Inputs
Run history
| Time | Rings | Distance (Å) | Angle (°) | Offset (Å) | ε | T (K) | Energy (kcal/mol) | Score | Category |
|---|---|---|---|---|---|---|---|---|---|
| No runs yet. | |||||||||
Example data table
These sample rows illustrate typical inputs and outputs using this estimator’s defaults.
| Ring A | Ring B | Distance (Å) | Angle (°) | Offset (Å) | ε | T (K) | Estimated energy (kcal/mol) | Category |
|---|---|---|---|---|---|---|---|---|
| Benzene | Benzene | 3.40 | 10 | 1.20 | 78.4 | 298.15 | -1.73 | Moderate |
| Indole | Naphthalene | 3.45 | 5 | 1.00 | 20 | 298.15 | -2.31 | Strong |
| Pyridine | Benzene | 3.80 | 25 | 1.60 | 78.4 | 310 | -0.95 | Moderate |
| Tryptophan ring | Tyrosine ring | 3.30 | 0 | 0.80 | 78.4 | 298.15 | -2.62 | Strong |
Formula used
This tool uses a simple, transparent heuristic that scales a base interaction energy by geometry and conditions.
Interpretation: more negative E suggests a more favorable interaction. Scores are derived from E magnitude and capped to 0–100 for quick comparison.
How to use this calculator
- Choose the aromatic partners for Ring A and Ring B.
- Enter centroid distance, relative angle, and lateral offset.
- Optionally add substituent σ values as electronic proxies.
- Set solvent dielectric and temperature to match conditions.
- Press Submit to see results above the form.
- Run multiple scenarios, then export CSV or PDF.
Why pi pi interactions matter
Pi pi contacts stabilize molecular recognition in pharmaceuticals, catalysts, and biomolecules. In protein–ligand complexes, aromatic side chains often stack against heteroaromatics, shaping potency and selectivity. Literature ranges commonly fall near 0.5–3.0 kcal/mol, but local context can shift values. This estimator converts key descriptors into a comparable interaction energy and a 0–100 score for rapid screening across design variants.
Geometry drives overlap and orientation
Centroid distance is the strongest predictor, with favorable stacking near 3.3–3.8 A. As distance increases, dispersion decays rapidly, so the calculator uses a Gaussian distance factor centered at 3.40 A with width 0.40 A. Angle separates parallel stacking from T-shaped motifs; intermediate angles can remain favorable when offset reduces quadrupole repulsion. The orientation term blends cos(theta)^2 with a partial sin(theta)^2 contribution to reflect residual attraction in edge contacts.
Offset controls quadrupole balance
Perfect face-to-face alignment is rarely optimal because aromatic quadrupoles can create repulsive regions. Lateral offset around 0.8–1.6 A can improve complementarity by shifting electron-rich and electron-poor zones. The tool penalizes very large offsets because overlap and contact area diminish. When both distance and offset are high, expect a steep reduction in energy magnitude and a lower score.
Substituents and ring identity effects
Different rings polarize differently, so the estimator applies ring factors for common aromatics and fused systems. Electron donating groups often increase pi density, while withdrawing groups reduce it. The optional sigma inputs act as a compact electronic proxy and scale energy modestly, enabling quick comparison of substituted analogs. Keep sigma values within about -1.0 to +1.0; shifts of 0.10 can meaningfully reorder close candidates.
Solvent, temperature, and decision use
Higher dielectric media can damp electrostatic components, while dispersion is less sensitive. The solvent factor gently increases toward water-like dielectric values to keep comparisons consistent. Temperature weakens net binding by increasing thermal motion, so energy is scaled using 298.15/T within capped bounds. Use history runs and exports to document assumptions, then validate finalists with higher fidelity modeling and experiments.
For structure-based projects, pair this score with docking poses and contact maps.
FAQs
1) What does a more negative energy mean?
More negative values indicate a more favorable predicted interaction under the selected geometry and conditions, so candidates can be ranked by magnitude before deeper modeling.
2) Which inputs usually change the result most?
Distance typically dominates. Angle and offset can strongly reshape the estimate when distance is near optimal, while substituent and solvent terms usually provide smaller adjustments.
3) How should I choose sigma values?
Use sigma as a simple electronic proxy when comparing substituted rings. Keep values within about -1.0 to +1.0, and focus on relative differences rather than exact constants.
4) Does the dielectric input represent a specific solvent model?
It is a practical scaling term, not a full solvation model. Use representative dielectric values to compare environments consistently, then confirm key cases with more rigorous solvation methods.
5) Can I use the score as an absolute binding predictor?
No. The score is a normalized ranking aid derived from the estimated energy. Use it for prioritization, then validate with experiments, higher fidelity calculations, and full binding-site context.
6) How do I export my runs for reporting?
Each submit adds a row to the history table. Use Download CSV for spreadsheets, or Download PDF for a printable summary of your recorded runs.