Egon has spotted a bug in our code for assignment of charges to atoms:
The example shown by Peter was nicely chosen: something is wrong with that example. It uncovers a bug in the pipeline, that could have been uncovered by a simple agent monitoring the RSS feed. That is why this technology is important! It allows pipelining of information between services.
Anyway, before you read on, check the structure in the example yourself (Bis(pyrimidine-2-carboxylato-K2N,O)copper(II)).
Done? Checked it? You saw the problem, right? Good.
The charges in the structure are indeed wrong. There are two challenges…
- for structures with more than one moiety (isolated fragment) in the structure it is formally impossible to know the changes if the author doesn’t give them. The authors can give them in _chemical_formula_moiety but they are often difficult to parse correctly and in any case they often aren’t given. In those cases we don’t try to assign charges. (The crystallographic experiment itself cannot determine charges).
- In cases where the fragment contains only light atoms it is usually (but not always) possible to allocate charges by machine. In cases with metals it’s usually impossible to do a good job. The molecule in questions is:
The molecule itself is neutral. The easiest way is not to put any charges. Anything else in uncomfortable. We can have + charges on the N’s which is natural, but then there are 2 – charges on the CU. That’s formally correct but since the mertal is usually described as Cu(II) it’s not happy. Or we can play around with thearomaticity, or dissociate the Cu-N or C-O bonds but that’s not happy either. And this is simple compared with may metal structures.
What we have been doing is to disoociate the metal, do the aromaticity and charges, and then add the metal back. In doing so it’s easy to forget the charges and that is what has happened. We’ll try to fix it.
But in the end the only thing that matters is the total electron count and the spin state (which normally isn’t given except in the text). Cu2+ is d9 so it has one unpaired electron. But Fe is much more difficult and it’s virtually impossible to do anythig automatic. We’ll probably simply leave the charges off…