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I’m trying to get a name for the structure above using MarvinSketch for my undergraduate senior thesis. This is the first time I’ve had to draw a metal complex in MarvinSketch, and I’m having trouble getting the program to name it as is.

Right now, using the “structure to name” feature, the name I’m getting is 8,14‐dimethyl‐2-λ-4,20-λ-4,21-λ-4,27-λ-4‐tetraaza‐1-cobaltaheptacyclo[12.6.6.11,9.02,7.015,20.021,26.013,27]-heptacosa2(7),3,5,9(27),10,12,15(20),16,18,21(26),22,24‐dodecaene‐1,1‐diol, and I’m pretty darn sure that’s wrong.

I think this issue is that I drew the water molecules as being attached to the carbon via coordinate bonds but the polypyridine ligand as being attached by normal single bonds. I did this because the program wouldn’t even give a name if all bonds were drawn as coordinate bonds, and if I try to show the water molecules being attached by normal bonds, the program always either gives the waters a formal charge or removes one of the hydrogens to make it an -OH bonded to the cobalt.

I was wondering if someone could help me figure out how to get the program to properly name this complex, and perhaps also help me get the program to stop adding a formal charge/removing one of the hydrogens from the waters if I change the bond type to not be coordinate.

This is not a very important part of my thesis so if there’s no relatively easy way to get the IUPAC name I’m not going to worry about it (though it would be nice). I also unfortunately don’t have access to books on nomenclature from my school with us being remote.

Thank you very muchcobalt complex

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    $\begingroup$ You should just name the ligand and then it's a small step to whole complex that program won't make, but you should be able to do easily. $\endgroup$
    – Mithoron
    Oct 19, 2020 at 0:38
  • $\begingroup$ Hello, thanks for the response! So if I just name the ligand in MarvinSketch, I get the name: 2‐[1,1‐bis(pyridin‐2‐yl)ethyl]‐6‐[1‐(pyridin‐2‐yl)ethyl]pyridine. Now that I have that, how would I go about naming the metal complex? I've not taken inorganic yet* and I've never learned IUPAC nomenclature for metal complexes. *The class is only offered in the spring and unfortunately, I've had to wait for senior year spring to take it. $\endgroup$
    – Planejerle18
    Oct 19, 2020 at 3:38
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    $\begingroup$ As I said this is the easy part. You can check for example Wikipedia for details. $\endgroup$
    – Mithoron
    Oct 19, 2020 at 14:45
  • $\begingroup$ Thanks for the link! Would the name therefore be: diaqua(2‐[1,1‐bis(pyridin‐2‐yl)ethyl]‐6‐[1‐(pyridin‐2‐yl)ethyl]pyridine)cobalt(III)? $\endgroup$
    – Planejerle18
    Oct 19, 2020 at 16:07
  • $\begingroup$ Well, there's probably need for curly bracket, but more importantly, is this Co(II) or (III) 'cause (II) is more probable. $\endgroup$
    – Mithoron
    Oct 19, 2020 at 18:02

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