Isothermal Disorder-to-Order Transitions of DNA Origami Structures Induced by Alternative Component Subsets

DNA origami technology has shown potential across various applications, including the construction of molecular machines. Among these, mimicking the complex structural transitions of natural biomolecules in physiological environments remains a long-standing pursuit. Here, inspired by intrinsically disordered proteins, we propose a strategy for inducing disorder-to-order transitions in DNA origami structures at room temperature using alternative component subsets. In a triangular DNA origami model, we define three subsets of its constitutional DNA staples based on their spatial distributions along the scaffold. Atomic force microscopy and molecular dynamics simulations show that the individual subsets result in metastable assemblies with disordered morphologies and elevated free-energy fluctuations compared with those generated by the complete set of staples. Notably, after the addition of the remaining staples, the irregular structures transform into ordered triangular architectures within 2 h at room temperature, achieving yields of up to ∼60%. These findings suggest that these controlled folding pathways in DNA origami can robustly converge on the global energy minimum at room temperature, thereby providing a promising alternative strategy for engineering biomimetic DNA molecular machines.

Heterogeneously catalyzed supramolecular polymerization: essential roles of nucleation and fragmentation-induced autocatalysis in chiral transfer

The complexity of multi-component molecular assembly demands precise control strategies to enhance both efficiency and selectivity. Heterogeneous nucleation and the autocatalytic secondary pathway, as key regulatory strategies, have attracted widespread attention for their crucial roles in crystal growth and amyloid protein aggregation. Here, we apply a heterogeneous nucleation strategy to supramolecular polymer systems and report the first direct observation of surface-enrichment-induced primary nucleation and a spontaneous fragmentation-driven autocatalytic secondary process. A heterogeneous nucleating agent promotes primary nucleation, facilitating supramolecular chiral induction. The resulting chiral polymers undergo a catalytic cycle of fragmentation and re-growth at their termini, with the fragments also acting as seeds for nucleation and growth. These pathways play a crucial role in the polymerization process and are essential for chiral transfer and asymmetry amplification, enabling the achievement of maximum enantioselectivity with as little as 0.5% molar equivalent of the heterogeneous nucleating agent. Furthermore, we reveal the existence of an optimal equivalent in their catalytic kinetics, arising from a surface assembly mechanism. In this mechanism, monomers adsorbed on the surface of the heterogeneous nucleating agent assemble with those in solution, rather than through surface diffusion and assembly. This process resembles the surface-catalyzed Eley-Rideal mechanism. Our study highlights the potential of heterogeneous nucleation as an effective strategy for controlling supramolecular polymerization and offers new insights into its underlying mechanism.

High-Fidelity Supramolecular Chirality Transportation Enabled Through Chalcogen Bonding

The formation of asymmetric microenvironments in proteins benefits from precise transportation of chirality across multiple levels through weak bonds in the folding and assembly process, which inspires the rational design and fabrication of artificial chiral materials. Herein, the chalcogen bonding-directed precise transportation of supramolecular chirality toward multiple levels is reported to aid the fabrication of chiroptical materials. Benzochalcogenadiazole (O, S, Se) motifs are conjugated to amino acid residues, and the solid-state assemblies afforded selective supramolecular chirality with handedness depending on the kinds of chalcogen atoms and amino acids. The chalcogen-N sequence assisted by hydrogen bonding synergistically allows for the complexation with pyrene conjugated aryl carboxylic acids to give macroscopic helical structures with active circular dichroism and circularly polarized luminescence, of which handedness is precisely determined by the pristine chiral species. Then the further application of chiral benzochalcogenadiazole motifs as seeds in directing handedness of benzamide via symmetry breaking is realized. Behaving as the dopants, embedding into the matrix of benzophenone induces the room temperature phosphorescence, whereby the thermal chiroptical switch is fabricated with color-tunable phosphorescent circularly polarized luminescence. This work utilized benzochalcogenadiazole-based chiral building units to accomplish precise transportation of supramolecular chirality in coassemblies with high-fidelity, achieving flexible manipulation of chiroptical properties and macroscopic helical sense.

Implementation of Digital Computing by Colloidal Crystal Engineering with DNA

Toehold-mediated strand displacement (TMSD) provides a versatile toolbox for developing DNA digital computing systems. Although different logic circuits with diverse functions have achieved good performance in terms of complexity and scalability, most previous DNA logic circuits perform information processing only at the molecular level, and nonspecific signal leakages are often difficult to avoid. Here, we demonstrate the feasibility of constructing leakless digital computing systems in three-dimensionally ordered colloidal supercrystals. These systems possess a unique signal leakage resistance by integrating different TMSD-based logic gates with the catalytic assembly of DNA-functionalized gold colloids. A complete set of basic Boolean logic gates and different cascaded logic circuits is constructed on the basis of the catalytic assembly strategy enabled by a facilely designed catassembler, where the output signals are recognized by determining whether specific colloidal supercrystals are formed or not. In addition, a half adder is built through a combination of XOR and AND logic gates with two distinct crystal types as readouts. Finally, a leakless two-digit DNA keypad lock for information security protection is demonstrated. The combination of TMSD-based logic circuits with the universal nanoparticle catalytic assembly offers the possibility to develop highly complicated and leakage-free digital computing systems and promotes macroscopic colloidal superlattice materials with programmable logic functions.

Tuning Surface Organic Structures by Small Gas Molecules through Catassembly and Coassembly

The field of molecular assembly has seen remarkable advancements across various domains, such as materials science, nanotechnology, and biomedicine. Small gas molecules serve as pivotal modulators, capable of altering the architecture of assemblies via tuning a spectrum of intermolecular forces including hydrogen bonding, dipole-dipole interactions, and metal coordination. Surface techniques, notably scanning tunneling microscopy and atomic force microscopy, have proven instrumental in dissecting the structural metamorphosis and characteristic features of these assemblies at an unparalleled single-molecule resolution. Recent research has spotlighted two innovative approaches for modulating surface molecular assemblies with the aid of small gas molecules: "catassembly" and "coassembly". This Perspective delves into these methodologies through the lens of varying molecular interaction types. The strategies discussed here for regulating molecular assembly structures using small gas molecules can aid in understanding various complex assembly processes and structures and provide guidance for the further fabrication of complex surface structures.

Molecular Face-Rotating Polyhedra: Chiral Cages Inspired by Mathematics

ConspectusMolecular polyhedral cages, notable for their enclosed inner cavities, can possess varying degrees of symmetry, spanning from regular Platonic polyhedra to lower symmetry forms that may display chirality. Crafting chiral molecular cages typically involves using building blocks containing stereogenic elements or arranging achiral components in a manner that lacks mirror and inversion symmetries. Achieving precise control over their chirality poses both significance and challenges.In this Account, we present an overview of our research endeavors in the realm of chiral molecular polyhedral cages, drawing inspiration from Buckminster Fuller's "Face-Rotating Polyhedra (FRP)". Mathematically, FRP introduce a unique form of chirality distinguished by a rotating pattern around the center of each face, setting it apart from regular polyhedra.Molecular FRP can be constructed using two types of facial building blocks. The first includes rigid, planar molecules such as truxene and triazatruxene, which exhibit either clockwise or counterclockwise rotations in two dimensions. The second category involves propeller-like molecules, e.g., tetraphenylethylene, 1,2,3,4,5-penta(4-phenylaldehyde)pyrrole, and tridurylborane, displaying dynamic stereochemistry.The synthesis of FRP may potentially yield a diverse array of stereoisomers. Achieving high stereoselectivity becomes feasible through the selection of building blocks with specific substitution patterns and rigidity. Prominent noncovalent repulsive forces within the resulting cages often play a pivotal role in the dynamic covalent assembly process, ultimately leading to the formation of thermodynamically stable FRP products.The capacity to generate a multitude of stereoisomers, combined with the integration of chiral vertices, has facilitated investigations into phenomena such as chiral self-sorting and the "sergeant and soldiers" chiral amplification effect in FRP. Even the inclusion of one chiral vertex significantly impacts the stereochemical configuration of the entire cage. While many facial building blocks establish a stable rotational pattern in FRP, other units, such as tridurylborane, can dynamically transition between P and M configurations within the cage structures. The kinetic characteristics of such stereolabile FRP can be elucidated through physicochemical investigations.Our research extends beyond the FRP concept to encompass mathematical analysis of these structures. Graph theory, particularly the coloring problem, sheds light on the intricate facial patterns exhibited by various FRP stereoisomers and serves as an efficient tool to facilitate the discovery of novel FRP structures. This approach offers a fresh paradigm for designing and analyzing chiral molecular polyhedral cages, showcasing in our work the synergy between mathematics and molecular design.

Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions

Nucleosome, the building block of chromatin, plays pivotal roles in all DNA-related processes. While cryogenic-electron microscopy (cryo-EM) has significantly advanced our understanding of nucleosome structures, the emerging field of single-molecule force spectroscopy is illuminating their dynamic properties. This technique is crucial for revealing how nucleosome behavior is influenced by chaperones, remodelers, histone variants, and post-translational modifications, particularly in their folding and unfolding mechanisms under tension. Such insights are vital for deciphering the complex interplay in nucleosome assembly and structural regulation, highlighting the nucleosome's versatility in response to DNA activities. In this Perspective, we aim to consolidate the latest advancements in nucleosome dynamics, with a special focus on the revelations brought forth by single-molecule manipulation. Our objective is to highlight the insights gained from studying nucleosome dynamics through this innovative approach, emphasizing the transformative impact of single-molecule manipulation techniques in the field of chromatin research.

What can molecular assembly learn from catalysed assembly in living organisms?

Molecular assembly is the process of organizing individual molecules into larger structures and complex systems. The self-assembly approach is predominantly utilized in creating artificial molecular assemblies, and was believed to be the primary mode of molecular assembly in living organisms as well. However, it has been shown that the assembly of many biological complexes is "catalysed" by other molecules, rather than relying solely on self-assembly. In this review, we summarize these catalysed-assembly (catassembly) phenomena in living organisms and systematically analyse their mechanisms. We then expand on these phenomena and discuss related concepts, including catalysed-disassembly and catalysed-reassembly. Catassembly proves to be an efficient and highly selective strategy for synergistically controlling and manipulating various noncovalent interactions, especially in hierarchical molecular assemblies. Overreliance on self-assembly may, to some extent, hinder the advancement of artificial molecular assembly with powerful features. Furthermore, inspired by the biological catassembly phenomena, we propose guidelines for designing artificial catassembly systems and developing characterization and theoretical methods, and review pioneering works along this new direction. Overall, this approach may broaden and deepen our understanding of molecular assembly, enabling the construction and control of intelligent assembly systems with advanced functionality.

Revealing the Electrocatalytic Self-Assembly Route from Building Blocks into Giant Mo-Blue Clusters

The assembly of single-core molybdate into hundreds of cores of giant molybdenum blue (Mo-blue) clusters has remained a long-standing unresolved scientific puzzle. To reveal this fascinating self-assembly behavior, we demonstrate an aqueous flowing in-operando Raman characterization system to capture the building blocks' evolution from the "black box" reaction process. We successfully visualized the sequential transformation of Na2MoO4 into Mo7O246- ({Mo7}), high nuclear Mo36O1128- ({Mo36}) cluster, and finally polymerization product of [H6K2Mo3O12(SO4)]n ({Mo3(SO4)}n) during the H2SO4 acidification. Notably, the facile conversion of {Mo3(SO4)}n back to the {Mo36} cluster by simple dilution is also discovered. Furthermore, we identified {Mo36} and {Mo3(SO4)}n as exclusive precursors responsible for driving the electrochemical self-assembly of {Mo154} and {Mo102}, respectively. The study also unravels a pivotal intermediate, the pentagonal reduced state fragment [H18MoVI4MoVO24]-, originating from {Mo36}, which catalyzes the autocatalytic self-assembly of {Mo154} with electron and proton injection during electrochemical processes. Concurrently, {Mo3(SO4)}n serves as the indispensable precursor for {Mo102} formation, generating sulfation pentagon building blocks of [H2Na2O2(H4MoVMoVI4O16SO4)4]4- that facilitate the consecutive assembly of giant {Mo102} sphere clusters. As a result, a complete elucidation of the assembly pathway of giant Mo-blue clusters derived from single-core molybdate was obtained, and H+/e- redox couple is revealed to play a critical role in catalyzing the deassembly of the precursor, leading to the formation of thermodynamically stable intermediates essential for further self-assembly of reduced state giant clusters.

Three-Phase Catassembly of 10 nm Au Nanoparticles for Sensitive and Stable Surface-Enhanced Raman Scattering Detection

Interfacial self-assembly with the advantage of providing large-area, high-density plasmonic hot spots is conducive to achieving high sensitivity and stable surface-enhanced Raman scattering (SERS) sensing. However, rapid and simple assembly of highly repeatable large-scale multilayers with small nanoparticles remains a challenge. Here, we proposed a catassembly approach, where the "catassembly" means the increase in the rate and control of nanoparticle assembly dynamics. The catassembly approach was dropping heated Au sols onto oil chloroform (CHCl3), which triggers a rapid assembly of plasmonic multilayers within 15 s at the oil-water-air (O/W/A) interface. A mixture of heated sol and CHCl3 constructs a continuous liquid-air interfacial tension gradient; thus, the plasmonic multilayer film can form rapidly without adding functional ligands. Also, the dynamic assembly process of the three-phase catassembly ranging from cluster to interfacial film formation was observed through experimental characterization and COMSOL simulation. Importantly, the plasmonic multilayers of 10 nm Au NPs for SERS sensing demonstrated high sensitivity with the 1 nM level for crystal violet molecules and excellent stability with an RSD of about 10.0%, which is comparable to the detection level of 50 nm Au NPs with layer-by-layer assembly, as well as breaking the traditional and intrinsic understanding of small particles of plasmon properties. These plasmonic multilayers of 10 nm Au NPs through the three-phase catassembly method illustrate high SERS sensitivity and stability, paving the way for small-nanoparticle SERS sensing applications.

Biotemplated precise assembly approach toward ultra-scaled high-performance electronics

Structural DNA nanotechnology can be programmed into complex designer structures with molecular precision for directing a wide range of inorganic and biological materials. However, the use of DNA-templated approaches for the fabrication and performance requirements of ultra-scaled semiconductor electronics is limited by its assembly disorder and destructive interface composition. In this protocol, using carbon nanotubes (CNTs) as model semiconductors, we provide a stepwise process to build ultra-scaled, high-performance field-effect transistors (FETs) from micron-scale three-dimensional DNA templates. We apply the approach to assemble CNT arrays with uniform pitches scaled between 24.1 and 10.4 nm with yields of more than 95%, which exceeds the resolution limits of conventional lithography. To achieve highly clean CNT interfaces, we detail a rinsing-after-fixing step to remove residual DNA template and salt contaminations present around the contact and the channel regions, without modifying the alignment of the CNT arrays. The DNA-templated CNT FETs display both high on-state current (4-15 μA per CNT) and small subthreshold swing (60-100 mV per decade), which are superior to previous examples of biotemplated electronics and match the performance metrics of high-performance, silicon-based electronics. The scalable assembly of defect-free three-dimensional DNA templates requires 1 week and the CNT arrays can be synthesized within half a day. The interface engineering requires 1-2 d, while the fabrication of high-performance FET and logic gate circuits requires 2-4 d. The structural and performance characterizations of molecular-precise DNA self-assembly and high-performance electronics requires 1-2 d. The protocol is suited for users with expertise in DNA nanotechnology and semiconductor electronics.

Structure transformation from Sierpiński triangles to chains assisted by gas molecules

Reversible transformations between fractals and periodic structures are of fundamental importance for understanding the formation mechanism of fractals. Currently, it is still a challenge to controllably achieve such a transformation. We investigate the effect of CO and CO2 molecules on Sierpiński triangles (STs) assembled from Fe atoms and 4,4″-dicyano-1,1':3',1″-terphenyl (C3PC) molecules on Au surfaces. Using scanning tunneling microscopy, we discover that the gas molecules induce a transition from STs into 1D chains. Based on density functional theory modeling, we propose that the atomistic mechanism involves the transformation of a stable 3-fold coordination Fe(C3PC)3 motif to Fe(C3PC)4 with an axially bonded CO molecule. CO2 causes the structural transformation through a molecular catassembly process.

Catalytic-assembly of programmable atom equivalents

Escape from metastable states in self-assembly of colloids is an intractable problem. Unlike the commonly adopted approach of thermal annealing, the recently developed enthalpy-mediated strategy provided a different option to address this dilemma in a dynamically controllable manner at room temperature. However, it required a complex catalytic-assembly DNA strand-displacement circuitry to mediate interaction between multiple components. In this work, we present a simple but effective way to achieve catalytic-assembly of DNA-functionalized colloidal nanoparticles, i.e., programmable atom equivalents, in a far-from-equilibrium system. A removable molecule named "catassembler" that acts as a catalyst was employed to rectify imperfect linkages and help the system escape from metastability without affecting the assembled framework. Notably, catalytic efficiency of the catassembler can be effectively improved by changing the seesaw catassembler in toehold length design or numbers of the repeat units. Leveraging this tractable catalytic-assembly approach, different ordered architectures were easily produced by directly mixing all reactants, as in chemical reactions. By switching bonding identities, solid-solid phase transformations between different colloidal crystals were achieved. This work opens up an avenue for programming colloid assembly in a far-from-equilibrium system.

Evolution of Transient Luminescent Assemblies Regulated by Trace Water in Organic Solvents

Trace water in organic solvents can play a crucial role in the construction of supramolecular assemblies, which has not gained enough attention until very recent years. Herein, we demonstrate that residual water in organic solvents plays a decisive role in the regulation of the evolution of assembled structures and their functionality. By adding Mg(ClO₄)₂ into a multi-component organic solution containing terpyridine-based ligand 3Tpy and monodentate imidazole-based ligand M2, the system underwent an unexpected kinetic evolution. Metallo-supramolecular polymers (MSP) formed first by the coordination of 3Tpy and Mg²⁺, but they subsequently decomposed due to the interference of M2, resulting in a transient MSP system. Further investigation revealed that this occurred because residual water in the solvent and M2 cooperatively coordinated with Mg²⁺. This allowed M2 to capture Mg²⁺ from MSP, which led to depolymerization. However, owing to the slow reaction between trace water/M2/Mg²⁺, the formation of MSP still occurred first. Therefore, water regulated both the thermodynamics and kinetics of the system and was the key factor for constructing the transient MSP. Fine-tuning the water content and other assembly motifs regulated the assembly evolution pathway, tuned the MSP lifetime, and made the luminescent color of the system undergo intriguing transition processes over time.

Supramolecular copolymerization through self-correction of non-polymerizable transient intermediates

Kinetic control over structures and functions of complex assembly systems has aroused widespread interest. Understanding the complex pathway and transient intermediates is helpful to decipher how multiple components evolve into complex assemblies. However, for supramolecular polymerizations, thorough and quantitative kinetic analysis is often overlooked. Challenges remain in collecting the information of structure and content of transient intermediates in situ with high temporal and spatial resolution. Here, the unsolved evolution mechanism of a classical self-sorting supramolecular copolymerization system was addressed by employing multidimensional NMR techniques coupled with a microfluidic technique. Unexpected complex pathways were revealed and quantitatively analyzed. A counterintuitive pathway involving polymerization through the 'error-correction' of non-polymerizable transient intermediates was identified. Moreover, a 'non-classical' step-growth polymerization process controlled by the self-sorting mechanism was unraveled based on the kinetic study. Realizing the existence of transient intermediates during self-sorting can encourage the exploitation of this strategy to construct kinetic steady state assembly systems. Moreover, the strategy of coupling a microfluidic technique with various characterization techniques can provide a kinetic analysis toolkit for versatile assembly systems. The combined approach of coupling thermodynamic and kinetic analyses is indispensable for understanding the assembly mechanisms, the rules of emergence, and the engineering of complex assembly systems.

Cyclodextrin-catalyzed self-assembly of a coordinating fluorescent molecule into microflowers

We report that γ-cyclodextrin (γ-CD) is able to catalyze the self-assembly process of the coordinating fluorescent molecule pyrenebutyrate with Zn²⁺. The direct interaction between pyrenebutyrate and Zn²⁺ would simply lead to amorphous precipitates, whereas addition of Zn²⁺ to the host-guest complex of pyrenebutyrate @ γ-CD would generate well-defined microflowers that have exactly the same composition as the amorphous pyrenebutyrate/Zn²⁺. The evidence of host-guest formation between 1-PBA and γ-CD and the absence of γ-CD in the final microflowers manifest that γ-CD acts as a catalyst in the self-assembly process. We envision that this dynamic host-guest chemistry would be very promising in creating catassemblies.

Electron-catalysed molecular recognition

Molecular recognition^1-4 and supramolecular assembly^5-8 cover a broad spectrum^9-11 of non-covalently orchestrated phenomena between molecules. Catalysis¹² of such processes, however, unlike that for the formation of covalent bonds, is limited to approaches^13-16 that rely on sophisticated catalyst design. Here we establish a simple and versatile strategy to facilitate molecular recognition by extending electron catalysis¹⁷, which is widely applied^18-21 in synthetic covalent chemistry, into the realm of supramolecular non-covalent chemistry. As a proof of principle, we show that the formation of a trisradical complex²² between a macrocyclic host and a dumbbell-shaped guest-a molecular recognition process that is kinetically forbidden under ambient conditions-can be accelerated substantially on the addition of catalytic amounts of a chemical electron source. It is, therefore, electrochemically possible to control²³ the molecular recognition temporally and produce a nearly arbitrary molar ratio between the substrates and complexes ranging between zero and the equilibrium value. Such kinetically stable supramolecular systems²⁴ are difficult to obtain precisely by other means. The use of the electron as a catalyst in molecular recognition will inspire chemists and biologists to explore strategies that can be used to fine-tune non-covalent events, control assembly at different length scales^25-27 and ultimately create new forms of complex matter^28-30.

α-Cyclodextrin-Catalyzed Symmetry Breaking and Precise Regulation of Supramolecular Self-Assembly Handedness with Harata-Kodaka's Rule

Harata-Kodaka's rule predicting the induced chirality of the guest molecules by cyclodextrins has been discovered in the 1970-1990s, yet its ability to control the supramolecular handedness of self-assembled structures has not been sufficiently recognized. Here we show that in a coordinating self-assembly system that is able to form racemic cone shells symmetry breaking occurs if the ligand is prethreaded into α-cyclodextrin prior to metal ion addition, and the handedness of cone shells can be rationally manipulated by creating the two scenarios of the Harata-Kadaka rule through controlling the host-guest dynamics. Since the coordination complexes have strong self-assembling ability, the coordinating ligand would dethread from the cavity of α-cyclodextrin but leaving the induced chirality to the coordinating self-assembly, thus catalyzing symmetry breaking. This work reveals that the dynamic factors such as concentration and molar ratio may play important roles in symmetry breaking at the supramolecular level. The current strategy provides a promising method for the symmetry breaking and manipulation of the handedness of self-assembled materials formed by achiral molecules.

Nonlinear Amplification of Chirality in Self-Assembled Plasmonic Nanostructures

Molecular chirality transfer and amplification is at the heart of the fundamental understanding of chiral origin and fabrication of artificial chiral materials. We investigate here the nonlinear amplification effect in the chiral transfer from small molecules to assembled plasmonic nanoparticles. Our results show clearly a recognizable nonlinear behavior of the electronic and plasmonic circular dichroism activities, demonstrating the validity of the "majority-rules" principle operating in both the three-dimensional interface-confined molecularly chiral environment and the assembled plasmonic nanoparticles. Such twin "majority-rules" effects from the self-assembled organic-inorganic nanocomposite system have not been reported previously. By establishing a direct correlation between the dynamic template of the molecularly chiral environment and the nonlinear chiral amplification in the nanoparticle assemblies, this study may provide an insightful understanding of the hierarchical and cooperative chiral information transfer from molecular levels to nanoscales.

Programming colloidal bonding using DNA strand-displacement circuitry

As a strategy for regulating entropy, thermal annealing is a commonly adopted approach for controlling dynamic pathways in colloid assembly. By coupling DNA strand-displacement circuits with DNA-functionalized colloid assembly, we developed an enthalpy-mediated strategy for achieving the same goal while working at a constant temperature. Using this tractable approach allows colloidal bonding to be programmed for synchronization with colloid assembly, thereby realizing the optimal programmability of DNA-functionalized colloids. We applied this strategy to conditionally activate colloid assembly and dynamically switch colloid identities by reconfiguring DNA molecular architectures, thereby achieving orderly structural transformations; leveraging the advantage of room-temperature assembly, we used this method to prepare a lattice of temperature-sensitive proteins and gold nanoparticles. This approach bridges two subfields: dynamic DNA nanotechnology and DNA-functionalized colloid programming.

Metal-directed supramolecular architectures based on the bifunctional ligand 2,5-bis(1H-1,2,4-triazol-1-yl)terephthalic acid

By the solvothermal reactions of 2,5-bis(1H-1,2,4-triazol-1-yl)terephthalic acid (H₂L) with transition-metal ions, two novel polymeric complexes, namely, poly[diaqua[μ₄-2,5-bis(1H-1,2,4-triazol-1-yl)terephthalato]cobalt(II)], [Co(C₁₂H₆N₆O₄)(H₂O)₂]_n, (1), and poly[[diaqua[μ₄-2,5-bis(1H-1,2,4-triazol-1-yl)terephthalato]nickel(II)] dihydrate], {[Ni(C₁₂H₆N₆O₄)(H₂O)₂]·2H₂O}_n, (2), were isolated. Both polymers have been characterized by FT-IR spectroscopy, elemental analysis and single-crystal X-ray diffraction analysis. The complexes have similar two-dimensional layered structures and coordination modes. Furthermore, the two-dimensional layered structures bear distinct intermolecular hydrogen-bonding interactions and π-π stacking interactions to form two different three-dimensional supramolecular networks based on 4⁴-subnets. The structural variation depends on the nature of the metal cations. The results of variable-temperature magnetization measurements (χ_MT-T and χ_M^-1-T) show that complexes (1) and (2) display antiferromagnetic behaviour.

Electric-field-induced supramolecular phase transitions at the liquid/solid interface: cat-assembly from solvent additives

The electrically triggered phase transformations of trimesic acid can be efficiently promoted to occur in an environment where trace levels of a highly polar solvent additive are present at the liquid/solid interface, as revealed by STM and DFT simulations.

Chaperone-like chiral cages for catalyzing enantio-selective supramolecular polymerization

Chiral organic cages can assist enantio-selective supramolecular polymerization through a catalyzed assembly (catassembly) strategy, like chaperones assist the assembly of biomolecules.

Cage catalysis has emerged as an important approach for mimicking enzymatic reactions by increasing the reaction rate and/or product selectivity of various types of covalent reactions. Here, we extend the catalytic application of cage compounds to the field of non-covalent molecular assembly. Acid-stable chiral imine cages are found to catalyze the supramolecular polymerization of porphyrins with an accelerated assembling rate and increased product enantioselectivity. Because the imine cages have a stronger interaction with porphyrin monomers and a weaker interaction with porphyrin assemblies, they can fully automatically detach from the assembled products without being consumed during the catalytic process. We reveal the kinetics of the auto-detachment of cages and the chirality growth of the assemblies using spectroscopic characterization studies. We find that the passivation groups attached to the cages are important for maintaining the structural stability of the cages during catalyzed assembly, and that the steric geometries of the cages can profoundly affect the efficiency of chiral regulation. This strategy demonstrates a new type of catalytic application of cage compounds in the field of molecular assembly, and paves the way to controlling supramolecular polymerization through a catalytic pathway.

Morphologies Transformation of BODIPY-Based Main Chain Supramolecular Polymers Amphiphiles: From Helical Nanowires to Nanosheets

The aggregate morphologies of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) main chain supramolecular polymer amphiphiles (SPA) are tunable by a fine balance of different non-covalent interactions. When the BODIPY segments and sodium cholate are mixed in aqueous solution, they form SPA by electrostatic attraction and hydrogen-bonds. This SPA displays helical nanowires' morphology. After the third component dimeric β-cyclodextrin (β-CD-C) is added, the hydrogen bonds between the cholate are substituted by the host-guest interaction between cholate and β-CD-C. Therefore, these SPA transform their aggregate morphologies into nanosheets' architecture. Therefore, a simple and effective way to regulate self-assembly by non-covalent forces is developed. This supramolecular method may provide an effective way to prepare various nanostructures in aqueous solution and show promising application in the future.

Programming chain-growth copolymerization of DNA hairpin tiles for in-vitro hierarchical supramolecular organization

Formation of biological filaments via intracellular supramolecular polymerization of proteins or protein/nucleic acid complexes is under programmable and spatiotemporal control to maintain cellular and genomic integrity. Here we devise a bioinspired, catassembly-like isothermal chain-growth approach to copolymerize DNA hairpin tiles (DHTs) into nanofilaments with desirable composition, chain length and function. By designing metastable DNA hairpins with shape-defining intramolecular hydrogen bonds, we generate two types of DHT monomers for copolymerization with high cooperativity and low dispersity indexes. Quantitative single-molecule dissection methods reveal that catalytic opening of a DHT motif harbouring a toehold triggers successive branch migration, which autonomously propagates to form copolymers with alternate tile units. We find that these shape-defined supramolecular nanostructures become substrates for efficient endocytosis by living mammalian cells in a stiffness-dependent manner. Hence, this catassembly-like in-vitro reconstruction approach provides clues for understanding structure-function relationship of biological filaments under physiological and pathological conditions.

Molecular engineering of polymeric supra-amphiphiles

Polymeric supra-amphiphiles are amphiphiles that are fabricated by linking polymeric segments, or small molecules and polymeric segments, by noncovalent interactions or dynamic covalent bonds. Compared with conventional amphiphilic polymers, polymeric supra-amphiphiles are advantageous in that they possess dynamic features and their preparation may be to some extent more facile. Moreover, polymeric supra-amphiphiles are endowed with richer structure and higher stability compared with small-molecule supra-amphiphiles. Owing to these properties, polymeric supra-amphiphiles have so far shown great promise as surfactants, nanocarriers and in therapies. In this tutorial review, recent work on polymeric supra-amphiphiles, from molecular architectures to functional assemblies, is presented and summarized. Different polymeric supra-amphiphile topologies and related applications are highlighted. By combining polymer chemistry with supramolecular chemistry and colloid science, we anticipate that the study of polymeric supra-amphiphiles will promote the continued development of the molecular engineering of functional supramolecular systems, and lead to practical applications, especially in drug delivery.

An Intrinsically Disordered Peptide-Peptide Stapler for Highly Efficient Protein Ligation Both in Vivo and in Vitro

Herein, we report an intrinsically disordered protein SpyStapler that can catalyze the isopeptide bond formation between two peptide tags, that is, SpyTag and BDTag, both in vitro and in vivo. SpyStapler and BDTag are developed by splitting SpyCatcher-the cognate protein partner of SpyTag-at the more solvent exposed second loop region. Regardless of their locations in protein constructs, SpyStapler enables efficient covalent coupling of SpyTag and BDTag under a variety of mild conditions in vitro (yield ∼80%). Co-expression of SpyStapler with telechelic dihydrofolate reductase (DHFR) bearing a SpyTag at N-terminus and a BDTag at C-terminus leads to direct cellular synthesis of a circular DHFR. Mechanistic studies involving circular dichroism and nuclear magnetic resonance spectrometry reveal that SpyStapler alone is disordered in solution and forms a stable folded structure ( T_m ∼ 55 °C) in the presence of both SpyTag and BDTag upon isopeptide bonding. No ordered structure can be formed in the absence of either tag. The catalytically inactive SpyStapler-EQ mutant cannot form a stable physical complex with SpyTag and BDTag, but it can fold into ordered structure in the presence of the ligated product (SpyTag-BDTag). It suggests that the isopeptide bond is important in stabilizing the complex. Given its efficiency, resilience, and robustness, SpyStapler provides new opportunities for bioconjugation and creation of complex protein architectures.

Stacking modular DNA circuitry in cascading self-assembly of spherical nucleic acids

Integrated circuitries are successfully built through using the cascaded modular strategy with the assistance of stochastic simulations.

Supramolecular assembly of fluorogenic glyco-dots from perylenediimide-based glycoclusters for targeted imaging of cancer cells

Supramolecular self-assembly between perylenediimide-based glycoclusters and a red-emitting fluorophore produces structurally uniform and stable glyco-dots amenable to targeted fluorogenic imaging of liver and triple-negative breast cancer cells.

Kinetic trapping - a strategy for directing the self-assembly of unique functional nanostructures

Supramolecular self-assembly into various nano- or microscopic structures based on non-covalent interactions between molecules has been recognized as a very efficient approach that leads to functional materials. Since most non-covalent interactions are relatively weak and form and break without significant activation barriers, the thermodynamic equilibrium of many supramolecular systems can be easily influenced by processing pathways that allow the system to stay in a kinetically trapped state. Thus far, kinetic traps have been found to be very important in producing more elaborate structural and functional diversity of self-assembled systems. In this review, we try to summarize the approaches that can produce kinetically trapped self-assemblies based on examples made by us. We focus on the following subjects: (1) supramolecular pathway dependent self-assembly, including kinetically trapped self-assemblies facilitated by host-guest chemistry, coordination chemistry, and electrostatic interactions; (2) physical processing pathway dependent self-assembly, including solvent quality controlled self-assembly, evaporation induced self-assembly and crystallization induced self-assembly.

Peptide self-assembly: thermodynamics and kinetics

Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.

Catalysis with two-dimensional materials and their heterostructures

Graphene and other 2D atomic crystals are of considerable interest in catalysis because of their unique structural and electronic properties. Over the past decade, the materials have been used in a variety of reactions, including the oxygen reduction reaction, water splitting and CO2 activation, and have been shown to exhibit a range of catalytic mechanisms. Here, we review recent advances in the use of graphene and other 2D materials in catalytic applications, focusing in particular on the catalytic activity of heterogeneous systems such as van der Waals heterostructures (stacks of several 2D crystals). We discuss the advantages of these materials for catalysis and the different routes available to tune their electronic states and active sites. We also explore the future opportunities of these catalytic materials and the challenges they face in terms of both fundamental understanding and the development of industrial applications.