (D) anchored catalysts that remain in contact with a substrate via multiple catalytic interactions (see frontispiece).

Kinetic enantio-recognition of chiral viologen guests by planar-chiral porphyrin cages

The kinetic enantio-recognition of chiral viologen guests by planar-chiral porphyrin cage compounds, measured in terms of ΔΔG‡on, is determined by the planar-chirality of the host and influenced by the size, as measured by ion mobility-mass spectrometry, but not the chirality of its substituents.

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.

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.

Rigidity and Flexibility in Rotaxanes and Their Relatives; On Being Stubborn and Easy-Going

Rotaxanes are an emerging class of molecules composed of two building blocks: macrocycles and threads. Rotaxanes, and their pseudorotaxane and polyrotaxane relatives, serve as prototypes for molecular-level switches and machines and as components in materials like elastic polymers and 3D printing inks. The rigidity and flexibility of these molecules is a characteristic feature of their design. However, the mechanical properties of the assembled rotaxane and its components are rarely examined directly, and the translation of these properties from molecules to bulk materials is understudied. In this Review, we consider the mechanical properties of rotaxanes by making use of concepts borrowed from physical organic chemistry. Rigid molecules have fewer accessible conformations with higher energy barriers while flexible molecules have more accessible conformations and lower energy barriers. The macrocycles and threads become rigidified when threaded together as rotaxanes in which the formation of intermolecular interactions and increased steric contacts collectively reduce the conformational space and raise barriers. Conversely, rotational and translational isomerism in rotaxanes adds novel modes of flexibility. We find that rigidification in rotaxanes is almost universal, but novel degrees of flexibility can be introduced. Both have roles to play in the function of rotaxanes.

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.

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.

Enantioselective synthesis of chiral porphyrin macrocyclic hosts and kinetic enantiorecognition of viologen guests

The construction of macromolecular hosts that are able to thread chiral guests in a stereoselective fashion is a big challenge. We herein describe the asymmetric synthesis of two enantiomeric C 2-symmetric porphyrin macrocyclic hosts that thread and bind different viologen guests. Time-resolved fluorescence studies show that these hosts display a factor 3 kinetic preference (ΔΔG ‡ on = 3 kJ mol-1) for threading onto the different enantiomers of a viologen guest appended with bulky chiral 1-phenylethoxy termini. A smaller kinetic selectivity (ΔΔG ‡ on = 1 kJ mol-1) is observed for viologens equipped with small chiral sec-butoxy termini. Kinetic selectivity is absent when the C 2-symmetric hosts are threaded onto chiral viologens appended with chiral tails in which the chiral moieties are located in the centers of the chains, rather than at the chain termini. The reason is that the termini of the latter guests, which engage in the initial stages of the threading process (entron effect), cannot discriminate because they are achiral, in contrast to the chiral termini of the former guests. Finally, our experiments show that the threading and de-threading rates are balanced in such a way that the observed binding constants are highly similar for all the investigated host-guest complexes, i.e. there is no thermodynamic selectivity.

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.

Constitutional Dynamic Networks-Guided Synthesis of Programmed "Genes", Transcription of mRNAs, and Translation of Proteins

Inspired by nature, where dynamic networks control the levels of gene expression and the activities of transcribed/translated proteins, we introduce nucleic acid-based constitutional dynamic networks (CDNs) as functional modules mimicking native circuits by demonstrating CDNs-guided programmed synthesis of genes, controlled transcription of RNAs, and dictated transcription/translation synthesis of proteins. An auxiliary CDN consisting of four dynamically equilibrated constituents AA', AB', BA', and BB' is orthogonally triggered by two different inputs yielding two different compositionally reconfigured CDNs. Subjecting the parent auxiliary CDN to two hairpins, H_A and H_B, and two templates T_A and T_B and a nicking/replication machinery leads to the cleavage of the hairpins and to the activation of the nicking/replication machineries that synthesize two "genes", e.g., the histidine-dependent DNAzyme g1 and the Zn²⁺-ion-dependent DNAzyme g2. The triggered orthogonal reconfiguration of the parent CDN to the respective CDNs leads to the programmed preferred CDN-guided synthesis of g1 or g2. Similarly, the triggered reconfigured CDNs are subjected to two hairpins H_C and H_D, the templates I'/I and J'/J, and the RNA polymerase (RNAp)/NTPs machinery. While the cleavage of the hairpins by the constituents associated with the parent CDN leads to the transcription of the broccoli aptamer recognizing the DFHBI ligand and of the aptamer recognizing the malachite green (MG) ligand, the orthogonally triggered CDNs lead to the CDNs-guided enhanced transcription of either the DFHBI aptamer or the MG aptamer. In addition, subjecting the triggered reconfigured CDNs to predesigned hairpins H_E and H_F, the templates M'/M and N'/N, the RNAp/NTPs machinery, and the cell-free ribosome t-RNA machinery leads to the CDNs-guided transcription/translation of the green fluorescence protein (GFP) or red fluorescence protein (RFP).

Molecular motor-functionalized porphyrin macrocycles

Molecular motors and switches change conformation under the influence of an external stimulus, e.g. light. They can be incorporated into functional systems, allowing the construction of adaptive materials and switchable catalysts. Here, we present two molecular motor-functionalized porphyrin macrocycles for future photo-switchable catalysis. They display helical, planar and point chirality, and are diastereomers, which differ in the relative orientation of the motor and macrocyclic components. Fluorescence, UV-vis, and ¹H NMR experiments reveal that the motor-functionalized macrocycles can bind and thread different variants of viologen guests, including a one-side blocked polymeric one of 30 repeat units. The latter feature indicates that the motor systems can find the open end of a polymer chain, thread on it, and move along the chain to eventually bind at the viologen trap, opening possibilities for catalytic writing on single polymer chains via chemical routes.

Molecular motors and switches change conformation under the influence of an external stimulus and can be incorporated into functional systems, allowing the construction of adaptive materials and switchable catalysts. Here, the authors present two molecular motor-functionalized porphyrin macrocycles for future photo-switchable catalysis.

A precise polyrotaxane synthesizer

Mechanically interlocked molecules are likely candidates for the design and synthesis of artificial molecular machines. Although polyrotaxanes have already found niche applications in exotic materials with specialized mechanical properties, efficient synthetic protocols to produce them with precise numbers of rings encircling their polymer dumbbells are still lacking. We report the assembly line-like emergence of poly[n]rotaxanes with increasingly higher energies by harnessing artificial molecular pumps to deliver rings in pairs by cyclical redox-driven processes. This programmable strategy leads to the precise incorporation of two, four, six, eight, and 10 rings carrying 8+, 16+, 24+, 32+, and 40+ charges, respectively, onto hexacationic polymer dumbbells. This strategy depends precisely on the number of redox cycles applied chemically or electrochemically, in both stepwise and one-pot manners.

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.

Directional Threading and Sliding of a Dissymmetrical Foldamer Helix on Dissymmetrical Axles

We have investigated the self-assembly of a dissymmetrical aromatic oligoamide helix on linear amido-carbamate rods. A dissymmetric sequence bearing two differentiated ends is able to wrap around dissymmetric dumbbell guest molecules. Structural and thermodynamic investigations allowed us to decipher the mode of binding of the helix that can bind specifically to the amide and carbamate groups of the rod. In parallel kinetic studies of threading and sliding of the helix along linear axles were also monitored by ¹ H NMR. Results show that threading of a dissymmetrical host can be kinetically biased by the nature of the guest terminus allowing a preferential sense of sliding of the helix. The study presented below further demonstrates the valuable potential of foldaxanes to combine designed molecular recognition patterns with fine control of self-assembly kinetics to conceive complex supramolecular events.

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.

Directional control of a processive molecular hopper

Intrigued by the potential of nanoscale machines, scientists have long attempted to control molecular motion. We monitored the individual 0.7-nanometer steps of a single molecular hopper as it moved in an electric field along a track in a nanopore controlled by a chemical ratchet. The hopper demonstrated characteristics desired in a moving molecule: defined start and end points, processivity, no chemical fuel requirement, directional motion, and external control. The hopper was readily functionalized to carry cargos. For example, a DNA molecule could be ratcheted along the track in either direction, a prerequisite for nanopore sequencing.

Securing a Supramolecular Architecture by Tying a Stopper Knot

We report on a rotaxane-like architecture secured by the in situ tying of an overhand knot in the tris(2,6-pyridyldicarboxamide) region of the axle through complexation with a lanthanide ion (Lu3+ ). The increase in steric bulk caused by the knotting locks a crown ether onto the thread. Removal of the lutetium ion unties the knot, and when the axle binding site for the ring is deactivated, the macrocycle spontaneously dethreads. When the binding interaction is switched on again, the crown ether rethreads over the 10 nm length of the untangled strand. The overhand knot can be retied, relocking the threaded structure, by once again adding lutetium ions.

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.

Chemoselective guest-triggered shaping of a polynuclear CuII calix[6]complex into a molecular host

A new calix[6]arene scaffold bearing a tris-imidazole binding site at the small rim and three tetradentate aza ligands at the large rim was synthesized. The system binds three Cu^II ions at the large rim sites and is unable to bind a fourth one, which remains in solution. The charge repulsion between the complexes, together with the flexibility of the scaffold, disorganizes the small rim site for binding and prevents its use for host-guest studies. Although the presence of MeCN or DMF guests does not alter this state, the addition of a heptylamine guest, which further displays Brønsted basicity, restores its receptor ability by stabilizing the extra Cu^II ion at the tris-imidazole site with concomitant guest encapsulation and binding of an exo hydroxo ligand. This chemoselective nuclearity switch yields a tetranuclear complex in which the guest backbone is preorganized in front of three potentially reactive Cu(ii) complexes, reminiscent of polynuclear Cu^II enzyme active sites.

Pseudorotaxane formation via the slippage process with chemically cyclized oligonucleotides

Circular nucleic acids have been utilized for versatile applications by taking advantage of the unique characteristic of their circular structure. In our previous study, we found that the chemically-cyclized ODN (cyODN) with double-tailed parts formed a pseudorotaxane structure with the target via the slippage process. We now report the investigation of the slippage properties and the mechanism of the slippage process using six different cyODNs. Our results indicate that the formation efficiency significantly depend on the temperature, the ring size, the target length and the mismatched position of the target. The kinetic studies also showed that this pseudorotaxane formation would proceed via a non-threaded structure which hybridizes with the target at the double-tailed parts. In addition, the resulting pseudorotaxanes showed interesting characteristics unlike the canonical duplex such as the hysteresis loop in the T_m measurements and the kinetic stabilization by lengthening the target. This information will be fundamentally important for finding new functions of circular nucleic acids and elucidating the threading mechanism regarding other synthetic small molecules and biopolymers.

Structural Control of Kinetics for Macrocycle Threading by Fluorescent Squaraine Dye in Water

While the general concept of steric speed bumps has been demonstrated in rotaxane shuttles and macrocycle threading systems, the sensitivity of speed bump effects has not been evaluated as a function of structural geometry. Values of K_a and k_on for macrocycle threading in water are reported for a series of homologous squaraine dyes with different substituents (speed bumps) on the flanking chains and two macrocycles with different cavity sizes. Sensitivity to a steric speed bump effect was found to depend on (a) structural location, being lowest when the speed bump was near the end of a flanking chain, and (b) macrocycle cavity size, which was enhanced when the cavity was constricted. This new insight is broadly applicable to many types of molecular threading systems.

Unexpected Interactions between Alkyl Straps and Pyridine Ligands in Sulfur-Strapped Porphyrin Nanorings

Strapped or “basket-handle” porphyrins have been investigated previously as hemoglobin mimics and catalysts. The facial selectivity of their interactions with axial ligands is a sensitive test for noncovalent bonding. Here the binding of pyridyl ligands to zinc porphyrins with thioester-linked alkyl straps is investigated in solution by NMR spectroscopy and UV–vis titration, and in the solid state by X-ray crystallography. We expected that coordination of the axial ligand would occur on the less hindered face of the porphyrin, away from the strap. Surprisingly, attractive interactions between the strap and the ligand direct axial coordination to the strapped face of the porphyrin, except when the strap is short and tight. The strapped porphyrins were incorporated into π-conjugated cyclic porphyrin hexamers using template-directed synthesis. The strap and the sulfur substituents are located either inside or outside the porphyrin nanoring, depending on the length of the strap. Six-porphyrin nanorings with outwardly pointing sulfur anchors were prepared for exploring quantum interference effects in single-molecule charge transport.

Accelerating chemical reactions by molecular sledding

The speed-up of covalent bond formation was achieved between a sulfhydryl group and a 2-bromopropionic acid derivative by utilizing sliding peptide-modified substrates. Moreover, a new type of DNA cleaving reagent was developed, consisting of pVIc covalently coupled to verteporfin. This peptide-porphyrin conjugate allowed targeting of DNA and resulted in increased photodegradation of double-stranded nucleic acids.

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.

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.

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.

Asymmetric Catalysis with a Mechanically Point-Chiral Rotaxane

Mechanical point-chirality in a [2]rotaxane is utilized for asymmetric catalysis. Stable enantiomers of the rotaxane result from a bulky group in the middle of the thread preventing a benzylic amide macrocycle shuttling between different sides of a prochiral center, creating point chirality in the vicinity of a secondary amine group. The resulting mechanochirogenesis delivers enantioselective organocatalysis via both enamine (up to 71:29 er) and iminium (up to 68:32 er) activation modes.

Celebrating Soft Matter's 10th Anniversary: Topology matters: structure and dynamics of ring polymers

Considering topology among all polymer architectures polymer rings are unique, as they are the simplest closed structures without ends. In this review we present recent experimental advances addressing the structure and dynamics of rings. We focus mainly on neutron scattering results that reveal experimental insight on a molecular scale. We first briefly reflect on the progress in ring chemistry that made the experimental access possible. Structural investigations characterizing rings as compact objects in the melts are put into theoretical context. In contrast to the plateau regime common for all other high molecular weight polymer systems, the dynamic modulus of pure ring systems is characterized by a power law decay, while the viscosity displays a much weaker molecular weight dependence as a corresponding linear melt. The dynamics of ring melts is uniquely addressed by neutron spin-echo spectroscopy. The sub-diffusive center of mass motion at short times agrees well with simulation as well as theoretical concepts. In the internal dynamics the basic length scale of the ring molecule, the loop size, manifests itself clearly. The experiments reveal strong evidence for loop motions and call for further theoretical work describing them. Finally, small fractions of ring molecules in linear melts turn out to be very sensitive probes in order to scrutinize the dynamics of the host with the potential to reveal fundamental aspects of the dynamics of branched polymer systems.

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.

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.

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.