Experimental and Computational Evidence for “Double Pancake Bonds”: The Role of Dispersion-Corrected DFT Methods in Strongly Dimerized 5-Aryl-1λ<sup>2</sup>,3λ<sup>2</sup>-dithia-2,4,6-triazines
Bibliographic record
Abstract
Abstract Crystal structures are reported for bicyclic 3-CF3C6H4CN5S3 and monocyclic 3-CF3C6H4CN3S2, the latter of which is strongly dimerized in a cis-cofacial geometry [3-CF3C6H4CN3S2]2. The title compounds have previously been characterized in solution by NMR, displaying spectra that are consistent with the structure of [3-CF3C6H4CN3S2]2 in the crystal with anti-oriented CF3 substituents. The interannular binding was investigated using density functional theory (DFT) methods. However, the DFT-optimized geometry spreads the aryl rings too far apart (centroid–centroid distances of ≥4.353 Å versus experimental distance of 3.850 Å). Significant improvements are obtained with dispersion-corrected DFT functionals B3LYP-D3, B3LYP-D3BJ, M062X, and APFD using the 6-311+G(2d,p) basis set. However, all of these overbind the aryl rings with centroid–centroid distances of 3.612, 3.570, 3.526, and 3.511 Å, respectively. After selecting B3LYP-D3BJ/6-311+G(2d,p) as the best method, five alternative dimer geometries were tested, and all were found to be binding; however, anti cofacial-4 (matching the structure in the solid state) is the most stable. Computed energies of the remainder are as follows: +7.0 kJ mol–1 (syn-cofacial-5), +26.7 kJ mol–1 (anti-cofacial-64), +27.0 kJ mol–1 (syn-cofacial-150), +102.0 kJ mol–1 (S,S-antarafacial), and +103.7 kJ mol–1 (S,N-antarafacial), where the suffixes are torsional angles around the CN3S2 thiazyl ring centroids. The binding in the four most stable cofacial dimers may be described by “double pancake bonding”.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.008 | 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".