News
News

Solvent effects

We're going to follow a bimolecular substitution reaction, and the effect of solvent on it.

  1. Construct the Br-···CH3Cl system
  2. Choose the following setup:
    • XC functional: OPBE (GGA)
    • Relativity: Scalar
    • Basis set: TZP
    • Frozen core: Small
    • Numerical quality: Good
    • Total charge: -1
  3. Choose as Task: Transition State
    • Select "Yes" at "Frequencies:"
    • Then click on the arrow at the right-hand side of Task:Transition State, to go to the [Model]:[Transition State search] submenu
    • Select the Cl and the C atoms, and click on the [+] sign next to "Reaction coordinate"
    • Select the Br and the C atoms, and click on the [+] sign next to "Reaction coordinate"
  4. Save
  5. Run

Analysis

  1. Check the frequencies, to make sure one imaginary frequency was found
  2. Add COSMO Solvation (Water as solvent)
  3. Check its effect on the structure and frequency

Explicit solvation

  1. Add one explicit water molecule, and rerun
  2. Check its effect on the structure and frequency

QM/QMM setup for explicit water molecules

  1. Now add a few more water molecules surrounding the Br···CH3Cl system
  2. Then select the Hybrid program
  3. Choose again the "Transition State" task
  4. Go to [Model]:[Regions] menu, select all waters and click on [+] for creating a new region (Solvent)
  5. Then choose "Invert selection" at the "Select" menu, and create a second region for the Substrate
  6. Go back to the "Main" menu of the Hybrid program, and set up the QM/QM multi-level scheme:
    • At the first line of the "Energy terms" choose DFTB as the Engine
    • Click on [+] to add a second/third energy term
    • Choose the Substrate region for both the second and third energy term
    • Set -1 as the Charge for all three energy terms
    • Choose DFTB 1 for the third energy term as Engine
    • Choose ADF for the second energy term as Engine
    • Click on the "ADF 1" submenu at the bottom, and select the OPBE as density functional
  7. Save
  8. Run

Further reading

members