I can’t find a tool to link two specified atoms together with a bond. The draw tool doesn’t seem to do it, and the bond-centric tool requires an existing bond.
Here is an example of what I want to do. If I wanted to make a benzene ring , I should be able to start with cis-hexa-1,3,5-triene, planarize it if necessary, remove the two endo hydrogens at C1 and C6, and draw a bond between C1 and C6. This should give a benzene ring.
Now, I know you can just insert benzene in the build menu or insert a phenyl group in the template tool, but I need to be able to change arbitrary pairs of adjacent carbon atoms into a benzene ring, in order to make something like hexacene or Clar’s hydrocarbon. Is this possible?
I did have to use Build => Bond => Bond Selected atoms, because dragging from one atom to another in the Draw tool often creates a new methyl group in front of or behind the other atom, instead of making a bond to that atom.
@davidshobe While constructing the molecules with a mouse, the selection of the atoms of interest can be facilitated with a quick i) reset of the molecule’s position (view → center), ii) a pivot and iii) adjustment of scale (via the gimbal / navigation icon, either moving the mouse while left mouse button is pressed, or using the scroll wheel [if accessible]), iv) pan/move of the scene. To drag individual atoms (by the hand icon) equally can be an option to increase access of the atoms eventually to be connected. Then continue with the construction of the molecule (pen / draw tool).
