A Novel Computer Lab Experiment

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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
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.
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CHM 348F (Organic Reaction Mechanisms)

• Lectures
• Wet labs
• Computer labs

The Diels-Alder Reaction

a diene
a dienophile
transition state
a cyclohexene derivative
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Dienes
Dienophiles
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Molecular 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 bonding 
• most weakly held electrons
• characteristic for nucleophilic component

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Molecular Orbital Analysis of Diels-Alder
reaction
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Molecular Orbital Analysis cont.
Therefore the reaction is said to be a "symmetry
allowed"
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Molecular Orbital Analysis cont.
energy difference larger, less overlap - lower
stabilization
energy difference smaller, more overlap - more
stabilization
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An 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
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LUMO
HOMO
dienes
dienophiles
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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
?E 0.10006 (-0.29698) 0.39704 Hartree
246.76
kcal/mol
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LUMO
HOMO
dienes
dienophiles
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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
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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

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Linux 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
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Foundation of the project

• WebMo Pro interactive computer interface
• Hope College, Holland, MI, US
  http//www.webmo.net/index.html

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CHM348 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

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Building 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.
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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.
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Monitoring 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.
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Evaluating Results
Energy
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To view orbital, click here
HOMO Energy
LUMO Energy
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Comparing HOMO LUMO orbitals
Diene - HOMO
Dienophile - LUMO
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Energy
Endo Product
Diels Alder Reaction
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Energy
B3LYP/6-31G
-609.07
0.51 kcal/mol
-609.08
-609.09
-609.10
-609.11
1.89 kcal/mol
Reaction progress
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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.

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Benefits to the educational process

• relates the theoretical knowledge of the students
  gained in the courses to real problems, from the
  real environment.

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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.

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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.

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Acknowledgments

• Andrew P. Dicks
• Scott Browning, Jamie Donaldson
• Andrew Woolley
• Frank Buries, Michael Yoo
• Chemistry Department, University of
  Toronto
• Instructional Technology Courseware
  Development Fund