Kinetic Analysis as a Tool to Distinguish Pathway Complexity in Molecular Assembly: An Unexpected Outcome of Structures in Competition

Impact of Temperature on the Chiroptical Properties of Thin Films of Chiral Thiophene-based Oligomers

According to the theoretical model based on the Mueller matrix approach, the experimental electronic circular dichroism (ECD) for thin films of chiral organic dyes can be expressed as the sum of several contributions, two of which are the most significant: 1) an intrinsic component (CDiso) invariant upon sample orientation, reflecting the molecular and/or supramolecular chirality, due to 3D-chiral nanoscopic structures; 2) a non-reciprocal component (LDLB) which inverts its sign upon sample flipping, which arises from the interaction of linear dichroism and linear birefringence in locally anisotropic domains, expression of 2D-chiral micro/mesoscopic structures. In this work, we followed in parallel through ECD and differential scanning calorimetry (DSC) the temperature evolution of the supramolecular arrangements of thin films of five structurally related chiral thiophene-based oligomers with different LDLB/CDiso ratio. By increasing the temperature, regardless of phase transitions observed by DSC analysis, systems with strong CDiso revealed no changes in the ECD spectrum, while compounds with dominant LDLB contribution underwent a gradual (and reversible) reduction of (apparent) ECD signals. These findings demonstrated that the concomitant occurrence of intrinsic and non-reciprocal components in the ECD spectrum of thin films of chiral organic dyes is strictly correlated with solid-state organizations of different stability.

Consequences of Vibrational Strong Coupling on Supramolecular Polymerization of Porphyrins

Supramolecular polymers display interesting optoelectronic properties and, thus, deploy multiple applications based on their molecular arrangement. However, controlling supramolecular interactions to achieve a desirable molecular organization is not straightforward. Over the past decade, light-matter strong coupling has emerged as a new tool for modifying chemical and material properties. This novel approach has also been shown to alter the morphology of supramolecular organization by coupling the vibrational bands of solute and solvent to the optical modes of a Fabry-Perot cavity (vibrational strong coupling, VSC). Here, we study the effect of VSC on the supramolecular polymerization of chiral zinc-porphyrins (S-Zn) via a cooperative effect. Electronic circular dichroism (ECD) measurements indicate that the elongation temperature (Te) of the supramolecular polymerization is lowered by ∼10 °C under VSC. We have also generalized this effect by exploring other supramolecular systems under strong coupling conditions. The results indicate that the solute-solvent interactions are modified under VSC, which destabilizes the nuclei of the supramolecular polymer at higher temperatures. These findings demonstrate that the VSC can indeed be used as a tool to control the energy landscape of supramolecular polymerization. Furthermore, we use this unique approach to switch between the states formed under ON- and OFF-resonance conditions, achieved by simply tuning the optical cavity in and out of resonance.

Strategies for Synthesizing Supramolecular Block Copolymers

Over the past decade, controlled supramolecular polymerization has been extensively studied and gradually shifted to supramolecular block copolymerization. Supramolecular block copolymers (BCPs) are considered the holy grail for developing supramolecular materials with new functionalities due to their fascinating structures and ability to introduce diverse functions. From a thermodynamic view to kinetic aspects, great progress has been made in the synthetic strategies of BCPs in the past few years. This Concept summarizes various strategies to realize supramolecular block copolymerization. The focus is on providing researchers with a methodological basis for achieving heterogeneous nucleation-elongation.

Exploring Host-Guest Interactions within a 600 kDa DegP Protease Cage Complex Using Hydrodynamics Measurements and Methyl-TROSY NMR

The DegP protease-chaperone operates within the periplasm of Gram-negative bacteria, where it assists in the regulation of protein homeostasis, promotes virulence, and is essential to survival under stress. To carry out these tasks, DegP forms a network of preorganized apo oligomers that facilitate the capture of substrates within distributions of cage-like complexes which expand to encapsulate clients of various sizes. Although the architectures of DegP cage complexes are well understood, little is known about the structures, dynamics, and interactions of client proteins within DegP cages and the relationship between client structural dynamics and function. Here, we probe host-guest interactions within a 600 kDa DegP cage complex throughout the DegP activation cycle using a model α-helical client protein through a combination of hydrodynamics measurements, methyl-transverse relaxation optimized spectroscopy-based solution nuclear magnetic resonance studies, and proteolytic activity assays. We find that in the presence of the client, DegP cages assemble cooperatively with few intermediates. Our data further show that the N-terminal half of the bound client, which projects into the interior of the cages, is predominantly unfolded and flexible, and exchanges between multiple conformational states over a wide range of time scales. Finally, we show that a concerted structural transition of the protease domains of DegP occurs upon client engagement, leading to activation. Together, our findings support a model of DegP as a highly cooperative and dynamic molecular machine that stabilizes unfolded states of clients, primarily via interactions with their C-termini, giving rise to efficient cleavage.

Supramolecular Hydrolase Mimics in Equilibrium and Kinetically Trapped States

The folding of proteins into intricate three-dimensional structures to achieve biological functions, such as catalysis, is governed by both kinetic and thermodynamic controls. The quest to design artificial enzymes using minimalist peptides seeks to emulate supramolecular structures existing in a catalytically active state. Drawing inspiration from the nuanced process of protein folding, our study explores the enzyme-like activity of amphiphilic peptide nanosystems in both equilibrium and non-equilibrium states, featuring the formation of supramolecular nanofibrils and nanosheets. In contrast to thermodynamically stable nanosheets, the kinetically trapped nanofibrils exhibit dynamic characteristics (e.g., rapid molecular exchange and relatively weak intermolecular packing), resulting in a higher hydrolase-mimicking activity. We emphasize that a supramolecular microenvironment characterized by an optimal local polarity, microviscosity, and β-sheet hydrogen bonding is conducive to both substrate binding and ester bond hydrolysis. Our work underscores the pivotal role of both thermodynamic and kinetic control in impacting biomimetic catalysis and sheds a light on the development of artificial enzymes.

Multiple hydrogen bonding driven supramolecular architectures and their biomedical applications

Supramolecular chemistry combines the strength of molecular assembly via various molecular interactions. Hydrogen bonding facilitated self-assembly with the advantages of directionality, specificity, reversibility, and strength is a promising approach for constructing advanced supramolecules. There are still some challenges in hydrogen bonding based supramolecular polymers, such as complexity originating from tautomerism of the molecular building modules, the assembly process, and structure versatility of building blocks. In this review, examples are selected to give insights into multiple hydrogen bonding driven emerging supramolecular architectures. We focus on chiral supramolecular assemblies, multiple hydrogen bonding modules as stimuli responsive sources, interpenetrating polymer networks, multiple hydrogen bonding assisted organic frameworks, supramolecular adhesives, energy dissipators, and quantitative analysis of nano-adhesion. The applications in biomedical materials are focused with detailed examples including drug design evolution for myotonic dystrophy, molecular assembly for advanced drug delivery, an indicator displacement strategy for DNA detection, tissue engineering, and self-assembly complexes as gene delivery vectors for gene transfection. In addition, insights into the current challenges and future perspectives of this field to propel the development of multiple hydrogen bonding facilitated supramolecular materials are proposed.

Stimuli-responsive synthetic helical polymers

Synthetic dynamic helical polymers (supramolecular and covalent) and foldamers share the helix as a structural motif. Although the materials are different, these systems also share many structural properties, such as helix induction or conformational communication mechanisms. The introduction of stimuli responsive building blocks or monomer repeating units in these materials triggers conformational or structural changes, due to the presence/absence of the external stimulus, which are transmitted to the helix resulting in different effects, such as assymetry amplification, helix inversion or even changes in the helical scaffold (elongation, J/H helical aggregates). In this review, we show through selected examples how different stimuli (e.g., temperature, solvents, cations, anions, redox, chiral additives, pH or light) can alter the helical structures of dynamic helical polymers (covalent and supramolecular) and foldamers acting on the conformational composition or molecular structure of their components, which is also transmitted to the macromolecular helical structure.

Supramolecular Polymerization of a Pyrene-Substituted Diamide and Its Ensemble of Kinetically Trapped Configurations

The prevalence of kinetically accessible states in supramolecular polymerization pathways has been exploited to control the growth of the polymer and thereby to obtain niche morphologies. Yet, these pathways themselves are not easily amenable for experimental delineation but could potentially be understood through molecular dynamics (MD) simulations. Herein, we report an extensive investigation of the self-assembly of pyrene-substituted diamide (PDA) monomers in solution, conducted using atomistic MD simulations and advanced sampling methods. We characterize such kinetic and thermodynamic states as well as the transition pathways and free energy barriers between them. PDA forms a dimeric segment with the N- to C-termini vectors of the diamide moieties arranged either in parallel or anti-parallel fashion. This characteristic, combined with the molecule's torsional flexibility and pyrene-solvent interactions, presents an ensemble of molecular configurations contributing to the kinetic state in the polymerization pathway. While this ensemble primarily comprises short oligomers containing a mix of anti-parallel and parallel dimeric segments, the thermodynamic state of the assembly is a right-handed polymer featuring parallel ones only. Our work thus offers an approach by which the landscape of any specific supramolecular polymerization can be deconstructed.

Supramolecular Polymer Polymorphism: Spontaneous Helix-Helicoid Transition through Dislocation of Hydrogen-Bonded π-Rosettes

Polymorphism, a phenomenon whereby disparate self-assembled products can be formed from identical molecules, has incited interest in the field of supramolecular polymers. Conventionally, the monomers that constitute supramolecular polymers are engineered to facilitate one-dimensional aggregation and, consequently, their polymorphism surfaces primarily when the states of assembly differ significantly. This engenders polymorphs of divergent dimensionalities such as one- and two-dimensional aggregates. Notwithstanding, realizing supramolecular polymer polymorphism, wherein polymorphs maintain one-dimensional aggregation, persists as a daunting challenge. In this work, we expound upon the manifestation of two supramolecular polymer polymorphs formed from a large discotic supramolecular monomer (rosette), which consists of six hydrogen-bonded molecules with an extended π-conjugated core. These polymorphs are generated in mixtures of chloroform and methylcyclohexane, attributable to distinctly different disc stacking arrangements. The face-to-face (minimal displacement) and offset (large displacement) stacking arrangements can be predicated on their distinctive photophysical properties. The face-to-face stacking results in a twisted helix structure. Conversely, the offset stacking induces inherent curvature in the supramolecular fiber, thereby culminating in a hollow helical coil (helicoid). While both polymorphs exhibit bistability in nonpolar solvent compositions, the face-to-face stacking attains stability purely in a kinetic sense within a polar solvent composition and undergoes conversion into offset stacking through a dislocation of stacked rosettes. This occurs without the dissociation and nucleation of monomers, leading to unprecedented helicoidal folding of supramolecular polymers. Our findings augment our understanding of supramolecular polymer polymorphism, but they also highlight a distinctive method for achieving helicoidal folding in supramolecular polymers.

Programmable supramolecular chirality in non-equilibrium systems affording a multistate chiroptical switch

The dynamic regulation of supramolecular chirality in non-equilibrium systems can provide valuable insights into molecular self-assembly in living systems. Herein, we demonstrate the use of chemical fuels for regulating self-assembly pathway, which thereby controls the supramolecular chirality of assembly in non-equilibrium systems. Depending on the nature of different fuel acids, the system shows pathway-dependent non-equilibrium self-assembly, resulting in either dynamic self-assembly with transient supramolecular chirality or kinetically trapped self-assembly with inverse supramolecular chirality. More importantly, successive conducting of chemical-fueled process and thermal annealing process allows for the sequential programmability of the supramolecular chirality between four different chiral hydrogels, affording a new example of a multistate supramolecular chiroptical switch that can be recycled multiple times. The current finding sheds new light on the design of future supramolecular chiral materials, offering access to alternative self-assembly pathways and kinetically controlled non-equilibrium states.

Temperature-Controlled Pathway Complexity in Self-Assembly of Perylene Diimide-Polydiacetylene Supramolecule

Self-assembly process represents one of the most powerful and efficient methods for designing functional nanomaterials. For generating optimal functional materials, understanding the pathway complexity during self-assembly is essential, which involves the aggregation of molecules into thermodynamically or kinetically favored pathways. Herein, a functional perylene diimide (PDI) derivative by introducing diacetylene (DA) chains (PDI-DA) is designed. Temperature control pathway complexity with the evolution of distinct morphology for the kinetic and thermodynamic product of PDI-DA is investigated in detail. A facile strategy of UV-induced polymerization is adopted to trap and capture metastable kinetic intermediates to understand the self-assembly mechanism. PDI-DA showed two kinetic intermediates having the morphology of nanosheets and nanoparticles before transforming into the thermodynamic product having fibrous morphology. Spectroscopic studies revealed the existence of distinct H- and J-aggregates for kinetic and thermodynamic products respectively. The polymerized fibrous PDI-DA displayed reversible switching between J-aggregate and H-aggregate.

Impact of Hydrophobic/Hydrophilic Balance on Aggregation Pathways, Morphologies, and Excited-State Dynamics of Amphiphilic Diketopyrrolopyrrole Dyes in Aqueous Media

We report the thermodynamic and kinetic aqueous self-assembly of a series of amide-functionalized dithienyldiketopyrrolopyrroles (TDPPs) that bear various hydrophilic oligoethylene glycol (OEG) and hydrophobic alkyl chains. Spectroscopic and microscopic studies showed that the TDPP-based amphiphiles with an octyl group form sheet-like aggregates with J-type exciton coupling. The effect of the alkyl chains on the aggregated structure and the internal molecular orientation was examined via computational studies combining MD simulations and TD-DFT calculations. Furthermore, solvent and thermal denaturation experiments provided a state diagram that indicates the formation of unexpected nanoparticles during the self-assembly into nanosheets when longer OEG side chains are introduced. A kinetic analysis revealed that the nanoparticles were obtained selectively as an on-pathway intermediate state toward the formation of thermodynamically controlled nanosheets. The metastable aggregates were used for seed-initiated supramolecular assembly, which allowed establishing control over the assembly kinetics and the aggregate size. The sheet-like aggregates prepared using the seeding method exhibited coherent vibration in the excited state, indicating a well-ordered orientation of the TDPP units. These results underline the significance of fine tuning of the hydrophobic/hydrophilic balance in the molecular design to kinetically control the assembly of amphiphilic π-conjugated molecules into two-dimensional nanostructures in aqueous media.

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.

Elucidating the Supramolecular Copolymerization of N- and C-Centered Benzene-1,3,5-Tricarboxamides: The Role of Parallel and Antiparallel Packing of Amide Groups in the Copolymer Microstructure

An in‐depth study of the supramolecular copolymerization behavior of N‐ and C‐centered benzene‐1,3,5‐tricarboxamides (N‐ and C‐BTAs) has been conducted in methylcyclohexane and in the solid state. The connectivity of the amide groups in the BTAs differs, and mixing N‐ and C‐BTAs results in supramolecular copolymers with a blocky microstructure in solution. The blocky microstructure results from the formation of weaker and less organized, antiparallel hydrogen bonds between N‐ and C‐BTAs. In methylcyclohexane, the helical threefold hydrogen‐bonding network present in C‐ and N‐BTAs is retained in the mixtures. In the solid state, in contrast, the hydrogen bonds of pure BTAs as well as their mixtures organize in a sheet‐like pattern, and in the mixtures long‐range order is lost. Drop‐casting to kinetically trap the solution microstructures shows that C‐BTAs retain the helical hydrogen bonds, but N‐BTAs immediately adopt the sheet‐like pattern, a direct consequence of the lower stabilization energy of the helical hydrogen bonds. In the copolymers, the stability of the helical aggregates depends on the copolymer composition, and helical aggregates are only preserved when a high amount of C‐BTAs is present. The method outlined here is generally applicable to elucidate the copolymerization behavior of supramolecular monomers both in solution as well as in the solid state.

Competing stress-dependent oligomerization pathways regulate self-assembly of the periplasmic protease-chaperone DegP

DegP is an oligomeric protein with dual protease and chaperone activity that regulates protein homeostasis and virulence factor trafficking in the periplasm of gram-negative bacteria. A number of oligomeric architectures adopted by DegP are thought to facilitate its function. For example, DegP can form a "resting" hexamer when not engaged to substrates, mitigating undesired proteolysis of cellular proteins. When bound to substrate proteins or lipid membranes, DegP has been shown to populate a variety of cage- or bowl-like oligomeric states that have increased proteolytic activity. Though a number of DegP's substrate-engaged structures have been robustly characterized, detailed mechanistic information underpinning its remarkable oligomeric plasticity and the corresponding interplay between these dynamics and biological function has remained elusive. Here, we have used a combination of hydrodynamics and NMR spectroscopy methodologies in combination with cryogenic electron microscopy to shed light on the apo-DegP self-assembly mechanism. We find that, in the absence of bound substrates, DegP populates an ensemble of oligomeric states, mediated by self-assembly of trimers, that are distinct from those observed in the presence of substrate. The oligomeric distribution is sensitive to solution ionic strength and temperature and is shifted toward larger oligomeric assemblies under physiological conditions. Substrate proteins may guide DegP toward canonical cage-like structures by binding to these preorganized oligomers, leading to changes in conformation. The properties of DegP self-assembly identified here suggest that apo-DegP can rapidly shift its oligomeric distribution in order to respond to a variety of biological insults.

Competing stress-dependent oligomerization pathways regulate self-assembly of the periplasmic protease-chaperone DegP

DegP is an oligomeric protein with dual protease and chaperone activity that regulates protein homeostasis and virulence factor trafficking in the periplasm of gram-negative bacteria. A number of oligomeric architectures adopted by DegP are thought to facilitate its function. For example, DegP can form a "resting" hexamer when not engaged to substrates, mitigating undesired proteolysis of cellular proteins. When bound to substrate proteins or lipid membranes, DegP has been shown to populate a variety of cage- or bowl-like oligomeric states that have increased proteolytic activity. Though a number of DegP's substrate-engaged structures have been robustly characterized, detailed mechanistic information underpinning its remarkable oligomeric plasticity and the corresponding interplay between these dynamics and biological function has remained elusive. Here, we have used a combination of hydrodynamics and NMR spectroscopy methodologies in combination with cryogenic electron microscopy to shed light on the apo-DegP self-assembly mechanism. We find that, in the absence of bound substrates, DegP populates an ensemble of oligomeric states, mediated by self-assembly of trimers, that are distinct from those observed in the presence of substrate. The oligomeric distribution is sensitive to solution ionic strength and temperature and is shifted toward larger oligomeric assemblies under physiological conditions. Substrate proteins may guide DegP toward canonical cage-like structures by binding to these preorganized oligomers, leading to changes in conformation. The properties of DegP self-assembly identified here suggest that apo-DegP can rapidly shift its oligomeric distribution in order to respond to a variety of biological insults.

Energetics of Competing Chiral Supramolecular Polymers

Chirality can have unexpected consequences including on properties other than spectroscopic. We show herein that a racemic mixture of bis-urea stereoisomers forms thermodynamically stable supramolecular polymers that result in a more viscous solution than for the pure stereoisomer. The origin of this macroscopic property was probed by characterizing the structure and stability of the assemblies. Both racemic and non-racemic bis-urea stereoisomers form two competing helical supramolecular polymers in solution: a double and a single helical structure at low and high temperature, respectively. The transition temperature between these assemblies, as probed by spectroscopic and calorimetric analyses, is strongly influenced by the composition (by up to 70 °C). A simple model that accounts for the thermodynamics of this system, indicates that the stereochemical defects (chiral mismatches and helix reversals) affect much more the stability of single helices. Therefore, the heterochiral double helical structure predominates over the single helical structure (whilst the opposite holds for the homochiral structures), which explains the aforementioned higher viscosity of the racemic bis-urea solution. This rationale constitutes a new basis to tune the macroscopic properties of the increasing number of supramolecular polymers reported to exhibit competing chiral nanostructures.

Pathway Complexity in Supramolecular Porphyrin Self-Assembly at an Immiscible Liquid-Liquid Interface

Nanostructures that are inaccessible through spontaneous thermodynamic processes may be formed by supramolecular self-assembly under kinetic control. In the past decade, the dynamics of pathway complexity in self-assembly have been elucidated through kinetic models based on aggregate growth by sequential monomer association and dissociation. Immiscible liquid–liquid interfaces are an attractive platform to develop well-ordered self-assembled nanostructures, unattainable in bulk solution, due to the templating interaction of the interface with adsorbed molecules. Here, we report time-resolved in situ UV–vis spectroscopic observations of the self-assembly of zinc(II) meso-tetrakis(4-carboxyphenyl)porphyrin (ZnTPPc) at an immiscible aqueous–organic interface. We show that the kinetically favored metastable J-type nanostructures form quickly, but then transform into stable thermodynamically favored H-type nanostructures. Numerical modeling revealed two parallel and competing cooperative pathways leading to the different porphyrin nanostructures. These insights demonstrate that pathway complexity is not unique to self-assembly processes in bulk solution and is equally valid for interfacial self-assembly. Subsequently, the interfacial electrostatic environment was tuned using a kosmotropic anion (citrate) in order to influence the pathway selection. At high concentrations, interfacial nanostructure formation was forced completely down the kinetically favored pathway, and only J-type nanostructures were obtained. Furthermore, we found by atomic force microscopy and scanning electron microscopy that the J- and H-type nanostructures obtained at low and high citric acid concentrations, respectively, are morphologically distinct, which illustrates the pathway-dependent material properties.

Diarylethene-Powered Light-Induced Folding of Supramolecular Polymers

Helical folding of randomly coiled linear polymers is an essential organization process not only for biological polypeptides but also for synthetic functional polymers. Realization of this dynamic process in supramolecular polymers (SPs) is, however, a formidable challenge because of their inherent lability of main chains upon changing an external environment that can drive the folding process (e.g., solvent, concentration, and temperature). We herein report a photoinduced reversible folding/unfolding of rosette-based SPs driven by photoisomerization of a diarylethene (DAE). Temperature-controlled supramolecular polymerization of a barbiturate-functionalized DAE (open isomer) in nonpolar solvent results in the formation of intrinsically curved, but randomly coiled, SPs due to the presence of defects. Irradiation of the randomly coiled SPs with UV light causes efficient ring-closure reaction of the DAE moieties, which induces helical folding of the randomly coiled structures into helicoidal ones, as evidenced by atomic force microscopy and small-angle X-ray scattering. The helical folding is driven by internal structure ordering of the SP fiber that repairs the defects and interloop interaction occurring only for the resulting helicoidal structure. In contrast, direct supramolecular polymerization of the ring-closed DAE monomers by temperature control affords linearly extended ribbon-like SPs lacking intrinsic curvature that are thermodynamically less stable compared to the helicoidal SPs. The finding represents an important concept applicable to other SP systems; that is, postpolymerization (photo)reaction of preorganized kinetic structures can lead to more thermodynamically stable structures that are inaccessible directly through temperature-controlled protocols.

Influence of the Z/E Isomerism on the Pathway Complexity of a Squaramide-Based Macrocycle

The rising interest on pathway complexity in supramolecular polymerization has prompted the finding of novel monomer designs able to stabilize kinetically trapped species and generate supramolecular polymorphs. In the present work, the exploitation of the Z/E (geometrical) isomerism of squaramide (SQ) units to produce various self-assembled isoforms and complex supramolecular polymerization pathways in methylcyclohexane/CHCl₃ mixtures is reported for the first time. This is achieved by using a new bissquaramidic macrocycle (MSq) that self-assembles into two markedly different thermodynamic aggregates, AggA (discrete cyclic structures) and AggB (fibrillar structures), depending on the solvent composition and concentration. Remarkably, UV-vis, ¹ H NMR, and FT-IR experiments together with quantum-chemical calculations indicate that these two distinct aggregates are formed via two different hydrogen bonding patterns (side-to-side in AggA and head-to-tail in AggB) due to different conformations in the SQ units (Z,E in AggA and Z,Z in AggB). The ability of MSq to supramolecularly polymerize into two distinct aggregates is utilized to induce the kinetic-to-thermodynamic transformation from AggA to AggB, which occurs via an on-pathway mechanism. It is believed that this system provides new insights for the design of potential supramolecular polymorphic materials by using squaramide units.

Solute-Solvent Interactions in Modern Physical Organic Chemistry: Supramolecular Polymers as a Muse

Interactions between solvents and solutes are a cornerstone of physical organic chemistry and have been the subject of investigations over the last century. In recent years, a renewed interest in fundamental aspects of solute-solvent interactions has been sparked in the field of supramolecular chemistry in general and that of supramolecular polymers in particular. Although solvent effects in supramolecular chemistry have been recognized for a long time, the unique opportunities that supramolecular polymers offer to gain insight into solute-solvent interactions have become clear relatively recently. The multiple interactions that hold the supramolecular polymeric structure together are similar in strength to those between solute and solvent. The cooperativity found in ordered supramolecular polymers leads to the possibility of amplifying these solute-solvent effects and will shed light on extremely subtle solvation phenomena. As a result, many exciting effects of solute-solvent interactions in modern physical organic chemistry can be studied using supramolecular polymers. Our aim is to put the recent progress into a historical context and provide avenues toward a more comprehensive understanding of solvents in multicomponent supramolecular systems.

Control of self-assembly pathways toward conglomerate and racemic supramolecular polymers

Homo- and heterochiral aggregation during crystallization of organic molecules has significance both for fundamental questions related to the origin of life as well as for the separation of homochiral compounds from their racemates in industrial processes. Herein, we analyse these phenomena at the lowest level of hierarchy – that is the self-assembly of a racemic mixture of (R,R)- and (S,S)-PBI into 1D supramolecular polymers. By a combination of UV/vis and NMR spectroscopy as well as atomic force microscopy, we demonstrate that homochiral aggregation of the racemic mixture leads to the formation of two types of supramolecular conglomerates under kinetic control, while under thermodynamic control heterochiral aggregation is preferred, affording a racemic supramolecular polymer. FT-IR spectroscopy and quantum-chemical calculations reveal unique packing arrangements and hydrogen-bonding patterns within these supramolecular polymers. Time-, concentration- and temperature-dependent UV/vis experiments provide further insights into the kinetic and thermodynamic control of the conglomerate and racemic supramolecular polymer formation.

Homo- and heterochiral aggregation is a process of interest to prebiotic and chiral separation chemistry. Here, the authors analyze the self-assembly of a racemic mixture into 1D supramolecular polymers and find homochiral aggregation into conglomerates under kinetic control, while under thermodynamic control a racemic polymer is formed.

Microstructural Capture of Living Ultrathin Polymer Brush Evolution via Kinetic Simulation Studies

Performing dynamic off-lattice multicanonical Monte Carlo simulations, we study the statics, dynamics, and scission-recombination kinetics of a self-assembled in situ-polymerized polydisperse living polymer brush (LPB), designed by surface-initiated living polymerization. The living brush is initially grown from a two-dimensional substrate by end-monomer polymerization-depolymerization reactions through seeding of initiator arrays on the grafting plane which come in contact with a solution of nonbonded monomers under good solvent conditions. The polydispersity is shown to significantly deviate from the Flory-Schulz type for low temperatures because of pronounced diffusion limitation effects on the rate of the equilibration reaction. The self-avoiding chains take up fairly compact structures of typical size R_g(N) ∼ N^ν in rigorously two-dimensional (d = 2) melt, with ν being the inverse fractal dimension (ν = 1/d). The Kratky description of the intramolecular structure factor F(q), in keeping with the concept of generalized Porod scattering from compact particles with fractal contour, discloses a robust nonmonotonic fashion with q^dF(q) ∼ (qR_g)^-3/4 in the intermediate-q regime. It is found that the kinetics of LPB growth, given by the variation of the mean chain length, follows a power law ⟨N(t)⟩ ∝ t^1/3 with elapsed time after the onset of polymerization, whereby the instantaneous molecular weight distribution (MWD) of the chains c(N) retains its functional form. The variation of ⟨N(t)⟩ during quenches of the LPB to different temperatures T can be described by a single master curve in units of dimensionless time t/τ_∞, where τ_∞ is the typical (final temperature T^∞-dependent) relaxation time which is found to scale as τ_∞ ∝ ⟨N(t = ∞)⟩⁵ with the ultimate average length of the chains. The equilibrium monomer density profile ϕ(z) of the LPB varies as ϕ(z) ∝ ϕ^-α with the concentration of segments ϕ in the system and the probability distribution c(N) of chain lengths N in the brush layer scales as c(N) ∝ N^-τ. The computed exponents α ≈ 0.64 and τ ≈ 1.70 are in good agreement with those predicted within the context of the Diffusion-Limited Aggregation theory, α = 2/3 and τ = 7/4.

Self-Sorting Supramolecular Polymerization: Helical and Lamellar Aggregates of Tetra-Bay-Acyloxy Perylene Bisimide

A new perylene bisimide (PBI), with a fluorescence quantum yield up to unity, self‐assembles into two polymorphic supramolecular polymers. This PBI bears four solubilizing acyloxy substituents at the bay positions and is unsubstituted at the imide position, thereby allowing hydrogen‐bond‐directed self‐assembly in nonpolar solvents. The formation of the polymorphs is controlled by the cooling rate of hot monomer solutions. They show distinctive absorption profiles and morphologies and can be isolated in different polymorphic liquid‐crystalline states. The interchromophoric arrangement causing the spectral features was elucidated, revealing the formation of columnar and lamellar phases, which are formed by either homo‐ or heterochiral self‐assembly, respectively, of the atropoenantiomeric PBIs. Kinetic studies reveal a narcissistic self‐sorting process upon fast cooling, and that the transformation into the heterochiral (racemic) sheetlike self‐assemblies proceeds by dissociation via the monomeric state.

N-Annulated Perylene Bisimides to Bias the Differentiation of Metastable Supramolecular Assemblies into J- and H-Aggregates

The unique self-assembling features of N-annulated perylene bisimides (PBIs) 1 and 2 are reported. The stability of the aggregates of diester 1, in which no H-bonding interactions are operative, corroborates the significance of long-range van der Waals and dipole-dipole electrostatic interactions in the construction of stable supramolecular assemblies. The incorporation of amide functional groups within the N-annulated PBI in 2 stimulates pathway differentiation to achieve up to three J-type aggregates and a fourth H-type aggregate depending on the experimental conditions. The results presented demonstrate unprecedented levels of control over synthetic supramolecular self-assembly and the rich differentiation that N-annulated PBIs exhibit, opening the door to new, complex, functional supramolecular materials.

Supramolecular polymerization provides non-equilibrium product distributions of imine-linked macrocycles

Supramolecular polymerization of imine-linked macrocycles has been coupled to dynamic imine bond exchange within a series of macrocycles and oligomers. In this way, macrocycle synthesis is driven by supramolecular assembly, either into small aggregates supported by π–π interactions, or high-aspect ratio nanotubes stabilized primarily by electrostatic and solvophobic interactions. For the latter, supramolecular polymerization into nanotubes restricts imine exchange, thereby conferring chemical stability to the assemblies and their constituent macrocycles. Competition in the formation and component exchange among macrocycles favored pyridine-2,6-diimine-linked species due to their rapid synthesis, thermodynamic stability, and assembly into high-aspect ratio nanotubes under the reaction conditions. In addition, the pyridine-containing nanotubes inhibit the formation of similar macrocycles containing benzene-1,3-diimine-linkages, presumably by disrupting their assembly and templation. Finally, we exploit rapid imine exchange within weak, low-aspect ratio macrocycle aggregates to carry out monomer exchange reactions to macrocycles bearing pyridine moieties. Once a pyridine-containing dialdehyde has exchanged into a macrocycle, the macrocycle becomes capable of nanotube formation, which dramatically slows further imine exchange. This kinetic trap provides chemically diverse macrocycles that are not attainable by direct synthetic methods. Together these findings provide new insights into coupling supramolecular polymerization and dynamic covalent bond-forming processes and leverages this insight to target asymmetric nanotubes. We envision these findings spurring further research efforts in the synthesis of nanostructures with designed and emergent properties.

Supramolecular polymerization of imine-linked macrocycles has been coupled to dynamic imine bond exchange within a series of macrocycles and oligomers.

Controlled supramolecular polymerization of π-systems

Externally-initiated controlled supramolecular polymerization of the kinetically trapped aggregated state in a chain growth mechanism can produce well-defined living supramolecular polymers and copolymers.

Controlling the supramolecular polymerization of dinuclear isocyanide gold(i) arylethynylene complexes through tuning the central π-conjugated moiety

Tuning the middle chromophores of dinuclear gold(i) arylethynyl complexes has been demonstrated to exhibit a pronounced effect on the photophysical properties, self-assembly mechanisms and morphologies.

Revising Complex Supramolecular Polymerization under Kinetic and Thermodynamic Control

Pathway complexity, hierarchical organization, out of equilibrium, and metastable or kinetically trapped species are common terms widely used in recent, high-quality publications in the field of supramolecular polymers. Often, the terminologies used to describe the different self-assembly pathways, the species involved, as well as their relationship and relative stability are not trivial. Different terms and classifications are commonly found in the literature, however, in many cases, without clear definitions or guidelines on how to use them and how to determine them experimentally. The aim of this Minireview is to classify, differentiate, and correlate the existing concepts with the help of recent literature reports to provide the reader with a general insight into thermodynamic and kinetic aspects of complex supramolecular polymerization processes. A good comprehension of these terms and concepts should contribute to the development of new complex, functional materials.

A Competing Hydrogen Bonding Pattern to Yield a Thermo-Thickening Supramolecular Polymer

Introduction of competing interactions in the design of a supramolecular polymer (SP) creates pathway complexity. Ester-bis-ureas contain both a strong bis-urea sticker that is responsible for the build-up of long rod-like objects by hydrogen bonding and ester groups that can interfere with this main pattern in a subtle way. Spectroscopic (FTIR and CD), calorimetric (DSC), and scattering (SANS) techniques show that such ester-bis-ureas self-assemble into three competing rod-like SPs. The previously unreported low-temperature SP is stabilized by hydrogen bonds between the interfering ester groups and the urea moieties. It also features a weak macroscopic alignment of the rods. The other structures form isotropic dispersions of rods stabilized by the more classical urea-urea hydrogen bonding pattern. The transition from the low-temperature structure to the next occurs reversibly by heating and is accompanied by an increase in viscosity, a rare feature for solutions in hydrocarbons.

Equilibrium Model for Supramolecular Copolymerizations

The coassembly of different building blocks into supramolecular copolymers provides a promising avenue to control their properties and to thereby expand the potential of supramolecular polymers in applications. However, contrary to covalent copolymerization which nowadays can be well controlled, the control over sequence, polymer length, and morphology in supramolecular copolymers is to date less developed, and their structures are more determined by the delicate balance in binding free energies between the distinct building blocks than by kinetics. Consequently, to rationalize the structures of supramolecular copolymers, a thorough understanding of their thermodynamic behavior is needed. Though this is well established for single-component assemblies and over the past years several models have been proposed for specific copolymerization cases, a generally applicable model for supramolecular cooperative copolymers is still lacking. Here, we provide a generalization of our earlier mass-balance models for supramolecular copolymerizations that encompasses all our earlier models. In this model, the binding free energies of each pair of monomer types in each aggregate type can be set independently. We provide scripts to solve the model numerically for any (co)polymerization of one or two types of monomer into an arbitrary number of distinct aggregate types. We illustrate the applicability of the model on data from literature as well as on new experimental data of triarylamine triamide-based copolymers in three distinct solvents. We show that apart from common properties such as the degree of polymerization and length distributions, our approach also allows us to investigate properties such as the copolymer microstructure, that is, the internal ordering of monomers within the copolymers. Moreover, we show that in some cases, also intriguing analytical approximations can be derived from the mass balances.

Off-Pathway Assembly: A Broad-Spectrum Mechanism of Action for Drugs That Undermine Controlled HIV-1 Viral Capsid Formation

The early and late stages of human immunodeficiency virus (HIV) replication are orchestrated by the capsid (CA) protein, which self-assembles into a conical protein shell during viral maturation. Small molecule drugs known as capsid inhibitors (CIs) impede the highly regulated activity of CA. Intriguingly, a few CIs, such as PF-3450074 (PF74) and GS-CA1, exhibit effects at multiple stages of the viral lifecycle at effective concentrations in the pM to nM regimes, while the majority of CIs target a single stage of the viral lifecycle and are effective at nM to μM concentrations. In this work, we use coarse-grained molecular dynamics simulations to elucidate the molecular mechanisms that enable CIs to have such curious broad-spectrum activity. Our quantitatively analyzed findings show that CIs can have a profound impact on the hierarchical self-assembly of CA by perturbing populations of small CA oligomers. The self-assembly process is accelerated by the emergence of alternative assembly pathways that favor the rapid incorporation of CA pentamers, and leads to increased structural pleomorphism in mature capsids. Two relevant phenotypes are observed: (1) eccentric capsid formation that may fail to encase the viral genome and (2) rapid disassembly of the capsid, which express at late and early stages of infection, respectively. Finally, our study emphasizes the importance of adopting a dynamical perspective on inhibitory mechanisms and provides a basis for the design of future therapeutics that are effective at low stoichiometric ratios of drug to protein.

Large Synthetic Molecule that either Folds or Aggregates through Weak Supramolecular Interactions Determined by Solvent

Weak noncovalent interactions between large disclike molecules in poorly solvating media generally lead to the formation of fibers where the molecules stack atop one another. Here, we show that a particular chiral spacing group between large aromatic moieties, which usually lead to columnar stacks, in this case gives rise to an intramolecularly folded structure in relatively polar solvents, but in very apolar solvents forms finite aggregates. The molecule that displays this behavior has a C 3 symmetric benzene-1,3,5-tris(3,3'-diamido-2,2'-bipyridine) (BTAB) core with three metalloporphyrin units appended to it through short chiral spacers. Quite well-defined chromophore arrangements are evident by circular dichroism (CD) spectroscopy of this compound in solution, where clear exciton coupled bands of porphyrins are observed. In more polar solvents where the molecules are dispersed, a relatively weak CD signal is observed as a result of intramolecular folding, a feature confirmed by molecular modeling. The intramolecular folding was confirmed by measuring the CD of a C 2 symmetric analogue. The C 3 symmetric BTAB cores that would normally be expected to stack in a chiral arrangement in apolar solvents show no indication of CD, suggesting that there is no transfer of chirality through it (although the expected planar conformation of the 2,2'-bipyridine unit is confirmed by NMR spectroscopy). The incorporation of the porphyrins on the 3,3'-diamino-2,2'-bipyridine moiety spaced by a chiral unit leaves the latter incapable of assembling through supramolecular π-π stacking. Rather, modeling indicates that the three metalloporphyrin units interact, thanks to van der Waals interactions, favoring their close interactions over that of the BTAB units. Atomic force microscopy shows that, in contrast to other examples of molecules with the same core, disclike aggregates (rather than fibrillar one dimensional aggregates) are favored by the C 3 symmetric molecule. The closed structures are formed through nondirectional interlocking of porphyrin rings. The chiral spacer between the rigid core and the porphyrin moieties is undoubtedly important in determining the outcome in polar or less polar solvents, as modeling shows that this joint in the molecule has two favored conformations that render the molecule relatively flat or convex.

Kinetic Control of a Self-Assembly Pathway towards Hidden Chiral Microcoils

Manipulating the self-assembly pathway is essentially important in the supramolecular synthesis of organic nano- and microarchitectures. Herein, we design a series of photoisomerizable chiral molecules, and realize precise control over pathway complexity with external light stimuli. The hidden single-handed microcoils, rather than the straight microribbons through spontaneous assembly, are obtained through a kinetically controlled pathway. The competition between molecular interactions in metastable photostationary intermediates gives rise to a variety of molecular packing and thereby the possibility of chirality transfer from molecules to supramolecular assemblies.

Future of Supramolecular Copolymers Unveiled by Reflecting on Covalent Copolymerization

Supramolecular copolymers are an emerging class of materials, and in the last years their potential has been demonstrated on a broad scale. Implementing noncovalent polymers with multiple components can bring together useful features such as dynamicity and new functionalities. However, mastering and tuning the microstructure of these systems is still an open challenge. In this Perspective, we aim to trace the general principles of supramolecular copolymerization by analyzing them through the lens of the well-established field of covalent copolymerization. Our goal is to delineate guidelines to classify and analyze supramolecular copolymers in order to create a fruitful platform to design and investigate new multicomponent systems.

Supramolecular polymerization: challenges and advantages of various methods in assessing the aggregation mechanism

Oligothiophenes with branched alkyl end groups show distinct aggregation in organic solvents. The process of supramolecular polymerization is assessed by three different methods (UV-vis absorption and fluorescence emission spectroscopy and dynamic light scattering) to exclude artifacts. An apparent dependence of the degree of aggregation on the concentration of the oligomers is observed. Above the upper limit of concentration (a lower micromolar range for the present class of compounds), experimental data delivered conflicting results and the concentration should not therefore be exceeded. Scanning force microscopy and molecular dynamics simulations confirm the formation of one-dimensional aggregates with presumably helical arrangement of the achiral monomers.

Cooperative supramolecular polymerization of phosphorescent alkynyl-gold(i)–isocyanide complexes

In this work, coil–rod–coil organogold(i) complexes have been successfully assembled into supramolecular polymers with green phosphorescent emission signal.

Regression Analysis for Nucleation-Elongation Model of Supramolecular Assembly: How To Determine Nucleus Size

Nucleation-elongation is known to give satisfactory descriptions of many supramolecular polymerization systems in thermal equilibrium. Its key feature is the necessity to form a "nucleus" consisting of a certain number of monomer units before being able to grow into a longer polymer chain. The size of the nucleus has significant implications for the understanding of the supramolecular polymerization mechanism. Here we investigate how experiments can give information on the nucleus size by regression analysis of various types of measurements. The measurements of free monomer concentrations, diffusion coefficients, and calorimetric response as functions of concentration or temperature are considered. The nucleation-elongation model with a general value for the nucleus size is used to provide mathematical expressions for these experimental observables. Numerical experiments are performed where experimental errors are simulated by computer-generated random numbers, and it is investigated whether least-squares fitting analyses can give the correct values of the nucleus size in the presence of experimental errors. It is recommended that the calorimetric measurements such as differential scanning calorimetry (DSC) or isothermal titration calorimetry (ITC) be performed under various conditions to correctly determine the nucleus size experimentally.