Thursday, August 10, 2017

Predicting most labile CH bond using semiempirical methods



Yesterday, I mentioned on Twitter that I had written some prototype code to predict labile proton using PM3/COSMO.  A few people expressed interest so I put the code on GitHub.

The code is based on some previous work and removes all CH protons/hydrides/H atoms and finds the position with the lowest free energy.  I've just finished the code so I have no idea how well it works or if PM3/COSMO is the best choice.  Also, there are very few comments and some aspects of the setup (paths, etc) are particular to my machine and needs to be changed.

In its current form the method doesn't consider different reference molecules, so the prediction is "pure PM3/COSMO".  The basic code to do it is there but I haven't extended it yet. Also, the code only considers CH groups, so if have other groups (OH, NH, etc) with lower pKa they won't be considered.  This is very much a work in progress but if you have suggestions, test cases, ideas, or any other kind of feedback please let me know.  I hope you find it useful.


This work is licensed under a Creative Commons Attribution 4.0
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