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If you look up the above CAS numbers, you will sometimes find this structure:

enter image description here

which, I think correctly, our chemistry validation software tags as 'bad valence'.

In other websites you will find the structure without any bond between N and B:

https://www.chemspider.com/Chemical-Structure.22439675.html?rid=0012f539-17bd-4c38-b4eb-410b3a14bd7a

enter image description here

or some with fancy 'dative' bonds:

enter image description here

or some with charges on B and N:

enter image description here

What representation, if any of the above, or some other, is the 'recommended' one for this kind of compound?

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  • $\begingroup$ out of curiosity, what is "our chemistry validation software"? $\endgroup$
    – Andrew
    Feb 20 at 12:27
  • $\begingroup$ In this specific case, Biovia's/3DS' Pipeline Pilot. But even ChemDraw will tag B and N as problematic if I don't put the charges on. $\endgroup$ Feb 20 at 17:55
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    $\begingroup$ On a side note, I would really like to know what the downvoters had to object to my question. It is based on a real life case; I am a professional cheminformatician who is asking a group of people with chemistry knowledge for advice on structural representation standards. If anyone has got problems with that, please come forward and justify your negative reaction. I've always found absolutely infuriating this vile, cowardly, completely moronic downvoting people indulge in, behind the anonymity that's unfortunately still offered by StackExchange. Either contribute or be gone already(!) $\endgroup$ Feb 20 at 18:05

1 Answer 1

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These are so-called N-methyl-iminodiacetic acid (MIDA) boronates. They were first prepared in 1986 (ref. 1) and started becoming popular after 2007 due to their use as protected boron functionalities. (ref. 2)

There is ample evidence that the B-N bond exists and is very strong, with a typical bond energy of >120 kJ/mol. Many crystals of MIDA boronates have been obtained, directly showing short B···N distances of around 1.6 Å, much smaller than the sum of the van der Waals radii of the atoms and consistent with a covalent B-N single bond. This is true in alkyl, alkenyl, alkynyl and aryl MIDA boronates.

(Visualization of a MIDA boronate structure based on crystallographic data from ref 1. Boron atom shown in pink, nitrogen atom shown in blue.)

Furthermore, NMR spectroscopic data also indicates the presence of the B-N bond in solution, and not only in the solid state. 1H-NMR data of MIDA boronates show two magnetically inequivalent proton signals for the methylene hydrogens next to the carbonyls with a typical geminal coupling constant of 15-18 Hz, meaning they do not interconvert due to restricted motion (i.e. formation of the bicyclic cage). This remains the case even at 125 °C in solution, from which lower bounds on activation energy for B-N bond scission could be established. 11B-NMR and 10B-NMR measurements can also be performed, and the boron shifts (ca. +10 ppm for 11B, relative to the $\ce{BF3.Et2O}$ standard) are consistent with tetracoordinate boron with a negative formal charge.

(Magnetically-inequivalent methylene protons in a MIDA boronate in MeCN-d3 solution, from ref. 1)

With these data in mind, the structure without any B-N bond is outright incorrect. The structure with a dative bond is also technically incorrect, because dative bonds are a deprecated concept, as they are indistinguishable from a standard covalent bond. This leaves the first and last structures you show, and both are arguably correct, as the formal charges are implicit even if not drawn.


References:

(1): Mancilla, T.; Contreras, R.; Wrackmeyer, B. New bicyclic organylboronic esters derived from iminodiacetic acids. J. Organomet. Chem. 1986, 307 (1), 1–6 DOI: http://dx.doi.org/10.1016/0022-328X(86)80169-3

(2): Gillis, E. P.; Burke, M. D. A Simple and Modular Strategy for Small Molecule Synthesis: Iterative Suzuki−Miyaura Coupling of B-Protected Haloboronic Acid Building Blocks. J. Am. Chem. Soc. 2007, 129 (21), 6716–6717 DOI: http://dx.doi.org/10.1021/ja0716204.

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  • $\begingroup$ Thanks! A very comprehensive and knowledgeable answer. I am just puzzled by the sentence "the formal charges are implicit even if not drawn". No chemistry drawing or validation software I have ever used professionally accepts structures where a nitrogen atom has 4 bonds and no charge on it. So if I had to choose I would at least put the charges on, not because I particularly insist on that, but because otherwise our software rejects the molecule :D $\endgroup$ Feb 20 at 17:54
  • $\begingroup$ Yeah If I had to pick one correct answer then it would be with the formal charges. The software complains because it can't be sure you drew what you wanted, it needs to call the error in order to cover other situations where you actually may have incorrect bonding. In a sense, the structure with the implicit charges is "human-readable but not machine-readable". $\endgroup$ Feb 20 at 21:05
  • $\begingroup$ I see... OK so I will change the representation in our system to the one still with the B-N bond, but with the required charges. Thanks again for looking into this! $\endgroup$ Feb 21 at 6:58

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