SN2 TS generated from SMILES

In the following example we will generate conformers of the SN2 transition state involving a cloride ion and fluoromethane in water.

SMILES

FC.[Cl-]

nocov_ts_chemdraw

nocov_ts_3D

In the following example we need a mapped SMILES to set up the constraints. We can either use rdkit for it in python, in a jupyter notebook (see python example ) or we can write the SMILES by ourselves (not recommended).

The mapped smiles that we will be using is the following one:

mapping

[Cl-:3].[F:1][C:2]([H:4])([H:5])[H:6]

Now that we have the mapping, we can easily proceed to set up the constraints. In this case we want the C-F and the Cl-C bond distances to be constrained and equal to 1.8 angstroms and we want the angle Cl-C-F to be of 180º.

As a consequence the distance constraints will be "[[1,2,1.8],[2,3,1.8]]" and the angle constrains "[[1,2,3,180]]"

Finally we proceed to the conformer generation using CREST

python -m aqme --csearch --name "TS-example" --nprocs 12 --program crest --cregen --crest_keywords "--alpb h2o" --xtb_keywords "--alpb h2o" --constraints_dist "[[1,2,1.8],[2,3,1.8]]" --constraints_angle "[[1,2,3,180]]" --smi "[Cl-:3].[F:1][C:2]([H:4])([H:5])[H:6]"