Reaction Coordinate Diagram
Chart overview
Reaction coordinate diagrams display the relative potential energy of reactants, transition states, intermediates, and products along a conceptual reaction pathway, illustrating activation energies and thermodynamic driving forces.
Key points
- Computational and physical organic chemists use these diagrams to compare catalytic mechanisms, rationalize reaction selectivity, and present DFT-calculated energy surfaces.
- Plotting multi-step pathways with rate-determining step annotation is standard in mechanistic chemistry publications.
Example Visualization
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"Create a reaction coordinate diagram from my data. Plot reaction coordinate on the x-axis and relative energy (kJ/mol or kcal/mol) on the y-axis. Connect energy levels with smooth curves passing through the transition state maxima. Label each stationary point with its name and relative energy value. Annotate activation energy barriers with double-headed arrows. Use journal formatting with Arial font and no top or right spines."
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Python Code Example
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Common Use Cases
- 1Presenting DFT-calculated energy profiles for catalytic reaction mechanism proposals
- 2Comparing uncatalyzed versus enzyme-catalyzed activation barriers in biochemistry
- 3Illustrating multi-step organic synthesis pathways with competing reaction channels
- 4Visualizing conformational energy landscapes of drug molecules for structure-activity relationships
Pro Tips
Use matplotlib Bezier control points to draw smooth curves through stationary point energies rather than straight lines
Annotate delta-G-double-dagger activation free energy with a bidirectional arrow spanning each barrier
Draw transition state structures as a dagger symbol above the barrier peak following IUPAC conventions
Use relative energies (reactants set to 0) to allow consistent comparison across different reaction series
Scientific Chart Selection Cheat Sheet
Not sure whether to use a Violin Plot, Box Plot, or Ridge Plot? Download our single-page reference mapping the most-used scientific chart types, exactly when to use them, and the core Matplotlib/Seaborn functions.