Posted: Sat Jan 10, 2015 1:39 amPost subject: Prediction the log P for Pt(II) complexes
I found in some publication, that the authors calculated the log P values for the platinum(II) complexes, using Marvin Sketch. Now, I am trying to do the same thing, but is it now possible. Is it some kind of problems with my software or the authors lied??
Jozsef ChemAxon personnel
Joined: 25 May 2004
I would like to predict the log P / log D for a coordination complex with keto groups as donors. When I draw a regular bond from the ketone oxygen to the metal Marvin assigns a negative charge to O and does not allow to predict the log P because it considers it an "Inconsistent molecular structure".
In the example above this problem did not occur because the amino donor had a proton that could be omitted to draw the bond without a negative bond to appear. How should I proceed? Using coordination bonds does not work either, as discussed above.
Do I need to use partial charges Pt(2+) and O(-) for the ketone, or should I even draw the ketone with only a single bond (C--O--M) instead of (C==O--M)? This way the simulation works but I wonder how reliable this is in representing my actual molecule?
Another thing I noticed is that the 3D geometry of the molecule is not correctly represented. Marvin draws the Pt complexes in a tetrahedral instead of square planar geometry. Does this affect the log P prediction?
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