CARBOT: A Mathematically Verified Rule-Based Molecule Generator for π-Conjugated and Aromatic Hydrocarbons

22 May 2025, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

π-Conjugated and aromatic hydrocarbons are foundational molecular scaffolds in materials science. Their design and discovery, however, remain limited by the lack of systematic frameworks for exploring the vast chemical space while ensuring structural validity. To address this, we present a rule-based molecular generation framework for π-conjugated and aromatic hydrocarbons. This framework defines a minimal set of chemically inspired transformation rules, each corresponding to fundamental structural modifications while preserving π-conjugation. We provide rigorous proof that the method is sound and complete, as it generates only chemically valid π-conjugated hydrocarbons and can construct all such molecules within the defined space using a finite sequence of rules. The generated structures are further analyzed in terms of size, topology, and conjugation patterns, revealing an expansive and chemically meaningful design space. This framework enables the rediscovery of any π-conjugated hydrocarbon within the defined space and offers a systematic basis for data-driven design and discovery of functional π-conjugated materials.

Keywords

Molecular Generation
Chemical Space
π-Conjugation
Hydrocarbon
Aromatic Compounds

Supplementary materials

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Supporting Information
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General Information, Supporting Figures, and Mathematical Proof of Correctness of CARBOT (PDF)
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List of generated structure (unit)
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List of generated structure by exhaustive structure generation via iterative unit transformations, up to distance 10
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List of generated structure (unit+comp.)
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List of generated structure by exhaustive structure generation via iterative unit and composite transformations, up to distance 6
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Supplementary weblinks

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