Molecular Property Calculations

Hi,

In the Molecular Properties node, is it possible to add a few extra descriptors for;

- "Most Acidic pKa"

- "Most Basic pKa"

- "sp3 character (%)"

 

Thanks,

Simon.

Getting SP3 character [division by sp3 count/ no of carbons]is very easy using smarts ref. http://bioinformatics.oxfordjournals.org/cgi/content-nw/full/22/17/2099/TBL1?ck=nck

Type Id. SMARTS string Description

C.3G 1 [C^3] Generic sp3 carbon
C.3X 2 [$([C^3][Cl,Br,I,$(C#N),$(N(~O)~O), $(OS(=O)=O)]),$(ON=O)] sp3 carbon connected to strong electron withdrawing group
C.3H 3 [$([C^3]([#6^3,#1])([#6^3,#1])([6^3,#1])[#6^3,#1])] sp3 carbon connected to sp3 carbon or hydrogen

 

Many thanks for this.

Simon.

Hi,

if I am not entirely mistaken, CDK doesn't support pKa calculation. It would be great to have a tool for protonation or pKa caluclation though. Any takers? :)

ChemAxon's JChem can deal pKa calculations and is freely available under an academic license if that is of any help to you.

Regarding the "sp3 character": All atoms have atom types assigned to them in CDK. Instead of using SMILES or SMARTS, I count all sp3 hybridized Carbon atoms and divide the count by all atoms in the molecule (including H). Values range from 0 to 1. You can change to the "Percentage renderer" for percent. Molecules with unconfigured carbons ,e.g., due to unknown valences, return a missing cell. Is that what you are looking for?

Best regards,

Stephan

Yes, I can see that the sp3 character can be achieved by the process you described, I just thought it may make the process more user friendly for chemists if this was an available option straight from the Molecular Property node instead of getting the two properties, and then using a Maths node to undertake the division. Just a thought!

In terms of the pKa calculations, this is somewhat of a gap in KNIME from the Community Contributions at the moment. It would be very nice if anyone can implement this. There was this blog about Open Source pKa calculations and how this could be achieved with CDK??

http://chem-bla-ics.blogspot.co.uk/2008/10/pka-prediction-or-how-to-convert-jcim.html

 and

http://blueobelisk.shapado.com/questions/is-there-an-open-source-pka-or-logd-tool-available

Simon.

My mistake. I should have said that I have added the option to the node. Just wanted to get feedback on the method I am using. Should be in the repository soon.

Yes, a pKa calculator has been on the wish list for way too long!

Hi Stephan,

Many many thanks for the inclusion of the sp3 character descriptor. I tried it out this morning and its working great. This is a really useful and common descriptor to use so thanks for the very quick implementation!

Simon.