Coordinating solvent molecules: THF and LDA

duartegroup / autodE

automated reaction profile generation

https://duartegroup.github.io/autodE/

MIT License

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Coordinating solvent molecules: THF and LDA #240

Closed eneas77 closed 1 year ago

eneas77 commented 1 year ago

Is there any present way autodE incorporates solvent molecules around metal centers?

Lets say I want to evaluate a deprotonation at the alpha position of a carbonyl with LDA. It is known there are several studies that incorporta at least one molecule of THF coordinating the Li center... Any way to include it via smiles or any other workaround?

Thank you for you hard work!

E77

t-young31 commented 1 year ago

Hi!

Yes there is – if you define everything as covalent bonds and assign formal charges appropriately then everything should be fine. e.g.

>>> import autode as ade
>>> lda_thf = ade.Molecule(smiles="CC(N([Li-][O+]1CCCC1)C(C)C)C")

Aside: this comes with the caveat that any graph based approach to finding TSs – like autodE – will struggle when there's not well defined 'bonds' present, like M-solv interactions. Good luck!