Synthesis and Dynamics of Nanosized Phenylene-Ethynylene-Butadiynylene Rotaxanes and the Role of Shape Persistence

Pretzelanes, [1]rotaxanes and molecular figures-of-eight - crossing the bridge from fundamentals to functional applications

There are myriad [2]catenanes and [2]rotaxanes that consist of two interlocked molecular components. On occasion, supramolecular chemists prepare interlocked molecules where there are covalent linkages between the interlocked molecular components. In this review, progress on pretzelanes ([1]catenanes), [1]rotaxanes and molecular figures-of-eight is surveyed. Particular attention is paid to the application of such molecules, especially where the interlocked structure and/or the covalent linkage(s) play a key functional role.

Covalent Template-Directed Synthesis: A Powerful Tool for the Construction of Complex Molecules

Template-directed synthesis has become a powerful methodology to access complex molecules. Noncovalent templating has been widely used in the last few decades, but less attention has been paid to covalent template-directed synthesis, despite the fact that this methodology was used for the first reported synthesis of a catenane. This review highlights the evolution of covalent templating over the last 60 years, thereby providing a toolbox for the design of efficient covalent templating processes. Covalent templating represents a useful synthetic tool for accessing complex molecules, and the examples described here include the synthesis of macrocycles, mechanically interlocked molecules, linear oligomers, polydisperse linear polymers, and cross-linked polymer networks.

Boronic ester-templated pre-rotaxanes as versatile intermediates for rotaxane endo-functionalisation

We report on the synthesis of [2]rotaxanes from vicinal diols through dynamic covalent boronic ester templates, as well as the use of the boronic ester for rotaxane post-functionalisation. A boronic acid pincer ligand with two alkene-appended arms was condensed with a linear diol-containing thread, and ring-closing metathesis established a pre-rotaxane architecture along with a non-entangled isomer. Advanced NMR spectroscopy and mass spectrometry unambiguously assigned the isomers and revealed that the pre-rotaxane was in equilibrium with its hydrolyzed free [2]rotaxane form. The boronic ester handle in the pre-rotaxane could be synthetically addressed in a multitude of ways to obtain different endo-functionalised [2]rotaxanes, including with direct oxidation reactions, protodeboronation, functional group interconversions and Pd-catalysed cross-couplings.

From π-Conjugated Rods to Shape-Persistent Rings, Wheels, and Ladders: The Question of Rigidity

ConspectusRigid-rod oligomers and polymers are mostly based on (hetero)aromatic rings connected with each other, either directly or via ethynylene or butadiynylene linkers, or by a combination of both structural elements. Although they are much more rigid than vinyl polymers, they exhibit considerable structural flexibility, often more than would be expected merely from their chemical structure. This disparity holds for both linear as well as for cyclic structures. The flexibility of rigid-rod polymers, which is directly observable for defined oligomers of different lengths at the solid-liquid interface by means of scanning-tunneling microscopy, also impacts their optical and electronic properties. The flexibility can be used, for example, to control whether an oligomer with two different fluorescent end-groups emits from either the one or the other. The flexibility of shape-persistent macrocycles also has an impact on the overall thermal stability of mechanically interlocked molecular architectures. However, the degree of flexibility can be reduced when rigid struts are covalently mounted into the inside of the rings, leading to the formation of so-called molecular spoked wheels. The combination of these two elements─rings and rods─stiffens both of them: the ring perimeter is prevented from collapsing and the internal rods from bending. These compounds have been further developed as platform molecules, where three spokes stiffen the ring and together form a tripod-like platform, while a fourth arm points─after adsorption to a solid substrate─above the plane of the molecule. This pillar makes it possible to decouple a functional group at the end of the arm from the surface. Rigidity enhancement by the introduction of rigid spacer elements can also be applied to the case of rigid-rod polymers and is visualized by sophisticated molecular dynamics simulations. In this case, formation of single-stranded oligomers and polymers, and a subsequent zipping reaction to form ladder-like structures, directly allows, by means of single-molecule fluorescence spectroscopy, a comparison of the single- and double-stranded molecules. In particular in the case of the polymers, which can be up to 100 nm in length, the enhancement of rigidity is quite remarkable. Overall, the covalent connection of two or more rigid molecular entities has a self-reinforcing effect: all parts of the molecule gain rigidity. Since overall synthetic yields for such complex high-molecular weight covalently bound shape-persistent structures can still be low, scanning tunneling microscopy and single-molecule fluorescence spectroscopy are the methods of choice for structural analyses. Preliminary results illustrate how these compounds can serve as versatile sources of deterministic single photons on demand, since rigidity also enhances the intramolecular flow of excitation energy, and suggest a range of applications in optoelectronic devices.

Modular Synthesis of Improbable Rotaxanes with All-Benzene Scaffolds

"Improbable" rotaxanes consisting of interlocked conjugated components represent non-trivial synthetic targets, not to mention those with all-benzene scaffolds. Herein, a modular synthetic strategy has been established using an isolable azo-linked pre-rotaxane as the core module, in which the azo group functions as a tracelessly removable template to direct mechanical bond formations. Through versatile connections of the pre-rotaxane and other customizable modules, [2]- and [3]rotaxanes derived from all-benzene scaffolds have been accomplished, demonstrating the utility and potential of the synthetic design for all-benzene interlocked supramolecules.

Synthesis of 'Impossible' Rotaxanes

'Impossible' rotaxanes, which are constituted by interlocked components without obvious binding motifs, have attracted the interest of the mechanically interlocked molecules (MIMs) community. Within the synthetic efforts reported in the last decades towards the preparation of MIMs, some innovative protocols for accessing 'impossible' rotaxanes have been developed. This short review highlights different selected synthetic examples of 'impossible' rotaxanes, as well as suggests some future directions of this research area.

Threading a Linear Molecule Through a Macrocycle Thanks to Boron: Optical Properties of the Threaded Species and Synthesis of a Rotaxane

Two BODIPYs and two boron β-diketonates were threaded through a macrocycle bearing a 2,2'-biphenol unit, showing thus the ability of boron to act as a gathering atom. The new threaded species were characterized by 1D and 2D NMR spectroscopy as well as by X-ray crystallography for one of them and their properties rationalized with quantum chemistry to unravel the vibronic contributions. The BODIPYs exhibited interesting fluorescence features with quantum yields up to 91 % and enhanced photostability compared to their non-threaded homologues. A rotaxane was synthesized using this threading strategy after stoppering and removing the boron with potassium hydroxide.

Flexible Phenanthracene Nanotubes for Explosive Detection

Phenanthracene nanotubes with arylene-ethynylene-butadiynylene rims and phenanthracene walls are synthesized in a modular bottom-up approach. One of the rims carries hexadecyloxy side chains, mediating the affinity to highly oriented pyrolytic graphite. Molecular dynamics simulations show that the nanotubes are much more flexible than their structural formulas suggest: In 12, the phenanthracene units act as hinges that flip the two macrocycles relative to each other to one of two possible sites, as quantum mechanical models suggest and scanning tunneling microscopy investigations prove. Unexpectedly, both theory and experiment show for 13 that the three phenanthracene hinges are deflected from the upright position, accompanied by a deformation of both macrocycles from their idealized sturdy macroporous geometry. This flexibility together with their affinity to carbon-rich substrates allows for an efficient host-guest chemistry at the solid/gas interface opening the potential for applications in single-walled carbon nanotube-based sensing, and the applicability to build new sensors for the detection of 2,4,6-trinitrotoluene via nitroaromatic markers is shown.

Rapid Access to Encapsulated Molecular Rotors via Coordination-Driven Macrocycle Formation

Macrocycle formation that relies upon trans metal coordination of appropriately placed pyridine ligands within an arylene ethynylene construct provides rapid and reliable access to molecular rotators encapsulated within macrocyclic stators. Showing no significant close contacts to the central rotators, X-ray crystallography of AgI -coordinated macrocycles provides plausibility for unobstructed rotation or wobbling of rotators within the central cavity. Solid-state 13 C NMR of PdII -coordinated macrocycles supports the notion of unobstructed movement of simple arenes in the crystal lattice. Solution 1 H NMR studies indicate complete and immediate macrocycle formation upon the introduction of PdII to the pyridyl-based ligand at room temperature. Moreover, the formed macrocycle is stable in solution; a lack of significant changes in the 1 H NMR spectrum upon cooling to -50 °C is consistent with the absence of dynamic behavior. The synthetic route to these macrocycles is expedient and modular, providing access to rather complex constructs in four simple steps involving Sonogashira coupling and deprotection reactions.

Knotting matters: orderly molecular entanglements

Entangling strands in a well-ordered manner can produce useful effects, from shoelaces and fishing nets to brown paper packages tied up with strings. At the nanoscale, non-crystalline polymer chains of sufficient length and flexibility randomly form tangled mixtures containing open knots of different sizes, shapes and complexity. However, discrete molecular knots of precise topology can also be obtained by controlling the number, sequence and stereochemistry of strand crossings: orderly molecular entanglements. During the last decade, substantial progress in the nascent field of molecular nanotopology has been made, with general synthetic strategies and new knotting motifs introduced, along with insights into the properties and functions of ordered tangle sequences. Conformational restrictions imparted by knotting can induce allostery, strong and selective anion binding, catalytic activity, lead to effective chiral expression across length scales, binding modes in conformations efficacious for drug delivery, and facilitate mechanical function at the molecular level. As complex molecular topologies become increasingly synthetically accessible they have the potential to play a significant role in molecular and materials design strategies. We highlight particular examples of molecular knots to illustrate why these are a few of our favourite things.

Ring-Over-Ring Deslipping From Imine-Bridged Heterorotaxanes

Ring-over-ring slippage and ring-through-ring penetration are important processes in the construction of ring-in-ring multiple interlocked architectures. We have successfully observed “ring-over-ring deslipping” on the rotaxane axle by exploiting the dynamic covalent nature of imine bonds in imine-bridged heterorotaxanes R1 and R2 with two macrocycles of different ring sizes on the axle. When the imine bridges of R1 were cleaved, a hydrolyzed hetero[4]rotaxane [4]R1′ was formed as an intermediate under dynamic equilibrium, and the larger 38-membered macrocycle M was deslipped over the 24-membered ring (24C8 or DB24C8) to dissociate into a [3]rotaxane [3]R3 and a macrocycle M. The time dependent NMR measurement and the determined thermodynamic parameters revealed that the rate-limiting step of the deslipping process was attributed to steric hindrance between two rings and reduced mobility of M due to proximity to the crown ether, which was bound to the anilinium on the axle molecule.

Condensation of pyrylium salts with mixed anhydrides: aryl ethers, aryl amines and sterically congested aromatics

Condensation of 2,4,6-triaryl pyrylium salts with mixed anhydrides, formed in situ from α-functionalized sodium acetates and an anhydride solvent, leads in good yields to the corresponding 2,4,6-triaryl benzenes functionalized at their 1-position.

Precision synthesis of linear oligorotaxanes and polyrotaxanes achieving well-defined positions and numbers of cyclic components on the axle

Interest in macromolecules has increased because of their functional properties, which can be tuned using precise organic synthetic methods. For example, desired functions have been imparted by controlling the nanoscale structures of such macromolecules. In particular, compounds with interlocked structures, including rotaxanes, have attracted attention because of their unique supramolecular structures. In such supramolecular structures, the mobility and freedom of the macrocycles are restricted by an axle and dependent on those of other macrocycles, which imparts unique functions to these threaded structures. Recently, methods for the ultrafine engineering and synthesis, as well as functions, of "defined" rotaxane structures that are not statistically dispersed on the axle (i.e., control over the number and position of cyclic molecules) have been reported. Various synthetic strategies allow access to such well-defined linear oligo- and polyrotaxanes, including [1]rotaxanes and [n]rotaxanes (mostly n > 3). These state-of-the-art synthetic methods have resulted in unique functions of these oligo-and polyrotaxane materials. Herein, we review the effective synthetic protocols and functions of precisely constructed one-dimensional oligomers and polymers bearing defined threaded structures, and discuss the latest reports and trends.

Covalently Templated Syntheses of Mechanically Interlocked Molecules

Mechanically interlocked molecules (MiMs), such as catenanes and rotaxanes, exhibit unique properties due to the mechanical bond which unites their components. The translational and rotational freedom present in these compounds may be harnessed to create stimuli-responsive MiMs, which find potential application as artificial molecular machines. Mechanically interlocked structures such as lasso peptides have also been found in nature, making MiMs promising albeit elusive targets for drug discovery. Although the first syntheses of MiMs were based on covalent strategies, approaches based on non-covalent interactions rose to prominence thereafter and have remained dominant. Non-covalent strategies are generally short and efficient, but do require particular structural motifs which are difficult to alter. In a covalent approach, MiMs can be more easily modified while the components may have increased rotational and translational freedom. Both approaches have complementary merits and combining the unmatched efficiency of non-covalent approaches with the scope of covalent syntheses may open up vast opportunities. In this review, recent covalently templated syntheses of MiMs are discussed to show their complementarity and anticipate future developments in this field.

1 Introduction

2 Tetrahedral Templates

2.1 A Carbonate Template for Non-Rusty Catenanes

2.2 All-Benzene Catenanes on a Silicon Template

2.3 Backfolding from Quaternary Carbon

3 Planar Templates

3.1 Rotaxanes Constructed in a Ring

3.2 Hydrindacene as a Dynamic Covalent Template

3.3 Templating on Tri- and Tetrasubstituted Benzenes

4 Conclusion

A review of oligo(arylene ethynylene) derivatives in molecular junctions

Oligo(arylene ethynylene) (OAE) derivatives are the "workhorse" molecules of molecular electronics. Their ease of synthesis and flexibility of functionalisation mean that a diverse array of OAE molecular wires have been designed, synthesised and studied theoretically and experimentally in molecular junctions using both single-molecule and ensemble methods. This review summarises the breadth of molecular designs that have been investigated with emphasis on structure-property relationships with respect to the electronic conductance of OAEs. The factors considered include molecular length, connectivity, conjugation, (anti)aromaticity, heteroatom effects and quantum interference (QI). Growing interest in the thermoelectric properties of OAE derivatives, which are expected to be at the forefront of research into organic thermoelectric devices, is also explored.

Nanopatterns of molecular spoked wheels as giant homologues of benzene tricarboxylic acids

Molecular spoked wheels with D_3h and C_s symmetry are synthesized by Vollhardt trimerization of C_2v-symmetric dumbbell structures with central acetylene units and subsequent intramolecular ring closure. Scanning tunneling microscopy of the D_3h-symmetric species at the solid/liquid interface on graphite reveals triporous chiral honeycomb nanopatterns in which the alkoxy side chains dominate the packing over the carboxylic acid groups, which remain unpaired. In contrast, C_s-symmetric isomers partially allow for pairing of the carboxylic acids, which therefore act as a probe for the reduced alkoxy chain nanopattern stabilization. This observation also reflects the adsorbate substrate symmetry mismatch, which leads to an increase of nanopattern complexity and unexpected templating of alkoxy side chains along the graphite armchair directions. State-of-the-art GFN-FF calculations confirm the overall structure of this packing and attribute the unusual side-chain orientation to a steric constraint in a confined environment. These calculations go far beyond conventional simple space-filling models and are therefore particularly suitable for this special case of molecular packing.

Scanning tunneling microscopy investigations of phenylene-based molecular spoked wheels with D_3h and C_s symmetries on graphite show the competitive or complementary effects of carboxylic acid groups and alkoxy chains on the nanopattern formation.

Replication of Sequence Information in Synthetic Oligomers

The holy grail identified by Orgel in his 1995 Account was the development of novel chemical systems that evolve using reactions in which replication and information transfer occur together. There has been some success in the adaption of nucleic acids to make artificial analogues and in templating oligomerization reactions to form synthetic homopolymers, but replication of sequence information in synthetic polymers remains a major unsolved problem. In this Account, we describe our efforts in this direction based on a covalent base-pairing strategy to transfer sequence information between a parent template and a daughter copy. Oligotriazoles, which carry information as a sequence of phenol and benzoic acid side chains, have been prepared from bifunctional monomers equipped with an azide and an alkyne. Formation of esters between phenols and benzoic acids is used as the equivalent of nucleic base pairing to covalently attach monomer building blocks to a template oligomer. Sequential protection of the phenol side chains on the template, ester coupling of the benzoic acid side chains, and deprotection and ester coupling of the phenol side chains allow quantitative selective base-pair formation on a mixed sequence template. Copper catalyzed azide alkyne cycloaddition (CuAAC) is then used to oligomerize the monomers on the template. Finally, cleavage of the ester base pairs in the product duplex by hydrolysis releases the copy strand. This covalent template-directed synthesis strategy has been successfully used to copy the information encoded in a trimer template into a sequence-complementary oligomer in high yield.The use of covalent base pairing provides opportunities to manipulate the nature of the information transferred in the replication process. By using traceless linkers to connect the phenol and benzoic acid units, it is possible to carry out direct replication, reciprocal replication, and mutation. These preliminary results are promising, and methods have been developed to eliminate some of the side reactions that compete with the CuAAC process that zips up the duplex. In situ end-capping of the copy strand was found to be an effective general method for blocking intermolecular reactions between product duplexes. By selecting an appropriate concentration of an external capping agent, it is also possible to intercept macrocyclization of the reactive chain ends in the product duplex. The other side reaction observed is miscoupling of monomer units that are not attached to adjacent sites on the template, and optimization is required to eliminate these reactions. We are still some way from an evolvable synthetic polymer, but the chemical approach to molecular replication outlined here has some promise.

[2]Catenane Synthesis via Covalent Templating

After earlier unsuccessful attempts, this work reports the application of covalent templating for the synthesis of mechanically interlocked molecules (MiMs) bearing no supramolecular recognition sites. Two linear strands were covalently connected in a perpendicular fashion by a central ketal linkage. After subsequent attachment of the first strand to a template via temporary benzylic linkages, the second was linked to the template in a backfolding macrocyclization. The resulting pseudo[1]rotaxane structure was successfully converted to a [2]catenane via a second macrocyclization and cleavage of the ketal and temporary linkages.

Self-division of 2-D sheets in aromatic macrocycle assembly

2-D Sheets from macrocycle assembly undergoes reversible lengthwise division in response to temperature change.

Over one century after discovery: pyrylium salt chemistry emerging as a powerful approach for the construction of complex macrocycles and metallo-supramolecules

Over one century after its discovery, pyrylium salt chemistry has been extensively applied in preparing light emitters, photocatalysts, and sensitizers. In most of these studies, pyrylium salts acted as versatile precursors for the preparation of small molecules (such as furan, pyridines, phosphines, pyridinium salts, thiopyryliums and betaine dyes) and poly(pyridinium salt)s. In recent decades, pyrylium salt chemistry has emerged as a powerful approach for constructing complex macrocycles and metallo-supramolecules. In this perspective, we attempt to summarize the representative efforts of synthesizing and self-assembling large, complex architectures using pyrylium salt chemistry. We believe that this perspective not only highlights the recent achievements in pyrylium salt chemistry, but also inspires us to revisit this chemistry to design and construct macrocycles and metallo-supramolecules with increasing complexity and desired function.

A Covalent and Modular Synthesis of Homo- and Hetero[n]rotaxanes

Incorporation of 2,5-dihydroxyterephthalate as a covalent scaffold in the axis of a 30-membered all-carbon macrocycle provides access to a modular series of rotaxanes. Installment of tethered alkynes or azides onto the terephthalic phenolic hydroxyl functionalities, which are situated at opposite sides of the macrocycle, gives versatile prerotaxane building blocks. The corresponding [2]rotaxanes are obtained by introduction of bulky stoppering (“capping”) units at the tethers and subsequent cleavage of the covalent ring/thread ester linkages. Extension of this strategy via coupling of two prerotaxanes bearing complementary linker functionalities (i.e., azide and alkyne) and follow-up attachment of stopper groups provide efficient access to [n]rotaxanes. The applicability and modular nature of this novel approach were demonstrated by the synthesis of a series of [2]-, [3]-, and [4]rotaxanes. Furthermore, it is shown that the prerotaxanes allow late-stage functionalization of the ring fragment introducing further structural diversity.

Molecular replication using covalent base-pairs with traceless linkers

A unique feature of kinetically inert covalent base-pairing is that the nature of the chemical information that is transferred can be modulated by changing the chemical connectivity between the two bases. Formation of esters between phenols and benzoic acids has been used as a base-pairing strategy for sequence information transfer in template-directed synthesis of linear oligomers, but the copy strand produced by this process has the complementary sequence to the template strand. It is possible to form a base-pair between two benzoic acids by using a hydroquinone linker, which is eliminated when the product duplex is hydrolysed. Using this approach, covalent template-directed synthesis was carried out using a benzoic acid 3-mer template to produce an identical copy. This direct replication process was used in iterative rounds of replication leading to an increase of the population of the copied oligomer.

Capping Strategies for Covalent Template-Directed Synthesis of Linear Oligomers Using CuAAC

Covalent templating provides an attractive solution to the controlled synthesis of linear oligomers because a template oligomer can be used to define the precise length and sequence of the product. If the monomer units are attached to the template using kinetically inert covalent bonds it should be possible to operate at high dilution to favor intramolecular over intermolecular reaction. However, for oligomerization reactions using copper-catalyzed azide alkyne cycloaddition (CuAAC) this is not the case. The rate-limiting step is formation of an activated copper complex, so any alkyne that is activated by copper reacts rapidly with the nearest available azide. As a result, every time a chain end alkyne is activated, rapid intermolecular reaction takes place with a different oligomer leading to the formation of higher order products. It proved possible to block these intermolecular reactions by adding an excess of an azide capping agent that intercepts the chain end of the growing oligomer on the template. By adjusting the concentration of the capping agent to compete effectively with the unwanted intermolecular reactions without interfering with the desired intramolecular reactions, it was possible to obtain quantitative yields of copy strands from covalent template-directed oligomerization reactions. Remarkably, the capping agent could also be used to control the stereochemistry of the duplex formed in the templated oligomerization reaction to give exclusively the antiparallel product.

Sequence information transfer using covalent template-directed synthesis

Kinetically inert ester bonds were used to attach monomers to a template, dictating the sequence of the polymer product.

Template-directed synthesis is the biological method for the assembly of oligomers of defined sequence, providing the molecular basis for replication and the process of evolution. To apply analogous processes to synthetic oligomeric molecules, methods are required for the transfer of sequence information from a template to a daughter strand. We show that covalent template-directed synthesis is a promising approach for the molecular replication of sequence information in synthetic oligomers. Two monomer building blocks were synthesized: a phenol monomer and a benzoic acid monomer, each bearing an alkyne and an azide for oligomerization via copper catalyzed azide alkyne cycloaddition (CuAAC) reactions. Stepwise synthesis was used to prepare oligomers, where information was encoded as the sequence of phenol (P) and benzoic acid (A) units. Ester base-pairing was used to attach monomers to a mixed sequence template, and CuAAC was used to zip up the backbone. Hydrolysis of the ester base-pairs gave back the starting template and the sequence complementary copy. When the AAP trimer was used as the template, the complementary sequence PPA was obtained as the major product, with a small amount of scrambling resulting in PAP as a side-product. This covalent base-pairing strategy represents a general approach that can be implemented in different formats for the replication of sequence information in synthetic oligomers.

Cap control: cyclic versus linear oligomerisation in covalent template-directed synthesis

Covalent template-directed synthesis was used to oligomerise monomer building blocks in a controlled manner to give exclusively the linear trimer. Competing reaction pathways were blocked by addition of a large excess of a monomeric capping agent. At a concentration of 1 mM, the cap selectively prevented further reaction of the product chain ends to give polymeric and macrocyclic products, but did not interfere with the templating process.

The right concentration of capping agent is required to control the product distribution in covalent template-directed synthesis of linear oligomers using CuAAC.

Template-Directed Synthesis of Molecular Nanorings and Cages

This Account is about templates as construction tools: molecules for making molecules. A template organizes the reactants and provides information to promote formation of a specific product, but it is not part of the final product. We have developed many different strategies for using oligopyridines as templates for the synthesis of alkyne-linked π-conjugated metalloporphyrin oligomers. These compounds include some of the largest macrocycles ever synthesized, such as a 50-porphyrin ring with a diameter of 21 nm containing a ring of 750 C-C bonds. Metalloporphyrins are excellent models for exploring template directed synthesis, as they can be functionalized in many different positions and the central metal (typically Zn or Mg) provides a handle for coordination to templates. Classical template-directed macrocyclization reactions have a 1:1 complementarity between the template and the product. This strategy works well for preparing nanorings of 5-7 porphyrin units, but larger templates are laborious to synthesize. Rings of 8 or more porphyrin units are most easily prepared using "nonclassical" strategies, in which several small templates work together to direct the formation of a large ring. In the Vernier approach, a mismatch between the number of binding sites on the template and the building block leads to a mathematical amplification of the length scale: the number of binding sites in the product is the lowest common multiple of those in the template and the building block. For example, a 40-porphyrin ring can be prepared by coupling a linear decamer in the presence of an octadentate template. Linear Vernier templating opens up intriguing possibilities for self-replication. When several small radial oligopyridine templates bind inside a large nanoring they can form complexes with some vacant coordination sites that display correlated motion like the caterpillar tracks of a bulldozer. These caterpillar track complexes can be used in template-directed synthesis and they provide the most convenient route to 8- and 10-porphyrin rings. Russian doll complexes provide another strategy for template-directed synthesis: a number of specifically designed ligands bind to a central nanoring to form a template for constructing a larger concentric nanoring. The same oligopyridine templates that are used to prepare nanorings can also be used to synthesize three-dimensional nanotubes and nanoballs. Again, nonclassical approaches, in which several small templates work together cooperatively, are much simpler than creating a single large template with sufficient binding sites to define the whole geometry of the product. Oligopyridine ligands can also be used as shadow mask templates to control the demetalation of magnesium porphyrin nanorings, because metal centers that are not coordinated by the template can be selectively demetalated with acid. Thus, the template forms a permanent shadow on the porphyrin nanostructure that remains after the template has been removed. Shadow mask templates provide a simple route to heterometalated molecular architectures. The insights emerging from these studies are widely applicable, and there are many opportunities for inventing new ways of using templates to control reactions.

Supramolecular nanopatterns of H-shaped molecules

Alkoxy-substituted phenylene-ethynylene-butadiynylenes (PEBs) are connected via 1H-benzimidazole units to form H-shaped molecular scaffolds that self-assemble on graphite at the solid/liquid interface. Spacer lengths and end groups determine supramolecular tiling patterns, as shown via scanning tunneling microscopy (STM).

A Nanosized Phenylene-Ethynylene-Butadiynylene [2]Catenane

In a convergent, template-directed synthesis, an efficient route to a phenylene-ethynylene-butadiynylene based [2]catenane is described. The key step is performed by the aminolysis of the corresponding precatenane, which is obtained by a sequence of metal-catalyzed cross-coupling and desilylation reactions. The cyclization reaction leads besides the [2]precatenane to a variety of larger precatenanes and offers an attractive approach to mechanically interlocked structures of different size.

Dynamic or undynamic chirality generated by helical arrangement of a shape-persistent ring and rod doubly bridged in a molecule

Dynamic or undynamic chirality is generated in either threaded or unthreaded form of an assembly of phenylene–ethynylene-based ring and rod.

Synthesis of spiro quasi[1]catenanes and quasi[1]rotaxanes via a templated backfolding strategy

Due to their well-defined three-dimensional geometry, spiro compounds are widely utilized in drug research. From the central tetrahedral carbon atom, besides the regular structure, an inverted spiro connectivity may be envisioned. Here we disclose the synthesis of this molecule class that we have coined quasi[1]catenanes. Next to their fascinating and aesthetic shape, the higher compactness as compared to regular spiro bicycles is noteworthy. To enable synthetic access to compact entangled multimacrocyclic molecules, we have developed a new strategy. The key element is a template, which is covalently connected to the linear precursors, and spatially directs the sterically congested backfolding macrocyclizations that are required to give quasi[1]catenanes. Similarly, quasi[1]rotaxanes are made.

Spiro compounds contain two or more rings linked together through one common atom. Here the authors provide a method to backfold both rings, producing spiro quasi[1]catenanes, via a strategy of temporarily linking the linear intermediates with covalent bonds.

Interactions between shape-persistent macromolecules as probed by AFM

Water-soluble shape-persistent cyclodextrin (CD) polymers with amino-functionalized end groups were prepared starting from diacetylene-modified cyclodextrin monomers by a combined Glaser coupling/click chemistry approach. Structural perfection of the neutral CD polymers and inclusion complex formation with ditopic and monotopic guest molecules were proven by MALDI-TOF and UV-vis measurements. Small-angle neutron and X-ray (SANS/SAXS) scattering experiments confirm the stiffness of the polymer chains with an apparent contour length of about 130 Å. Surface modification of planar silicon wafers as well as AFM tips was realized by covalent bound formation between the terminal amino groups of the CD polymer and a reactive isothiocyanate-silane monolayer. Atomic force measurements of CD polymer decorated surfaces show enhanced supramolecular interaction energies which can be attributed to multiple inclusion complexes based on the rigidity of the polymer backbone and the regular configuration of the CD moieties. Depending on the geometrical configuration of attachment anisotropic adhesion characteristics of the polymer system can be distinguished between a peeling and a shearing mechanism.

A Short Covalent Synthesis of an All-Carbon-Ring [2]Rotaxane

While the current supramolecular syntheses of [2]rotaxanes are generally efficient, the final product always retains the functional groups required for non-covalent preorganization. A short and high-yielding covalent-template-assisted approach is reported for the synthesis of a [2]rotaxane. A terephthalic acid template core preorganizes the covalently connected ring precursor fragments to induce a clipping-type cyclization over the thread moiety. Cleavage of the temporary ester bonds that connect the ring and thread fragments liberates the [2]rotaxane.

Macrocyclic shape-persistency of cyclo[6]aramide results in enhanced multipoint recognition for the highly efficient template-directed synthesis of rotaxanes

Examples of using two-dimensional shape-persistent macrocycles, i.e. those having noncollapsible and geometrically well-defined skeletons, for constructing mechanically interlocked molecules are scarce, which contrasts the many applications of these macrocycles in molecular recognition and functional self-assembly. Herein, we report the crucial role played by macrocyclic shape-persistency in enhancing multipoint recognition for the highly efficient template-directed synthesis of rotaxanes. Cyclo[6]aramides, with a near-planar conformation, are found to act as powerful hosts that bind bipyridinium salts with high affinities. This unique recognition module, composed of two macrocyclic molecules with one bipyridinium ion thread through the cavity, is observed both in the solid state and in solution, with unusually high binding constants ranging from ∼10¹³ M^-2 to ∼10¹⁵ M^-2 in acetone. The high efficacy of this recognition motif is embodied by the formation of compact [3]rotaxanes in excellent yields based on either a "click-capping" (91%) or "facile one-pot" (85%) approach, underscoring the great advantage of using H-bonded aromatic amide macrocycles for the highly efficient template-directed synthesis of mechanically interlocked structures. Furthermore, three cyclo[6]aramides bearing different peripheral chains 1-3 demonstrate high specificity in the synthesis of a [3]rotaxane from 1 and 2, and a [2]rotaxane from 3via a "facile one-pot" approach, in each case as the only isolated product. Analysis of the crystal structure of the [3]rotaxane reveals a highly compact binding mode that would be difficult to access using other macrocycles with a flexible backbone. Leveraging this unique recognition motif, resulting from the shape-persistency of these oligoamide macrocycles, in the template-directed synthesis of compact rotaxanes may open up new opportunities for the development of higher order interlocked molecules and artificial molecular machines.

Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles

Shape-persistent macrocycles are attractive functional targets for synthesis, molecular recognition, and hierarchical self-assembly. Such macrocycles are noncollapsible and geometrically well-defined, and they are traditionally characterized by having repeat units and low conformational flexibility. Here, we find it necessary to refine these ideas in the face of highly flexible yet shape-persistent macrocycles. A molecule is shape-persistent if it has a small change in shape when perturbed by external stimuli (e.g., heat, light, and redox chemistry). In support of this idea, we provide the first examination of the relationships between a macrocycle's shape persistence, its conformational space, and the resulting functions. We do this with a star-shaped macrocycle called cyanostar that is flexible as well as being shape-persistent. We employed molecular dynamics (MD), density functional theory (DFT), and NMR experiments. Considering a thermal bath as a stimulus, we found a single macrocycle has 332 accessible conformers with olefins undergoing rapid interconversion by up-down and in-out motions on short time scales (0.2 ns). These many interconverting conformations classify single cyanostars as flexible. To determine and confirm that cyanostars are shape-persistent, we show that they have a high 87% shape similarity across these conformations. To further test the idea, we use the binding of diglyme to the single macrocycle as guest-induced stimulation. This guest has almost no effect on the conformational space. However, formation of a 2:1 sandwich complex involving two macrocycles enhances rigidity and dramatically shifts the conformer distribution toward perfect bowls. Overall, the present study expands the scope of shape-persistent macrocycles to include flexible macrocycles if, and only if, their conformers have similar shapes.

Synthesis and Dynamics of Nanosized Phenylene-Ethynylene-Butadiynylene Rotaxanes and the Role of Shape Persistence

Phenylacetylene‐based [2]rotaxanes were synthesized by a covalent‐template approach by aminolysis of the corresponding prerotaxanes. The wheel and the bulky stoppers are made of phenylene–ethynylene–butadiynylene macrocycles of the same size. The stoppers are large enough to enable the synthesis and purification of the rotaxane. However, the wheel unthreads from the axle at elevated temperatures. The deslipping kinetics and the activation parameters were determined. We described theoretically the unthreading by state‐of‐the‐art DFT‐based molecular‐mechanics models and a string method for the simulation of rare events. This approach enabled us to characterize in detail the unthreading mechanism, which involves the folding of the stopper during its passage through the wheel opening, a process that defies intuitive geometrical considerations. The conformational and energetic features of the transition allowed us to infer the molecular residues controlling the disassembly timescale.