• Question: Why the bonds or trajectories between the non-bonded atoms in the AIM molecular graph is not straight?

    Asked by anon-198476 to Alex on 15 Mar 2019.
    • Photo: Alexander Allen

      Alexander Allen answered on 15 Mar 2019:


      I mean a fantastic question…I love it – mostly because the wording is so distinct that I can put it into google and find an exact copy of this question on ResearchGate… The problem was you didn’t include the particular model that they referred to so I needed to find the actual image. Now I’ve found it – I’ll aim to give you an answer, that may be wrong but it’s my best guess.

      Here is the image:

      And as a good scientist I should point out that this is courtesy of Soares, B. et al (2014) J. Braz. Chem. Soc., Vol. 25, No. 4, 629-638
      With the title:
      Experimental and NMR Theoretical Methodology Applied to Geometric Analysis of the Bioactive Clerodane trans-Dehydrocrotonin

      Molecules are networks made up of atoms and here we see a framework of atoms connected in a structure. The problem is that in simple molecules we see a 2D structure because all the molecules are lying flat together. More complicated molecules are not flat and some parts come toward or away from the plane that the diagram is drawn in. There are lots of ways of trying to communicate the fact that the particular bond should come OUT OF THE PAGE in a correct drawing.

      I BELIEVE though I’m not sure – that this is simply the authors way of showing that these particular bonds are coming out of (or going into) the page.

      Real molecular bonds are always straight – there’s no such thing as a curvy bond.

      Also massive points for this question!

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