A General Synthetic Approach for Polymethine Modified Trimethine Cyanines Gives Access to Viscosity Sensitive Probes
Bibliographic record
Abstract
Polymethine functionalization of trimethine cyanine (Cy3) fluorophores remains challenging due to limited synthetic strategies. Here, we report a versatile synthetic strategy for accessing both symmetric and unsymmetric meso-substituted Cy3 fluorophores using activated carboxyl intermediates. This three-step, high-yielding approach enables polymethine modified Cy3. Through systematic variation of acyl chloride precursors and indolenine derivatives, we generated a structurally diverse library of Cy3 dyes featuring aliphatic, aromatic, and electron-withdrawing meso-substituents. The approach is compatible with a broad range of indolenines. The Cy3 fluorophores have absorption and emission maxima between 550–590 nm and 560–650 nm, respectively. Unsymmetric Cy3 derivatives have larger Stokes shifts (up to 100 nm) as compared to symmetrical Cy3. Additionally, we demonstrate a new approach to synthesize viscosity sensitive probes. We show that meso-substituted benzothiazole-containing analogs exhibit up to 20-fold enhancement in quantum yield in high-viscosity environments, and, as such, could be used as molecular rotors for viscosity sensing. Complementary time-dependent density functional theory (TD-DFT) calculations further support the experimental observations by accurately reproducing the substituent‐dependent trends in absorption, emission, and Stokes shifts across the series. The computed absorption wavelengths and Stokes shifts are consistent with the experimental results. This work establishes a general synthetic scheme for meso-functionalized Cy3, offering new opportunities to fine-tune photophysical properties for imaging, sensing, and bioconjugation applications.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".