Influence of Electron-Donating and Electron-Withdrawing Groups on One- and Two-Photon Absorption Properties on Modified Adenine and Guanine Nucleobases
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Bibliographic record
Abstract
Fluorescent nucleobase analogues are valuable probes for nucleic acid structure and dynamics, yet rational design remains challenging. Here, we investigate one-and two-photon absorption (1PA and 2PA) properties of 66 modified adenine and guanine derivatives using quadratic response theory and the two-state model (2SM), employing RI-CC2 and time-dependent density functional theory (CAM-B3LYP and MN15) approaches. Each system includes either electron-donating groups (EDGs: CH3, NH2, OCH3, OH) or electron-withdrawing groups (EWGs: CF3, NO2, COOH, CN) attached at different positions on a phenyl ring appended to the parent adenine or guanine nucleobase. Phenylation enhances the brightness of the parent nucleobases and red-shifts the excitation wavelengths, λ1PA, by up to 47 nm (i.e., 94 nm for λ2PA), while EDG/EWG substitution induces further shifts of up to 113 nm in λ1PA (i.e., 226 nm for λ2PA), thereby extending 2PA activity into the near-infrared region. The largest 2PA responses are associated with substantial permanent dipole changes upon excitation (|∆μ| = |μ11 − μ00| ≈ 13 Debye) and near-colinear alignment between the change in the permanent dipole moment (∆μ) and the transition dipole moment (μ01), cos2θ ≈ 1, as captured by the 2SM. While EDG substitution enhances the photophysical response relative to the parent nucleobases, EWG substitution leads to the most pronounced improvements.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 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 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 it