8
$\begingroup$

Looking at, for example, the bond lengths of styrene:

Entity["Chemical", "Styrene"][EntityProperty["Chemical", "BondLengths"]]

I get a list of three bond lengths:

{Quantity[1.4, "Angstroms"], Quantity[1.4, "Angstroms"], Quantity[1.1, "Angstroms"]}

But which bonds do these represent?

I understand why there's three: carbon-carbon aromatic bonds, carbon-carbon single bonds, and carbon-hydrogen bonds.

But which number goes with which bond type?

$\endgroup$
6
$\begingroup$

When you request the "BondLengths" property,

In[18]:= Entity["Chemical", "Styrene"]["BondLengths"]

Out[18]= {Quantity[1.4, "Angstroms"], Quantity[1.4, "Angstroms"], 
 Quantity[1.1, "Angstroms"]}

you are getting the average bond length for the three "types" of bonds. These types of bonds are given by

In[19]:= Entity["Chemical", "Styrene"]["BondCounts"]

Out[19]= <|{{Entity["Element", "Carbon"], 
    Entity["Element", "Carbon"]}, 2} -> 
  4, {{Entity["Element", "Carbon"], Entity["Element", "Carbon"]}, 
   1} -> 4, {{Entity["Element", "Carbon"], 
    Entity["Element", "Hydrogen"]}, 1} -> 8|>

These properties were introduced long before Molecule and haven't been updated - they should.

If I wanted to see all the bond lengths in styrene, and know which bonds they belong to I would use the 3-argument form of BondList:

In[17]:= BondList[
 Entity["Chemical", "Styrene"], All, {"BondedAtomIndices", 
  "BondLength"}]

Out[17]= {{{1, 2}, Quantity[1.40783, "Angstroms"]}, {{1, 3}, 
  Quantity[1.39844, "Angstroms"]}, {{1, 7}, 
  Quantity[1.50116, "Angstroms"]}, {{2, 4}, ......}

where you can see exactly which bond goes with which length.

One method to visualize this would be with the resource function MoleculeValuePlot3D:

ResourceFunction["MoleculeValuePlot3D"][
 Entity["Chemical", "Styrene"], "BondLength"]

enter image description here

$\endgroup$
1
  • $\begingroup$ Would never have thought to look in BondCounts. And I had no idea I could extract bond lengths from the BondList. I see now in the BondList documentation, though, that it gives the possible properties. Thanks! $\endgroup$
    – user54038
    Sep 6 '20 at 3:23
11
$\begingroup$

There must be a better way, but here is a first pass. This method is based on [Experimental] functions, two of which are new in MMA 12, BondList and MoleculePlot3D. In MMA 12.1.0, we start by defining our molecule and obtain a list of its bonds:

mol = Molecule[Entity["Chemical","Styrene"]];
bond = BondList[mol]

(*  {Bond[{1, 2}, "Aromatic"], Bond[{1, 3}, "Aromatic"], 
     Bond[{1, 7}, "Single"],   Bond[{2, 4}, "Aromatic"], 
     Bond[{2, 9}, "Single"],   Bond[{3, 5}, "Aromatic"], 
     Bond[{3, 10}, "Single"],  Bond[{4, 6}, "Aromatic"], 
     Bond[{4, 11}, "Single"],  Bond[{5, 6}, "Aromatic"], 
     Bond[{5, 12}, "Single"],  Bond[{6, 13}, "Single"], 
     Bond[{7, 8}, "Double"],   Bond[{7, 14}, "Single"], 
     Bond[{8, 15}, "Single"],  Bond[{8, 16}, "Single"]}   *)

Examining the list above, we might be interested in atom 1, which is connected to atoms 2, 3 and 7. We can get the first atom's three bond lengths like this:

len = BondList[mol,Bond[{1,#},_],"BondLength"]& /@ {2,3,7}

(*  {{1.40783Å},{1.39844Å},{1.50116Å}}  *)

We can use the bond lengths in the plot legend of either MoleculePlot or MoleculePlot3Dto visualize which is atom 1 and which are the bonds like this:

MoleculePlot3D[mol, Bond[{1,_},_], PlotLegends -> Flatten@len]

enter image description here

The above is awkward because selecting other bonds requires changing both the atom list used to the len = statement and the bond pattern in the plot statement. A better approach is to select the bonds first as the variable sel, then get their lengths and do the plot like this:

sel = bond[[1;;3]];
len = BondList[mol, #, "BondLength"]&  /@  sel;
MoleculePlot3D[mol, sel, PlotLegends -> Flatten@len]

We can select the six aromatic bonds and find their lengths like this:

aromatic = Cases[bond, Bond[_, "Aromatic"]];
lenA = BondList[mol, #, "BondLength"] &  /@ aromatic

(*  {{1.40783Å},{1.39844Å},{1.40212Å},{1.39967Å},{1.39844Å},{1.40938Å}}  *)

Then we can select and highlight the 3 shortest of the aromatic bonds like this:

sel = aromatic[[{2, 4, 5}]];
len = BondList[mol, #, "BondLength"] &  /@ sel
MoleculePlot3D[mol, sel, PlotLegends -> Flatten@len]

enter image description here

$\endgroup$
1
  • $\begingroup$ I see. The most important takeaway is that I can get the bond lengths from BondList, I don't need to get them directly from the properties of the Chemical entity. Thanks--I'm accepting the other answer which I think communicated the information more directly, but both were helpful. $\endgroup$
    – user54038
    Sep 6 '20 at 3:21

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

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