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Transition State


The transition state is a saddle point in the energy surface. The perfect analogy is the mountain pass which in hiking is the easiest way to travel between two valleys. In mathematics this point is where all the derivatives are cero or possitive, except one. The frequency analisys depicts the small changes in geometry with respect to the energy, a possitive frequency implies that in that direction the energy increases, so in the transition state all the geometry displacements will increase the energy except one: the direction that take us into another energy minimum.

Finding the transition state that conect the reactants and products is, sometimes, a handmade carving work. But if we make use of the chemical intuition and the geometry tools that ORCA provides is relatively easy to find it.

ORCA provides the optTS module, which if a good guess of the transition state geometry is provided will find the sadle point. Here we are going to make use of our geometry scan calculation for the malonic acid.

Hint: make a surface scan.
As in the previous excercise, perform a geometry scan in the direction where you intuit the transition state is. See in the plot the maximum energy point and propose it as the inital geometry for the transtition state calculation.

From the past energy vs geometry plot we see that the fifth and sixth generated geometry have the maximum energy. We choose the sixth one as the initial geometry for our transition state search.
[emma@pople]$ vi trans_state.inp


#DFT Transition State Search
! RKS PBE TZVP
! PMODEL TightSCF
! PAL8

! OptTS #Search the trans state
! NumFreq #Verify the state

%method
  Grid  2
  FinalGrid  4
end

#Coordinates of the 6th geom scan step
#Type  Charge   Multiplicity
* xyz    0   1
O   -0.067   -0.044   0.017
H    1.752   0.023  -0.056
C   -0.503   1.084   0.089
O   -1.376   1.852   0.342
C    1.147   2.323  -0.570
H    0.980   1.904  -1.562
H    0.887   3.371  -0.433
C    2.205   1.833   0.161
O    2.569   0.548   0.176
O    2.898   2.603   1.010
H    3.423   2.015   1.590
*
[emma@pople]$/path/to/orca trans_state.inp


After the calculation ends

[emma@pople]$ grep -A32 'IR ' trans_state.out
IR SPECTRUM
-------------
Mode   freq(cm**-1)
-------------
 6:    -306.96 cm**-1
       .
       .
 25:    1412.27 cm**-1
       .
 29:    2839.66 cm**-1

Generate the ir vibration.

[emma@pople]$ orca_pltvib malonic_acid.hess 6
-306.96 cm**-1