I just bought a molecular modeling kit for my toddler ("Snatoms").

To use the kit to play with her, I want to start out by memorizing a list of all molecules (isomers) fitting these criteria:

  • only contains C, H, and/or O
  • contains a maximum of 6 atoms

I started out by noodling around with Lewis diagrams and wikipedia... but then I ran into the various isomers of C2H2O2:

isomer Lewis diagrams from https://en.wikipedia.org/wiki/C2H2O2

I wanted to do this search on a chemical database (like chemspider.com) but I couldn't find a criterion that would filter the search by number of atoms in the molecule (isomer).

Is there a name for this "number"?

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    $\begingroup$ For molecules of an element, it's called the “atomicity,” and from a bit of web searching, it looks like that word (also terms like “hexatomic”) is sometimes applied to non-elemental compounds as well. $\endgroup$ – Steve Kass Nov 13 '17 at 0:49
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    $\begingroup$ Are you only interested in structures that are real chemicals, or do you want to include all possible ways of connecting the atoms? That is, do you also want very chemically unlikely compounds that will not be in a database? $\endgroup$ – gilleain Nov 13 '17 at 16:55
  • $\begingroup$ @SteveKass thanks much! Certainly that should be the answer. As helpful as SteffX's answer was, I would "accept" your "answer" if you added one for the sake of site conformity. $\endgroup$ – stevenbhardwaj Nov 14 '17 at 3:54
  • $\begingroup$ @gilleain thanks for your interest! For the didactic purpose at hand, I was thinking that I would want to list and memorize any chemical compound with enough relevance and existence to have a reasonably canonically accepted name in English. I wanted to make the list as best I could myself, before asking the question you are describing on the stackexchange, as a separate question. But feel free to ask it yourself in the meantime if you're curious now! $\endgroup$ – stevenbhardwaj Nov 14 '17 at 3:58

The "number of atoms"'s name is... the number of atoms. I am not aware of any special word for that. Databases may not let you search/filter that kind of criterion, i.e. the total number of atoms, but usually let you search by "chemical formula" which is, in your case, C2H2O2.

I have just tried with Chemspider by typing "C2H2O2" in the search box and it disappointingly gave me just 3 results, i.e. glyoxal (OHC-CHO, not in your list), 42879-41-4 and 16005-17-7.

DID YOU KNOW? Just to expand the scope, did you know that the last digit in CAS# is actually a check digit? It helps any software checking that you did not mistyped the number.

  • $\begingroup$ Interesting idea -- thanks! I guess I can try some different databases and exhaustively search all the different combinatorically possible molecular formulas. I suppose that might work, but as you noted, with that method, ChemSpider doesn't even report all the isomers that wikipedia's image seems to identify. I guess I'll let the question stand for a little while in case someone comes up with a jargon term before I accept the "negative result". :) Three cheers for negative results in academic literature though!!! $\endgroup$ – stevenbhardwaj Nov 12 '17 at 17:20
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    $\begingroup$ I would recommend PubChem as a database. Unfortunately, I just tried it and the results are more than poor 😩 with their online interface. I am sure it can be helpful, but you would need to look at advanced search. $\endgroup$ – SteffX Nov 12 '17 at 17:32
  • $\begingroup$ Awesome! So PubChem seems to do pretty well. I typed in C2H2O2 and it gave me 978 results... seems that asks for any molecule including at least 2 carbons, 2 hydrogens, 2 oxygens. But after filtering those by the molecular weight of C2H2O2, got down to 17 results, of which 13 aren't ions. It's a little more effort than I imagined it'd be, but no pain, no gain I guess! $\endgroup$ – stevenbhardwaj Nov 12 '17 at 18:03
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    $\begingroup$ Glyoxal is in the asker's picture, see top middle, has number 107-22-2. $\endgroup$ – Jeppe Stig Nielsen Nov 12 '17 at 18:31

So this addresses the part about going from (number of atoms, element symbols) -> set of structure spaces. For this case, the input is (6, "CHO").

The steps I would go through are:

  1. List all the (weak?) compositions of 6 - e.g. [3, 2, 1], [2, 3, 1], [2, 2, 2], ...
  2. Turn each of these into a formula like C3H2O, C2H3O, C2H2O2, ...
  3. List all the structures with that formula

Of course, step 3 might involve looking them up in a database to see if they are real structures or not.

For step 1, a 'composition' is a breakdown of a number into parts (like a partition) but where the order matters. So [3, 2, 1] is not the same as [2, 3, 1]. A weak composition allows zeros, so you can have [3, 3, 0] which means C3H3 - but that depends on whether you want to include all atoms or not.


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