Resonance bond rendering differs from Java/PubChem

[arouinfar]

For phetsims/qa#538 and possibly related to #151.

Occasionally, a double bond is rendered as a single bond in the ball-and-stick representation. Here are a few instances:

Molecule	Sim	PubChem 3D
Phosgene
1,1-dicholoroethylene/vinylidene chloride
acetic acid methyl ester/methyl acetate

These structures are regular neutral molecules (not ions or radicals) so I'm not sure why the double bonds are incorrectly rendered.

[arouinfar]

@Denz1994 these structures are correctly rendered in the Java sim.

[arouinfar]

@Denz1994 I tested several older dev versions, and it doesn't appear to be a new issue. It existed in dev.50 (post- #151) and dev.40 (pre- #151).

[arouinfar]

I think I've figured it out. These molecules have resonance bonding, which means there is a delocalized electron. The most probable location for that electron would be where PubChem shows a double bond.

A classic example of a molecule with resonance bonding is benzene. PubChem shows double bonds in its 3D rendering

I no longer think this is a bug, so I will close this issue and add a note about resonance structures to the Teacher Tips.

[arouinfar]

On second thought, I am going to reopen and defer. It would be nice to understand the difference between the Java and HTML5 behavior, but it should not impact publication.

[oliver-phet]

A user report this behavior:

3d image of propionic acid does not show double bond between C and O in carboxyl group

[oliver-phet]

Another user reported:

Playground mode - Acetone does not show the double bond between oxygen and carbon.