A while back I got this question
”I’m about to hit the tedious part of writing my chemistry PhD thesis in Microsoft Word: having all mentioned compounds numbered in text and in the chemdraw imported files. My question: is there any automated option for this task or do I have to insert every number manually? In particular renumbering after adding a new compound in the middle of the text”
There are a couple of ways to do this in LaTex (http://www.jkwchui.com/2010/03/writing-chemistry-with-latex-33/) and (http://piti.exroot.org/konwerter/) but in my experience LaTex is not particularly popular among chemists. However help is at hand, I’ve just been sent details of a brilliant applescript that works with ChemBioDraw and Word.
The process is described in detail here (http://www.martinp23.com/blog/2013/03/chemdraw-and-word-compound-numbering-on-mac/) so I won’t give anymore details just to add that one thing I’ve been using in recent Chemdraw scripts is
tell application id "com.cambridgesoft.ChemDraw"
It avoids the problems with application naming with different versions of Chem(Bio)Draw Std/Pro/Ultra.
There are many more applescripts here.