Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations

Abstract

We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of π–π interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the π–π interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, π–π stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.

Cyclic Photoisomerization of Azobenzene in Atomistic Simulations: Modeling the Effect of Light on Columnar Aggregates of Azo Stars

“…The different parts of the stacked molecules contribute in different proportions to the binding of the cluster, see Figure 10 and Ref. [41]. In particular, the intermolecular (or binding) energies of the clusters are dominated by the dispersion interactions (π-π stacking) between the azobenzene arms of directly neighboring molecules.…”

“…[24] has hydrogen atoms (R = H) in place of dimethylamino groups and will be named TrisAzo-H from here on. These substituent groups have only a marginal influence on the intermolecular interactions between such molecules [41].…”

“…This initial stack arrangement is considered because it has been the most long-time stable in the columnar shape, as determined in a closely related simulation study of the equilibrium structure of TrisAzo stacks [41]. Thus, after the equilibration period, the simulations can be continued with a still column-shaped stack (Figure 2b).…”

“…The equilibrium structure of the TrisAzo is analyzed in detail in another work [41]. Nevertheless, the most important structural properties are summarized below.…”

“…A detailed simulation study has focused on the introduction of defects in supramolecular tubules of another multiazobenzene compound [39]. We have previously investigated the self-assembly and stability of aggregates formed by three-arm azobenzene stars [40,41] and we have analyzed how highly intense light irradiation influences the binding of these supramolecular stacks [29]. In a proof-of-principle manner, it was found that the photoisomerization of all trans-azo groups to cis does not result in breaking or disassembly of the column-shaped aggregate but strongly disorders it.…”