Deciphering Substrate-Driven Hierarchical Self-Assembly of 1,3,6,8-Tetrabromopyrene (Br4Py): First-Principles Insights into Interfacial Halogen Bonding and Strain-Mediated Epitaxy

chemistry Medicinal and pharmaceutical chemistry Nano- and molecular-scale electronics Nano-biomaterials and bioscience Nanomagnetics Nanomaterials, thin films and nanointerfaces Nanomedicine Nanometrology and nanomechanics Nano-optics Nanopatterning, self-assembly and nanofabrication Nanostructures for energy and sensing applications Natural products chemistry Organo main group chemistry Other nanotechnology (unclassified) Other organic chemistry (unclassified) Photochemistry and photovoltaics Physical organic chemistry Supramolecular chemistry The hierarchical self-assembly of 1,3,6,8-tetrabromopyrene (Br4Py) into two-dimensional monolayers was systematically elucidated through first-principles calculations, revealing complementary Br–H hydrogen bonding and Br–Br halogen interactions as synergistic driving forces. During the assembly process, three distinct molecular chain intermediates were identified, which further organize into two thermodynamically stable monolayer configurations with nearly identical binding energies. Structural parameters derived from CASTEP simulations exhibit excellent agreement with experimental scanning tunneling microscopy (STM) data, with deviations below 6% in lattice constants (b/c = 2.170 nm) and Br–H bond lengths (0.323 nm). Detailed electron density analysis quantifies the competitive nature of intermolecular interactions, showing charge accumulation at Br–H bonding regions and depletion zones in Br–Br repulsive domains. Notably, substrate-mediated strain effects from Au(111) induce lattice distortions of up to 5.8%, underscoring the critical influence of surface-molecule coupling in dictating final configurations. This computational-experimental correlation establishes a mechanistic framework for designing substrate-selective functional materials via halogen-mediated self-assembly, with potential applications in surface-confined molecular electronics or photonic materials.

Hierarchical Self-Assembly; Surface-Mediated Molecular Assembly; Halogen-Hydrogen Cooperative Bonding; Interfacial Strain Engineering; Intermolecular Halogen-Hydrogen Competition When a peer-reviewed version of this preprint is available, this information will be updated in the information box above. If no peer-reviewed version is available, please cite this preprint using the following information: Ye, J.; Wu, T.; Yu, B.; Yan, S. Beilstein Arch. 2025, 202540. doi:10.3762/bxiv.2025.40.v1 Citation data can be downloaded as file using the "Download" button or used for copy/paste from the text window below. Citation data in RIS format can be imported by all major citation management software, including EndNote, ProCite, RefWorks, and Zotero. © 2025 Ye et al.; licensee Beilstein-Institut. This is an open access work licensed under the terms of the Beilstein-Institut Open Access License Agreement (https://www.beilstein-archives.org/xiv/terms), which is identical to the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0). The reuse of material under this license requires that the author(s), source and license are credited. Third-party material in this work could be subject to other licenses (typically indicated in the credit line), and in this case, users are required to obtain permission from the license holder to reuse the material.