Optimal Self-Assembly of Linked Constructs and Catenanes via Spatial Confinement

How to direct the self-assembly of simple templates toward constructs with complex shape and topology is still an open problem. Recent advancements have made it possible to self-assemble various types of knotted constructs, but targeting general multicomponent topologies, that is, links and catenanes, has proved much harder. Here, we study how the yield and complexity of self-assembled links depends on both intrinsic and extrinsic system properties and, particularly, template shape and spatial confinement. We show that slit confinement does not necessarily suppress linking but can rather enhance it significantly thanks to entropic effects. We also found that only a limited set of binary links are recurrent for different template shapes. These privileged topologies include all those experimentally realized so far plus a few additional ones, such as the 7₇² and 7₈² links that, hence, ought to be ideal candidates for broadening the current class of constructs with addressable topology.

Experimental Binding Energies in Supramolecular Complexes

On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.

Exploiting recognition-mediated assembly and reactivity in [2]rotaxane formation

A small molecular reaction network exploits recognition-mediated reactive processes in order to drive the assembly and formation of both a self-replicating linear template (thread) and a [2]rotaxane, in which the linear template is encircled by a diamide macrocycle. Complementary recognition sites, placed at strategic positions on the reactive building blocks, drive these assembly and replication processes. Template-instructed experiments show that the thread is capable of efficient self-replication and that no cross-catalytic relationships exist between the thread and the [2]rotaxane. The rate of [2]rotaxane formation is insensitive to the addition of a preformed template, however, [2]rotaxane formation does show enhanced diastereoselectivity, most likely originating from its recognition-mediated formation through a ternary reactive complex.

Dynamic covalent synthesis of aryleneethynylene cages through alkyne metathesis: dimer, tetramer, or interlocked complex?

A modular dynamic covalent approach towards rigid aryleneethynylene covalent organic polyhedrons (COPs) and the mechanistic features were explored.

A dynamic covalent approach towards rigid aryleneethynylene covalent organic polyhedrons (COPs) was explored. Our study on the relationship of the COP structures and the geometry of their building blocks reveals that the topology of aryleneethynylene COPs strongly depends on the size of the building blocks. A tetramer (D_2h symmetric), dimer, or interlocked complex can be formed from monomers with the same face-to-edge angle but in different sizes. As alkyne metathesis is a self-exchange reaction and non-directional, the cyclooligomerization of multi-alkyne monomers involves both intramolecular cyclization and intermolecular metathesis reaction, resulting in complicated thermodynamic process disturbed by kinetic competition. Although a tetrahedron-shaped tetramer (T_d symmetric) has comparable thermodynamic stability to a D_2h symmetric tetramer, its formation is kinetically disfavored and was not observed experimentally. Aryleneethynylene COPs consist of purely unsaturated carbon backbones and exhibit large internal cavities, which would have interesting applications in host–guest chemistry and development of porous materials.

Kinetically Trapped Tetrahedral Cages via Alkyne Metathesis

In dynamic covalent synthesis, kinetic traps are perceived as disadvantageous, hindering the system from reaching its thermodynamic equilibrium. Here we present the near-quantitative preparation of tetrahedral cages from simple tritopic precursors using alkyne metathesis. While the cages are the presumed thermodynamic sink, we experimentally demonstrate that the products no longer exchange their vertices once they have formed. The example reported here illustrates that kinetically trapped products may facilitate high yields of complex products from dynamic covalent synthesis.

Mechanochemical Encapsulation of Fullerenes in Peptidic Containers Prepared by Dynamic Chiral Self-Sorting and Self-Assembly

Molecular capsules composed of amino acid or peptide derivatives connected to resorcin[4]arene scaffolds through acylhydrazone linkers have been synthesized using dynamic covalent chemistry (DCC) and hydrogen-bond-based self-assembly. The dynamic character of the linkers and the preference of the peptides towards self-assembly into β-barrel-type motifs lead to the spontaneous amplification of formation of homochiral capsules from mixtures of different substrates. The capsules have cavities of around 800 Å(3) and exhibit good kinetic stability. Although they retain their dynamic character, which allows processes such as chiral self-sorting and chiral self-assembly to operate with high fidelity, guest complexation is hindered in solution. However, the quantitative complexation of even very large guests, such as fullerene C60 or C70 , is possible through the utilization of reversible covalent bonds or the application of mechanochemical methods. The NMR spectra show the influence of the chiral environment on the symmetry of the fullerene molecules, which results in the differentiation of diastereotopic carbon atoms for C70 , and the X-ray structures provide unique information on the modes of peptide-fullerene interactions.

A Hierarchical Self-Assembly System Built Up from Preorganized Tripodal Helical Metal Complexes

The hierarchical organization strategy has realized elaborate supramolecular structures that are difficult to achieve by a one-pot thermodynamically driven self-assembly. Self-assembly via Schiff base formation of the preorganized tripodal helical unit 2(2+), which is composed of the tris(bipyridyl) ligand 1 and octahedral metal ion (Ru(II) and Fe(II)), lead to two supramolecular structures, i.e., a macrobicyclic dimer and an interlocked helicate. Notably, the interlocked helicate had a unique motif with an elongated shape (∼ 58 Å) and linearly aligned metal centers with homochiral configurations (all-Δ or all-Λ), which shows potential for allosteric regulation based on the long-range transmittance of the structural information.

On-Demand Cyclophanes: Substituent-Directed Self-Assembling, Folding, and Binding

A family of p-cyclophanes based on bis- or tetrafunctionalized 1,4-bisthiophenol units linked by disulfide bridges was obtained by self-assembly on a gram scale and without any chromatographic purification. The nature of the functionalities borne by these so-called dyn[4]arenes plays a crucial role on their structural features as well as their molecular recognition abilities. Tuning these functions on demand yields tailored receptors for cations, anions, or zwitterions in organic or aqueous media.

Single-Handed Towards Nanosized Organic Molecules

Hand in hand: Enantiopure reactants have been used to generate rigid molecular tweezers by Buchwald-Hartwig aminations. These result in the phenazine units curving in only one direction with formation of one product exclusively.

Discoveries from a phenanthroline-based dynamic combinatorial library: catenane from a copper(i) or copper(ii) template?

We report here a DCL study of a phenanthroline-based building block focusing on catenane formation with copper templates.

Helical supramolecular organization of a 1,2-diol appended naphthalene diimide organogelator via an extended intermolecular H-bonding network

Hydrogen bonded self-assembly of a 1,2-diol linked naphthalene diimide derivative features M-helical and J-type aggregation. In MCH/CHCl₃, the compound exhibits intense yellow excimer and thermoreversible “sol–gel” behavior.

Instructable Nanoparticles Using Dynamic Combinatorial Chemistry

The application of nanoparticles to the multivalent recognition of biomacromolecules or programmed self-assembly requires control over the relative placement of chemical groups on their surface. We have developed a method to direct the functionalization of surfaces of aldehyde-equipped gold nanoparticles using a DNA template. An error-correction mechanism is built into the functionalization process thanks to the thermodynamic control enabled by the hydrazone exchange reaction. This reversible reaction can be conveniently switched off by removing the catalyst, preserving the functionalization.

Anion-templated hexagonal nanotubes

Hydrogen bonding between bromide anions and a tetrahydroxytriptycene ligand was used to assemble crystalline hexagonal tubes with nanometer diameters in good yield. Use of a hexahydroxytriptycene ligand again gave hexagonal nanotubes, but containing the spontaneously-oxidised quinone-tetrahydroxy ligand. The surprisingly robust nanotubes are stable to heat, vacuum and water, and represent an unprecedented use of O-H···anion coordination to assemble complex three-dimensional structures.

Molecular knots in biology and chemistry

Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.

Self-assembly of nanostructured materials through irreversible covalent bond formation

Over the past decades, numerous efforts have been devoted to synthesizing nanostructured materials with specific morphology because their size and shape play an important role in determining their functions. Self-assembly using weak and reversible interactions or bonds has provided synthetic routes toward various nanostructures because it allows a "self-checking" and "self-error-correcting" process under thermodynamic control. By contrast, the use of irreversible covalent bonds, despite the potential to generate more robust structures, has been disfavored in the synthesis of well-defined nanomaterials largely due to the lack of such self-error-correcting mechanisms. To date, the use of irreversible bonds is largely limited to covalent fixation of preorganized building blocks on a template, which, though capable of producing shape-persistent and robust nanostructured materials, often requires a laborious and time-consuming multistep processes. Constructing well-defined nanostructures by self-assembly using irreversible covalent bonds without help of templates or preorganization of components remains a challenge. This Account describes our recent discoveries and progress in self-assembly of nanostructured materials through strong, practically irreversible covalent bond formation and their applications in various areas including drug delivery, anticancer therapy, and heterogeneous catalysis. The key to the success of this approach is the use of rationally designed building blocks possessing multiple in-plane reactive groups at the periphery. These blocks can then successfully grow into flat oligomeric patches through irreversible covalent bond formation without the aid of preorganization or templates. Further growth of the patches with or without curvature generation drives the system to the formation of polymer nanocapsules, two-dimensional (2D) polymer films, and toroidal nanotubular microrings. Remarkably, the final morphology can be specified by a few simple parameters: the reaction medium, bending rigidity of the system, and orientation of the reactive groups. Theoretical studies support the spontaneous formation of such nanostructured materials in terms of energetics and successfully predict or explain their size distributions. Although the lack of self-error-correcting mechanisms results in defect sites in these nanostructures, the high efficiency and relative simplicity of our novel approach demonstrates the potential power of using irreversible covalent bonds to generate a diverse range of shape-persistent and robust nanostructures that is likely to enrich the repertoire of self-assembled nanomaterials.

Lanthanide Template Synthesis of Trefoil Knots of Single Handedness

We report on the assembly of 2,6-pyridinedicarboxamide ligands (1) with point chirality about lanthanide metal ion (Ln(3+)) templates, in which the helical chirality of the resulting entwined 3:1 ligand:metal complexes is covalently captured by ring-closing olefin metathesis to form topologically chiral molecular trefoil knots of single handedness. The ligands do not self-sort (racemic ligands form a near-statistical mixture of homoleptic and heteroleptic lanthanide complexes), but the use of only (R,R)-1 leads solely to a trefoil knot of Λ-handedness, whereas (S,S)-1 forms the Δ-trefoil knot with complete stereoselectivity. The knots and their isomeric unknot macrocycles were characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography and the expression of the chirality that results from the topology of the knots studied by circular dichroism.

Dynamic combinatorial chemistry on a monolayer protected gold nanoparticle

Here, we show that the addition of Hg(2+) or Ag(+) metal ions to a dynamic system composed of monolayer protected gold nanoparticles (Au NPs) and a mixture of four nucleotides (dGMP, dAMP, TMP, and dCMP) leads to the self-selection of TMP or dGMP, respectively, on the monolayer surface.

Chirality- and sequence-selective successive self-sorting via specific homo- and complementary-duplex formations

Self-recognition and self-discrimination within complex mixtures are of fundamental importance in biological systems, which entirely rely on the preprogrammed monomer sequences and homochirality of biological macromolecules. Here we report artificial chirality- and sequence-selective successive self-sorting of chiral dimeric strands bearing carboxylic acid or amidine groups joined by chiral amide linkers with different sequences through homo- and complementary-duplex formations. A mixture of carboxylic acid dimers linked by racemic-1,2-cyclohexane bis-amides with different amide sequences (NHCO or CONH) self-associate to form homoduplexes in a completely sequence-selective way, the structures of which are different from each other depending on the linker amide sequences. The further addition of an enantiopure amide-linked amidine dimer to a mixture of the racemic carboxylic acid dimers resulted in the formation of a single optically pure complementary duplex with a 100% diastereoselectivity and complete sequence specificity stabilized by the amidinium–carboxylate salt bridges, leading to the perfect chirality- and sequence-selective duplex formation.

The recognition and self-sorting of chiral molecules is a vital feature of many biomolecules. Here, the authors report chirality- and sequence-specific self-sorting of organic strands containing carboxylic acid or amidine groups, leading to selective duplex formation.

[2]Pseudorotaxane composed of heteroditopic macrobicycle and pyridine N-oxide based axle: recognition site dependent axle orientation

A strategy for threading an axle having a hydrogen bond acceptor unit in the cavity of a C3v symmetric amido-amine macrobicycle is investigated. The macrobicycle acts as a wheel in its neutral as well as triprotonated states to form threaded architectures with a pyridine N-oxide derivative. The negative oxygen dipole of the axle is capable of [2]pseudorotaxane formation in two different orientations with the wheel in its neutral and triprotonated states.

Constitutional self-selection from dynamic combinatorial libraries in aqueous solution through supramolecular interactions

We describe the predominant formation of a specific constitution arising from the combination of building blocks with different topologies through disulphide chemistry in a Dynamic Combinatorial Library (DCL). The supramolecular interactions established by a zwitterionic cysteine moiety are responsible for the self-selection of one product from all the virtual members of a large library.

A trefoil knotted polymer produced through ring expansion

A synthetic strategy is reported for the production of a trefoil knotted polymer from a copper(I)-templated helical knot precursor through ring expansion. The expected changes in the properties of the knotted polymer compared to a linear analogue, for example, reduced hydrodynamic radius and lower intrinsic viscosity, together with an atomic force microscopy (AFM) image of individual molecular knots, confirmed the formation of the resulting trefoil knotted polymer. The strategies employed here could be utilized to enrich the variety of available polymers with new architectures.

Supramolecular systems chemistry

The field of supramolecular chemistry focuses on the non-covalent interactions between molecules that give rise to molecular recognition and self-assembly processes. Since most non-covalent interactions are relatively weak and form and break without significant activation barriers, many supramolecular systems are under thermodynamic control. Hence, traditionally, supramolecular chemistry has focused predominantly on systems at equilibrium. However, more recently, self-assembly processes that are governed by kinetics, where the outcome of the assembly process is dictated by the assembly pathway rather than the free energy of the final assembled state, are becoming topical. Within the kinetic regime it is possible to distinguish between systems that reside in a kinetic trap and systems that are far from equilibrium and require a continuous supply of energy to maintain a stationary state. In particular, the latter systems have vast functional potential, as they allow, in principle, for more elaborate structural and functional diversity of self-assembled systems - indeed, life is a prime example of a far-from-equilibrium system. In this Review, we compare the different thermodynamic regimes using some selected examples and discuss some of the challenges that need to be addressed when developing new functional supramolecular systems.

Energy transfer within responsive pi-conjugated coassembled peptide-based nanostructures in aqueous environments

Steady-state and time-resolved photophysical measurements demonstrate energy transfer within π-conjugated peptide nanostructures composed of oligo-(p-phenylenevinylene)-based donor units and quaterthiophene-based acceptor units in completely aqueous environments. These peptide-based assemblies encourage energy migration along the stacking axis, thus resulting in the quenching of donor emission peaks along with the development of new spectral features reminiscent of acceptor emission. These spectral changes were observed even at minute amounts of the acceptor (starting at 1 mol%), suggesting that exciton migration is involved in energy transport and supporting a funnel-like energy transduction mechanism. The reversibility of nanostructure formation and the associated photophysical responses under different conditions (pH, temperature) were also studied. This unique material design incorporates two different semiconducting units coassembled within peptide nanostructures and offers a new platform for the engineering of energy migration through bioelectronic materials in aqueous environments.

Orthoester exchange: a tripodal tool for dynamic covalent and systems chemistry

Reversible covalent reactions have become an important tool in supramolecular chemistry and materials science. Here we introduce the acid-catalyzed exchange of O,O,O-orthoesters to the toolbox of dynamic covalent chemistry. We demonstrate that orthoesters readily exchange with a wide range of alcohols under mild conditions and we disclose the first report of an orthoester metathesis reaction. We also show that dynamic orthoester systems give rise to pronounced metal template effects, which can best be understood by agonistic relationships in a three-dimensional network analysis. Due to the tripodal architecture of orthoesters, the exchange process described herein could find unique applications in dynamic polymers, porous materials and host-guest architectures.

Origin of metastable knots in single flexible chains

Recent theoretical progress has explained the physics of knotting of semiflexible polymers, yet knotting of flexible polymers is relatively unexplored. We herein develop a new theory for the size distribution of knots on a flexible polymer and the existence of metastable knots. We show the free energy of a flexible molecule in a tube can be mapped to quantitatively reproduce the free energy distribution of a knot on a flexible chain. The size distribution of knots on flexible chains is expected to be universal and might be observed at a macroscopic scale, such as a string of hard balls.

Self-assembled capsules based on tetrafunctionalized calix[4]resorcinarene cavitands

The hemispherical structures of calix[4]resorcinarene cavitands are suitable for forming capsular assemblies with guest encapsulations through various intermolecular interactions.

How to make a porphyrin flip: dynamics of asymmetric porphyrin oligomers

The pathways and energy barriers from computational and experimental methods reveal the dynamics of asymmetric porphyrin oligomers.

Disulfide exchange: exposing supramolecular reactivity through dynamic covalent chemistry

A Tutorial Review of the subtle supramolecular interactions influencing the outcomes of equilibrating systems, focusing on the dynamic covalent chemistry (DCC) of disulfide exchange reactions, is presented. We discuss the topics of cation-π interactions (2.1), hydrophobic effects (2.2), hydrogen bonding interactions (2.3) aromatic donor-acceptor interactions (2.4), and metal-ligand interactions (2.5) in the context of dynamic disulfide chemistry.