Simple SN2 reaction

In this tutorial, we will investigate an SN2 reaction through a one-dimensional scan based on a linear combination of multiple interatomic distances. For this purpose, we will use the semiempirical PM6 method, natively implemented in pDynamo3.

The SN2 reaction between the bromide ion (Br⁻) and methyl chloride (CH₃Cl) is a classic example of bimolecular nucleophilic substitution. In this mechanism, the bromide acts as a nucleophile, attacking the carbon atom of CH₃Cl from the opposite side of the leaving group (Cl), simultaneously promoting the breaking of the C–Cl bond and the formation of the new C–Br bond.

This process occurs in a single concerted step, characterized by a pentacoordinate transition state and by inversion of configuration at the central carbon, a phenomenon known as Walden inversion.

• Step 1 - Loading your system: File 

a) Go to Main Menu -> File -> New

b) Set the system type to: "other(*.pdb, *.xyz, *.mol2)" (it means there is no MM parameters)

c) Load the coordinate file "SN2_tutorial.xyz"

d) Click Import System

• Step2 - Setup your QC theory level

a) Go  to EasyHybrid toolbar and click on the "Quantum Chemistry" icon. 

b) Choose your theory level and the system charge. For this tutorial,  semi-empirical - PM6  and total charge -1. 

• Step3 - Reaction coordinate scan

a) Go to Main Toolbar -> Reaction Coordinate Scans.

b) Using the picking mode selection, select , as showed in the Figure, the Chloride , Carbon and Bromide  atoms (selections #1 , #2 and #3), and press the button “Import from Picking Selection”.

c) Set the “Step Size” as 0.05 and the Number of Steps to 30. As #1 and #3 are different atoms, set Apply Mass Weighted Restraints  as True.

d) Check the working folder  and  Trajectory Name, and push the Run Button. 

Once it is done, a new structure will be generated in the interactive interface.

Step 4 – Importing the Trajectory and Potential Energy Profile Data

a) In the system header, right-click to access the treeview menu. Select the option "Import Data...".

b) Change the format to "pkl folder – pDynamo trajectory" and select the folder generated by the scan. Note that, if everything went correctly, EasyHybrid will automatically detect that there is a log file associated with the trajectory folder. Click "Import".

Step 5 – Analysis

a) Access the "Analysis" item in the main menu and select the "PES Analysis" option.

b) In this window, you can inspect the energy value obtained at each frame. Use the scroll bar at the bottom to change the frames along the trajectory.

Step6 - Comparing results

Access: www.uni-pc.gwdg.de/botschwina/sschmat/jcp110_9483.ps and compare your results. The SMO used in this tutorial is good enough to reproduce the experimental data?

references:

S Schmatz, DC Clary - Journal of chemical physics, 1999 - uni-pc.gwdg.de