Why does the Dative bond type only affect the valence of the end atom? #7261
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jasondbiggs
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Like many users of the RDKit I am not overly familiar with coordinate-covalent bonds or organometallic compounds in general, except that they are a class of compounds I need to turn off sanitization to work with. In recent versions of the RDKit I notice that the automatic cleanup will convert some bonds between metals and nonmetals into dative bonds, and that this in general leads to fewer valence errors.
But I don't really understand how the valence accounting is done with dative bonds. As I understand it, they are like a normal 2-electron single bond except both electrons come from one atom. But the RDKit documentation says
I would have thought the dative bond would affect both atoms, albeit in different ways. What is the rationale behind this? Are the electrons from the start atom still effectively a lone pair?
And how can I use dative bonds to represent the common example of an ammonia boron trifluoride aduct? The SMILES strings
'[NH3]->[B](F)(F)F'
and'[NH3]<-[B](F)(F)F'
both fail with valence errors, but the charge-separated form'[NH3+]-[B-](F)(F)F'
needs no dative bonds at all.Beta Was this translation helpful? Give feedback.
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