Influence of Electron-Donating and Electron-Withdrawing Groups on One- and Two-Photon Absorption Properties on Modified Adenine and Guanine Nucleobases
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 linear response for 1PA and quadratic response theory combined with the two-state model (2SM) for 2PA, employing RI-CC2 and time-dependent density functional theory (CAM-B3LYP and MN15) approaches. Each system includes either electron-donating groups (EDGs: CH 3, NH 2, OCH 3, OH) or electron-withdrawing groups (EWGs: CF 3, NO 2, 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, λ 1PA, by up to 47 nm (i.e., 94 nm for λ 2PA ), while EDG/EWG substitution induces further shifts of up to 113 nm in λ 1PA (i.e., 226 nm for λ 2PA ), thereby extending 2PA activity into the near-infrared region. The largest 2PA responses are associated with substantial permanent dipole changes upon excitation (|Δμ| = [(μ 11, x – μ 00, x ) 2 + (μ 11, y – μ 00, y ) 2 + (μ 11, z – μ 00, z ) 2 ] 1/2 ≈ 13 Debye) and near-colinear alignment between the change in the permanent dipole moment (Δ μ ) and the transition dipole moment (μ 01 ), cos 2 θ ≈ 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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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 | 0.000 |
| 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".