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Use of template structures

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vingman edited this page May 6, 2021 · 3 revisions

AaronJr can load template structure files and process modifications to these files by setting the appropriate options in the INI configuration file associated with your workflow.

Table of Contents

Using the [Geometry] section

See here

Using the [Reaction] section

This is used when loading templates from your personal $AARONLIB library. The file structure is as follows:

  • $AARONLIB/template_geoms - the parent directory for storing template files
  • $AARONLIB/template_geoms/<reaction> - store template files for similar reaction types here
  • $AARONLIB/template_geoms/<reaction>/<template> - optional, but useful to further sub-divide your template files.
If your template files are for a selective reaction, create R, S, cis, trans, etc. sub-directories within the $AARONLIB/template_geom/<reaction>/<template> directory and store your template files accordingly. This will allow AaronJr to include selectivity estimations when displaying results.

Setting options using the comment line in XYZ files

AaronJr will automatically read in certain options using the comment line of XYZ files:

  • constraints for constrained job types
  • key atoms for ligand mapping
  • defining the "center" atom
  • defining sub-structural components

Constraints

F:1-2;3-4-5;6-7-8-9 constrains the 1-2 bond length, the 3-4-5 bond angle, and the 6-7-8-9 dihedral

Constraints can also be specified using the "constrain" option in the [Geometry] section. However, constraints set in the [Geometry] section will be used for all template files. Thus, using the comment line form allows for setting different constraints for different template files.

Key atoms

K:1,2 atoms 1 and 2 will be used as anchors for mapping new ligands

"Key atoms" are used for defining how a new ligand will be mapped to the template structure. For ligands coordinated to the only transition metal in the structure, detection is done automatically (the key atoms are the ones coordinated to the metal). For ligands coordinated to another type of atom (for example, a Si-centered catalyst) or if transition metals are found elsewhere in the structure (for example, ferrocenyl phospine ligands), the key atoms will be detected automatically only if the center atom is defined (see next section). For other types of systems, it will be necessary to define the key atoms prior to ligand mapping. The new key atoms are mapped to the old key atoms, so it may be helpful to look at the AaronTools ligand library when choosing your key atoms, as they should correspond to the key atoms of the new ligand.

Center atoms

C:23 ligands are coordinated to atom 23

C:23,24 two center atoms (eg: bimetallic catalyst)

If the center atom(s) are transition metals AND no other transition metals are present in the structure, this does not need to be set.

Defining sub-structural components

L:1-10;11-20,22 Atoms belonging to the same component are given as ranges or individual atom numbers separated by commas. The semicolon is used to separate one component from another. Any atoms not included in the definition will be automatically partitioned by the component detection algorithm. 




AaronTools will automatically partition the structure into sub-structural components (eg: ligands/substrates) based on their inter-atomic distances.
However, there may be systems for which our detection algorithm fails (we would love a bug report if you find one).
For this reason, sub-structural components can be defined manually.



Example: Recursively load all template files found in $AARONLIB/template_geoms/cycloaddition.


[Reaction]
reaction = cycloaddition




Example: Recursively load all template files found in $AARONLIB/template_geoms/cycloaddition/ethene_ozone.


[Reaction]
reaction = cycloaddition
template = ethene_ozone




Example: TS structure templates for an asymmetric Heck reaction


[Reaction]
reaction = Heck
template = 2a


The snippet above instructs AaronJr to load all template files in $AARONLIB/template_geoms/Heck/2a. Using the directory structure below will allow for selectivity analysis when using the AaronJr results command:


$AARONLIB/template_geoms/
  Heck/
    2a/
      R/
        TS1.xyz
        TS2.xyz
        TS3.xyz
        TS4.xyz
      S/
        TS1.xyz
        TS2.xyz
        TS3.xyz
        TS4.xyz






Making changes to the template files





See here for substitutions.



See here for ligand mapping. Note that substitutions to the ligand being mapped are not yet supported, but this will be implemented soon! For now, you can use AaronTools to modify the ligand ahead of time and save it to your personal ligand library.

              


          



  
          

            


            
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