ReactionMechanismGenerator / ReactionMechanismGenerator/ARC

Optical isomer number may be incorrect

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#413 2 comments 0 reactions 1 assignee View on GitHub

@xiaoruiDong is already working on this.

Since Jul 27, 2020.

Priority: Critical Topic: Arkane Topic: Thermo Type: Bug
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Python
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Description

Describe the bug

declaration
I am directly calling the APIs. But from my preliminary check, the ARC workflow can be also suffering from this issue.

Currently, in ARC, the opticalIsomers used to create ARC input (file) is automatically generated from PointGroupCalculator.

https://github.com/ReactionMechanismGenerator/ARC/blob/b179c764b3f546c4bdcca34ae5b4064079408e4a/arc/common.py#L592

PointGroupCalculator is an RMG-Py built-in module calling the GNU Symmetry package and calculating the point group based on the provided geometry. However, the chirality of a certain conformer geometry is not equivalent to the chirality of the molecule. For example. as we know, propanol has no chiral center, but optical_isomers=2 will be assigned if I use the following geometry (lowest at B3LYP/CBSB7):

image

This is a geometry that cannot overlap with its mirror image. I would say if we are using Multi-Structure method to calculate thermo, the value is correctly assigned. However, we are calculating thermo with Single-Structure method, so it is improper to go with optical_isomers=2 and we should use optical_isomers=1, I think.

This issue is not rare. In my personal calculation database, 250/700 species are impacted.

Please correct me if my thought is wrong. Otherwise, we should fix this, and probably let users aware of this, especially for their previous job.

Fix the issue?
A naive idea is that for wells, we can use RDKit to detect the chiral centers (based on CIP). However, this is not currently available for TSs.

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