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.
Python Tutorial
How to create a reaction coordinate diagram in Python
Use the full tutorial for implementation details, troubleshooting, and chart variations in matplotlib, seaborn, and plotly.
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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
Long-tail keyword opportunities
High-intent chart variations
Library comparison for this chart
matplotlib
Best when you need full control over axis formatting, annotation placement, and journal-specific styling for reaction-coordinate-diagram.
numpy
Useful in specialized workflows that complement core Python plotting libraries for reaction-coordinate-diagram analysis tasks.
scipy
Useful in specialized workflows that complement core Python plotting libraries for reaction-coordinate-diagram analysis tasks.
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