MoleditPy PySCF Calculator Plugin Tutorial

Objective

Visualize the π-electron system molecular orbitals of 1,3-butadiene and verify the regularity that the number of "Nodes" increases as the energy level rises.

Instructions

Step 1: Build Molecular Model & Run Calculation

1. Draw the Structure:
   • On the main 2D canvas, select the Carbon tool.
   • Draw a chain of 4 Carbon atoms.
   • Create Double Bond: Draw a single bond to an Oxygen atom first. Then, hover over the bond and press '2' (or select the "Double Bond" tool and click the bond) to convert it to a C=C double bond.
   • Ensure the structure represents 1,3-Butadiene.
2. Convert to 3D: Locate the toolbar and click the "Convert 2D to 3D" button.
3. Wait for the 3D structure to generate.
4. Launch Plugin:
   • Go to the menu bar: Extensions > PySCF Calculator.
   • This will open the PySCF Calculator interface.
5. Configure Calculation:
   • Navigate to the Calculation tab.
   • Set Job Type to Geometry Optimization.
   • Set Method to RKS (Restricted Kohn-Sham).
   • Set Functional to b3lyp.
   • Set Basis to sto-3g (Minimal basis set for speed).
   • Click the Run Calculation button to start the calculation.
   

Step 2: Generate Orbital Data (Post-Calculation Analysis)

Wait for the calculation to finish. The status bar will indicate completion, and the Post-Calculation Analysis area at the bottom will become active.

1. Select Orbitals:
   • Scroll through the orbital list in the analysis panel.
   • Check the boxes for HOMO-1, HOMO (Highest Occupied Molecular Orbital), LUMO (Lowest Unoccupied Molecular Orbital), and LUMO+1.

   Pro Tip: Click the Orbital Energy Diagram button to open an interactive dialog. This is useful for checking energy gaps (HOMO-LUMO gap) and selecting orbitals directly from the diagram.

   

2. Generate Cubes:
   • Click the Generate & Visualize Selected button.
   • Note: The application will calculate the orbital values on a grid and save them as .cube files. This may take a few seconds.
3. Verify Output: check that new files with a .cube extension appear in the Visualization Files list.

Step 3: Compare Orbitals

Select each file from the Visualization Files list to view the shape. Notice how the number of "nodes" (change in phase/color) increases with energy.

1. HOMO-1 (Orb 14) 0 Nodes (Lowest Energy)

2. HOMO (Orb 15) 1 Node

3. LUMO (Orb 16) 2 Nodes

4. LUMO+1 (Orb 17) 3 Nodes (Highest Energy)