Iminopyrrole-Based Self-Assembly: A Route to Intrinsically Flexible Molecular Links and Knots

The use of 2,5-diformylpyrrole in self-assembly reactions with diamines and Zn(II)/Cd(II) salts allowed the preparation of [2]catenane, trefoil knot, and Borromean rings. The intrinsically dynamic nature of the diiminopyrrole motif rendered all of the formed assemblies intramolecularly flexible. The presence of diiminopyrrole revealed new coordination motifs and influenced the host-guest chemistry of the systems, as illustrated by hexafluorophosphate encapsulation by Borromean rings.

Synthesis, Characterization, and Encapsulation Properties of Rigid and Flexible Porphyrin Cages Assembled from N-Heterocyclic Carbene-Metal Bonds

Four porphyrins equipped with imidazolium rings on the para positions of their meso aryl groups were prepared and used as tetrakis(N-heterocyclic carbene) (NHC) precursors for the synthesis of porphyrin cages assembled from eight NHC-M bonds (M = Ag⁺ or Au⁺). The conformation of the obtained porphyrin cages in solution and their encapsulation properties strongly depend on the structure of the spacer -(CH₂)_n- (n = 0 or 1) between meso aryl groups and peripheral NHC ligands. In the absence of methylene groups (n = 0), porphyrin cages are rather rigid and the short porphyrin-porphyrin distance prevents the encapsulation of guest molecules like 1,4-diazabicyclo[2.2.2]octane (DABCO). By contrast, the presence of methylene functions (n = 1) between meso aryl groups and peripheral NHCs offers additional flexibility to the system, allowing the inner space between the two porphyrins to expand enough to encapsulate guest molecules like water molecules or DABCO. The peripheral NHC-wingtip groups also play a significant role in the encapsulation properties of the porphyrin cages.

A Giant [8+12] Boronic Ester Cage with 48 Terminal Alkene Units in the Periphery for Postsynthetic Alkene Metathesis

Dynamic covalent chemistry (DCC) is a powerful synthetic tool to construct large defined molecules in one step from rather simple precursors. The advantage of the intrinsic dynamics of the applied reversible reaction steps is a self‐correction under the chosen conditions, to achieve high yields of the target compound. To date, only a few examples are known, in which DCC was used to build up a molecular defined but larger product that was chemically transferred to a more stable congener in a second (irreversible) step. Here, we present a nanometer‐sized [8+12] boronic ester cage containing 48 peripheral terminal alkene units which allows to put a hydrocarbon exoskeleton around the cage via alkene metathesis.

Coordination-Directed Construction of Molecular Links

Since the emergence of the concept of chemical topology, interlocked molecular assemblies have graduated from academic curiosities and poorly defined species to become synthetic realities. Coordination-directed synthesis provides powerful, diverse, and increasingly sophisticated protocols for accessing interlocked molecules. Originally, metal ions were employed solely as templates to gather and position building blocks in entwined or threaded arrangements. Recently, metal centers have increasingly featured within the backbones of the integral structural elements, which in turn use noncovalent interactions to self-assemble into intricate topologies. By outlining ingenious recent examples as well as seminal classic cases, this Review focuses on the role of metal-ligand paradigms in assembling molecular links. In addition, the ever-evolving approaches to efficient assembly, the structural features of the resulting architectures, and their prospects for the future are also presented.

A hydrogen-bonded polymer constructed from mechanically interlocked, suit[1]ane monomers

A T-shaped 2,4,7-substituted benzimidazolium “axle” with two ester functionalities and a 24-membered crown ether “wheel” with appendages containing terminal olefin groups were threaded — axle through wheel — to form a [2]pseudorotaxane. Grubbs’ ring-closing metathesis (RCM) was then used to form a third loop and create a bicyclic cage that fully encapsulates the axle and permanently interlocks the two molecular components creating a suit[1]ane. There are no bulky groups on the axle to prevent unthreading, but the axle is trapped due to the cage-like nature of the newly created polyether host. After hydrolysis of the esters groups to carboxylic acids, this novel mechanically interlocked molecule (MIM) polymerizes in the solid state. The structure of the resulting supramolecular polymer was determined by single-crystal X-ray diffraction and contains linear one-dimensional tapes of suit[1]ane monomers linked by intermolecular hydrogen bonding between the carboxylic acid groups.

Pyrroloindole-Based Dynamic Combinatorial Chemistry

We report a new class of building blocks for Dynamic Combinatorial Chemistry (DCC) based on the pyrroloindole scaffold. The attachment of l-cysteine on the α, α′ positions of the core makes the molecule suitable for disulfide exchange in aqueous dynamic combinatorial libraries (DCLs). The synthesis of the core follows a modified version of the Knoevenagel–Hemetsberger approach. The new building block (l-PI) is fluorescent (Φ = 48%) and relatively stable towards thermal and photodegradation. The chirality of the cysteine is transferred to the electron-rich pyrroloindole core. Homo- and heterochiral DCLs of l-PI with electron-deficient l- and d-naphthalenediimide (NDI) lead to similar library distributions regardless of the enantiomer used. When no salt is present, the major component is a dimer, while dimers and tetramers are obtained at increased ionic strength.

Subcomponent Self-Assembly of Covalent Metallacycles Templated by Catalytically Active Seven-Coordinate Transition Metal Centers

Coordination geometries of transition metals play vital roles in the self-assembly process of supramolecular coordination complexes. Herein, seven-coordinate 3d metal ions were applied as templates and catalytically active sites for subcomponent self-assembly that resulted in a new category of covalent metallacycles. Single-crystal structures showed that the sizes, configurations, and functionalization of covalent metallacycles could be tuned by the selection of rigid dihydrazide, transition metal ions, and prefunctionalized subcomponents, respectively. Moreover, metallacycles decorated with carboxylic groups could be employed as precursors to prepare aerogels through hierarchical self-assembly, which also exhibited high catalytic activity for cycloaddition of CO₂ into cyclic carbonates.

DNA Origami Catenanes Templated by Gold Nanoparticles

Mechanically interlocked molecules have marked a breakthrough in the field of topological chemistry and boosted the vigorous development of molecular machinery. As an archetypal example of the interlocked molecules, catenanes comprise macrocycles that are threaded through one another like links in a chain. Inspired by the transition metal-templated approach of catenanes synthesis, the hierarchical assembly of DNA origami catenanes templated by gold nanoparticles is demonstrated in this work. DNA origami catenanes, which contain two, three or four interlocked rings are successfully created. In particular, the origami rings within the individual catenanes can be set free with respect to one another by releasing the interconnecting gold nanoparticles. This work will set the basis for rich progress toward DNA-based molecular architectures with unique structural programmability and well-defined topology.

Molecular knot with nine crossings: Structure and electronic properties from density functional theory computation

The electronic structure of a molecule with nine-crossing composite knots 9₇³ link denoted by the Alexander-Briggs notation (complex-1) are studied by means of theoretical methods (DFT). The most interesting feature of this kind of molecules is their capability to capture anion spices inside the cage. Stability and chemical reactivity were evaluated taking advantage of the criteria chemical hardness and chemical potential. The simulation of the infrared spectra is also included and shows the characteristic signal of the molecule in a range 1000-1600 cm^-1. The frontier molecular orbitals were also analyzed. Whereas the capability to capture chlorine ion into the cavity of the complex-1 is explored by means the analysis of bond energy. Also, the electron density distribution of the chlorine complex was studied by means the quantum theory of atoms in molecules (QTAIM) formalism in order to stablish its bonding properties as well as the electron transfer between chlorine ion and complex-1 which was approached by the natural bonding orbital (NBO) and Hirshfeld charge. Ours results revels semiconductor behaviors for both compounds.

Exploring and Exploiting the Symmetry-Breaking Effect of Cyclodextrins in Mechanomolecules

Cyclodextrins (CDs) are cone-shaped molecular rings that have been widely employed in supramolecular/host–guest chemistry because of their low cost, high biocompatibility, stability, wide availability in multiple sizes, and their promiscuity for binding a range of molecular guests in water. Consequently, CD-based host–guest complexes are often employed as templates for the synthesis of mechanically bonded molecules (mechanomolecules) such as catenanes, rotaxanes, and polyrotaxanes in particular. The conical shape and cyclodirectionality of the CD “bead” gives rise to a symmetry-breaking effect when it is threaded onto a molecular “string”; even symmetrical guests are rendered asymmetric by the presence of an encircling CD host. This review focuses on the stereochemical implications of this symmetry-breaking effect in mechanomolecules, including orientational isomerism, mechanically planar chirality, and topological chirality, as well as how they support applications in regioselective and stereoselective chemical synthesis, the design of molecular machine prototypes, and the development of advanced materials.

Molecular Borromean Rings Based on Half-Sandwich Organometallic Rectangles

Over the last two decades, interlocked molecular species have received considerable attention, not only because of their intriguing structures and topological importance, but also because of their potential applications as smart materials, nanoscale devices, and molecular machines. Through judicious choice of metal centers and their adjoining ligands, a range of interesting interlocked structures have been realized by coordination-driven self-assembly. In addition, researchers have extensively developed synthetic methodologies for the construction of organized self-assemblies. One fascinating and challenging synthetic target in this field is the family of molecular Borromean rings, which consist of three chemically independent rings that are locked in such a way that no two of the three rings are linked with each other. Toward this goal, we have developed a template-free self-assembly method for synthesizing molecular Borromean rings by rationally designing metal-containing precursors and organic ligands. In this Account, we present our recent work, focusing on interlocked structures comprising half-sandwich iridium- and rhodium-based organometallic assemblies obtained by rational design. We first describe a series of template-free self-assembled organometallic molecular Borromean rings, which we constructed from preorganized binuclear half-sandwich molecular clips and suitable pyridyl ligands. These molecular Borromean rings can be sorted into four types according to their different bridging ligands, including those based on metallaligands, dihalogenated ligands, naphthazarin and π-acceptor ligands. By single-crystal X-ray crystallographic analysis, NMR experiment, and DFT calculation, we discuss their driving forces and the inter-ring interactions. Furthermore, we took advantage of the dissimilarity in their interactions to realize selective, reversible conversions between molecular Borromean rings and monomeric rectangles by the use of suitable solvents or guest molecules. Subsequently, a stepwise chemoseparation method based on molecular Borromean rings was established, with the molecular Borromean rings used in the separation being recoverable and recyclable. Due to their structural complexity and difficult synthesis, useful guidelines or rules to help design complicated interlocked molecules are highly desirable. We also highlight our efforts to develop empirical guidelines to uncover the relationship between the aspect ratio of metallarectangles and the formation or stability of molecular Borromean rings. An empirical formula has further been established to show the approximate ratio of lengths of the short arm and the long arm in molecular Borromean rings based on π-π (or p-π) stacking. We then demonstrate how to use these guidelines to design new molecular Borromean rings and further lead to other interlocked structures, for example, [2]- and [3]catenane structures. Taken together, our results may lead to a promising future for the design of fascinating and useful interlocked structures by coordination-driven self-assembly.

Discovering privileged topologies of molecular knots with self-assembling models

Despite the several available strategies to build complex supramolecular constructs, only a handful of different molecular knots have been synthesised so far. Here, in response to the quest for further designable topologies, we use Monte Carlo sampling and molecular dynamics simulations, informed by general principles of supramolecular assembly, as a discovery tool for thermodynamically and kinetically accessible knot types made of helical templates. By combining this approach with the exhaustive enumeration of molecular braiding patterns applicable to more general template geometries, we find that only few selected shapes have the closed, symmetric and quasi-planar character typical of synthetic knots. The corresponding collection of admissible topologies is extremely restricted. It covers all known molecular knots but it especially includes a limited set of novel complex ones that have not yet been obtained experimentally, such as 10124 and 15n41185, making them privileged targets for future self-assembling experiments.

Chirality in rotaxanes and catenanes

Although chiral mechanically interlocked molecules (MIMs) have been synthesised and studied, enantiopure examples are relatively under-represented in the pantheon of reported catenanes and rotaxanes and the underlying chirality of the system is often even overlooked. This is changing with the advent of new applications of MIMs in catalysis, sensing and materials and the appearance of new methods to access unusual stereogenic units unique to the mechanical bond. Here we discuss the different stereogenic units that have been investigated in catenanes and rotaxanes, examples of their application, methods for assigning absolute stereochemistry and provide a perspective on future developments.

Post-synthetic modifications of cadmium-based knots and links

Three topologically non-trivial cadmium(ii)-based complexes-Cd-[2]C, Cd-TK and Cd-SL-were simultaneously self-assembled in a dynamic library, individually isolated and fully characterized using solid-state, gas-phase and solution-phase techniques. Post-synthetic modifications, including reduction and transmetalation, were subsequently achieved. Imine bond reduction followed by demetallation led to the isolation of the corresponding organic molecules [2]C, TK and SL. Transmetalation of Cd-TK and Cd-SL with the zinc(ii) cation resulted in isolation of the corresponding zinc(ii)-containing complexes Zn-TK and Zn-SL.

Interlocked DNA topologies for nanotechnology

Interlocked molecular architectures are well known in supramolecular chemistry and are widely used for various applications like sensors, molecular machines and logic gates. The use of DNA for constructing these interlocked structures has increased significantly within the current decade. Because of Watson-Crick base pairing rules, DNA is an excellent material for the self-assembly of well-defined interlocked nanoarchitectures. These DNA nanostructures exhibit sufficient stability, good solubility in aqueous media, biocompatibility, and can be easily combined with other biomolecules in bio-hybrid nano-assemblies. Therefore, the study of novel DNA-based interlocked systems is of interest for nanotechnology, synthetic biology, supramolecular chemistry, biotechnology, and for sensing purposes. Here we summarize recent developments and applications of interlocked supramolecular architectures made of DNA. Examples illustrating that these systems can be precisely controlled by switching on and off the molecular motion of its mechanically trapped components are discussed. Introducing different triggers into such systems creates molecular assemblies capable of performing logic gate operations and/or catalytic activity control. Interlocked DNA-based nanostructures thus represent promising frameworks for building increasingly complex and dynamic nanomachines with highly controllable functionality.

Reversible mechanical protection: building a 3D "suit" around a T-shaped benzimidazole axle

The T-shaped benzimidazolium/crown ether recognition motif was used to prepare suit[1]anes. These novel mechanically interlocked molecules (MIMs) were fully characterized by 1H and 13C NMR spectroscopy, single-crystal X-ray diffraction, UV-vis absorption and fluorescence spectroscopy. By conversion to a suit[1]ane, a simple benzimidazole was shown to be protected from deprotonation by strong base. Moreover, it was demonstrated that this unique three-dimensional encapsulation can be made reversible, thus introducing the concept of "reversible mechanical protection"; a protecting methodology that may have potential applications in synthetic organic chemistry and the design of molecular machinery.

Pseudopeptidic compounds for the generation of dynamic combinatorial libraries of chemically diverse macrocycles in aqueous media

The combination of pseudopeptidic dithiol building blocks leads to the generation of highly diverse dynamic libraries of macrocycles in aqueous media.

Catenanes: fifty years of molecular links

Half a century after Schill and Lüttringhaus carried out the first directed synthesis of a [2]catenane, a plethora of strategies now exist for the construction of molecular Hopf links (singly interlocked rings), the simplest type of catenane. The precision and effectiveness with which suitable templates and/or noncovalent interactions can arrange building blocks has also enabled the synthesis of intricate and often beautiful higher order interlocked systems, including Solomon links, Borromean rings, and a Star of David catenane. This Review outlines the diverse strategies that exist for synthesizing catenanes in the 21st century and examines their emerging applications and the challenges that still exist for the synthesis of more complex topologies.

Perspectives in chemistry--aspects of adaptive chemistry and materials

Chemistry, pure and applied, is a science and an industry. By its power over the expressions of matter, it also displays the creativity of art. It has expanded from molecular to supramolecular chemistry and then, by way of constitutional dynamic chemistry, towards adaptive chemistry. Constitutional dynamics allow for adaptation, through component exchange and selection in response to physical stimuli (e.g. light, photoselection), to chemical effectors (e.g. metal ions, metalloselection) or to environmental effects (e.g. phase change) in equilibrium or out-of-equilibrium conditions, towards the generation of the best-adapted/fittest constituent(s) in a dynamic set. Such dynamic systems can be represented by two-dimensional or three-dimensional dynamic networks that define the agonistic and antagonistic relationships between the different constituents linked through component exchange. The introduction of constitutional dynamics into materials science opens perspectives towards adaptive materials and technologies, presenting attractive behavioral features (such as self-healing). In particular, dynamic polymers may undergo modification of their properties (mechanical, optical, etc.) through component exchange and recombination in response to physical or chemical agents. Constitutional adaptive materials open towards a systems materials science and offer numerous opportunities for soft-matter technologies.

Kinetically controlled phenomena in dynamic combinatorial libraries

Dynamic combinatorial libraries (DCLs) are collections of structurally related compounds that can interconvert through reversible chemical reaction(s). Such reversibility endows DCLs with adaptability to external stimuli, as rapid interconversion allows quick expression of those DCL components which best respond to the disturbing stimulus. This Tutorial Review focuses on the kinetically controlled phenomena that occur within DCLs. Specifically, it will describe dynamic chiral resolution of DCLs, their self-sorting under the influence of irreversible chemical and physical stimuli, and the autocatalytic behaviours within DCLs which can result in self-replicating systems. A brief discussion of precipitation-induced phenomena will follow and the review will conclude with the presentation of covalent organic frameworks (COFs)-porous materials whose synthesis critically depends on the fine tuning of the crystal growth and error correction rates within large DCLs.

The self-sorting behavior of circular helicates and molecular knots and links

We report on multicomponent self-sorting to form open circular helicates of different sizes from a primary monoamine, Fe(II) ions, and dialdehyde ligand strands that differ in length and structure by only two oxygen atoms. The corresponding closed circular helicates that are formed from a diamine--a molecular Solomon link and a pentafoil knot--also self-sort, but up to two of the Solomon-link-forming ligand strands can be accommodated within the pentafoil knot structure and are either incorporated or omitted depending on the stage that the components are mixed.

How Small Can a Catenane Be?

Catenanes are playing an increasingly important role in supramolecular chemistry. In attempting to identify the minimum number of carbon atoms in a viable catenane, the B3LYP, BP86, M06-2X, MM3, and MM4 methods were applied to study representative [2]catenane models, which consist of two mechanically interlocked saturated n-cycloalkanes ([CnH2n]2). The structures, energy variations, and electron density differences vary nearly monotonically from n = 18 to 11. For example, the B3LYP/DZP++ dissociation energies [CnH2n]2 → 2CnH2n are 101, 121, 159, 191, 222, 252, 290, and 323 kcal/mol from n = 18 to 11, respectively. However, there is much variation among the energetic predictions with the B3LYP, BP86, M06-2X, MM3, and MM4 methods. The distances of the longest C-C single bond in each catenane are 1.593 (n = 18), 1.604 (n = 17), 1.631 (n = 16), 1.640 (n = 15), 1.667 (n = 14), 1.669 (n = 13), 1.680 (n = 12), and 1.689 Å (n = 11). These results display something of a shoulder in the vicinity of n = 14. This may suggest that [C15H30]2 is the smallest catenane that will resist fragmentation under specified laboratory conditions.

Solvent-driven selective π-cation templating in dynamic assembly of interlocked molecules

The different solvent responses for bipyridinium and trispyridinium-based dynamic imine [2]rotaxanes allow their interconversion with high selectivity.