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

Korlepara, Divya B.; Henderson, Will R; Castellano, Ronald K.; Balasubramanian, Sundaram

doi:10.1039/c9cc01058k

Cited by 21 publications

(38 citation statements)

References 43 publications

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“…The angle Ω defined as the rotation angle of the upper star is shown schematically in Figure 3. Such a systematic rotation of the consecutive stars along the column leads to the formation of the helical structures found in literature for BTA-centred molecules [44,58,[62][63][64]. It was discussed that this twisting allows the binding of the stars through hydrogen bonding, in which all three amide groups of the BTA are involved.…”

Section: Binding Energy Diagramsmentioning

confidence: 88%

“…Let us now compare the literature data with our predictions. The most common rotational angle between consecutive unmoved (l=k=0) BTA-centred monomers is 60-65 o [44,58,[62][63][64]. The calculations show that the binding energy corresponding to these coordinates is about -73 kJ mol −1 for the azo-BTA star (marked with yellow colour).…”

Section: Binding Energy Diagramsmentioning

confidence: 97%

“…As descriptors of cooperativity, the following features are analysed as functions of N or depending on the position of the star in the stack: binding energies, the length of hydrogen bonds, and macrodipoles. These descriptors have been used by many researchers for the classification of the self-assembly mechanisms in BTA-containing systems [44,61,64,67]. The stacks of azo-BTA stars are analysed using data sets from molecular dynamics (MD) simulations [29] and from experiments [17] applying density functional theory and classical modelling techniques.…”

Section: On the Cooperative Nature Of Self-assemblymentioning

confidence: 99%

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

Savchenko

Koch

Pavlov

et al. 2019

Preprint

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In this paper, the columnar supramolecular aggregates of photosensitive star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core and azobenzene arms are analysed theoretically applying a combination of computer simulation techniques. Without a light stimulus, the trans-stars 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. Upon UV light exposure, the azobenzene arms isomerise from thermodynamically stable planar trans- to a metastable kinked cis-state influencing the aggregate morphology. Here, we determine the most favourable mutual orientations of the \textit{trans}-stars in the stack in terms of (i) the pi-pi distance between the cores lengthwise the aggregate, (ii) the star slipped displacements and (iii) the rotation promoting the helical twist and chirality of the aggregate by calculating 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 made of trans-azobenzene stars in crystals are quantified using Hirshfeld surface analysis. Finally, to characterize the self-assembly mechanism of such stars in solution, we calculate the hydrogen bond lengths, the normalized dipole moment and the binding energies as the functions of the columnar length using molecular dynamics trajectories, and conclude about the cooperative nature of this process.

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Section: Binding Energy Diagramsmentioning

confidence: 88%

Section: Binding Energy Diagramsmentioning

confidence: 97%

Section: On the Cooperative Nature Of Self-assemblymentioning

confidence: 99%

See 1 more Smart Citation

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

Savchenko

Koch

Pavlov

et al. 2019

Preprint

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“…Therefore, the assembly of [2.2]-pCpTA under thermodynamic control is likely comprised of the anti-conformer, and this hypothesis is consistent with recent computational investigations. [55] The characterization of (�)-1b and alkylated comparator (�)-1c allowed the assignment of both intermolecular and transannularly H-…”

Section: Discussionmentioning

confidence: 99%

“…[54] Computational data suggests that the anti-conformer is the predominant assembling species, but both conformers will exist in solution. [55] We envision that the two conformers, because of their structural similarities and electronic differences, will be useful models for understanding structureÀ mechanism relationships in supramolecular polymers. [56] Reported here are the design, synthesis, and investigation of simpler disubstituted [2.2]pCp systems to closely examine transannular H-bonding independent of strong intermolecular assembly (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

Transannular Hydrogen Bonding in Planar‐Chiral [2.2]Paracyclophane‐Bisamides

Henderson

Fagnani

Grolms

et al. 2019

Helvetica Chimica Acta

Self Cite

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A series of [2.2]paracyclophane‐bisamide regioisomers and alkylated comparators were designed, synthesized, and characterized in order to better understand the transannular hydrogen bonding of [2.2]paracyclophane‐based molecular recognition units. X‐Ray crystallography shows that transannular hydrogen bonding is maintained in the solid‐state, but no stereospecific self‐recognition is observed. The assignment of both transannularly and intermolecularly hydrogen bonded N−H stretches could be made by infrared spectroscopy, and the effect of transannular hydrogen bonding on amide bond rotation dynamics is observed by 1H‐NMR in nonpolar solvents. The consequences of transannular hydrogen bonding on the optical properties of [2.2]paracyclophane is observed by comparing alkylated and non‐alkylated pseudo‐ortho 4,12‐[2.2]paracyclophane‐bisamides. Finally, optical resolution of 4‐mono‐[2.2]paracyclophane and pseudo‐ortho 4,12‐[2.2]paracyclophane‐bisamides was achieved through the corresponding sulfinyl diastereoisomers for circular dichroism studies. Transannular hydrogen bonding in [2.2]paracyclophane‐amides allows preorganization for self‐complementary intermolecular assembly, but is weak enough to allow rapid rotation of the amides even in nonpolar solvents.

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Molecular Insights into [2.2]Paracyclophane‐Based Functional Materials: Chemical Aspects Behind Functions

Hassan

2024

Adv Funct Materials

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Many of the functions and features of practically useful materials are the province of molecular‐level chemistry and their modulation at different length‐scale. This report illustrates the molecular‐level chemistry behind functions and features of the [2.2]paracyclophane‐based materials with a particular focus on the most recent explorations on through‐space conjugated small‐molecule organic emitters, π‐stacked macrocyclic molecules and polymers, poly(p‐phenylenevinylene)s featuring well‐defined donor‐acceptors sequence control, and surface engineering of technologically‐relevant parylenes that finds broad applications across the field of chemical science and technology. This report largely deals with the potential and opportunities associated with molecular features and functions of planar chirality, conformational behaviors, strain‐induced non‐planarity of the aromatics, the profound impacts of through‐space conjugation and π‐electron interactions/delocalization on optoelectronic properties of the π‐conjugated organic emitters, polymers and extended structures consisting of cyclophanes. A special focus is put on the concept of supramolecular polymers using chemically‐programmed chiral cyclophanes via non‐covalent stacking and controlled conformational arrangements. Illustrating cyclophane as precursors/monomers and fabrication strategies for their incorporation in structurally‐controlled (poly(p‐xylylene)s formed via chemical vapor deposition polymerization and post‐deposition fabrication for interface engineering is described. Demonstrating a rather different approach of electronically‐dictated ring‐opening metathesis polymerization employing strained cyclophane‐diene precursors that generate conjugated poly(p‐phenylenevinylene)s with well‐defined (i.e., low dispersity) and donor‐acceptor sequence control is also discussed. This report will serve as an indispensable one‐stop reference for organic, and polymer chemists, as well as material scientists working with cyclophanes for research innovations.

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

Abstract: 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.

Cited by 21 publications

References 43 publications

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

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

Transannular Hydrogen Bonding in Planar‐Chiral [2.2]Paracyclophane‐Bisamides

Molecular Insights into [2.2]Paracyclophane‐Based Functional Materials: Chemical Aspects Behind Functions

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