## Sunday, August 2, 2009

### Finding a transition state: an Sn2 reaction

Here is a screencast I made about finding a transition state for the reaction

F- + CH3Cl -> Cl- + CH3F

The general approach is as follows

1. Build the structure (F- + CH3Cl)
2. Optimize the geometry while constraining a key distance (between the F and C atom) to a certain value (2.0 Å)
3. Compute the frequencies for the optimized geometry to check for an imaginary frequency
4. If there is an imaginary frequency, use this geometry and frequency information as a starting point for the TS search

The distance constraint is imposed using

\$zmat ifzmat(1)=1,1,6 fvalue(1)=2.0 \$end

which is used in conjunction with the delocalized internal coordinates I discussed previously. 1,1,6 defines the distance (denoted with the first "1") between atoms 1 and 6. Note that this distance does not have be 2.0 Å in the guess geometry (though the closer it is to 2.0 Å the faster the optimization will converge).

I also show how the frequency information contained in the \$HESS group, found at the end of the .dat file that GAMESS produces along with the output file, can be transferred to the input file for the TS search, where hess=read is used in \$statpt. Any text editor can be used for this. Note that the hssend=.t. keyword has to be used to cause the frequencies to be computed at the end of the optimization. I have showed the use of this keyword in a screencast in a previous post.

The complete \$statpt groups looks like this

\$statpt opttol=0.0005 nstep=50 hess=read ihrep=5 hssend=.t. \$end

ihrep=5 causes the frequencies to be recomputed at every 5th step. This really helps convergence but is computationally expensive.

Note that there are no constraints imposed when searching for the TS.

The key question is of course why I chose the C-F distance and 2.0 Å for the constraint value. This is simply the first thing that popped into my head and it happened to work. If it hadn't, I would have tried some other values and, if none worked, I would have tried to the C-Cl distance. Future posts will show examples of trying difference distances.

Because you may have to try different constraints before succeeding, it is a good idea to find the TS at a cheap level of theory, such as PM3. The C-F distance in the PM3 TS structure (2.10 Å) should provide a good guess for TS searches at higher levels of theory.

I tried it for this reaction using RHF/3-21G, but with no luck. That is because I forgot the very first step in searching for a TS: make sure there is one! In the screencast below I show how a RHF/3-21G geometry optimization (with no constraints) starting from F- + CH3Cl leads to Cl- + CH3F, meaning that the former structure is not a minimum on the gas phase RHF/3-21G potential energy surface. So there is not much point in looking for the corresponding TS.