Computational Chem: Calculating Transition States for SN2 Reactions " I need an organic chemistry expert"

Calculating Transition States for SN2 ReactionChem 420 Spring 2023
We will use Spartan to perform these computations.
SN2 reactions proceed via bimolecular inversion. The rate is dependent on both the nucleophile
and the electrophile. There are many other factors that affect the success or failure of this
reaction. Factors include: solvent, polarizability of nucleophile, steric bulk around the leaving
group, and much more.
In this experiment, we will calculate the activation energy (Ea) for a few SN2 reactions.
Rate = k [Nuc][E+]
Use the following components for your SN2 reactions:
Nuc: Chloride, bromide or iodide ions
LG: Chlorine
Part 1:
We will start with chloride attacking chloromethane in an SN2 reaction.
Build chloromethane
Add chloride ready to attack from the backside. Delete the valence from chloride (yellow bond).
‘Minimize’ with button in bottom right corner.
Select Build – Transition State
Indicate electron flow by selecting the following atoms/bonds (don’t rotate molecule as you’re
doing this):
● Click: Carbon, then LG, then LG again
● Then Nuc to carbon then Nuc
This should show the appropriate mechanistic arrows.
Then click the blue arrows button in the bottom right corner. This searches for a transition state.
(Ignore if it says: “No Match”)
Select Geometry – Constrain bond distance
Select the C – LG bond
Click ‘Lock’ – and Profile checkbox
Set distances to 1.767 to 5 Å (in subsequent experiments you will need to look up a typical bond
length for your C-LG. See table below)
Constrain the other bond (Nuc — C) to 5.000 to 1.767 Å
11 steps for each constraint
Calculations
Setup – Calculations Calculate: Energy Profile
PM3
Set total charge to anion
Unpaired electrons set to 0
When computations are complete, open the new document.
Open Spreadsheet
Add : Energy (note the units)
Click on the “constrained bond for the C-LG” (not C-Nucleophile)
Click the ‘download button’ (a yellow down arrow in the lower right corner), which adds this data
to spreadsheet.
Plot this data.
Energy on the y-axis, Constrained distance on the x- axis.
Display: plots
Click green plus sign. Assign the axes.
Find activation energy by difference.
Convert the value to kJ/mol (if needed).
In the plot of Energy vs bond distance, do some plots have two maxima? Why is this?
Repeat with a different nucleophile (Br- or I-)
Calculate the activation energy with respect to the Br- (or I-) as the Nuc orLG. You can do this
from the same energy plot.
Do your results match what we learned in lecture?
BONUS
1. Calculate the Ea for chloride attacking 2-chloropropane
2. Calculate the Ea for chloride attacking chloromethane at a higher level of theory than
PM3. For example: Hartree-Fock.
a. Then repeat this computation using a polar solvent instead of gas. Compare
these answers. Is this what you expected?
3. OR repeat the first calculation with solvent set to XXXX
(For fun, you can overlay various surfaces on your molecule. Go to ‘Display-Surfaces’, click
ADD – either density, or HOMO, or any other). Click the ‘play’ button to see these surfaces
change as the reaction proceeds.YAY)
Table of bond lengths
C-LG
Bond length (pm)
C-Cl
176.7 pm
C-Br
193 pm
C-I
213 pm
Data/Results
Record the following information on a separate sheet of paper.
1. Chloride attacking chloromethane in an SN2 reaction.
Ea = _______ kJ/mol
Sketch the plot of Energy vs bond length.
2. Draw the reaction you chose for your second experiment.
Ea = _______ kJ/mol (with _____ as the Nuc and _____ as LG)
Ea = _______ kJ/mol (with _____ as the Nuc and _____ as LG)
3. BONUS experiment
Ea = _______ kJ/mol (with _______ as the level of theory)
Ea = _______ kJ/mol (with _______ as the level of theory and polar solvent instead of gas)