MoleditPy PySCF Calculator Plugin Tutorial

Objective

Scan the Potential Energy Surface (PES) by rotating the C-C single bond of an ethane molecule to observe the correlation between energy changes and molecular structure. The rotational barrier is experimentally known to be approximately 12 kJ/mol.

Instructions

Step 1: Build Molecular Model

1. Draw Ethane:
   • On the main canvas, draw a 2-carbon chain (C-C).
   • The tool implies hydrogen saturation, so this represents Ethane (C₂H₆).
2. Convert and Launch:
   • Click "Convert 2D to 3D" to generate the 3D model.
   • Go to Extensions > PySCF Calculator to open the plugin.

Step 2: Scan Settings & Execution

1. Select Job Type:
   • In the Calculation tab, set Job Type to Relaxed Surface Scan.
   • Set Method to RKS / Functional to b3lyp / Basis to sto-3g.
   • This tells the solver to optimize the geometry at each step of the scan.
2. Configure Scan Variables:
   • Click the Configure Scan button.
   • Action: The application enters "Surface Scan Setup" mode.
3. Define Dihedral Angle:
   • Return to the Main 3D Viewport.
   • Select 4 atoms in sequence to define the dihedral angle: Hydrogen → Carbon → Carbon → Hydrogen.
   • Verify the selected atoms form the torsional angle you wish to rotate.
4. Set Parameters and Run:
   • A dialog will appear showing the current angle.
   • Set Start to 0.
   • Set End to 180.
   • Set Steps to 10.
   • Click OK to confirm, then click Run Calculation on the main tab.
   

Step 3: Play Results Animation

Wait for the entire scan to complete. A Scan Results window will pop up automatically.

1. Analyze the Graph:
   • Observe the potential energy curve displayed in the window.
   • Identify the Maxima (peaks) at 0° and 120°. These correspond to the unstable Eclipsed conformations.
   • Identify the Minima (valleys) at 60° and 180°. These correspond to the stable Staggered conformations.
   • Verify that the calculated energy barrier is approximately 12 kJ/mol, closer to the experimental value.
   
2. Visualize Rotation:
   • Click the Play button (or scrub the timeline slider) in the results window.
   • Watch the 3D molecule in the main view. It should rotate its C-C bond in sync with the graph, demonstrating the conformational changes.