Bond angles

Another shortcoming of shortcut groups is the bond angles upon expansion. For example, when a CN group is expanded, the C has a 120 degree bond angle, but the triple bond should clue you in that it should be 180 degrees. And the NO₂ group when expanded shows a N with two 90 degree bond angles, though they should be 120 degrees. (The pentavalency of that N is an issue for another day.)





Also, sometimes when a shortcut group is expanded, the atoms are placed on top of other atoms. For example, draw biphenyl with the Ph-Ph bond horizontal, then put a CO₂Me group on the upper ortho position of the right-hand ring, then expand it. The CH₃ of the CO₂Me group ends up on top of the upper ortho C atom of the left-hand phenyl ring. Could you calculate to see whether the expanded atoms are going to be placed on top of other atoms and, if so, put them somewhere else?





Finally, when adding H atoms, all the H atoms are added at 90 degree angles to one another, which means they often overlap with other H atoms. Can you add them at 60 degree angles instead?

We are enhancing the algorithm used for the coordinate calculation of ungrouped atoms, thus, you can expect improvements in a short time. However, placing atoms in limited space (like ortho substituted biphenyls) may result crowded layouts, especially when you also have explicit hydrogens. But I agree, overlapping atoms should be avoided.





Regarding the addition of explicit hydrogens: please explain the problem in more details. I attached an image of a simple example, which seems OK.

Here's an example. Even in your example, the 90 degree H-C-H bond angles look bad, particularly at the CH3 groups.

You are right, we will improve it soon!