Consequences of a Single Double Bond within a Side Group on the Ordering of Supramolecular Polymers

Abstract

By combining atomic force microscopy experiments and full-atomistic computer simulations, we compared the twodimensional ordering dynamics of two variants of supramolecular polymers of bis-urea molecules which differed only by a single cisdouble bond in their side groups. At early stages of ordering, the double bonds favored kinks at the level of individual molecules, which induced transient steric constraints hindering the spontaneous formation of long supramolecular polymers. In addition, due to these kinks, molecule−substrate interactions were disturbed. At later stages, however, due to a progressively increasing number of established directional hydrogen bonds between molecules, the self-assembly process improved and thereby increased the length of the supramolecular polymers. Large domains of micrometer-long and aligned supramolecular polymers were formed, epitaxially guided by the graphite substrate and having a constant width consistent with the length of the molecule. Thus, introducing flexible (kinked) side chains can reduce the nucleation probability and slow the growth of supramolecular polymers due to incommensurablility with the crystalline substrate. Such an elementary control of nucleation and growth via the introduction of a single double bond represents a powerful pathway for the formation of large ordered domains of aligned one-dimensional supramolecular polymers.

Engineering Long-Range Order in Supramolecular Assemblies on Surfaces: The Paramount Role of Internal Double Bonds in Discrete Long-Chain Naphthalenediimides

“…The hypothesis that various parameters could play a role in the overall stability of the on-surface assemblies could not be ruled out. More recently, Shokri et al suggested that the introduction of a Z -configured double bond in the side chains of bis­(urea) molecules leads to the formation of long-range ordered polymers on graphite . However, the study was conducted with one chain length only (C 18 ), and the influence of the internal double bond was visible only after storage of the modified surface for 1 year .…”

“…More recently, Shokri et al suggested that the introduction of a Z-configured double bond in the side chains of bis(urea) molecules leads to the formation of long-range ordered polymers on graphite. 45 However, the study was conducted with one chain length only (C 18 ), and the influence of the internal double bond was visible only after storage of the modified surface for 1 year. 45 Although both studies independently posed the question of the influence of internal double bonds on on-surface self-assembly processes, no further investigations followed in this direction.…”

Self-Assembly of Oligo(phenylene-thiophene)s on Monolayer Graphene: Molecular Dynamics Simulations

“…Atomistic molecular dynamics simulations are a promising and powerful tool to study the properties of nanosized systems, including the investigation of the structural characteristics of molecular self-assembly on surfaces at different temperatures. − …”

“…We use this algorithm to avoid fast lateral movement of graphene sheet as a whole, significant distortion of its planarity, and rearrangement of its atoms because our main goal is to investigate the self-assembly mechanism of the TBT oligomers on the surface of graphene. The described algorithm has been successfully used previously in our group to study the structure of the graphene-filled nanocomposites. , The length of the boxes in z -direction was set to 10 nm to prevent the effect of the opposite side of the surface . Then, the TBT oligomers were randomly distributed near the graphene monolayer.…”

“…32,33 The length of the boxes in z-direction was set to 10 nm to prevent the effect of the opposite side of the surface. 49 Then, the TBT oligomers were randomly distributed near the graphene monolayer. A 10 ns equilibration run was carried out at a temperature of 500 K to allow the molecules to settle on the surface of graphene until the formation of a monolayer (Figure 2).…”