MoleditPy PySCF Calculator Plugin Tutorial

Objective

Using the S_N2 substitution reaction between chloromethane (CH₃Cl) and bromide ion (Br^-) as an example, we will perform a reaction coordinate scan (Relaxed Scan) to estimate the energy barrier. Furthermore, using that structure as an initial guess, we will perform a Transition State (TS) calculation and frequency analysis to confirm the imaginary frequency.

Procedure

Step 1: Drawing and Arranging Molecules

1. Draw Molecules:
   • Draw Chloromethane (CH₃Cl).
   • Draw a Bromide ion (Br^-) nearby.
2. 3D Conversion:
   • Click "Convert 2D to 3D" on the toolbar to convert to a 3D structure.
   
3. Position Adjustment:
   • Use the "3D Edit > Move Group..." tool to place Br^- on the backside attack position of the carbon atom (opposite to Cl).
   
4. Bond Distance Adjustment:
   • Use the "3D Edit > Adjust Bond Length..." tool to set the C-Br distance to 2.8 Å.
   

Step 2: Relaxed Scan Calculation

1. Launch PySCF Calculator:
   • Open Extensions > PySCF Calculator.
2. Scan Configuration:
   • Set Mode to Relaxed Surface Scan.
   • Click the "Configure Scan" button and set the Distance tab as follows:
     • Start: 2.8 Å
     • End: 1.96 Å
     • Steps: 5
   • This setting calculates the process of Br approaching C.
   
3. Level of Theory Settings:
   • Method: RKS (B3LYP)
   • Basis: ma-def2-svp
   • Note: For anion calculations, basis sets containing diffuse functions (like ma-def2-svp) are recommended. It takes longer than STO-3G.
4. Run Calculation: Click "Run Calculation". Please wait as it takes some time.

Step 3: Energy Diagram and TS Estimation

1. Check Results:
   • After calculation finishes, check the Energy Diagram. An energy barrier (mountain-shaped graph) should be displayed.
   • Press the animation play button to see the reaction process.
   
2. Select TS Candidate:
   • Click the Highest Point on the graph.
   • This reflects the structure of that step in the main window. This serves as a good initial structure for the Transition State (TS).
   

Step 4: Transition State (TS) Calculation + Freq

1. Change Calculation Settings:
   • Return to the Calculation tab.
   • Change Job Type to TS Optimization + Frequency.
   • Do not change other settings (B3LYP / ma-def2-svp).
   
2. Run Calculation: Click "Run Calculation" again.

Step 5: Confirm Imaginary Frequency

1. Check Vibrational Modes:
   • After calculation completion, check the Vibrational Modes list.
   • Confirm that there is exactly one Imaginary Frequency (negative frequency). This indicates a transition state.
   • Select that mode and confirm via animation that atoms are moving along the reaction coordinate.