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Lab Book: Physical Computational Labs

Following the procedure detailed here
Written up here

The Cope rearrangement tutorial

Optimising the reactants and products

4/2/2014

Anti 1,5-hexadiene
  • Drew out 1,5-hexadiene (anti) in gaussian
  • Used the clean function
  • Used the Hartree-Fock 3-21G opmisation (file name: 15hexadiene HF321G optimisation)
  • Recorded energy: -234.06073048 a.u.

5/2/2014

  • Structure symmetrised
  • Point group C2h
  • Symmetrised stucture saved under file name: 15hexadiene HF321G optimisation symmetrised
Gauche 1,5-hexadiene
  • Drew out 1,5-hexadiene (gauche) in guassian
  • Would expect to have higher energy than anti 1,5-hexadiene
  • Used the clean function
  • Used the Hartree-Fock 3-21G optimisation (file name: gauche 15hexadiene HF321G optimisation)
  • "Severe Error" occured
  • Retried the Hartree-Fock 3-21G optimisation (file name: gauche_15hexadiene_HF321G_optimisation)
  • Error occured again
  • Redrew molecule, used clean again
  • Used the Hartree-Fock 3-21G optimisation (file name: gauche15hexadiene_HF321Gopti2)
  • Error occured once more!
  • Redrew molecule, used clean
  • Realised that adding in a double bond doesn't remove a hydrogen automatically, and that the anti calculation needs to be re-run!
  • So anyway, used the Hartree-Fock 3-21G optimisation (file name: gauche15hexadieneHF321Gopti3)
    • This time with correct number of hydrogens!
    • ...It worked!
  • Recorded energy: -231.69166 a.u.
  • Structure symmetrised
  • Point group C2
  • Corresponds to gauche2 in the table of low energy conformers
  • frequency calculation: gaucheHF321Gfreq
  • further optimisation: gaucheB3YLP631Gdoptifreq
Anti 1,5-hexadiene
  • Drew out anti 1,5-hexadiene again in guassian, this time remembering to remove hydrogens.
  • Used clean function
  • Used Hartree-Fock 3-21G optimisation (file name: anti15hexadieneHF321Gopti2)
  • Recorded energy: -231.69260235 a.u.
    • Lower than gauche conformation
  • Symmetrised structure
  • Point group C2
  • Corresponds to anti1 in the table of low energy conformers
Lowest energy conformer
  • First attempt is a slightly played with anti-conformation, which gave a very slightly lower energy of -231.69260237 a.u., saved under file name: tweakedanti15hexadieneHF321Gopti1
  • Further attempts gave higher energies such as -231.69253528 a.u. (file name: tweakedanti15hexadieneHF321Gopti4), which is closer in energy to anti2 om the table of low energy conformers.
  • If have time at the end: run calculations for all anti and gauche conformations
Anti2 1,5-hexadiene
  • First attempt at creating anti2 from the table of low energy conformers gave a molecule of energy -231.69253527 a.u., which correlates well with the table. File name: anti215hexadieneHF321Gopti1
  • Symmetrising gives the Ci point group.
  • Ran frequency calculation under the name anti215hexadieneHF321Gfreq1
    • Sum of electronic and zero-point Energies= -231.436741
    • Sum of electronic and thermal Energies= -231.430933
    • Sum of electronic and thermal Enthalpies= -231.429989
    • Sum of electronic and thermal Free Energies= -231.466250

6/2/2014

  • Reoptimized the structure using the B3LYP/6-31G(d) function (file name: anti215hexadieneDFTB3YLP631Gd-step2)
  • New energy: -234.61170290 a.u.
  • Point group remains: Ci, geometry looks much the same
  • A frequency calculation was run using the same B3YLP/6-31G(d)
    • Sum of electronic and zero-point energies: -234.469204
    • Sum of electronic and thermal energies: -234.461857
    • Sum of electronic and thermal enthalpies: -234.460913
    • Sum of electronic and thermal free energies: -234.500778

"Note that these corrections can also be calculated at other temperatures using the Temperature option in Gaussian, If you have time, try to re-calculate these quantities at 0 K as shown in the Advanced GaussView Tutorial."

Optimising the "Chair" and "Boat" Transition Structures

Chair
  • Drew out allyl fragment (using clean function)
  • Optimised using HF/3-21G (file name: allylHF321Gopti3)

7/2/2014

  • Created file "2xallylchairts2" from the optimised fragment.
  • Ran Opt+Freq, TS(Berny)Opt, with Opt=NoEigen on the allyl chair TS guess, file name 2xallylchairtsHF321GoptifreqTSBerny2
  • Imaginary frequency: -817.91cm-1
  • Ran Opt+Freq, minimum, with Opt=ModRedundant on the allyl chair TS guess, having fixed the positions of one end of the TS for one of the "bond breaking/making" bits. file name 2xallylchairtsHF321Goptifreqfreezbondmin
  • Distances between two ends of TS were 2.2Å and 1.62023Å

10/2/2014

  • Drew new TS, making sure to make both ends as close to 2.2Å away from each other as possible.
  • Ran Opt+Freq, minium, Opt=Mod redundant was already in the input. File name 2xallylchairtsHF321Goptifreqfreezbondmin2
  • File-saving started to become an issue - I think a file got overwritten somewhere along the way. So tried again, file name: 2xallylchairtsHF321Goptifreqfreezbondmin3
  • This structure was then further optimised fixing bonds as derivative in redundant bond menu. File name 2xallylchairtsHF321Goptifreqfreezbondmin3optideriv2
  • chk file won't open .. R group error or something?
  • starting again again again...
New molecules, new me
  • Drew out allyl fragment and optimised used HF/3-21G, file name: HF321Goptiallylfrag
  • Created chair TS guess file chairts.gjf
  • 1st optimisation using Opti+Freq Optimisation = TS Berny and 1 FC, HF/3-21G, file name chairtsoptifreqfc1TSBerny
  • Imaginary vibration at -817.9cm-1
  • 2nd optimisation freezing the 4 atoms involved in bond breaking/making, ran as if minimum, file name chairtsfreezbondzoptifreqfc1min
  • Optimised again as a TS chairtsderivbondoptifreqfcnTSBernyNE

NE = no Eigen, needed to prevent crashing when running a TS.

    • Sum of electronic and zero-point Energies= -231.466701
    • Sum of electronic and thermal Energies= -231.461341
    • Sum of electronic and thermal Enthalpies= -231.460397
    • Sum of electronic and thermal Free Energies= -231.495207
  • New bond lengths = 2.02Å compared with 2.20Å before optimisation
Boat
  • Took file of optimised anti2 structure (file name: anti215hexadieneDFTB3YLP631Gd-step2)
  • Duplicated in new window so that they are in seperate boxes (one reactant, one product)
  • Numbered appropriately for a before and after boat TS via Cope rearrangement: 1-2-3-4-5-6 reactant, 4-5-6-1-2-3 product
  • Ran Opt+Freq TS(QST2) HF/3-21G, didn't work as ends of structure too far apart spatially.
  • Changed dihedral 2-3-4-5 angle to 0o and 2-3-4 and 3-4-5 angles to 100o on reactant
  • Changed dihedral 5-6-1-2 angle to 0o and 5-6-1 and 6-1-2 angles to 100o on product
  • Ran QST2 optimisation again, file name boattsqst2
  • Got out boat TS
    • Sum of electronic and zero-point Energies= -231.450928
    • Sum of electronic and thermal Energies= -231.445299
    • Sum of electronic and thermal Enthalpies= -231.444355
    • Sum of electronic and thermal Free Energies= -231.479774
  • Imaginary frequency: -839.67cm-1
  • TRY QST3 IF HAVE TIME

11/2/2014

  • "Take a look at your optimized chair and boat transition structures. Which conformers of 1,5-hexadiene do you think they connect?"
  • Ran the IRC forward, calculating the force constants all the way, looking at 50 points on the chairtsderivbondoptifreqfcnTSBernyNE saved under filename chairtsTSBernyIRC50
  • Calculation stopped at point 44
    • Energy: -231.69157878 a.u.
  • Ran minimum optimisation on last point. filename point44optimin
    • Energy: -231.69166702 a.u.
  • Ran another IRC, this time on the other optimised chair structure; chairtsoptifreqfc1TSBerny giving the filename chairtsIRCplainBerny
  • Calculation stopped at point 44
    • Energy: -231.69157869 a.u.
    • RMS gradient: 0.00015227
  • Ran minimum optimisation to last point filename point44n2optimin
    • Energy: -231.69166702 a.u.
    • RMS gradient: 0.00000475 a.u.
Activation energies
  • Starting with chair structure optimised from the freeze/derivative bond thing: chairtsderivbondoptifreqfcnTSBernyNE, optimise using the B3YLP/6-31G(d) theory. file name chairEaoptifreqB3YLP631Gd
    • Energy: -234.55698303 a.u.
    • Compared to gauche2
    • Sum of electronic and zero-point Energies= -234.414929 a.u.
    • Sum of electronic and thermal Free Energies= -234.443814 a.u.
  • Boat structure optimised from boattsqst2, optimised with B3YLP/6-31G(d) theory. file name boatEaoptifreqB3YLP631Gd
    • Energy: - 234.54309307 a.u.
    • Compare to anti2
    • Sum of electronic and zero-point Energies= -234.402342 a.u.
    • Sum of electronic and thermal Free Energies= -234.431751 a.u.
  • Subtract the energy of the transition state from that of the reactant to get the activation energy, then convert to kcal/mol.

12/2/2014

  • Ran freqchk on boatEaoptifreqB3YLP631Gd at 1K:
    • z. point correction: 0.140751 <hartree/particle>
    • therm correct to G free energy: 0.140731
  • Ran freqchk on boatEaoptifreqB3YLP631Gd at 100K:
    • z. point correction: 0.140751 <hartree/particle>
    • therm correct to G free energy: 0.132867
    • Total thermal energy: 89.022 kcal/mol
  • Ran freqchk on boatEaoptifreqB3YLP631Gd at 298.15K:
    • z. point correction: 0.140751 <hartree/particle>
    • therm correct to G free energy: 0.111342
  • Ran freqchk on boatEaoptifreqB3YLP631Gd at 300K:
    • z. point correction: 0.140751 <hartree/particle>
    • therm correct to G free energy: 0.111114
  • Ran freqchk on boatEaoptifreqB3YLP631Gd at 400K:
    • z. point correction: 0.140751 <hartree/particle>
    • therm correct to G free energy: 0.098077
  • Ran freqchk on chairEaoptifreqB3YLP631Gd at 1K:
    • z. point correction: 0.142054 <hartree/particle>
    • therm correct to G free energy: 0.142034
  • Ran freqchk on chairEaoptifreqB3YLP631Gd at 100K:
    • z. point correction: 0.142054 <hartree/particle>
    • therm correct to G free energy: 0.134236
  • Ran freqchk on chairEaoptifreqB3YLP631Gd at 298.15K:
    • z. point correction: 0.142054 <hartree/particle>
    • therm correct to G free energy: 0.113169
  • Ran freqchk on chairEaoptifreqB3YLP631Gd at 300K:
    • z. point correction: 0.142054 <hartree/particle>
    • therm correct to G free energy: 0.112947
  • Ran freqchk on chairEaoptifreqB3YLP631Gd at 400K:
    • z. point correction: 0.142054 <hartree/particle>
    • therm correct to G free energy: 0.100255


The Diels Alder Cycloaddition

Optimising butadiene

  • Drew cis butadiene, used clean function
  • Optimised at the HF/3-21G level, file name cisbutadieneoptifc1HF321G
    • Energy: -154.05514025 a.u.
  • Further optimised at the B3YLP/6-31G(d) level, file name: cisbutadieneoptifc1B3YLP631Gd
    • Energy: -155.98648374 a.u.
  • Looking at MO visualisations (filenames: cisbutadieneHOMOLUMO, cisbutadieneHOMOLUMOotherside and cisbutadieneHOMOLUMOdiagoanlabove), the MOs seem to be strictly speakign antisymmetric due to the twisted structure of the molecule.

Transition State of prototype reaction

  • Using optimised boat structure from the tutorial as my skelton, filename boattsQST2, changed bonds to turn into Diels Alder transition state, also made dashed bonds ~2.2Å
  • Optimised with TSBerny HF/3-21G, fielname: butadieneethylenetsoptifreqTSBernyHF31G
    • It put a hydrogen in the middle of my C=C double bond...... hmmmmm
  • OK now trying making the ts from my recently optimised butadiene structure, then adding a ethylene in there somewhere (YOLO)
  • So I did that and hit the clean function... not very boaty anymore but lets have a look. Ran optimisation opti+freq TSBerny HF/3-21G, filename dielsalderprototypetsoptifreqTSBernyHF321G
    • Imaginary vibration: -818.66 cm-1, looks like a Diels Alder type of motion?
    • Energy: -231.60320845 a.u.
    • 3 nodal planes
    • Symmetric through the central plane

Studying the Regioselectivity of the Diels Alder Reaction

Reactants
  • Drew out a cyclohexa-1,3-diene, cleaned, optimised to a minimum using the HF/3-21G level of theory, filename cyclohexadieneoptiminHF321G
    • Energy: -230.54323108 a.u.
  • Drew out maleic anhydride, cleaned, optimised to a minimum using the HF/3-21G level of theory, filename maleicanhydrideoptiminHF321G
    • Energy: -375.10351323 a.u.
  • Reoptimised cyclohexa-1,3-diene to the B3YLP/6-31G(d) level, filename: cyclohexadieneoptiminB3YLP631Gd
    • Energy: -233.41893632 a.u.
  • Reoptimised maleic anhydride to the B3YLP/6-31G(d) level, filename: maleicanhydrideoptiminB3YLP631Gd
    • Energy: -379.28954468 a.u.
Exo
  • Combined reoptimised structures into a 3 exo ts with dashed bonds, kept original double bonds though, will do with new double bond placements aswell later.
  • Combined structure exo ts was optimised with TS Berny at HF/3-21G, filename cyhexmaanhytsoptifreqTSBernyHF321G
    • Energy: -605.60359124 a.u.
    • Imaginary frequency: -647.36 cm-1, looking quite transition-esque.
  • This time changed double bond placements to how they'd be in the product, reoptimised with TS Berny at HF/3-21G level, filename cyhexmaanhytsprodbondoptifreqTSBernyHF321G
    • Identical energy and imaginary frequncy; altering the bonding changes nothing.

13/2/2014

  • Drew out 3exo product, cleaned, optimised to a minimum at the HF/3-21G level of theory. file name exoprodoptiminHF321G
    • Energy: -605.71873542 a.u.
  • Put the two optimised reactants (file names: cyclohexadieneoptiminB3YLP631Gd & maleicanhydrideoptiminB3YLP631Gd) in the correct conformation, and in same file, different box, put the optimised exo product file name: exoprodoptiminHF321G.
  • Ran a QTS2 to find the TS between them. filename cyhexmaanhytsoptifreqTSQST2HF321G
    • Energy: -605.60359125 a.u.
    • Imaginary frequency: -647.48 cm-1
    • This would imply that my original guess structure for the TS was actually quite good.
  • Bond lengths were measured on the TS outputted by QST2 filename: bond lengths on exo product.ppt
Endo
  • Drew out 4 endo ts from the two previously optimised fragments (file names: cyclohexadieneoptiminB3YLP631Gd & maleicanhydrideoptiminB3YLP631Gd), ran a TSBerny opt+freq to the HF/3-21G level of theory. filename endotsTSBernyHF321G
    • Energy: -605.61036822 a.u.
    • Imaginary frequency: -643.58 cm-1
  • Drew out endo product, cleaned, optimised to the HF/3-21G level of theory, filename endoprodoptiminHF321G
    • Energy: -605.72132083 a.u.
  • Put the two optimised reactants (file names: cyclohexadieneoptiminB3YLP631Gd & maleicanhydrideoptiminB3YLP631Gd) in the correct conformation, and in same file, different box, put the optimised endo product file name: endoprodoptiminHF321G.
  • Ran a QTS2 to find the TS between them. filename endotsTSQST2HF321G
    • Energy: -605.61036811 a.u.
    • Imaginary frequency: -643.19 cm-1
    • This would imply that my original guess structure for the TS was actually quite good.
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