ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
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butterfly diborane(4) #4387

Open K-r-ll opened 1 year ago

K-r-ll commented 1 year ago

There is a bit of confusion in the databases as for "diborane(4)" actually is. This is because the name "diborane(4)" is compositional and only tells us that it has a formula B2H4. There are two known isomers of B2H4:

In ChEBI, diborane(4) (CHEBI:38288) corresponds to H2B‒BH2. It corresponds to Gmelin 24760. Blue Book (2014) gives it a preselected name "diborane(4)" [P-68.1.1.2.1] although it makes more sense to name it substitutively "boranylborane" (this is how it is also named in PubChem:29529).

Another isomer of B2H4 has two terminal hydrogen atoms and two bridging hydrogens. It corresponds to the structure (b) of the Fig. 1 in Brandejs et al. (2019):

![diboraneb2h4](https://github.com/ebi-chebi/ChEBI/assets/66882875/e9c259e1-38f0-48a1-98e6-da7598b398e1)

Here is a 2D MOL file:

B2H4
APtclcactv05192305012D 0   0.00000     0.00000

  6  7  0  0  0  0  0  0  0  0999 V2000
    3.0004   -0.4330    0.0000 B   0  4  0  0  0  0  0  0  0  0  0  0
    3.3104   -0.9699    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5004    0.4330    0.0000 H   0  4  0  0  0  0  0  0  0  0  0  0
    2.5004    0.4330    0.0000 B   0  4  0  0  0  0  0  0  0  0  0  0
    2.1904    0.9699    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000   -0.4333    0.0000 H   0  4  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  RAD  4   1   2   3   2   4   2   6   2
M  END

Here is a 3D MOL file:

B2H4
APtclcactv05172309253D 0   0.00000     0.00000

  6  7  0  0  0  0  0  0  0  0999 V2000
    0.7917   -0.0557    0.0515 B   0  4  0  0  0  0  0  0  0  0  0  0
    1.7441    0.5379   -0.2856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7917   -0.0557    0.0515 B   0  4  0  0  0  0  0  0  0  0  0  0
   -1.7441    0.5379   -0.2856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8058    0.0012 H   0  4  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.6877   -0.5349 H   0  4  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  1  5  1  0  0  0  0
  3  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  RAD  4   1   2   3   2   5   2   6   2
M  END

It was shown to be "butterfly-shaped" [PMID: 20509694]. It could be named additively, e.g. di-μ-hydrido-dihydridodiboron(BB) or di-μ-hydrido-bis(hydridoboron)(BB) [see Red Book (2005) IR-7.3.1]. The English Wikipedia https://en.wikipedia.org/wiki/Diborane(4) mentions only the "butterfly" isomer as "diborane(4)" while referring to (CHEBI:38288). Cf. French Wikipedia https://fr.wikipedia.org/wiki/Diborane(4) which describes both B2H4 isomers, the "butterfly" one as à l'état fondamental (in the ground state) and H2B‒BH2 as à l'état excité (in the excited state).

PubMed references for "butterfly" isomer: PMID: 29861928 PMID: 21698334 PMID: 31153207 PMID: 27434758

So. I suggest to:

  1. rename (CHEBI:38288) to "boranylborane" while keeping "diborane(4)" as its IUPAC name;
  2. create another entry (CHEBI:XXX) for di-μ-hydrido-dihydridodiboron(BB)
  3. make them both is a children of a (new) entry (CHEBI:YYY) for "generic" diborane(4) which is a diborane;(CHEBI:51685) so

diborane(4) (CHEBI:YYY) is a diborane (CHEBI:51685) boranylborane (CHEBI:38288) is a diborane(4) (CHEBI:YYY) di-μ-hydrido-dihydridodiboron(BB) (CHEBI:XXX) is a diborane(4) (CHEBI:YYY)