7
$\begingroup$

Consider the following:

cacl = Molecule[{Atom["Ca"], Atom["Cl"]}, {Bond[{1, 2}, "Single"]}];
MoleculeValue[cacl, "CanonicalSMILES"]
(* Cl[CaH] *)

Notice the artificial insertion of the hydrogen atom to fill the valency of the calcium atom. I understand that this behaviour is mentioned in the official documentation:

"Hydrogen atoms may be omitted from the atom list if their presence can be inferred from the valence and bonding of the atoms present."

But is there a way to suppress this default behaviour? I want the SMILES representation of the molecule above to be Cl[Ca+], not Cl[CaH].

Improve this question
$\endgroup$
1
  • $\begingroup$ Unfortunately, there seems to be no way. I think this choice of default behaviour was a very short-sighted decision on the part of Wolfram Research. $\endgroup$
    – Shredderroy
    Commented Oct 8, 2019 at 16:34

2 Answers 2

Reset to default
5
$\begingroup$

You can use a SMILES string to create the molecule. In a SMILES string, wrapping an atomic symbol with brackets signifies that there should be no implicit hydrogens added.

mol = Molecule["[Ca][Cl]"]

enter image description here

Note that this does leave an unpaired electron on the calcium atom,

In[17]:= AtomList@mol

Out[17]= {Atom["Ca", "UnpairedElectronCount" -> 1], Atom["Cl"]}

which I think is what you are going for.

I think a reasonable way to input atoms like this would be something like 

Molecule[{"[Ca]", "Cl"}, {Bond[{1, 2}, "Single"]}]

I can make the above work for 12.1

Improve this answer
$\endgroup$
3
  • $\begingroup$ Perhaps explicitly indicating the formal charge of a specific atom might be sufficient? $\endgroup$
    – J. M.'s missing motivation ♦
    Commented Nov 17, 2019 at 22:29
  • $\begingroup$ I have accepted this because it answers the question as posed. Since you seem to be in charge of these features within Mathematica, it might be relevant to mention that what I would really like is the ability to start with the command Molecule[atoms, bonds] and have a way to suppress the automatic insertion of hydrogen atoms. I am doing some combinatorics on the graph structures of molecules, and generating SMILES only in the very end to record results. So, if Mathematica could accept a command like Molecule[atoms, bonds, InsertHydrogens -> False], that would be awesome. $\endgroup$
    – Shredderroy
    Commented Nov 18, 2019 at 16:46
  • $\begingroup$ I have something like this, try Molecule[{Atom["Ca"], Atom["Cl"]}, {Bond[{1, 2}, "Single"]}, IncludeHydrogens -> None]. From re-reading your question it seems you would like the calcium here to automatically be given a positive charge instead of a radical electron. I'm not sure if that is the right behavior for all applications. $\endgroup$
    – Jason B.
    Commented Nov 18, 2019 at 18:42
7
$\begingroup$

I imagine it's because CaCl is not a valid compound. If you want CaCl+, you can do:

cacl = Molecule[{Atom["Ca+"], Atom["Cl"]}, {Bond[{1, 2}, "Single"]}]

enter image description here

MoleculeValue[cacl, "CanonicalSMILES"]

"Cl[Ca+]"

For CaCl2:

cacl2 = Molecule[{Atom["Ca"], Atom["Cl"], Atom["Cl"]}, {Bond[{1, 2}, "Single"], Bond[{1, 3}, "Single"]}];
MoleculeValue[cacl2, "CanonicalSMILES"]

"Cl[Ca]Cl"

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.