Rep:Mod:Yunzhang Module3 Writeup2

Optimizing the "Chair" and "Boat" Transition Structures

Optimizing the "Chair" Transition Structures

(a) Draw a planar allyl fragment(CH2CHCH2)-> run a HF/3-21G level optimisation -> copy this structure to a new GaussView window 
    twice and orient for them to look like the chair transition state (translate one fragment: Shift Alt keys + Left Mouse button; 
    rotate: Alt key + Left)-> Bond distance between the terminal Cs of the CH2CHCH2 fragments ~ 2.2 Å -> Save as chair_ts_guess.

(b) Use Hartree Fock and the default basis set 3-21G for parts (b) to (f).
       Optimization by using Hessian:
          File → New → Create MolGroup -> copy and paste the guess structure into the window -> Calculation: Gaussian -> Job Type: 
          Opt+Freq; Optimization to a: TS (Berny); calculate force constants: Once; Additional keyword: Opt=NoEigen -> Submit. 
          After the job completes, it gives an imaginary frequency -817.897cm-1 due to the Cope rearrangement.

       Optimization by using Frozen coordinate:
(c) Frozen coordinate optimization: File → New → Create MolGroup -> copy and paste the guess structure into the window -> 
      Edit: Redundant Coord Editor -> click on Create a New Coordinate -> On GaussView window: select 2 of the terminal Cs from the 
      CH2CHCH2 fragments which form/break a bond during the rearrangement -> On coordinate editor: select Coordination: Bond; Freeze 
      Coordinate -> Set value: 2.2 -> click on Create a New Coordinate -> select the opposite 2 terminal Cs -> select Bond and Freeze 
      Coordinate -> Click OK -> Submit.
(d) Open the file after the job has finished -> Edit: Redundant Coord Editor -> create a new coordinate by clicking on Create 
      a New Coordinate -> Select one of the bonds that was frozen before -> Coordinative: Bond; Derivative -> Repeat this procedure for
      the other bond -> Calculate: Gaussian -> Job type: opt+freq; optimize to a: TS(Berny); Calulate Force Constants: Never ->  
      yun_opt_freq_redundant2 -> submit. This transition structure gives an imaginary frequency -817.947cm-1 due to the Cope rearrangement.

Results:

/	Chair transition structure(Optimized under Hessian)	Chair transition structure(Optimized under Redundant)
Jmol	Cyclopentasiloxane	Cyclopentasiloxane
Result summary
Imaginary frequency
Geometric information(atom list)

Optimizing the "Boat" Transition Structures

(e) Optimization by using the QST2 method: 
         Open the chk file of anti2 -> open a second window -> create a new MolGroup -> copy anti2 molecule into the new window 
         and select File → New → Add to MolGroup(the original molecule disappears and a green circle appearwith a 2 next to
         it -> copy and paste the reactant molecule again and we are going to make it the product molecule -> click on the 
         icon showing two molecules side by side -> View: select Labels and change the numbering.
         Set up the 1st QST2 optimization:
         On Gaussian menu -> Job Type: Opt+Freq; optimize to a: TS (QST2)-> Submit -> job fails. 

		The structure looks like chair transition state but with bonds more dissociated, this is because the calculation translated the top CH3CH2CH3 fragment but did not rotate it around the central bonds.

Set up your QST2 calculation again by going back to the original input file and this time modify the geometries of both molecules, for the reactant, make the central C-C-C-C dihedral angle 0 and the inside C-C-C angle 100. Repeat for the product molecule.

The QST2 calculation was then carried out.

Results:

Jmol of the boat transition state under QST2 method	Result summary	Imaginary vibration	Advantage and disadvantage of using the QST2 method
Cyclopentasiloxane			The QST2 method is easy to set up because it is fully automated, however the job has failed for serveal times before the correct optimisation was obtained due to the input guess transition structure is not close enough to the real one.

Optimization by using the QST3 method:

Result:

Input image	Result Summary and Imaginary vibration	Advantage of using the QST3 method
		The QST3 method is more reliable and the optimization is successfully carried out in one go.

(f) The Intrinisic Reaction Coordinate/IRC plots a series of points by taking small geometric steps follow the direction 
  in which the gradient is the steepest on the PE surface and this gives rise to the reaction path after the transition state.

  Open optimized chair/boat transition structures -> Calculate: Gaussian -> Job Type: IRC; forward; once; 50 -> Submit.
  Since the RMS gradient has not reached a minimum yet, the follwing methods are used in order further minimize it:
  (1) Copy and paste structure 51 obtained in IRC to a new molgroup and run a normal minimization;
  (2) Carry out IRC as the one above with number of points=200; 
  (3) Redo the IRC and choose force constants: always.

Results obtained by using three different methods above:

Boat TS	Method 1	Method 2	Method 3
Jmol of the final structure obtained	Cyclopentasiloxane	Cyclopentasiloxane	Cyclopentasiloxane
Result summary
IRC
Comment	Min. E= -231.69266121 a.u. Point group= C1 fastest/ end up in the wrong minimum if the starting structure is not close enough to a local minimum	Min. E= -231.69194563 a.u. Point group= C1 more reliable/ too many points may veer off in the wrong direction therefore end up wit the wrong minimum;	Min. E= -231.69266113 a.u. Point group= C1 the most reliable/ the most expensive and may not be feasible for large molecules.

Chair TS	Method 1	Method 2	Method 3
Jmol of the final structure obtained	Cyclopentasiloxane	Cyclopentasiloxane	Cyclopentasiloxane
Result summary
IRC
Comment	Min. E= -231.69166698 a.u. Point group= C2 fastest/ end up in the wrong minimum if the starting structure is not close enough to a local minimum	Min. E= -231.69164474 a.u. Point group= C2 more reliable/ too many points may veer off in the wrong direction therefore end up wit the wrong minimum;	Min. E= -231.69166674 a.u. Point group= C2 the most reliable/ the most expensive and may not be feasible for large molecules.

Conclusion: By using different approaches, the symmetry obtained for each is the same, C1 for the Boat structure and C2 for the Chair structure; the Boat structure obtained matches well with Gauche 3 whereas the Chair structure matches well with the Gauche 2, this tells us the conformers involved in the cope rearrangement; the energy obtained for the Boat structure is always lower than that of the chair in regardless of the method used, which indicates the Boat structure is the thermodynamically preferred structure.

(g)Calculate the activation energies for the reaction via both transition structures:

start from the HF/3-21G optimized structures -> carry out opt+freq for both chair and boat transition structures using B3LYP/6-31G(d).

1 Hartree= 627.509 391 kcal/mol therefore:

/	Jmol	Results summary	ΔE under B3LYP/6-31G(d) at 298.15K	Experimental ΔE at 0K
Chair	Cyclopentasiloxane		33.69	33.5±0.5
Boat	Cyclopentasiloxane		42.23	44.7±2.0

Conclusion:

The calculated activation energies match well with the experimental ones and the energy for each conformer obtained under the HF/3-21G and B3LYP/6-31G(d) methods are quite different in regardless of their similarity in geometry. Therefore, the higher level optimization could carried out based on the result obtained from the lower level of optimization in order to be more time efficient.