Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

NMR calculations and pH #84

Open
flatstik opened this issue Jun 27, 2022 · 1 comment
Open

NMR calculations and pH #84

flatstik opened this issue Jun 27, 2022 · 1 comment
Labels
enhancement New feature or request

Comments

@flatstik
Copy link

flatstik commented Jun 27, 2022

A great feature would be to print out NMR data prediction with J-couplings with/from the generated output with keyword "NMROUT(C, H, F...) etc". EPS would be mandatory to simulate the solvent (with keywords or better defined numerical values) and if EPS is used, optimization to that solvent with the most rigorous precision before optimization should be used).

pH function would be also be great for ionization of molecules. This is nice function in openbabel for adding hydrogens: -p adds hydrogens appropriate for pH (which use transforms in phmodel.txt)

@godotalgorithm
Copy link
Collaborator

godotalgorithm commented Jun 30, 2022

MOPAC does have a pKa feature already, but it is only for protonation of oxygen atoms in molecules, and it involves a limited, custom-built semiempirical model on top of a PM6 calculation. Without additional fits/corrections, pKa predictions suffer in accuracy from MOPAC's relatively poor description of the charge density around hydrogen atoms (which is why MOPAC needs explicit corrections for hydrogen bonding in PM6-D3H4 and PM7). Jimmy Stewart does not recommend "consistent" pKa estimates that are calculated directly with PM6/PM7 and without any additional correction factors. I have not explored this myself yet to have a more informed opinion.

NMR is a feature in the suite of tools associated with xTB. I am not familiar with that feature, but it appears that ab-initio quantum chemistry data is required as part of their prescribed process - they do not appear to trust NMR calculations based purely on semiempirical model calculations.

In both cases, the technical implementation might not be that hard (especially piggy-backing on some tools from the xTB suite), but it will be non-trivial research to fit and validate these features to be of usable accuracy in a purely semiempirical setting. Also, the result may simply be that MOPAC's models are just too crude to describe these effects to sufficient accuracy for any practical purpose. These are use cases for which MOPAC's models may very well be near their Pauling points, and something substantially more sophisticated might be needed for reliable semiempirical versions of these property calculations. Whatever the outcome, this would be a research project, not straightforward software development.

@godotalgorithm godotalgorithm added enhancement New feature or request labels Jun 30, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

2 participants