{"paper_id":"00effc96-659a-4b92-879d-de974e9393bb","body_text":"Submitting author affiliation:\nZhejiang University of Water Resources and Electric Power, Hangzhou, China\nBeilstein Arch. 2025, 202540. https://doi.org/10.3762/bxiv.2025.40.v1\nPublished 16 Jun 2025\nThis preprint has not been peer-reviewed. When a peer-reviewed version is available, this information\nwill be updated.\nShow All Preprints\nNanotechnology\nOrganic chemistry\nBioorganic chemistry / chemical biology\nCatalysis\nChemical methods and reactions\nFlow and process chemistry\nGreen and sustainable chemistry\nMaterials chemistry\nMedicinal and pharmaceutical chemistry\nNano- and molecular-scale electronics\nNano-biomaterials and bioscience\nNanomagnetics\nNanomaterials, thin films and nanointerfaces\nNanomedicine\nNanometrology and nanomechanics\nNano-optics\nNanopatterning, self-assembly and nanofabrication\nNanostructures for energy and sensing applications\nNatural products chemistry\nOrgano main group chemistry\nOther nanotechnology (unclassified)\nOther organic chemistry (unclassified)\nPhotochemistry and photovoltaics\nPhysical organic chemistry\nSupramolecular chemistry\nThe 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.\nKeywords: Hierarchical Self-Assembly; Surface-Mediated Molecular Assembly; Halogen-Hydrogen Cooperative Bonding; Interfacial Strain Engineering; Intermolecular Halogen-Hydrogen Competition\nWhen 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:\nYe, J.; Wu, T.; Yu, B.; Yan, S. Beilstein Arch. 2025, 202540. doi:10.3762/bxiv.2025.40.v1\nCitation data can be downloaded as file using the \"Download\" button or used for copy/paste from the text window below.\nCitation data in RIS format can be imported by all major citation management software, including EndNote, ProCite, RefWorks, and\nZotero.\n© 2025 Ye et al.; licensee Beilstein-Institut.\nThis 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.","source_license":"CC-BY-4.0","license_restricted":false}