Understanding Cooperativity in Hydrogen-Bond-Induced Supramolecular Polymerization: A Density Functional Theory Study

Dispersion-Driven Cooperativity in Alkyl Perylene Diimide Oligomers: Insights from Density Functional Theory

The cooperative mechanism is of paramount importance in the synthesis of supramolecular polymers with desired characteristics, including molecular mass, polydispersity, and morphology. It is primarily driven by the presence of intermolecular interactions, which encompass strong hydrogen bonding, metal-ligand interactions, and dipole-dipole interactions. In this study, we utilize density functional theory and energy decomposition analysis to investigate the cooperative behavior of perylene diimide (PDI) oligomers with alkyl chains at their imide positions, which lack the previously mentioned interactions. Our systematic examination reveals that dispersion interactions originating from the alkyl side-chain substituents play an important role in promoting cooperativity within these PDIs. This influence becomes even more pronounced for alkyl chain lengths beyond hexyl groups. The energy decomposition analysis reveals that the delicate balance between dispersion energy and Pauli repulsion energy is the key driver of cooperative behavior in PDIs. Additionally, we have developed a mathematical model capable of predicting the saturated binding energies for PDI oligomers of varying sizes and alkyl chain lengths. Overall, our findings emphasize the previously undervalued significance of dispersion forces in cooperative supramolecular polymerization, enhancing our overall understanding of the cooperative mechanism.

Strengthened cooperativity of DNA-based cyclic hydrogen-bonded rosettes by subtle functionalization

Cooperative effects cause extra stabilization of hydrogen-bonded supramolecular systems. In this work we have designed hydrogen-bonded rosettes derived from a guanine-cytosine Janus-type motif with the aim of finding a monomer that enhances the synergy of supramolecular systems. For this, relativistic dispersion-corrected density functional theory computations have been performed. Our proposal involves a monomer with three hydrogen-bonds pointing in the same direction, which translates into shorter bonds, stronger donor-acceptor interactions, and more attractive electrostatic interactions, thus giving rise to rosettes with strengthened cooperativity. This newly designed rosette has triple the cooperativity found for the naturally occurring guanine quadruplex.

A supramolecular and liquid crystalline water-based alignment medium based on azobenzene-substituted 1,3,5-benzenetricarboxamides

A supramolecular, lyotropic liquid crystalline alignment medium based on an azobenzene-containing 1,3,5-benzenetricarboxamide (BTA) building block is described and investigated. As we demonstrate, this water-based system is suitable for the investigation of various water-soluble analytes and allows for a scaling of alignment strength through variation of temperature. Additionally, alignment is shown to reversibly collapse above a certain temperature, yielding an isotropic solution. This collapse allows for isotropic reference measurements, which are typically needed in addition to those in an anisotropic environment, to be performed using the same sample just by varying the temperature. The medium described thus provides easy access to anisotropic NMR observables and simplifies structure elucidation techniques based thereon.

Muscle-Inspired Anisotropic Hydrogel Strain Sensors

Hydrogel strain sensors have attracted tremendous attention in medical monitoring, flexible wearable devices, and human-machine interfaces. However, traditional hydrogels exhibit isotropic sensing performance based on their isotropic structure. Therefore, it is challenging to fabricate a hydrogel with an anisotropic structure similar to human tissues for achieving anisotropic sensing characteristics. Herein, we proposed a simple and effective method for preparing anisotropic poly(vinyl alcohol) (PVA) conductive hydrogels, which demonstrated anisotropic mechanical properties and anisotropic ion conductivity. The anisotropic hydrogel was successfully constructed through first thermal stretching and then directional freezing. The mechanical strength of hydrogels along the parallel stretching direction (stress of 1596 kPa and toughness of 3.69 MJ/m³) was higher than that of the hydrogels along the vertical stretching direction (stress of 883.1 kPa and toughness of 1.96 MJ/m³). Moreover, the hydrogel showed anisotropic conductivity on the advantage of the different ion channels. The prepared hydrogel sensor exhibited anisotropic sensing for multidirectional stress in the strain range from 0.5 to 100%. The gauge factors (GF) parallel to the stretching direction were greater than the GF vertical to the stretching direction. The anisotropic hydrogel sensors are expected to have broad application prospects in flexible wearable devices and medical monitoring.

Cooperative Effect of Noncovalent Interactions on Tetrel Bonding in Halogenated Silanes

Tetrel bond, a weak noncovalent interaction between the  σ -hole of a Group IV element (Silicon in our case) and the cloud of an electronegative element (Oxygen in our case) is the focus of current work. The percentage strengthening of tetrel bond has been investigated by optimising 16 binary complexes of halogenated silane and water of general formula SiX n H 4 - n  - H 2 O and 16 ternary complexes, of general formula NaX - SiX n H 4 - n  -H 2 O, where X =F, Cl, Br and I and n = 1, 2, 3 and 4 at various levels of theory defined within the formalism of density functional theory (DFT). With the addition of NaX, tetrel bond between Si and O in SiX n H 4 - n  - H 2 O gets strengthened up to 49%, owing to cooperativity effect exerted by hydrogen bonding between X and H in the ternary complex NaX - SiX n H 4 - n  - H 2 O. In the series of complexes studied here, overall stabilization due to cooperativity lies between 10 kJ/mol to 170 kJ/mol. This large extent of reinforcement due to cooperativity has never been showcased before. The exceptional stabilization and reinforcement owe its genesis to the transformation of the ternary complex into a cluster orchestrated by the H-bonding in most of the cases and covalent bonding in few of the cases.

Computational prediction of the supramolecular self-assembling properties of organic molecules: the role of conformational flexibility of amide moieties

Two families of organic molecules with different backbones have been considered. The first family is based on a macrolactam-like unit that is constrained in a particular conformation. The second family is composed by a substituted central phenyl that allows a larger mobility for its substituents. They have however a common feature, three amide moieties (within the cycle for the macrolactam-like molecule and as substituents for the phenyl) that permit hydrogen bonding when molecules are stacked. In this study we propose a computational protocol to unravel the ability of the different families to self-assemble into organic nanotubes. Starting from the monomer and going towards larger assemblies like dimers, trimers, and pentamers we applied the different protocols to rationalize the behavior of the different assemblies. Both structures and thermodynamics were investigated to give a complete picture of the process. Thanks to the combination of a quantum mechanics approach and molecular dynamics simulations along with the use of tailored tools (non covalent interaction visualization) and techniques (umbrella sampling), we have been able to differentiate the two families and highlight the best candidate for self-assembling purposes.

Cooperative Self-Assembly Driven by Multiple Noncovalent Interactions: Investigating Molecular Origin and Reassessing Characterization

Cooperative interactions play a pivotal role in programmable supramolecular assembly. Emerging from a complex interplay of multiple noncovalent interactions, achieving cooperativity has largely relied on empirical knowledge. Its development as a rational design tool in molecular self-assembly requires a detailed characterization of the underlying interactions, which has hitherto been a challenge for assemblies that lack long-range order. We employ extensive one- and two-dimensional magic-angle-spinning (MAS) solid-state NMR spectroscopy to elucidate key structure-directing interactions in cooperatively bound aggregates of a perylene bisimide (PBI) chromophore. Analysis of ¹H-¹³C cross-polarization heteronuclear correlation (CP-HETCOR) and ¹H-¹H double-quantum single-quantum (DQ-SQ) correlation spectra allow the identification of through-space ¹H···¹³C and ¹H···¹H proximities in the assembled state and reveals the nature of molecular organization in the solid aggregates. Emergence of cooperativity from the synergistic interaction between a stronger π-stacking and a weaker interstack hydrogen-bonding is elucidated. Finally, using a combination of optical absorption, circular dichroism, and high-resolution MAS NMR spectroscopy based titration experiments, we investigate the anomalous solvent-induced disassembly of aggregates. Our results highlight the disparity between two well-established approaches of characterizing cooperativity, using thermal and good solvent-induced disassembly. The anomaly is explained by elucidating the difference between two disassembly pathways.

Consequences of Amide Connectivity in the Supramolecular Polymerization of Porphyrins: Spectroscopic Observations Rationalized by Theoretical Modelling

The correlation between molecular structure and mechanism of supramolecular polymerizations is a topic of great interest, with a special focus on the pathway complexity of porphyrin assemblies. Their cooperative polymerization typically yields highly ordered, long 1D polymers and is driven by a combination of π-stacking due to solvophobic effects and hydrogen bonding interactions. Subtle changes in molecular structure, however, have significant influence on the cooperativity factor and yield different aggregate types (J- versus H-aggregates) of different lengths. In this study, the influence of amide connectivity on the self-assembly behavior of porphyrin-based supramolecular monomers was investigated. While in nonpolar solvents, C=O centered monomers readily assemble into helical supramolecular polymers via a cooperative mechanism, their NH centered counterparts form short, non-helical J-type aggregates via an isodesmic pathway. A combination of spectroscopy and density functional theory modelling sheds light on the molecular origins causing this stunning difference in assembly properties and demonstrates the importance of molecular connectivity in the design of supramolecular systems. Finally, their mutual interference in copolymerization experiments is presented.

Predicted structure and selectivity of 3d transition metal complexes with glutamic N,N-bis(carboxymethyl) acid

Structure and selectivity of 3d transition metal complexes with glutamic N,N-bis(carboxymethyl) acid are analyzed and predicted from DFT calculations.

Controlling the Length of Cooperative Supramolecular Polymers with Chain Cappers

The design and the characterization of supramolecular additives to control the chain length of benzene-1,3,5-tricarboxamide (BTA) cooperative supramolecular polymers under thermodynamic equilibrium is unraveled. These additives act as chain cappers of supramolecular polymers and feature one face as reactive as the BTA discotic to interact strongly with the polymer end, whereas the other face is nonreactive and therefore impedes further polymerization. Such a design requires fine tuning of the conformational preorganization of the amides and the steric hindrance of the motif. The chain cappers studied are monotopic derivatives of BTA, modified by partial N-methylation of the amides or by positioning of a bulky cyclotriveratrylene cage on one face of the BTA unit. This study not only clarifies the interplay between structural variations and supramolecular interactions, but it also highlights the necessity to combine orthogonal characterization methods, spectroscopy and light scattering, to elucidate the structures and compositions of supramolecular systems.

Divergent Self-Assembly Pathways to Hierarchically Organized Networks of Isopeptide-Modified Discotics under Kinetic Control

Natural proteins traverse complex free energy landscapes to assemble into hierarchically organized structures, often through stimuli-directed kinetic pathways in response to relevant biological cues. Bioinspired strategies have sought to emulate the complexity, dynamicity, and modularity exhibited in these natural processes with synthetic analogues. However, these efforts are limited by many factors that complicate the rational design and predictable assembly of synthetic constructs, especially in aqueous environments. Herein, a model discotic amphiphile gelator is described that undergoes pathway-dependent structural maturation when exposed to varying application rates of a pH stimulus, investigated by electron microscopy, spectroscopy, and X-ray scattering techniques. Under the direction of a slowly changing pH stimulus, complex hierarchical assemblies result, characterized by mesoscale elongated "superstructure" bundles embedded in a percolated mesh of narrow nanofibers. In contrast, the assembly under a rapidly applied pH stimulus is characterized by homogeneous structures that are reminiscent of the superstructures arising from the more deliberate path, except with significantly reduced scale and concomitantly large increases in bulk rheological properties. This synthetic system bears resemblance to the pathway complexity and hierarchical ordering observed for native structures, such as collagen, and points to fundamental design principles that might be applied toward enhanced control of the properties of supramolecular self-assembly across length scales.

Stacks of Azobenzene Stars: Self-Assembly Scenario and Stabilising Forces Quantified in Computer Modelling

In this paper, the columnar supramolecular aggregates of photosensitive star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core and azobenzene arms are analyzed theoretically by applying a combination of computer simulation techniques. Without a light stimulus, the azobenzene arms adopt the trans-state and build one-dimensional columns of stacked molecules during the first stage of the noncovalent association. These columnar aggregates represent the structural elements of more complex experimentally observed morphologies-fibers, spheres, gels, and others. Here, we determine the most favorable mutual orientations of the trans-stars in the stack in terms of (i) the π - π distance between the cores lengthwise the aggregate, (ii) the lateral displacements due to slippage and (iii) the rotation promoting the helical twist and chirality of the aggregate. To this end, we calculate the binding energy diagrams using density functional theory. The model predictions are further compared with available experimental data. The intermolecular forces responsible for the stability of the stacks in crystals are quantified using Hirshfeld surface analysis. Finally, to characterize the self-assembly mechanism of the stars in solution, we calculate the hydrogen bond lengths, the normalized dipole moments and the binding energies as functions of the columnar length. For this, molecular dynamics trajectories are analyzed. Finally, we conclude about the cooperative nature of the self-assembly of star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core in aqueous solution.

Tuning the Length of Cooperative Supramolecular Polymers under Thermodynamic Control

In the field of supramolecular (co)polymerizations, the ability to predict and control the composition and length of the supramolecular (co)polymers is a topic of great interest. In this work, we elucidate the mechanism that controls the polymer length in a two-component cooperative supramolecular polymerization and unveil the role of the second component in the system. We focus on the supramolecular copolymerization between two derivatives of benzene-1,3,5-tricarboxamide (BTA) monomers: a-BTA and Nle-BTA. As a single component, a-BTA cooperatively polymerizes into long supramolecular polymers, whereas Nle-BTA only forms dimers. By mixing a-BTA and Nle-BTA in different ratios, two-component systems are obtained, which are analyzed in-depth by combining spectroscopy and light-scattering techniques with theoretical modeling. The results show that the length of the supramolecular polymers formed by a-BTA is controlled by competitive sequestration of a-BTA monomers by Nle-BTA, while the obvious alternative Nle-BTA acts as a chain-capper is not operative. This sequestration of a-BTA leads to short, stable species coexisting with long cooperative aggregates. The analysis of the experimental data by theoretical modeling elucidates the thermodynamic parameters of the copolymerization, the distributions of the various species, and the composition and length of the supramolecular polymers at various mixing ratios of a-BTA and Nle-BTA. Moreover, the model was used to generalize our results and to predict the impact of adding a chain-capper or a competitor on the length of the cooperative supramolecular polymers under thermodynamic control. Overall, this work unveils comprehensive guidelines to master the nature of supramolecular (co)polymers and brings the field one step closer to applications.

Detailed Approach to Investigate Thermodynamically Controlled Supramolecular Copolymerizations

Elucidating the microstructure of supramolecular copolymers remains challenging, despite the progress in the field of supramolecular polymers. In this work, we present a detailed approach to investigate supramolecular copolymerizations under thermodynamic control. Our approach provides insight into the interactions of different types of monomers and hereby allows elucidating the microstructure of copolymers. We select two monomers that undergo cooperative supramolecular polymerization by way of threefold intermolecular hydrogen bonding in a helical manner, namely, benzene-1,3,5-tricarboxamide (BTA) and benzene-1,3,5-tris(carbothioamide) (thioBTA). Two enantiomeric forms and an achiral analogue of BTA and thioBTA are synthesized and their homo- and copolymerizations are studied using light scattering techniques, infrared, ultraviolet, and circular dichroism spectroscopy. After quantifying the thermodynamic parameters describing the homopolymerizations, we outline a method to follow the self-assembly of thioBTA derivatives in the copolymerization with BTA, which involves monitoring a characteristic spectroscopic signature as a function of temperature and relative concentration. Using modified types of sergeants-and-soldiers and majority-rules experiments, we obtain insights into the degree of aggregation and the net helicity. In addition, we apply a theoretical model of supramolecular copolymerization to substantiate the experimental results. We find that the model describes the two-component system well and allows deriving the hetero-interaction energies. The interactions between the same kinds of monomers (BTA-BTA and thioBTA-thioBTA) are slightly more favorable than those between different monomers (BTA-thioBTA), corresponding to a nearly random copolymerization. Finally, to study the interactions of the monomers at the molecular level, we perform density functional theory-based computations. The results corroborate that the two-component system exhibits a random distribution of the two monomer units along the copolymer chain.

The Nature of Hydrogen Bonds: A Delineation of the Role of Different Energy Components on Hydrogen Bond Strengths and Lengths

Hydrogen bonds are a complex interplay between different energy components, and their nature is still subject of an ongoing debate. In this minireview, we therefore provide an overview of the different perspectives on hydrogen bonding. This will be done by discussing the following individual energy components: 1) electrostatic interactions, 2) charge-transfer interactions, 3) π-resonance assistance, 4) steric repulsion, 5) cooperative effects, 6) dispersion interactions and 7) secondary electrostatic interactions. We demonstrate how these energetic factors are essential in a correct description of the hydrogen bond, and discuss several examples of systems whose energetic and geometrical features are not captured by easy-to-use predictive models.

Self-Assembly of C3 Symmetric Rigid Macrolactams into Very Polar and Porous Trigonal Crystals

Cyclohexane and cyclotri-β-alanyl have been used as scaffolds for the design of new C₃ -symmetric rings incorporating conjugated alkenes and dienes. All three C₃ -symmetric lactams share the same triangular shape and their crystal system is trigonal. They all belong to the R3 space group, R3m, R3 and R3c, for the increasingly large 12-, 18- and 24-membered rigid rings, respectively. All lactams stack on top of each other, through H-bonds and van der Waals noncovalent interactions, leading to endless supramolecular cylinders and tubes. The largest member of the family leads to tubes, the central pores of which is wide enough to let water in. A common feature of all the lactams is their very large dipole, of around 9 D, according to DFT calculations. Surprisingly, all the resulting cylinders and tubes pack side by side in the crystals, with all the dipoles pointing to the same direction. As a result, all three crystals are anisotropic and appear to be the first members of a new kind of highly polar crystals.

Biomimetic anisotropic poly(vinyl alcohol) hydrogels with significantly enhanced mechanical properties by freezing–thawing under drawing

Anisotropic poly(vinyl alcohol) hydrogels with significantly enhanced mechanical properties are prepared by a freezing–thawing under drawing (FTD) method.

Differentiating the mechanism of self-assembly in supramolecular polymers through computation

The mechanism by which monomers in solution, beyond a certain concentration or below a certain temperature, self-assemble to form one dimensional supramolecular polymers determines much of the bulk properties of the polymer.

Nanoscale insight into silk-like protein self-assembly: effect of design and number of repeat units

By means of replica exchange molecular dynamics simulations we investigate how the length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary structure. We carry out simulations for two protein sizes consisting of three and five blocks, and study the stability of a single protein, a dimer, a trimer and a tetramer. Initial configurations of our simulations are β-roll and β-sheet structures. We find that for the triblock the secondary and quaternary structures upto and including the tetramer are unstable: the proteins melt into random coil structures and the aggregates disassemble either completely or partially. We attribute this to the competition between conformational entropy of the proteins and the formation of hydrogen bonds and hydrophobic interactions between proteins. This is confirmed by our simulations on the pentablock proteins, where we find that, as the number of monomers in the aggregate increases, individual monomers form more hydrogen bonds whereas their solvent accessible surface area decreases. For the pentablock β-sheet protein, the monomer and the dimer melt as well, although for the β-roll protein only the monomer melts. For both trimers and tetramers remain stable. Apparently, for these the entropy loss of forming β-rolls and β-sheets is compensated for in the free-energy gain due to the hydrogen-bonding and hydrophobic interactions. We also find that the middle monomers in the trimers and tetramers are conformationally much more stable than the ones on the top and the bottom. Interestingly, the latter are more stable on the tetramer than on the trimer, suggesting that as the number of monomers increases protein-protein interactions cooperatively stabilize the assembly. According to our simulations, the β-roll and β-sheet aggregates must be approximately equally stable.

Cooperativity Principles in Self-Assembled Nanomedicine

Nanomedicine is a discipline that applies nanoscience and nanotechnology principles to the prevention, diagnosis, and treatment of human diseases. Self-assembly of molecular components is becoming a common strategy in the design and syntheses of nanomaterials for biomedical applications. In both natural and synthetic self-assembled nanostructures, molecular cooperativity is emerging as an important hallmark. In many cases, interplay of many types of noncovalent interactions leads to dynamic nanosystems with emergent properties where the whole is bigger than the sum of the parts. In this review, we provide a comprehensive analysis of the cooperativity principles in multiple self-assembled nanostructures. We discuss the molecular origin and quantitative modeling of cooperative behaviors. In selected systems, we describe the examples on how to leverage molecular cooperativity to design nanomedicine with improved diagnostic precision and therapeutic efficacy in medicine.

Communication: Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering

Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper, we explore the utility of replica exchange with solute tempering (REST) (i.e., a variant of Hamiltonian replica exchange methods) to simulate the self-assembly of a supramolecular polymer in explicit solvent and compare the performance with temperature-based replica exchange MD (T-REMD) as well as cMD. As a test system, we consider a relatively simple all-atom model of supramolecular polymerization (namely, benzene-1,3,5-tricarboxamides in methylcyclohexane solvent). Our results show that both REST and T-REMD are able to predict highly ordered polymer structures with helical H-bonding patterns, in contrast to cMD which completely fails to obtain such a structure for the present model. At the same time, we have also experienced some technical challenge (i.e., aggregation-dispersion transition and the resulting bottleneck for replica traversal), which is illustrated numerically. Since the computational cost of REST scales more moderately than T-REMD, we expect that REST will be useful for studying the self-assembly of larger systems in solution with enhanced rearrangement of monomers.

Induced-Dipole-Directed, Cooperative Self-Assembly of a Benzotrithiophene

A benzotrithiophene derivative possessing phenylisoxazoles self-assembled to form stacks. The molecule isodesmically self-assembled in chloroform, whereas it self-assembled in a cooperative fashion in decalin and in methylcyclohexane. Thermodynamic studies based on isodesmic, van der Schoot, and Goldstein-Stryer mathematical models revealed that the self-assembly processes are enthalpically driven and entropically opposed. An enthalpy-entropy compensation plot indicates that the assembly processes in chloroform, decalin, and methylcyclohexane are closely related. The enthalpic gains in less-polar solvents are greater than those in more-polar solvents, resulting in the formation of large assemblies in decalin and in methylcyclohexane. The formation of large assemblies leads to cooperative assemblies. The elongation process is enthalpically more favored than the nucleation process, which drives the cooperativity of the self-assembly. DFT calculations suggested that a hexameric assembly is more stable than tetrameric or dimeric assemblies. Cooperative self-assemblies based on intermolecular interactions other than hydrogen bonding have rarely been reported. It is demonstrated herein that van der Waals interactions, including induced dipole-dipole interactions, can drive the cooperative assembly of planar π-conjugated molecules.

Effect of Concentration on the Supramolecular Polymerization Mechanism via Implicit-Solvent Coarse-Grained Simulations of Water-Soluble 1,3,5-Benzenetricarboxamide

We report an implicit-solvent coarse-grained (CG) model for a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer. The technical advances guaranteed by this CG model allow simulation of the self-assembly of 1000 BTA monomers and easy variation of the BTA concentration into the system down to experimental dilute conditions. In this way, we can monitor the mechanism of supramolecular polymerization as a function of the concentration at submolecular resolution exceeding the microsecond time scale. While increasing the concentration produces rapid formation of large disordered clusters that are then converted into BTA fibers, moving to very dilute concentrations favors early ordering of the oligomers in solution even at small sizes. Interestingly, we observe that below a certain concentration the oligomers that dynamically grow in solution during the self-assembly present the same level (and amplification) of order of prestacked equilibrated oligomers of the same size, meaning that concentration-dependent kinetic effects have disappeared from the polymerization mechanism.

Cooperativity Scale: A Structure-Mechanism Correlation in the Self-Assembly of Benzene-1,3,5-tricarboxamides

The self-assembly of small and well-defined molecules using noncovalent interactions to generate various nano- and microarchitectures has been extensively studied. Among various architectures, one-dimensional (1-D) nano-objects have garnered significant attention. It has become increasingly evident that a cooperative or nucleation-elongation mechanism of polymerization leads to highly ordered 1-D supramolecular polymers, analogous to shape-persistent biopolymers such as actin. With this in mind, achieving cooperativity in self-assembled structures has been actively pursued with significant success. Only recently, researchers are focusing on the origin of the mechanism at the molecular level in different synthetic systems. Taking a step further, a thorough quantitative structure-mechanism correlation is crucial to control the size, shape, and functions of supramolecular polymers, and this is currently lacking in the literature. Among a plethora of molecules, benzene-1,3,5-tricarboxamides (BTAs) provide a unique combination of important noncovalent interactions such as hydrogen bonding, π-stacking, and hydrophobic interactions, for self-assembly and synthetic ease. Due to the latter, a diverse range of BTA derivatives with all possible structural mutations have been synthesized and studied during the past decade, mainly from our group. With such a large body of experimental results on BTA self-assembly, it is time to embark on a structure-mechanism correlation in this family of molecules, and a first step toward this will form the main focus of this Account. The origin of the cooperative mechanism of self-assembly in BTAs has been ascribed to 3-fold intermolecular hydrogen bonding (HB) between monomers based on density-functional theory (DFT) calculations. The intermolecular hydrogen-bonding interaction forms the central premise of this work, in which we evaluate the effect of different moieties such as alkyl chains, and amino acids, attached to the core amides on the strength of intermolecular HB, which consequently governs the extent of cooperativity (quantified by the cooperativity factor, σ). In addition to this, we evaluate the effect of amide connectivity (C- vs N-centered), the role of solvents, amides vs thioamides, and finally the influence of the benzene vs cyclohexane core on the σ. Remarkably, every subtle structural change in the BTA monomer seems to affect the cooperativity factor in a systematic and rationalizable way. The take home message will be that the cooperativity factor (σ) in the BTA family forms a continuous spectrum from 1 (isodesmic) to <10^-6 (highly cooperative) and it can be tuned based on the appropriate modification of the BTA monomer. We anticipate that these correlations drawn from the BTA series will be applicable to other systems in which HB is the main driving force for cooperativity. Thus, the understanding gained from such correlations on a prototypical self-assembling motif such as BTA will aid in designing more complex systems with distinct functions.

Modeling cooperative effects in halogen-bonded infinite linear chains

Non-additivity in noncovalent interactions is an important aspect of complex systems that can lead to stronger (cooperative) interactions when three or more molecular units influence each other. The halogen bond (XB) is a highly-directional noncovalent interaction that has been found to be cooperative. Here the strength and nature of cooperativity arising in X-bonded infinite linear chains of cyanogen halides and 4-halopyridines are investigated by means of density functional theory calculations. It is found that cyanogen halide chains are highly cooperative (up to 77%), whereas pyridines are only slightly cooperative (below 21%). It is demonstrated that XB and its non-additivity can be modeled as the sum of a local term, which depends on first nearest-neighbors only, and long-range effective dipole-dipole attractions. It is shown that the local term in cyanogen halides primarily accounts for repulsive short-range screened Coulomb interactions, whereas in 4-halopyridines such a term also includes attractive contributions, which are particularly sizeable in some elongated XB conformations. This outcome reveals differences in the nature of the XBs formed in these molecular systems. Nevertheless, it is shown that both systems behave as effective point dipoles regarding cooperative effects, at any point of the XB dissociation path. As such, these results are useful contributions for the understanding and modeling of non-additive effects of noncovalent interactions.

Unravelling the Pathway Complexity in Conformationally Flexible N-Centered Triarylamine Trisamides

Two families of C3 -symmetrical triarylamine-trisamides comprising a triphenylamine- or a tri(pyrid-2-yl)amine core are presented. Both families self-assemble in apolar solvents via cooperative hydrogen-bonding interactions into helical supramolecular polymers as evidenced by a combination of spectroscopic measurements, and corroborated by DFT calculations. The introduction of a stereocenter in the side chains biases the helical sense of the supramolecular polymers formed. Compared to other C3 -symmetrical compounds, a much richer self-assembly landscape is observed. Temperature-dependent spectroscopy measurements highlight the presence of two self-assembled states of opposite handedness. One state is formed at high temperature from a molecularly dissolved solution via a nucleation-elongation mechanism. The second state is formed below room temperature through a sharp transition from the first assembled state. The change in helicity is proposed to be related to a conformational switch of the triarylamine core due to an equilibrium between a 3:0 and a 2:1 conformation. Thus, within a limited temperature window, a small conformational twist results in an assembled state of opposite helicity.

Ferroelectric switching and electrochemistry of pyrrole substituted trialkylbenzene-1,3,5-tricarboxamides

We explore a new approach to organic ferroelectric diodes using a benzene‐tricarboxamide (BTA) core connected with C10 alkyl chains to pyrrole groups, which can be polymerized to provide a semiconducting ferroelectric material. The compound possesses a columnar hexagonal liquid crystalline (LC) phase and exhibits ferroelectric switching. At low switching frequencies, an additional process occurs, which leads to a high hysteretic charge density of up to ∼1000 mC/m². Based on its slow rate, the formation of gas bubbles, and the emergence of characteristic polypyrrole absorption bands in the UV–Vis–NIR, the additional process is identified as the oxidative polymerization of pyrrole groups, enabled by the presence of amide groups. Polymerization of the pyrrole groups, which is essential to obtain semiconductivity, is limited to thin layers at the electrodes, amounting to ∼17 nm after cycling for 21 h. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017, 55, 673–683

From Cooperative Self-Assembly to Water-Soluble Supramolecular Polymers Using Coarse-Grained Simulations

Supramolecular polymers, formed via noncovalent self-assembly of elementary monomers, are extremely interesting for their dynamic bioinspired properties. In order to understand their behavior, it is necessary to access their dynamics while maintaining high resolution in the treatment of the monomer structure and monomer-monomer interactions, which is typically a difficult task, especially in aqueous solution. Focusing on 1,3,5-benzenetricarboxamide (BTA) water-soluble supramolecular polymers, we have developed a transferable coarse-grained model that allows studying BTA supramolecular polymerization in water, while preserving remarkable consistency with the atomistic models in the description of the key interactions between the monomers (hydrophobic, H-bonding, etc.), self-assembly cooperativity, and amplification of order into the growing fibers. This permitted us to monitor the amplification of the key interactions between the monomers (including H-bonding) in the BTA fibers during the dynamic polymerization process. Our molecular dynamics simulations provide a picture of a stepwise cooperative polymerization mechanism, where initial fast hydrophobic aggregation of the BTA monomers in water is followed by the slower reorganization of these disordered aggregates into ordered directional oligomers. Supramolecular polymer growth then proceeds on a slower time scale. We challenged our models via comparison with the experimental evidence, capturing the effect of temperature variations and subtle changes in the monomer structure on the polymerization and on the properties of the fibers seen in the real systems. This work provides a multiscale spatiotemporal characterization of BTA self-assembly in water and a useful platform to study a variety of BTA-based supramolecular polymers toward structure-property relationships.

Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs

For the AT pair, Symst and Strech peaks further shift toward the red, giving the H-bonds an amplified effect (orange arrows).

Columnar self-assembly of N,N′,N′′-trihexylbenzene-1,3,5-tricarboxamides investigated by means of NMR spectroscopy and computational methods in solution and the solid state

The columnar self-assembly resulting from units of N,N′,N′′-trihexylbenzene-1,3,5-tricarboxamide is investigated in solution and the solid state by means of NMR spectroscopy and DFT methods.

Influence of Metal, Ligand and Solvent on Supramolecular Polymerizations with Transition-Metal Compounds: A Theoretical Study

The nature of intermolecular interactions governing supramolecular polymerizations is very important for controlling their cooperativity. In order to address this problem, supramolecular columns made of Pt^II and Pd^II complexes of oligo(phenylene ethynylene)-based pyridine (OPE) and tetrazolylpyridine ligands (TEP) were investigated through the dispersion-corrected PM6 method. Aromatic, CH-π, M-Cl and metallophilic interactions helped stabilize the supramolecules studied, and their geometries and associated cooperativities were in excellent agreement with experimental data. The OPE ligand and/or the presence of Pt^II led to stronger metallophilic interactions and also to cooperative supramolecular polymerizations, which clearly suggests that metallophilic interactions are a key factor for controlling cooperativity. The results indicate that sequential monomer addition is in general less spontaneous than the combination of two larger preformed stacks. The present theoretical investigations contribute to the further understanding of the relation between the thermodynamics of supramolecular polymerizations and the nature of different synthons.

Cooperative Self-Assembly of Carbazole Derivatives Driven by Multiple Dipole-Dipole Interactions

Carbazole possessing phenylisoxazoles self-assembled in a cooperative manner in decalin. X-ray crystal structure analysis revealed that the isoxazole dipoles align in a head-to-tail fashion. DFT calculations suggested that the linear array of dipoles induced the polarization of each dipole, leading to an increase in dipole-dipole interactions. This dipole polarization resulted in cooperative assembly.

Supercoiled fibres of self-sorted donor-acceptor stacks: a turn-off/turn-on platform for sensing volatile aromatic compounds

To ensure the comfortable survival of living organisms, detection of different life threatening volatile organic compounds (VOCs) such as biological metabolites and carcinogenic molecules is of prime importance. Herein, we report the use of supercoiled supramolecular polymeric fibres of self-sorted donor-acceptor molecules as "turn-off/turn-on" fluorescent sensors for the detection of carcinogenic VOCs. For this purpose, a C3-symmetrical donor molecule based on oligo(p-phenylenevinylene), C3OPV, and a perylene bisimide based acceptor molecule, C3PBI, have been synthesized. When these two molecules were mixed together in toluene, in contrast to the usual charge transfer (CT) stacking, supramolecular fibres of self-sorted stacks were formed at the molecular level, primarily driven by their distinct self-assembly pathways. However, CT interaction at the macroscopic level allows these fibres to bundle together to form supercoiled ropes. An interfacial photoinduced electron transfer (PET) process from the donor to the acceptor fibres leads to an initial fluorescence quenching, which could be modulated by exposure to strong donor or acceptor type VOCs to regenerate the respective fluorescence of the individual molecular stacks. Thus, strong donors could regenerate the green fluorescence of C3OPV stacks and strong acceptors could reactivate the red fluorescence of C3PBI stacks. These supercoiled supramolecular ropes of self-sorted donor-acceptor stacks provide a simple tool for the detection of donor- or acceptor-type VOCs of biological relevance, using a "turn-off/turn-on" fluorescence mechanism as demonstrated with o-toluidine, which has been reported as a lung cancer marker.

Binding energies of nucleobase complexes: Relevance to homology recognition of DNA

The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and calculate their binding energies. At a second step, mismatches are incorporated into the Watson-Crick complexes in order to evaluate the variation in the binding energy with respect to the canonical Watson-Crick pairs. A linear variation of this binding energy with the degree of mismatching is observed. The binding energies for the duplets and triplets containing mismatches are further compared to the energies of the respective singlets in order to assess the degree of collectivity in these complexes. This study also suggests that mismatches do not considerably affect the energetics of canonical base pairs. Our work is highly relevant to the recognition process in DNA promoted through the RecA protein and suggests a clear distinction between recognition in singlets, and recognition in duplets or triplets. Our work assesses the importance of collectivity in the homology recognition of DNA.

Supramolecular polymerisation in water; elucidating the role of hydrophobic and hydrogen-bond interactions

Understanding the self-assembly of small molecules in water is crucial for the development of responsive, biocompatible soft materials. Here, a family of benzene-1,3,5-tricarboxamide (BTA) derivatives that comprise a BTA moiety connected to an amphiphilic chain is synthesised with the aim to elucidate the role of hydrophobic and hydrogen-bonding interactions in the self-assembly of these BTAs. The amphiphilic chain consists of an alkyl chain with a length of 10, 11, or 12 methylene units, connected to a tetraethylene glycol (at the periphery). The results show that an undecyl spacer is the minimum length required for these BTAs to self-assemble into supramolecular polymers. Interestingly, exchange studies reveal only minor differences in exchange rates between BTAs containing undecyl or dodecyl spacers. Additionally, IR spectroscopy provides the first experimental evidence that hydrogen-bonding is operative and contributes to the stabilisation of the supramolecular polymers in water.