Using Computational Chemistry to Study a Reaction Pathway

1
Using Computational Chemistry to Study a Reaction
Pathway

• Jessica L. Case
• Super Chem II
• April 30, 2002

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Goals of the Project

• Utilize Gaussian 98 and WebMO for various
  computational calculations
• Geometry Optimizations
• Frequency Calculations
• Transition State Determination
• IRC Calculations to find Intermediate Structures
• Determine the energies of the reactants,
  intermediates, transition state, and product
• Use these methods to determine a reaction pathway
• Draw a calculated reaction coordinate diagram

3
Reaction Under Study

• Why this reaction?
• Studied it last summer as a possible monomer unit
  to form ladder polymers

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Geometry Optimization2-methoxyfuran
Method Basis Set Energy (H) Energy (kcal/mol)
AM1 3-21G -0.055206032 -34.64230929
AM1 6-31G(d) -0.055206032 -34.64230929
AM1 6-311G(d,p) -0.055206032 -34.64230929
HF 3-21G -340.6059668 -2.13734105
HF 6-31G(d) -342.5083676 -2.14927105
HF 6-311G(d,p) -342.5987805 -2.14984105
B3LYP 3-21G -342.6481147 -2.15015105
B3LYP 6-31G(d) -344.5377379 -2.14945105
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Geometry Optimizationcyclobutylbenzyne
Method Basis Set Energy (H) Energy (kcal/mol)
AM1 3-21G 0.273878653 171.8614568
AM1 6-31G(d) 0.273878653 171.8614568
AM1 6-311G(d,p) 0.273878653 171.8614568
HF 3-21G -304.5375532 -1.91100105
HF 6-31G(d) -306.2532483 -1.92177105
HF 6-311G(d,p) -306.3209326 -1.92219105
B3LYP 3-21G -306.5968457 -1.92393105
B3LYP 6-31G(d) -308.2918719 -1.93456105
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Geometry Optimizationproduct
Method Basis Set Energy (H) Energy (kcal/mol)
AM1 3-21G 0.171341699 107.5185441
AM1 6-31G(d) 0.171341699 107.5185441
AM1 6-311G(d,p) 0.171341699 107.5185441
HF 3-21G -645.1633345 -4.04846105
HF 6-31G(d) -648.7899777 -4.07122105
B3LYP 3-21G -649.2513117 -4.07412105
B3LYP 6-31G(d) -652.8390400 -4.09663105
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Frequency Calculations
Molecule Method Basis Set ZPE (H)
2-MF HF 3-21G 0.108346
2-MF HF 6-31G(d) 0.108148
2-MF B3LYP 6-31G(d) 0.101644
CBB HF 3-21G 0.116369
CBB HF 6-31G(d) 0.115783
CBB B3LYP 6-31G(d) 0.109457
Product HF 3-21G 0.230598
Product HF 6-31G(d) 0.230935
Product B3LYP 6-31G(d) 0.215880
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Locating the Transition State

• First, combine the numbering of the atoms in the
  two reactant structures
• Second, combine the Z-matrices of the two
  geometry optimized reactants
• Third, determine the approximate approach of the
  two molecules will take to react together to form
  the product
• Vary distance between reactants
• Vary intermolecular angles
• Vary dihedral angles

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Lining Up the ReactantsHF / 6-31G(d)

• R 3 Angstroms
• E -648.6805142 H
• R 10 Angstroms
• E -648.7616681 H
• R 20 Angstroms
• E -648.7615803 H
• R 80 Angstroms
• E -648.7615669 H

• 2-methoxyfuran
• E -342.5083676 H
• cyclobutylbenzyne
• E -306.2532483 H
• sum of reactants
• E -648.7616159 H

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Determining the Transition State Structure

• Use the combined Z-matrix of the two reactants
  and the Z-matrix of the product as input
• The STQN method locates a transition structure
  with the QST2 keyword
• Utilizes the input structures to determine a
  structure of maximum energy in between the
  reactants and products structures

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The Transition State

• Two different inputs yielded very similar
  structures
• E1 -648.752134712 H -4.07098452053105
  kcal/mol
• E2 -648.752134717 H -4.07098452056105
  kcal/mol
• The transition state occurred at R 2.999
  Angstroms
• Frequency calculations yielded a zero point
  energy of 0.229644 H and one negative vibrational
  mode, which is expected for a transition state
  structure

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Locating the Intermediates

• IRC Calculations
• Takes the calculated structure and force field
  from the optimized transition state and
  determines intermediate structures along the
  reaction path
• Varied the number of steps away from the
  transition state
• 2 steps E -648.7522613 H
• 10 steps E -648.7555564 H
• 40 steps E -648.7571191 H

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The Intermediate Structures
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Reaction Coordinate Diagram
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And with that, my academic career at Hope College
is complete!!!
Booyah!