Rigid-Flexible Coupling Pore Engineering in Covalent Organic Frameworks Enables the Selective Identification of Nucleotide Analogues

Abstract Covalent organic frameworks (COFs) offer programmable pore architectures and tunable host–guest interactions, yet their rigid channels limit the selective recognition of structurally similar biomolecules─a longstanding challenge in sensor design. Inspired by enzymatic pockets that combine rigid active sites with flexible secondary coordination spheres, we report a rigid-flexible coupling pore engineering strategy that integrates spatially proximal rigid Fe single-atom switches and dynamic alkoxy chains within a light-emitting hydrazone COF scaffold. By strategically varying the alkoxy chain length from methoxy to heptyloxy, we demonstrate that elongated flexible chains modulate the coordination geometry of Fe single-atom sites through steric hindrance effect and enable adaptive binding of adenosine triphosphate (ATP) over its analogues adenosine monophosphate and adenosine diphosphate. This selective recognition, driven by synergistic coordination from the rigid Fe single-atom and multiple weak interactions (including hydrogen bond, C–H···π, and hydrophobic interactions) from the flexible heptyloxy chain, suppresses the photoinduced electron transfer from the COF skeleton to the Fe sites and ultimately triggers a fluorescence turn-on response exclusively for ATP, with a wide quantitative range from 10 nM to 50 μM and a limit of detection as low as 8.99 nM. This work establishes a biomimetic paradigm for designing COF-based sensors with tailored specificity toward structurally similar nucleotides.