Understanding the Origin of 2D Self-Assembly of Tricarbazole Macrocycles: An Integrated Quantum Mechanical/Molecular Dynamics Study

Abstract

The intermolecular interactions underlying self-assembly are important for designing supramolecular architectures with defined function and composition over various length scales. Here, an integrated quantum mechanical/molecular dynamics (QM/MD) approach is introduced to explore the intermolecular interactions governing the two-dimensional selfassembly of a shape-persistent macrocycle, that is, tricarbazolo triazolophane (tricarb), on highly ordered pyrolytic graphite (HOPG). Three structural motifs (row, zig-zag, and rosette) for the self-association and growth of tricarb oligomers are analyzed using dispersion-corrected density functional theory to reveal their relative stability. QM analysis shows that the major factor in the self-assembly, via H-bonding contributions to the interaction energies, originates from favorable local dipole orientations between triazole units in the zig-zag and rosette motifs. Closing of the macrocyclic loop leads to the formation of a tertiary structure, which induces stability for the rosette formation relative to other motifs. MD simulations of these motifs on HOPG demonstrate the stability of the rosette, corroborating the QM results. In addition, the effect of long alkyl chains on the selfassembly dynamics is explored by simulating preexisting honeycomb domains of tricarbs with various alkyl chain lengths, without and with the presence of an explicit solvent. MD simulations reveal that alkyl chains mediate the formation of a honeycomb pattern, as observed experimentally.

Solution-Mediated Annealing Pathways Are Critical for Supramolecular Ordering of Complex Macrocycles at Surfaces

“…These observations are consistent with our previous MD work simulating tricarb at the vacuum/HOPG interface, where interactions between peripheral groups and the macrocyclic core promote ordered packing. 56 These MD observations are made on a simulation time scale of up to 100 ns. We note that the computational cost of these atomistic simulations does not currently allow for the significantly longer time scales that would be required to simulate surface self-assembly starting from solution or structural transformations between surface structures.…”

“…The honeycomb structures were constructed with the guidance of STM images (Figure S3), following the strategy introduced in the Supporting Information in a recent report. 56 The preformed honeycomb structure of tricarb macrocycles was placed 3.5 Å above the HOPG with all alkyl tails desorbed from the HOPG. See the Supporting Information of our recent report for a detailed description of the initial configuration design.…”

“…Each system in Table S4 consisted of a four-layer AB-stacked graphene (HOPG), preformed honeycomb structure of tricarb molecules, and explicit solvent molecules (if not in a vacuum). The honeycomb structures were constructed with the guidance of STM images (Figure S3), following the strategy introduced in the Supporting Information in a recent report . The preformed honeycomb structure of tricarb macrocycles was placed 3.5 Å above the HOPG with all alkyl tails desorbed from the HOPG.…”

“…60 It was also observed in the STM experiments that the peripheral alkyl chains tend to be excluded from surface adsorption; that is, the chains back-fold into solution and do not directly impact structure. However, two recent experimental and computational studies using different peripheral alkyl chains of tricarb 9,56 reveal that chain length and functionalization symmetry can play a major role in tricarb self-assembly structure. We were therefore interested to examine the role of the chain length; this led to discovery of a disordered packing phase on the surface, 9 and here we report that the conversion of that disordered structure to an ordered structure demonstrates a solution-mediated annealing pathway.…”

Recent Advances in Heterocyclic Nanographenes and Other Polycyclic Heteroaromatic Compounds

“…These assemblies were stabilized by hydrogen bonding interactions between the triazole N atoms and the carbazole C–H units on the outside of the macrocycle, and their self-organization behavior was further studied using STM imaging and computational methods. 770 , 771 …”