Building a TS Library

Table of Contents IN PROGRESS Overview Constructing a TS Library for a single elementary step For simple reactions in which you only have one conformation per TS structure Directory Structure

IN PROGRESS

Overview

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.

Constructing a TS Library for a single elementary step

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.

For simple reactions in which you only have one conformation per TS structure

1. Save XYZ files for all TS structures, named tsXXX.xyz (e.g. ts1.xyz, ts2.xyz, etc.)

2.Re-order atoms in these XYZ files using the AaronTools convention: Substrate atoms, then metal center (if it exists), then ligand/catalyst atoms. It is recommended that you keep atom ordering as consistent as possible across different TS structures. It is mandatory that any atom being replaced have the same number in all TS structures.

3. For each XYZ file, specify the atoms involved in any forming/breaking bonds that need to be constrained in step 2 (this sometimes requires some trial and error) on the comment line:

For example,

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.