Explicit bonds between metal and hydrogen atoms must be kept

[gblanke02]

The current InChI releases including the development release (status version 1.07.4) delete any explicit terminal hydrogen atoms bound to a metal atom and keep the information in the /h layer.

Example: hydrido(dimethyl)iron: InChI=1/C2H7Fe/c1-3-2/h3H,1-2H3 with atom 1 and 2 as C, and atom 3 as Fe

To identify the stereochemistry of molecular inorganic compounds, any H atom directly bound to a metal atom must be kept, has to undergo the canonicalization process and must be listed in the connectivity string
Expected
InChI=1/C2H7Fe/c1-4(2)3/h1-2H3
With atom 1 and 2 as C, atom 3 as H and atom 4 as Fe. Note that the /h layer is adapted accordingly.

hydrido(dimethyl)iron
  ACCLDraw11182517382D

  4  3  0  0  0  0  0  0  0  0999 V2000
    6.0938   -6.6250    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    7.1166   -6.0344    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0709   -6.0344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0938   -7.8061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
M  END

iron_trihydride
  ACCLDraw11182517552D

  4  3  0  0  0  0  0  0  0  0999 V2000
    6.0938   -7.8061    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0709   -6.0344    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1166   -6.0344    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0938   -6.6250    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
M  END

Note: In case of metal hydrides like iron trihydride FeH3, the current implementation is sufficient as the connectivity string is not created: InChI=1/FeH3/h1H3.

[gblanke02]

Explicit bonds between one H atom and two metal atoms are already kept. B-H-B systems are handled as well. In both cases, the H atom gets an canonical atomnumber, is listed in the connectivity string and does not occur in the /h layer.

[schatzsc]

@gblanke02

To identify the stereochemistry of molecular inorganic compounds, any H atom directly bound to a metal atom must be kept, has to undergo the canonicalization process and must be listed in the connectivity string Expected InChI=1/C2H6ClFe/c1-4(2)3/h1-2H3 With atom 1 and 2 as C, atom 3 as H and atom 4 as Fe. Note that the /h layer is adapted accordingly.

The sum formula of your expected InChI example is not correct - with two methyl groups and a metal-coordinated hydrido ligand, it should be:

InChI=1/C2H7Fe/c1-4(2)3/h1-2H3

2x CH3 + 1x FeH = 6+1 = 7 H

And where is the Cl in your example coming from???

[schatzsc]

@gblanke02

Explicit bonds between one H atom and two metal atoms are already kept.

It actually does not matter if the two "other" atoms are metal or not - any bridging H atoms (those with coordination number/"actual valence" larger than one) of the type X(µ-H)X' must be kept, regardless which elements X and X' are.

[gblanke02]

Lieber Uli, Den Fehler hatte ich bislang nur auf den Folien korrigiert. In GtHub war ich noch nicht dazu gekommen. Vielen Dank, dass Du mich daran erinnert hast. Warum Cl? Ich brauchte die richtige Atomnummer für das H, damit der Connectivity String korrekt wird, obwohl es ein Mockup ist. Viele Grüße Gerd Von: Ulrich Schatzschneider ***@***.***> Gesendet: Donnerstag, 27. November 2025 15:39 An: IUPAC-InChI/InChI ***@***.***> Cc: ***@***.***; Mention ***@***.***> Betreff: Re: [IUPAC-InChI/InChI] Explicit bonds between metal and hydrogen atoms must be kept (Issue #168) [https://avatars.githubusercontent.com/u/88166560?s=20&v=4]schatzsc left a comment (IUPAC-InChI/InChI#168)<#168 (comment)> @gblanke02<https://github.com/gblanke02> To identify the stereochemistry of molecular inorganic compounds, any H atom directly bound to a metal atom must be kept, has to undergo the canonicalization process and must be listed in the connectivity string Expected InChI=1/C2H6ClFe/c1-4(2)3/h1-2H3 With atom 1 and 2 as C, atom 3 as H and atom 4 as Fe. Note that the /h layer is adapted accordingly. The sum formula of your expected InChI example is not correct - with two methyl groups and a metal-coordinated hydrido ligand, it should be: InChI=1/C2H7Fe/c1-4(2)3/h1-2H3 2x CH3 + 1x FeH = 6+1 = 7 H And where is the Cl in your example coming from??? — Reply to this email directly, view it on GitHub<#168 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AT3EDCKEKLPLX5ARUCPY5I3364EHLAVCNFSM6AAAAACMPJ7LWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKOBWGIYTKMZTGQ>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[gblanke02]

Yes you are right, but this issue is focused to explicit H atoms only. We do not have to test any other atom types for this case. Von: Ulrich Schatzschneider ***@***.***> Gesendet: Donnerstag, 27. November 2025 15:41 An: IUPAC-InChI/InChI ***@***.***> Cc: ***@***.***; Mention ***@***.***> Betreff: Re: [IUPAC-InChI/InChI] Explicit bonds between metal and hydrogen atoms must be kept (Issue #168) [https://avatars.githubusercontent.com/u/88166560?s=20&v=4]schatzsc left a comment (IUPAC-InChI/InChI#168)<#168 (comment)> @gblanke02<https://github.com/gblanke02> Explicit bonds between one H atom and two metal atoms are already kept. It actually does not matter if the two "other" atoms are metal or not - any bridging H atoms (those with coordination number/"actual valence" larger than one) of the type X(µ-H)X' must be kept, regardless which elements X and X' are. — Reply to this email directly, view it on GitHub<#168 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AT3EDCK26PPXRWYBTOKT3C3364EPBAVCNFSM6AAAAACMPJ7LWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKOBWGIZDOMRSGU>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

[gblanke02]

Any bridging H atoms (those with coordination number/"actual valence" larger than one) of the type X(µ-H)X' are kept already, but the atom numbers are the highest in the list, i.e. the H atom numbers of the type "X(µ-H)X" are counted from the highest atom number of the non H-atoms and are not listed in the /h layer.
To keep the approach equivalent for explicit H atoms bound to (one) metal atom they have to get the highest atom number positions. For our example above that means tah the explcit H atom gets the highest atom number:
InChI=1/C2H7Fe/c1-3(2)4/h1-2H3

[gblanke02]

The following 2 structures represent a Th complex where the two Th atoms are bridged by H atoms twice while each Th atom gets an additional H atom and 2 cyclopentadeiney rings.
The original example has been found in Reaxys whie teh second one is drawn by using the haptic bonds of Biovia/Draw

The 3rd example represents a Ru complex that has got H2 bound described by a haptic bond. The resulting INChI is calculated as : InChI=1B/H12O5Ru/c1-6(2,3,4,5)7-8-6/h1-5H2 with atom numbers 7 and 8 as explcit H atoms.

inchi3 org - Biovia - haptic adapted.mol.txt
inchi3 org.mol.txt
Ru(OH2)5H2 - Hydrogen complex.mol.txt

The following exmple contans metal-hydrogen atom bonds but handles all H atoms in the hydrogen layer.
H2PtNH2.mol.txt

[schatzsc]

@gblanke02

Is that the intended behaviour to keep the terminal hydrides in the /h layer?!?

For H2PtNH2.mol.txt the InChI is

InChI=1B/H5NPt/c1-2/h2H2,1H3

I have no problem with that - but is there a consistent treatment, like all bridging H in the /c layer and all terminal H in the /h layer, regardless if they were explicitly defined in the molfile or implicitly calculated?

[schatzsc]

@gblanke02

I also tried the ruthenium complex [Ru(H2)(H2O)5] which has the expected 12H count - but I'm a bit confused about the structure display in the lower right. Is it intentional that there are three white "spheres" shown - with the central one presumably the "* pseudo atom"?!? If that is indeed the case, it should be displayed differently from the hydrogen atoms.

Also, something does not seem to be right with the /c layer:

InChI=1B/H12O5Ru/c1-6(2,3,4,5)7-8-6/h1-5H2

It appears to me when you select the "canonical index" that the node number #6 is incorrectly assigned to the "* pseudo atom" and not one of the oxygen atoms, among which one remains un-labelled.

The canonical labels are: O1, O2, O3, O4, Ru5, H7, H8

Label #6 is on the "third white sphere" and one O has no canonical label at all - looks like an indexing problem

[gblanke02]

@gblanke02

Is that the intended behaviour to keep the terminal hydrides in the /h layer?!?

For H2PtNH2.mol.txt the InChI is

InChI=1B/H5NPt/c1-2/h2H2,1H3

I have no problem with that - but is there a consistent treatment, like all bridging H in the /c layer and all terminal H in the /h layer, regardless if they were explicitly defined in the molfile or implicitly calculated?

@schatzsc
The explicit H atoms directly bound to a metal atoms must be represented in the connectivity layer because we need the atom numbers for the representation of the stereochemistry. For the numbering we should follow the H atom number ssystem of the type "X(µ-H)X".

[gblanke02]

@gblanke02

I also tried the ruthenium complex [Ru(H2)(H2O)5] which has the expected 12H count - but I'm a bit confused about the structure display in the lower right. Is it intentional that there are three white "spheres" shown - with the central one presumably the "* pseudo atom"?!? If that is indeed the case, it should be displayed differently from the hydrogen atoms.

Also, something does not seem to be right with the /c layer:

InChI=1B/H12O5Ru/c1-6(2,3,4,5)7-8-6/h1-5H2

It appears to me when you select the "canonical index" that the node number #6 is incorrectly assigned to the "* pseudo atom" and not one of the oxygen atoms, among which one remains un-labelled.

The canonical labels are: O1, O2, O3, O4, Ru5, H7, H8

Label #6 is on the "third white sphere" and one O has no canonical label at all - looks like an indexing problem

@schatzsc
Ferrocene shows a similar issue in the structure display tool. The display in the structure display tools is based on information of the auxinfo. The auxinfo keeps the original * atoms that are taken out during the determination of the InChI in case of haptic bonds. The auxinfo is not adaptedaccordingly (it has to represent the original input structure). What you see in the "discrapncy" netween the original structure and the related InChI. I create a seaparte issue for that.

[schatzsc]

@gblanke02

The explicit H atoms directly bound to a metal atoms must be represented in the connectivity layer because we need the atom numbers for the representation of the stereochemistry. For the numbering we should follow the H atom number ssystem of the type "X(µ-H)X".

Ok, so in other words the following InChI is not the proper required format:

InChI=1B/H5NPt/c1-2/h2H2,1H3

Instead, it should be something like

InChI=1B/H5NPt/c1-2(3,4)/h1H3

But will H order higher or lower than N and Pt?!?

That's also something I still find confusing - canonical numbering in the InChI is by alphabetic order of the element systems, not the atomic number?!?