Hi I'm not sure but there might be an issue with displaying organic molecules that have some 3d structure. They are not the same as the images on e.g. wikipedia, here some examples:
https://en.wikipedia.org/wiki/Octanitrocubane https://en.wikipedia.org/wiki/Twistane also a large dissimilarity https://en.wikipedia.org/wiki/2.2.2-Propellane https://en.wikipedia.org/wiki/1.1.1-Propellane https://en.wikipedia.org/wiki/Bicyclo(1.1.1)pentane https://en.wikipedia.org/wiki/Adamantane displays some CH_2 https://en.wikipedia.org/wiki/Iceane I don't know how you'd render that https://en.wikipedia.org/wiki/Cubane
I've also filed this issue to https://github.com/lambdacasserole/avogadrio/issues/30 where I originally stumbled upon this.
Can you improve on this?