Title: A Novel Computer Lab Experiment
1A 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
Relationship between research and teaching
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.
2CHM 348F (Organic Reaction Mechanisms)
- Lectures
- Wet labs
- Computer labs
The Diels-Alder Reaction
a diene
a dienophile
transition state
a cyclohexene derivative
3(No Transcript)
4Dienes
Dienophiles
5Molecular Orbitals - review
The most important orbitals in molecules for
reactivity are the two so-called frontier
orbitals. These are called the HOMO and LUMO
LUMO 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 bondingÂ
- most weakly held electrons
- characteristic for nucleophilic component
6Molecular Orbital Analysis of Diels-Alder
reaction
7Molecular Orbital Analysis cont.
Therefore the reaction is said to be a "symmetry
allowed"
8Molecular Orbital Analysis cont.
energy difference larger, less overlap - lower
stabilization
energy difference smaller, more overlap - more
stabilization
9An example of a problem
Choose the best pair (one diene and one
dienophile) and calculate the energies of HOMO
and LUMO.
HOMO -0.32348 -0.38622 -0.34261
-0.29698
LUMO 0.1212 0.10006 0.19862
0.14441
10LUMO
HOMO
dienes
dienophiles
11An 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
?E 0.10006 (-0.29698) 0.39704 Hartree
246.76
kcal/mol
12LUMO
HOMO
dienes
dienophiles
13exo product
endo product
Experiment exo product more stable by 1.9
kcal/mol Ea lower for the endo product by 3.8
kcal/mol
14(No Transcript)
15The 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
16Linux Computer Cluster Zeus
- 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.
courtesy of Scott Browning
17Foundation of the project
- WebMo Pro interactive computer interface
-
- Hope College, Holland, MI, US
http//www.webmo.net/index.html
18CHM348 Diels Alder Reactions Computational
Experiment using Gaussian03 suit of programs and
WebMo interface
Before you begin
- Read these instructions beforehand and then start
working. - 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. - All energies are calculated in Hartree (Atomic
Unit for Energy) - Conversion factor to kcal/mol
- 1 Hartree 627.51 kcal/mol
19Building the Reactant Structures cont.
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.
20 Job Options
Job Options for Reactant and Product Geometry
Optimization (3 jobs)
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.
21Monitoring jobs progress
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.
22 Evaluating Results
Energy
23To view orbital, click here
HOMO Energy
LUMO Energy
24 Comparing HOMO LUMO orbitals
Diene - HOMO
Dienophile - LUMO
25Energy
Endo Product
Diels Alder Reaction
26Energy
B3LYP/6-31G
-609.07
0.51 kcal/mol
-609.08
-609.09
-609.10
-609.11
1.89 kcal/mol
Reaction progress
27Methodological 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.
28Benefits to the educational process
- relates the theoretical knowledge of the students
gained in the courses to real problems, from the
real environment.
29Benefits 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.
30Benefits 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.
31Acknowledgments
- Andrew P. Dicks
-
- Scott Browning, Jamie Donaldson
- Andrew Woolley
- Frank Buries, Michael Yoo
-
- Chemistry Department, University of
Toronto - Instructional Technology Courseware
Development Fund