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A Novel Computer Lab Experiment
Studies of Diels-Alder Reactions
Stanislaw Skonieczny and Mima Staikova
Department of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6
Why are research and teaching linked ?
research - an élite activity
scholars and scientists held hostage in classrooms
It is impossible to teach well without reflection, analysis, discussion.
Relationship between research and teaching
The Diels-Alder Reaction:
a diene
+H
O
a dienophile
H
O
H
O
transition state
a cyclohexene derivative
CHM 348F (Organic Reaction Mechanisms) :
- Lectures- “Wet” labs- Computer labs
Number of Research Papers on the Studies of Diels-Alder Reactions
0
50
100
150
200
250
300
350
400
2001 2002 2003 2004 2005
Year
Nu
mb
er o
f P
aper
s
S
MeO
O
MeO
O
Dienes:
Dienophiles:
C
C
H H
HHC
C
H C
HH
N
C
C
C C
HH
NN
C
C
H C
CH
N
N
C
C
H C
HC
N
N
O
OCH3
O
O
O
O
F
The most important orbitals in molecules for reactivity are the two so-called frontier orbitals. These are called the HOMO and LUMO
Molecular Orbitals - review
HOMO
LUMO
EnergyLUMO = lowest unoccupied molecular orbital
• lowest energy orbital available • LUMO receives electrons • characteristic for electrophilic component
HOMO = highest occupied molecular orbital
• electrons from the HOMO are donated • most available for bonding • most weakly held electrons • characteristic for nucleophilic component
ethene
HOMO LUMO
butadiene
HOMO-1 HOMO LUMO LUMO+1
Molecular Orbital Analysis of Diels-Alder
reaction
Molecular Orbital Analysis – cont.
Therefore the reaction is said to be a "symmetry allowed"
HOMO
LUMO
stabilizationHOMO
LUMO
HOMO
LUMO
energy difference larger,less overlap
- lower stabilization
energy difference smaller,more overlap
- more stabilization
Molecular Orbital Analysis – cont.
An example of a problem:
Choose the best pair (one diene and one dienophile) and calculate the energies of HOMO and LUMO.
O
HOMO: -0.32348 -0.38622 -0.34261 -0.29698
LUMO: 0.1212 0.10006 0.19862 0.14441
HOMO
LUMO
dienes dienophiles
0.20
0.10
0.00
- 0.10
- 0.20
- 0.30
- 0.40
0.20
0.10
0.00
- 0.10
- 0.20
- 0.30
- 0.40
O
An example of a problem:
Choose the best pair (one diene and one dienophile) and calculate the energy difference.
HOMO: -0.38622 -0.29698
LUMO: 0.10006 0.14441
O
E = 0.10006 – (-0.29698) = 0.39704 Hartree
= 246.76 kcal/mol
0.20
0.10
0.00
- 0.10
- 0.20
- 0.30
- 0.40
0.20
0.10
0.00
- 0.10
- 0.20
- 0.30
- 0.40
dienes dienophiles
C
C
C C
CC
N
N N
N
O
O
O
C
C
H C
CH
N
N
LUMO
HOMO
O
C
CO
O
O
O O
O
O
+
OO
O
O
O
O
O
O
O
CC
OO
O
exo product
endo product
Experiment: exo product more stable by 1.9 kcal/mol
Ea lower for the endo product by 3.8 kcal/mol
O O
O
O
+
E
Reaction progress
O O
O
O
+
OO
O
O
O
CC
OO
O
O
O
O
O
O
C
CO
O
O
3.8 kcal/mol
1.9 kcal/mol
The Undergraduate Computer Lab - UCL Chemistry Department
CHM 138 Introductory Organic Chemistry |
CHM 151 Chemistry: The Molecular Science
CHM 247 Introductory Organic Chemistry ||
CHM 348H Organic Reaction Mechanisms
CHM 379 Biomolecular Chemistry
CHM 415 Atmospheric Chemistry
CHM 441F Applications of Spectroscopy to Organic Structure Determination
CHM 443S Physical Organic Chemistry
CHM 447F Bio-Organic Chemistry
Linux Computer Cluster Linux Computer Cluster ZeusZeus
Zeus configuration*Main node: AMD Athlon 64 Dual 4800+ with 4 GB memory and 250 GB HD
*Computational nodes: 10 Dual Athlon CPUs at 2 GHz, each with 1 GB memory.
courtesycourtesy of Scott Browningof Scott Browning
Foundation of the project Foundation of the project
WebMo Pro interactive computer interface
Hope College, Holland, MI, US http://www.webmo.net/index.html
CHM348
Diels – Alder Reactions
Computational Experiment
using Gaussian03 suit of programs and WebMo interface
Before you begin:
1. Read these instructions beforehand and then start working.
2. You have to complete 7 calculation jobs: 3 jobs for Geometry Optimization – 2 Reactants, 1 Product 1 job for Transition State Optimization 1 job for Transition State Vibrations 2 jobs for Molecular Orbital Calculations – one for each Reactant.
3. All energies are calculated in Hartree (Atomic Unit for Energy) Conversion factor to kcal/mol: 1 Hartree = 627.51 kcal/mol
Select the appropriate substituents in the periodic table and construct the substituted diene and dienophile for your reaction.Prepare a separate job for each reactant.
Building the Reactant Structures – cont.
From the “Calculation” drop box select “Geometry Optimization”.Use “Theory”, “Basis set”, “Charge”, and “Multiplicity” as shown above.
When ready, send your job for calculation with the right blue arrow.
Job Options for Reactant and Product
Geometry Optimization (3 jobs)
Job Options
When your job is calculated (it will take some time) it will show a “complete” status.
Use the “view button” to see and evaluate the results and to use them for your next job preparation.
Monitoring jobs progress
Evaluating Results
Energy
HOMO Energy
LUMO Energy
To view orbital, click here:
Diene - HOMO
Dienophile - LUMO
Comparing HOMO – LUMO orbitals
Diels Alder ReactionDiels Alder Reaction
Endo Product
FURAN
Malonic Anhydride
Endo Transition State
Energy
Energy
1.89 kcal/mol
0.51 kcal/mol
B3LYP/6-31G
-609.11
-609.10
-609.08
-609.07
-609.09
Reaction progress
Methodological particularities:Methodological particularities:
calculations are performed at “research level”
each student has a different set of compounds, works independently.
project can be done in class or remotely at each student convenience.
Benefits to the educational process: Benefits to the educational process: relates the theoretical knowledge of the students
gained in the courses to real problems, from the real environment.
Benefits to the educational process: Benefits to the educational process: relates the theoretical knowledge of the students
gained in the courses to real problems, from the real environment.
facilitates the direct connection between macroscopic description of the chemistry phenomena and the microscopic world of molecular interactions that drive chemical processes.
Benefits to the educational process: Benefits to the educational process: relates the theoretical knowledge of the students
gained in the courses to real problems, from the real environment.
facilitates the direct connection between macroscopic description of the chemistry phenomena and the microscopic world of molecular interactions that drive chemical processes.
exposes the students to various theoretical methods and approaches in solving scientific problems as a parallel/alternative to the experimental approaches presented in the chemistry course.
AcknowledgmentsAcknowledgments
Andrew P. Dicks
Scott Browning, Jamie DonaldsonAndrew Woolley
Frank Buries, Michael Yoo
$$ Chemistry Department, University of Toronto$$ Instructional Technology Courseware Development Fund