Several options are available to restrict the search area and avoid exploration of unwanted pathways. An example for the Claisen rearrangement is shown below:
# SC-AFIR/B3LYP/6-31G
0 1
C -2.348573142273 -0.935085648340 -4.639035219979
H -3.294831555012 -0.909900166285 -5.165505604652
H -2.265520409294 -1.569755265262 -3.764502826845
C -1.323670838495 -0.187800168120 -5.053606036206
H -1.376099035933 0.455646220924 -5.932040727634
O -0.116512212492 -0.147042048223 -4.361394618504
C 1.038781163598 0.379514582718 -5.095548476611
H 1.401531586911 -0.372454818381 -5.807968751223
H 0.716697284928 1.266585513489 -5.664785329631
C 2.095220863649 0.740468623421 -4.097999098495
H 1.765012689228 1.390876923398 -3.290524814409
C 3.364961437537 0.328923419949 -4.170524858465
H 3.709442329648 -0.333531078363 -4.961162649841
H 4.109140272000 0.637257301074 -3.443193839506
Options
Add Interaction
Target = 1,4,10,12
GAMMA = 200
END
NoBondRearrange
There are two lines between the Add Interaction … END keywords. Target = 1,4,10,12 means that the fragments A and B in the AFIR function are generated only around these atoms (four sp2 carbons in this case); in default, the fragments are generated around all atoms. For details about how to generate the fragments automatically, see S. Maeda, et al., J. Comput. Chem., 2018, 39, 233–251. (this paper is Open Access). A simple but not precise explanation is, only paths mainly involving geometrical displacements of these four atoms are searched with this setting. The NoBondRearrange option disables the path searching starting from EQs that have different bond connectivity from the initial EQ.
Frequently used options
See Global reaction route mapping by single-component algorithm (SC-AFIR).