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Supramolecular Chemistry

Supramolecular chemistry specializes in non-covalent interactions. These weak and reversible forces—such as hydrogen bonds, hydrophobic forces, van der Waals forces, and metal–ligand coordination—are key to understanding biological processes and self-assembling systems, and to constructing complex materials and molecular machinery. In the several decades since its conception, supramolecular chemistry has become a truly interdisciplinary research area, providing insights into and spurring developments across biology, chemistry, nanotechnology, materials science, and physics.

In this collection, we highlight a selection of recent experimental and theoretical studies published in Nature Communications, which we hope reflect the true breadth of supramolecular chemistry as a discipline. The collection features advances in building discrete assemblies and extended material systems, all through the clever design of non-covalently organizing components. We also showcase fundamental research that furthers our understanding of the range of interactions that make up the supramolecular chemist’s toolbox.

Physical Principles

The halogen bond is well known for its ability to assemble supramolecules. Here, using NMR experiments, the authors reveal the role of these bonds in dynamic processes, finding that the halogen bond directly catalyzes dynamical rotation in solid cocrystals by reducing the associated energy barrier.

Article | open | | Nature Communications

Homo radical spin-pairing interactions between two identical aromatic radicals are common in supramolecular chemistry, but hetero interactions between two different aromatic radicals are seldom observed. Here, the authors find that hetero radical pairing between a radical cation and a radical anion, together with Coulombic attraction, can drive host-guest recognition, representing a new supramolecular recognition motif.

Article | open | | Nature Communications

Bottom-up fabrication via on-surface molecular self-assembly is a useful way to make nanomaterials, but finding appropriate precursor molecules for a given structure remains a challenge. Here the authors present an informatics technique linking self-assembled structures with precursor properties, helping identify molecules for target nanomaterials.

Article | open | | Nature Communications

Molecular self-assembly is controlled by chemical and entropic factors, but theory has not been able to differentiate the role of each. Here, the authors unambiguously address this question for self-assembly on metal surfaces, using a new computational method that bridges coarse-grained and atomistic approaches.

Article | open | | Nature Communications

Accessing the dynamics of soft self-assembled materials at high resolution is very difficult. Here the authors show atomistic and coarse-grained modelling combined with enhanced sampling to characterize the molecular mechanisms and kinetics of monomer exchange in synthetic supramolecular polymers.

Article | open | | Nature Communications

The weak and directional CH-π hydrogen bond has rarely been exploited in the design of supramolecular complexes and molecular machinery. Here, the authors construct a bowl-in-tube complex stabilized solely by concyclic CH-π hydrogen bonds, and show that the guest exhibits single-axis rotational motion despite tight association with the host.

Article | open | | Nature Communications

Though dynamics of molecules are generally restricted by intermolecular contacts, C60 fullerene is able to rotate freely despite being tightly bound inside a molecular host. Here, the authors study the solid-state dynamics of this host-guest system to understand the anomalous relationship between tight association and low friction.

Article | open | | Nature Communications

A deeper understanding of the mechanics of molecular machines is limited by the fast motions which are in the nanosecond or picosecond timescale. Here the authors present a real-time observation of structural changes in a rotaxane-based molecular shuttle by transient two-dimensional infrared spectroscopy.

Article | open | | Nature Communications

Discrete Assemblies

For interlocking ring structures, knot theory predicts that the number of topologically different links increases with ring and crossing number. Here, the authors use a peptide folding-and-assembly strategy to selectively realize two highly entangled catenanes with 4 rings and 12 crossings, representing two of the 100 predicted topologies with this complexity.

Article | open | | Nature Communications

Deracemization is a powerful method which allows transformation of racemic mixtures into excess enantiomer, but was applied only to small chiral molecular systems so far. Here the authors report deracemization of a kinetically stable bisporphyrin helicate upon encapsulation of chiral aromatic guests.

Article | open | | Nature Communications

Photoresponsive molecular capsules that can be used in water are rare. Here, the authors construct polyaromatic nanocapsules via self-assembly from photoswitch-bearing amphiphilic molecules in water. Light induces a structural change in the amphiphiles, triggering the capsule to disassemble into monomers and release encapsulated guests.

Article | open | | Nature Communications

The structures of fullerenes, or buckyballs, are often very difficult to resolve. Here, the authors describe a decapyrrylcorannulene host with ten flexible pyrryl groups that can efficiently co-crystallize with diverse fullerene derivatives in a ‘hand-ball-hand’ fashion, allowing crystallographic identification of commonly known types of fullerenes.

Article | open | | Nature Communications

Hierarchical non-intertwined ring-in-ring complexes are intriguing but challenging supramolecular targets. Here, the authors describe a box-in-box assembly based on radical-pairing interactions between two rigid diradical dicationic cyclophanes; the inner box can further accommodate guests to form Russian doll-like assemblies.

Article | open | | Nature Communications

Nested structures are common throughout nature and art, yet remain challenging synthetic targets in supramolecular chemistry. Here, the authors design multitopic terpyridine ligands that coordinate into nested concentric hexagons, and show that these discrete supramolecules display potent antimicrobial activity.

Article | open | | Nature Communications

Molecular capsules typically bind only guests with volumes smaller than their cavities. Here, the authors find that a polyaromatic capsule accommodates linear amphiphilic oligomers in a length-dependent manner, whereas short chains are fully crammed into the cavity, long chains can be incorporated into the capsule in a threaded fashion.

Article | open | | Nature Communications

Induced-fit binding, common in biological systems, is still relatively rare in artificial hosts. Here, the authors assemble a molecular cube from six gear-shaped faces, whose interdigitated design allows the cube to expand and contract in response to the size, shape, and charge of a guest molecule.

Article | open | | Nature Communications

Adapting the cavity of a coordination capsule generally involves the addition or removal of subcomponents. Here, the authors report two vanadium-organic coordination nanocapsules with the same number of components but variable cavity sizes—an expanded ball and contracted octahedron—whose solvent-controlled interconversion is attributed to the versatile coordination geometry of the vanadium centers.

Article | open | | Nature Communications

The complex, multicomponent structures often found in nature are difficult to mimic synthetically. Here, the authors assemble a molecular analogue of a peanut through coordinative and π-stacking interactions, in which a polyaromatic double capsule ‘pod’ held together by metal ions encapsulates fullerene ‘beans’.

Article | open | | Nature Communications

Host—guest assemblies can exploit stimuli-responsive guest binding and release for molecular recognition, but are typically governed by thermodynamics alone. Here, the authors design macrocycles with removable and exchangeable anion caps, allowing for the kinetic trapping and on-demand exchange of guest ions.

Article | open | | Nature Communications

One of the challenges of synthetic self-assembled capsules is achieving selective recognition of specific cargoes. Here, authors synthesize a self-assembled porphyrin cubic cage that is capable of sequestering imidazole and thiazole-containing small molecules and peptides, protecting them from proteolysis.

Article | open | | Nature Communications

Supramolecular assemblies remain of great importance to a variety of fields, yet their targeted design and synthesis remains highly challenging. Here, Cooper and colleagues combine computational screening with high-throughput robotic synthesis and discover 33 new organic cage molecules that form cleanly in one-pot syntheses.

Article | open | | Nature Communications

Molecules exhibiting Möbius topology are fascinating but challenging synthetic targets. Here, the authors report the elegant synthesis and crystal structure of a catenane formed from two fully conjugated, interlocked Möbius nanohoops, and use theoretical calculations to understand its conformational stability and aromaticity.

Article | open | | Nature Communications

Unidirectional rotation in a synthetic molecular motor is typically driven by intrinsic asymmetry or sequences of chemical transformations. Here, the authors control the direction of a molecule’s rotation through supramolecular binding of a chiral guest and subsequent transfer of its chiral information.

Article | open | | Nature Communications

Mechanically interlocked molecules are extensively applied as artificial molecular machines but rotaxane-branched dendrimers are rarely explored because of synthetic challenges. Here the authors present the construction of dual stimuli-responsive rotaxane-branched dendrimer which can be stimulated by DMSO or acetate ions.

Article | open | | Nature Communications

The complexity of rotaxane dendrimers poses a great synthetic challenge and the synthesis of higher generation rotaxane dendrimers has therefore rarely been reported. Here the authors report the synthesis of acid-base switchable rotaxane dendrimers up to generation 4 and demonstrate the uptake and release of guest molecules.

Article | open | | Nature Communications

Rotaxanes are interlocked molecules that can undergo sliding and rotational movements and can be used in artificial molecular machines and motors. Here, Simmel and co-workers show a rigid rotaxane structures consisting of DNA origami subunits that can slide over several hundreds of nanometres.

Article | open | | Nature Communications

In metal-based molecular motors, the motion is generally triggered by changes in the ligand coordination around the metal centre. Here, the authors synthesize a molecular gear that switches between states through photo- and thermally driven geometrical isomerization around a platinum ion.

Article | open | | Nature Communications

Materials Design

Long-chain polyamides could bridge the gap between traditional polyamides and polyethylenes. Here the authors show the preparation of diamide diene monomers derived from natural resources coupled by thiol-ene addition copolymerization to form long-chain amide-containing polymers for the synthesis of ultra-strong elastomers.

Article | open | | Nature Communications

Self-assembly of carbohydrates play an integral part in the design of higher ordered structures, but is limited to amphiphiles where the carbohydrate is covalently bound to a hydrophobic tail. Here the authors show that sugars direct the self-assembly of insoluble curcumin and the formation of well-defined capsules.

Article | open | | Nature Communications

Molecular tessellations of complex tilings are difficult to design and construct. Here, the authors show that molecular tessellations can be formed from a single building block that gives rise to two distinct supramolecular phases, whose self-similar subdomains serve as tiles in the periodic tessellations.

Article | open | | Nature Communications

Modulating the structural and transient characteristics of synthetic nanostructures can be achieved by temporal control of supramolecular assemblies. Here the authors show a biomimetic, ATP-selective and fuel-driven controlled supramolecular polymerization of a phosphate receptor functionalised monomer.

Article | open | | Nature Communications

Dynamically controlling the conformations of 1D elongated supramolecular polymers can induce functions comparable to protein folding/unfolding. Here the authors show light-induced conformational changes of azobenzene-based supramolecular polymers from helically coiled to extended/randomly coiled conformations.

Article | open | | Nature Communications

Nature can precisely control monomer sequences in biopolymers, but this is somewhat problematic in the formation of synthetic polymers. Here the authors show sequence-controlled supramolecular terpolymerization via self-sorting behavior among three sets of monomers possessing mismatched host-guest pairs.

Article | open | | Nature Communications

Porosity in metal–organic materials typically relies on highly ordered crystalline networks, which hinders material processing and morphological control. Here, the authors use metal–organic polyhedra as porous monomers in supramolecular polymerization to produce colloidal spheres and gels with intrinsic microporosity.

Article | open | | Nature Communications

Chirality transfer by chemical self-assembly has been studied intensively for years but chirality transfers along the same path remains elusive. Here the authors use a multiscale chemo-mechanical model to elucidate the mechanism underlying the chirality transfer via self-assembly in hierarchical camphorsulfonic acid doped polyaniline.

Article | open | | Nature Communications

Perylene bisimides (PBI) exhibit interesting photophysical and self-assembly properties but detailed understanding of the correlation between packing motif and spectroscopic properties is lacking. Here the authors report on self-assembling of PBIs in liquid crystalline phases to give aggregates with J- and H-type coupling contribution between the chromophores.

Article | open | | Nature Communications

Reaction-diffusion controls the spatial formation of many natural structures but is rarely applied to organic materials. Here, the authors couple reaction-diffusion to the self-assembly of a supramolecular gelator, introducing a strategy to forming soft, free-standing objects with controlled shape and functionality.

Article | open | | Nature Communications

Polymersomes have become a powerful tool in drug delivery and synthetic biology, but their use can be restricted by a lack of versatile methods for shape control. Here the authors demonstrate access to a range of non-spherical polymersome morphologies by exploiting hydrophobic directional aromatic perylene interactions within the membrane structure.

Article | open | | Nature Communications

Crystallization-driven processes play a vital role in preparing 2D nanostructures which makes structures with high symmetry hard to access. Here the authors present a non-crystallization approach which is based on π–π interactions of a copolymer for the fabrication of 2D symmetric structures with good dimensional control.

Article | open | | Nature Communications

Perylene diimide-bithiophene macrocycles are electroactive and shape-persistent hosts. Here, the authors describe their self-assembly into a cellular organic semiconducting film whose voids are electrically sensitive to different guests, and which can function as the active layer in a field-effect transistor device.

Article | open | | Nature Communications

Host–guest chemistry in hollow coordination cages can be exploited for a range of applications, but is often limited by inner cavity dimensions. Here, Schmitt and co-workers fabricate supramolecular keplerates that possess ultra-large cross-sectional diameters and are composed of multiple sub-cages.

Article | open | | Nature Communications

Systems

Temporal control over self-assembly processes is a desirable trait for discovering adaptable and controllable materials. Here the authors show that a chemical fuel driven system can not only self-assemble in a controlled manner, but can also result in precise control over the assembly and disassembly kinetics.

Article | open | | Nature Communications

In this paper, the authors study the temperature-controlled dynamic behavior of a system of nanocubes self-assembled from two different building blocks. Non-intuitively, the disordered, equilibrium state (a mixture of heteroleptic cubes) and the ordered, out-of-equilibrium state (a mixture of homoleptic cubes) are cycled by heating and subsequent rapid cooling.

Article | open | | Nature Communications

While many processes in biological cells can be understood in terms of molecular logic gates that process information sequentially and combinationally, the design and construction of such devices in the laboratory are unknown. Here the authors achieve this by the reversibly-controlled capture and release of guest molecules from host containers.

Article | open | | Nature Communications

Several cell functions are based on the fuel-driven assembly and disassembly of supramolecular polymers under non-equilibrium conditions. Here, the authors show controlled formation and breaking of a supramolecular polymer by enzymatic phosphorylation and dephosphorylation of a building block by continuously adding ATP fuel and removing waste products.

Article | open | | Nature Communications

Selection and persistence of chemical non-equilibrium species is crucial for the emergence of life and the exact mechanisms remain elusive. Here the authors show that phase separation is an efficient way to control selection of chemical species when primitive carboxylic acids are brought out-of-equilibrium by high-energy condensing agents.

Article | open | | Nature Communications

Unravelling the fundamental mechanisms of emergence of complex behaviour is key to understanding living systems. Here, the authors provide a simple experimental platform to investigate and control a rich set of complex phenomena, akin to those seen in living organisms, from a nonliving system of colloidal nanoparticles.

Article | open | | Nature Communications

Understanding self-replication and persistence in an out-of-equilibrium state is key to designing systems with new properties mimicking “living systems”. Here, the authors developed a synthetic small molecule system in which a transient surfactant replicator is responsible for both an autocatalytic aggregation pathway and a destructive pathway.

Article | open | | Nature Communications

Multistate molecular systems usually rely on external energy inputs to switch between states. Here, the authors show that a bispyridyl calixpyrrole system directed by only weak noncovalent interactions and metal coordination can access six discrete structural states, with directional and sequential control.

Article | open | | Nature Communications

One of the most dramatic effects of supramolecular assembly is the generation of homochirality in near-racemic systems. Here the authors rationalize the chiral amplification mechanism with a combined scanning tunneling microscopy and modelling study of surface-grown enantiomerically unbalanced supramolecular bilayers.

Article | open | | Nature Communications

Symmetry breaking and chiral amplification are fundamental principles in chemistry and biology but the control of initial chiral bias remains a great challenge. Here the authors show that chiral microvortices can lead to a selection of initial chiral bias of supramolecular systems composed of achiral molecules.

Article | open | | Nature Communications

Understanding why and how molecules transfer their chirality into helical superstructures, including crystals, remains a challenge. Here, the authors show that topological defects not only promote the growth, but also control the helical morphology of crystals formed by chiral rod-shaped particles.

Article | open | | Nature Communications

The sergeants-and-soldiers effect, in which a few chiral units induce chirality in a large number of achiral molecules, is difficult to quantify at the molecular level. Here, the authors devise an elegant strategy—combining theory and a system of pure organic polyhedra with chiral and achiral vertices—to understand the mechanism of chiral amplification in discrete molecular assemblies.

Article | open | | Nature Communications

Controlling the chirality of self-assembled polyhedra is a synthetic challenge. Here, the authors stereoselectively form emissive lanthanide tetrahedral cages from a series of chiral ligands, and use their circularly polarized luminescence to explore the effect of ligand point chirality on supramolecular architecture.

Article | open | | Nature Communications