Near-Atomic Resolution Structure of J-aggregated Helical Light Harvesting Nanotubes
Bibliographic record
Abstract
Function-oriented design of supramolecular self-assemblies represents a foundational goal in chemistry. Especially, chromophore self-assemblies display extreme photophysical changes from their monomers that are sensitive to the nanoscale molecular arrangements. Slip-stacked arrangements in J-aggregates lead to red shifts (>200 nm) and enhanced quantum yields. Actively introducing specific molecular arrangements using supramolecular chemistry provides a platform to tune the excitonic couplings and avail exotic photophysical properties. However, the nanoscale molecular arrangements have not yet been directly observed in these solution-state assemblies. Here, we present a high-resolution structure of the prototypical biomimetic light harvesting nanotubes (LHNs) of an amphiphilic cyanine dye (C8S3-Cl). We achieve a 3.3 Å resolution with helical reconstruction of cryo-EM images, directly visualizing the atomic scale parameters and packing arrangements that control the excitonic properties. Our structure clearly shows a brick layer arrangement of the molecules as opposed to the previously thought herringbone arrangement. Furthermore, we identify a new non-biological supramolecular motif – interlocking sulfonates, that may be responsible for the slip-stacked packing and ultimately the J-aggregate nature of LHNs. This motif may be relevant towards other amphiphilic self-assemblies, in general and provides a new chemical handle on predictable self-assemblies.
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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) | 0.000 | 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) | 0.001 | 0.000 |
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".