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