dorsal/arxiv
View SchemaGenerating readily synthesizable small molecule fluorophore scaffolds with reinforcement learning
| Authors | Ruhi Sayana, Kate Callon, Jennifer Xu, Jonathan Deutsch, Steven Chu, James Zou, John Janetzko, Rabindra V. Shivnaraine, Kyle Swanson |
|---|---|
| Categories | |
| ArXiv ID | 2601.07145vv1 |
| URL | https://arxiv.org/abs/2601.07145 |
| License | http://creativecommons.org/licenses/by/4.0/ |
Abstract
Developing new fluorophores for advanced imaging techniques requires exploring new chemical space. While generative AI approaches have shown promise in designing novel dye scaffolds, prior efforts often produced synthetically intractable candidates due to a lack of reaction constraints. Here, we developed SyntheFluor-RL, a generative AI model that employs known reaction libraries and molecular building blocks to create readily synthesizable fluorescent molecule scaffolds via reinforcement learning. To guide the generation of fluorophores, SyntheFluor-RL employs a scoring function built on multiple graph neural networks (GNNs) that predict key photophysical properties, including photoluminescence quantum yield, absorption, and emission wavelengths. These outputs are dynamically weighted and combined with a computed pi-conjugation score to prioritize candidates with desirable optical characteristics and synthetic feasibility. SyntheFluor-RL generated 11,590 candidate molecules, which were filtered to 19 structures predicted to possess dye-like properties. Of the 19 molecules, 14 were synthesized and 13 were experimentally confirmed. The top three were characterized, with the lead compound featuring a benzothiadiazole chromophore and exhibiting strong fluorescence (PLQY = 0.62), a large Stokes shift (97 nm), and a long excited-state lifetime (11.5 ns). These results demonstrate the effectiveness of SyntheFluor-RL in the identification of synthetically accessible fluorophores for further development.
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"abstract": "Developing new fluorophores for advanced imaging techniques requires exploring new chemical space. While generative AI approaches have shown promise in designing novel dye scaffolds, prior efforts often produced synthetically intractable candidates due to a lack of reaction constraints. Here, we developed SyntheFluor-RL, a generative AI model that employs known reaction libraries and molecular building blocks to create readily synthesizable fluorescent molecule scaffolds via reinforcement learning. To guide the generation of fluorophores, SyntheFluor-RL employs a scoring function built on multiple graph neural networks (GNNs) that predict key photophysical properties, including photoluminescence quantum yield, absorption, and emission wavelengths. These outputs are dynamically weighted and combined with a computed pi-conjugation score to prioritize candidates with desirable optical characteristics and synthetic feasibility. SyntheFluor-RL generated 11,590 candidate molecules, which were filtered to 19 structures predicted to possess dye-like properties. Of the 19 molecules, 14 were synthesized and 13 were experimentally confirmed. The top three were characterized, with the lead compound featuring a benzothiadiazole chromophore and exhibiting strong fluorescence (PLQY = 0.62), a large Stokes shift (97 nm), and a long excited-state lifetime (11.5 ns). These results demonstrate the effectiveness of SyntheFluor-RL in the identification of synthetically accessible fluorophores for further development.",
"arxiv_id": "2601.07145",
"authors": [
"Ruhi Sayana",
"Kate Callon",
"Jennifer Xu",
"Jonathan Deutsch",
"Steven Chu",
"James Zou",
"John Janetzko",
"Rabindra V. Shivnaraine",
"Kyle Swanson"
],
"categories": [
"cs.LG"
],
"license": "http://creativecommons.org/licenses/by/4.0/",
"title": "Generating readily synthesizable small molecule fluorophore scaffolds with reinforcement learning",
"url": "https://arxiv.org/abs/2601.07145",
"version": "v1"
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