SpaceFillingMolecularPlot using CAS number of a compound

Question

When I tried to get 3D graphics for the molecule with CAS number 52364-73-5 using Mathematica 10, it produced the following result:

ChemicalData["CAS52364-73-5", "SpaceFillingMoleculePlot"]

Missing["NotAvailable"]

but it makes a plot for caffeine:

ChemicalData["Caffeine", "SpaceFillingMoleculePlot"]

How can I get a structural diagram for my compound?

Answer 1

added 4/26/2020

Molecule[] + MoleculePlot3D[] can now do this directly in version 12.1:

MoleculePlot3D[Molecule["CAS52364-73-5"], PlotTheme -> "Spacefilling"]

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Original answer

Since the compound of interest does not have the required 3D structure within ChemicalData[], we must look for other sources. One possibility is to use the CACTUS Chemical Identifier Resolver, which can take e.g. a SMILES string and output a *.mol file that can the be displayed in 3D.

Generate the SMILES string:

smiles = ChemicalData["CAS52364-73-5", "SMILES"]
   "CCCCCCCCOC1=CC=C(C=C1)C2=CC=C(C=C2)C#N"

Here is a little routine that retrieves (or tries to) the corresponding *.mol file from CACTUS:

CactusGet[arg_String, opts___] := Import[StringTemplate[
      "https://cactus.nci.nih.gov/chemical/structure/`spec`/file?format=sdf&get3d=true"] @
      <|"spec" -> StringReplace[If[StringMatchQ[arg, "InChI*"], arg, URLEncode[arg]],
                                "+" -> "%20"]|>, "MOL", opts]

Here goes:

CactusGet[smiles, "Rendering" -> "Spacefilling"]

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Of course, not all known compounds are in CACTUS; one might then try to write routines for retrieving data from e.g. ChemSpider or PubChem.

Luckily, ServiceConnect[] and ServiceExecute[] allow one to access these sources directly from within Mathematica.

In the case of ChemSpider, you will need to register to obtain a security token, which Mathematica will prompt you for when you first use the service.

After doing that, you can then use this:

GetChemSpider[str_String, opts___] := Module[{res}, 
   res = ServiceExecute["ChemSpider", "Search", "Query" -> str] @ "ID"; 
   If[! FailureQ[res], 
      Import["http://www.chemspider.com/FilesHandler.ashx?type=str&3d=yes&id=" <> res,
             "MOL", opts], $Failed]]

I'll use some examples that are a bit more interesting than the one in the OP:

GetChemSpider[#, "Rendering" -> "Spacefilling"] & /@
{"4493-23-6", "4368-28-9", "1256580-46-7"} // GraphicsRow

For PubChem, you can query with CAS numbers like so:

ServiceExecute["PubChem", "CompoundSDF", {"Name" -> "138261-41-3"}]["Graphics3D", 1]

but as you can see, the result returned is "fake 3D"; this is probably a problem on PubChem's end, tho.

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Still another possibility presents itself if you happen to have OpenBabel also installed on your computer. Here's how to use OpenBabel's conversion capabilities from within Mathematica:

OpenBabelStructure[arg_String, opts___] := 
    ImportString[RunProcess[{"obabel", If[StringMatchQ[arg, "InChI*"], "-iinchi", ""], 
                             "-:" <> "\"" <> arg <> "\"", "-omol",
                             "--gen3d", "-c", "--minimize"}] @
                 "StandardOutput", "MOL", opts]

(See this for information on the command line options used.)

Using the same example as the CACTUS one:

smiles = ChemicalData["CAS52364-73-5", "SMILES"];
OpenBabelStructure[smiles, "Rendering" -> "Spacefilling"]

Answer 2

The information you ask for is simply not in Wolfram's curated database. The following works

ChemicalData["CAS52364-73-5", "CHBlackStructureDiagram"]

showing that queries on molecule CAS52364-73-5 are possible. My conclusion is that the 3D structure data needed to satisfy your query is not in the database.

I verified my conclusion by doing an Wolfram|Alpha query from Mathematica.