Tips & tricks for finding transition states, bonding analysis
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We already have some useful (advanced) teaching examples and workshop materials which contain useful tips & tricks, input files etc.
Here we highlight two aspects for which we regularly get questions: how to find a transition state, and how to perform energy decomposition analysis to get insight in chemical bonding.
Tips & Tricks: finding transition states, bonding analysis
Finding a transition state essentially comes down to this procedure
- Getting close to the maximum on the reaction pathway
- Get a good guess to the transition mode / Hessian
- Verify you have optimized a first-order saddle point
We have prepared a package with slides giving some hints on finding a good starting geometry as well as ways to get a good guess Hessian:
- Tips, tricks, examples and exercises for finding Transition States (pdf, input files)
It also contains hints and recommendations on the technical settings which may be a good starting point (of course consulting the recent literature is always good!). The rescan option for frequencies can help identify if low-lying imaginary modes are really spurious imaginary modes or not. It also introduces how you can use the energy decomposition analysis along the reaction pathway (the activation strain model by Bickelhaupt et al.) to understand catalysts in more detail with the ultimate goal to rationally design better catalysts.
For more insights and examples on how to perform and use EDA / ETS-NOCV analyses, check out:
- Energy Decomposition Analysis (Marc Raupach), files: 2sqrtX2sqrt_struc.xyz, 2X2_struc.xyz, sqrtXsqrt_struc.xyz
- Investigating Chemical Bonding with ADF, (Paul Jerabek, 2014): slides, input/output files
- ETS-NOCV workshop Marburg May 2015, slides, exercises by Mariusz Mitoraj
- Chemical bonding and activation strain models (slides from Matthias Bickelhaupt)
- Understanding H bonding through Kohn-Sham MO theory and EDA (slides from Celia Fonseca Guerra)
Scanning low-lying modes could help uncover whether low-lying imaginary modes for transition state are really spurious modes or not.