Building a TS Library

AARON relies on a library of pre-computed TS structures for a given reaction. These pre-computed TS structures are typically for a representative model catalyst/substrate. AARON then computes analogous structures for new catalysts/ligands or substrates as specified in the AARON input file, allowing the user to make predictions of selectivities, etc. for other ligands and substrates.

AARON comes with TS libraries for several reactions.

The first step in applying AARON to a new reaction is constructing a TS library. An ideal TS library should include all reasonable low-lying transition states for the reaction. This requires the user to manually explore different configurations and relative orientations of the substrate and catalyst. Note that even if a given configuration is relatively high in energy for a given catalyst does not mean it will be necessarily unimportant for other catalysts being screened.

Note 1: Keep atom ordering consistent It is important to keep the atom ordering as consistent as possible in the TS structures. If these are previously-computed structures (or those taken from the SI of another paper), this might require you to reorder atoms manually.

Note 2: Put substrate atoms first, then the transition metal, then the catalyst/ligand atoms It is vital that all substrate atoms come first, then the metal center, then any ligand atoms.

Note 3: All TS structures must be named tsxxx, and all intermediates minxxx Typically, xxx will be numbers (e.g. ts1.xyz, ts2.xyz, etc)

Directory Structure

Personal TS libraries should be located in

 $HOME/AARON_libs/TS_geoms

Each reaction type should be a subdirectory of TS_geoms:

 Heck_Allenylation
 Hydrogenation

Within a given reaction type, there should be a directory a given 'template', which is typically a family of catalysts/ligands. While AARON can replace a given ligand with another ligand type, you will often find faster TS convergence using templates for more similar ligands. For example, if you are screening over different substituted BINAP ligands, it would be best to have the TS library contain TS structures for an unsubstituted BINAP.

 BINAP

Within the template directory, you can have subdirectories specifying different stereoisomers or regioisomers:

 R
 S

Within each of these are the structures corresponding to different configurations and relative orientations (i.e. tsxxx, minxxx):

 ts1
 ts2
 ts3

For a given tsxxx, you can include TS structures corresponding to different conformers (or just one conformer):

 cf1.xyz
 cf2.xyz

See $QCHASM/Aaron/TS_geoms for examples.