Hi, I've spent a while beating my head against this without much success, so I figured I'd ask around.
The attached mol file contains a chiral phosphorus center; I'm trying to figure out whether the label for that center should be R or S. My usual approach to this is to draw the thing in Marvin Sketch and/or Chemdraw and see what they say. Both agree that the P is (R). The problem I have with that is that I can't really figure out why. I'm sure the answer is simple, but I haven't been able to find it. I've been singularly unsuccessful at coming up with the right search phrase to google for a result. The one explanation I was able to find for labeling these things: http://www.chemistry.ucsc.edu/courses/palleros/PhosphatesII.pdf makes sense to me (the O with the double bond is the highest priority atom), but that would lead to a label of (S) for the P in the attached molecule. I attempted to figure this out by going back to the original CIP papers, but that way leads to madness (and I didn't find anything in my skim of the papers anyway). Here's how I would go about doing the assignment... using the mol-file numbering of the atoms: P6 has neighbors: O4, O5, O7 Expand those out in shells... Shell 1: O4 : C2 O5 : C3 O7 : C9 O8 : (P) <- because of the double bond Shell 2: O4 : C2 : C1 O5 : C3 : C1, C10 O7 : C9 : O8 : (P) Now we have a ranking in order of increasing priority: O7, O4, O5, O8. This leads to an assignment of (S) to the P. The only way I can find to make the Marvin/ChemDraw assignment work is to ignore the double bond to O8 when doing the expansion and to treat it as a naked O: Shell 1: O4 : C2 O5 : C3 O7 : C9 O8 : Shell 2: O4 : C2 : C1 O5 : C3 : C1, C10 O7 : C9 : O8 : This gives the ranking O8, O7, O4, O5, which is consistent with an assignment of (R) to the P. I just can't figure out why one would do things this way. Anyone have any help or a clarification for this? -greg
chiral_phosphorous.1.mol
Description: Binary data
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