Physical Property Predictions – Filtering Out Potential Problematic Data on ChemSpider…or is it NOT a problem?Posted by: Antony Williams in ChemSpider Services
Copyright©2007 Antony Williams
During the past couple of weeks there have been a number of comments regarding the association of Physicochemical Properties with chemical structures inside the ChemSpider database. Specifically the comments have been directed at inorganic and organometallic compounds.
Based on this feedback we are considering a series of actions regarding physicochemical predictions and these are outlined below.
1) Filter the ChemSpider database and remove the following PhysChem predictions (ACD/LogP, ACD/LogD (pH 5.5), ACD/LogD (pH 7.4), Number of Rule of 5 Violations, Number of H bond acceptors, Number of H bond donors, Number of Freely Rotating Bonds, Polar Surface Area) for substances with the following properties:
â€¢ Exclude multi-component substances
â€¢ Exclude substances represented as a single atom
â€¢ Exclude radicals
â€¢ Exclude structures with a delocalized charge
â€¢ Exclude structures containing isotopes
â€¢ Exclude substances containing elements other than As,B,Br,C,Cl,F,Ge,H,I,N,O,P,Pb, S,Se,Si,Sn, the elements supported by ACD/PhysChem predictors
A question for readers..do you believe that structures with isotopes should be excluded from PhysChem prediction of the properties listed? I have my own opinions but would like community feedback as to whether this is necessary and is all inclusive for all isotopes. Also, should all multicomponent systems be excluded? For example, if there is one water of solvation present should the parameters NOT be calculated for the primary component?
2) For any future updates to the database pre-filter using the criteria listed above
3) Apply the criteria above prior to performing PhysChem predictions on the Services Page
Our predicted properties for certain structures have created a response suggesting that we should alter our application of such algorithms. The suggested path forward is listed above. We welcome feedback from the community! These questions have also been posted to PMR’s blog supporting the suggestions. Please provide your feedback at either site. It will be important in helping to make the decision. It is possible that there will not be sufficient feedback but a decision does need to be made and we will determine a path forward regardless.Stumble it!