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Why doesn't MoleculePlot show AgNO3 ?


(* IUPAC name: silver nitrate. Mathematica shows the 2d (iupac style) diagram but not 3D *)

In[3]:= ChemicalData["AgNO3", "MoleculePlot"]

Out[3]= Missing["NotAvailable"]

ChemicalData["HNO3", "MoleculePlot"] (* WORKS *)

(* is it just not in (small) database, database didn't download correctly, are metal to oxy-polyatomic ion not in data base? In other words is there something like "only organic chemistry is supported" limitation i'm not made aware of yet? *)

POSTED BY: John Hendrickson
14 days ago

I also get (is it just me?) ChemicalData["NO3"] is "not defined" but NO2 is defined. (both are common as pie in my chem 101 book)

I'm wondering how one would (best) use a system having simple things not yet complete? Is one supposed to "alter the .m or paclet" to include such minors mathematica doesn't have? Or is my MM install not working? (i might be asking this to bump the post). Are some people getting paclets that don't have this missing data?

11.3's chemistry certainly far superior to previous versions, of course.

POSTED BY: John Hendrickson
13 days ago

@John Hendrickson the reason there isn't a 3D plot for silver nitrate is that there are no 3D coordinates. You can check this via

In[99]:= ChemicalData["AgNO3", "AtomPositions"]

Out[99]= Missing["NotApplicable"]

One of the sources we use for ChemicalData is PubChem, which has 3D structures for millions of compounds - but not for silver nitrate, because it is a salt. The "MoleculePlot" property really is best suited for connected structures.

Regarding "NO3" - ChemicalData doesn't actually have any ions, only neutral molecules, and so "nitrate" isn't to be found.

Hope that helps

POSTED BY: Jason Biggs
12 days ago

To "plot" AgNO3 you have to plot a crystal-lattice with Ag+ cations and NO3- Anions. There is not such a thing like a "molecular plot". As Jason said: it is a salt !

POSTED BY: Hans Dolhaine
11 days ago

Thank you. I think you told me enough to understand how to best think of and use the data in this respect.

I'm playing with the idea that 3D "molecular plot" is intended to be a 3D representation of "Nomenclature of Organic Chemistry" (CRC) (so that non-planar molecules can be seen easier than they can be in the associated 2D chart). I'm unsure of this. (but this section contains many rules and abbreviations of chart that have nothing to do with bond angle or 3D structure: abbreviations useful for those saving paper as well as some that are for bond abbreviatons)

But According to new iupac pdf on graphical representation: what kind of bond isn't always specified but should be consistent - which i consider awful. (but that short document mentions salts are "non-structural" and ions are best kept separate rather than connected in the 2D graph).

I see "Everything has it's place", in this "historic 2D annotation model", is not true.

Thanks you answered my question. I see now Mathematica is doing "what is generally expected". It'll be much easier to navigate around knowing that.

POSTED BY: John Hendrickson
11 days ago

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