Rotatable bond count in JChem for Excel

User d190c185e7

11-02-2013 15:44:40


I am working with JChem for Excel (version and I have a used the chemical function "JCRotatableBondCount" to evaluate a series of compounds (such as the one attached).

was wondering how the rotatable bonds are calculated, since the number of rotatable bonds calculated for the attached compound is 1 according to JChem for Excel, but according to the criteria established by Veber in his original article (i.e. "Rotatable bonds were defined as any single bond, not in a ring, bound to a nonterminal heavy (i.e., non-hydrogen) atom. Excluded from the count were amide C-N bonds because of their high rotational energy barrier") it seems that the number of rotatable bonds would be 3 (two single C-O bonds and one single C-C bond).

Are not the single C-O bonds in this compound counted by JChem? Why? Which is the rotatable bond found by JChem?

Thanks in advance.



ChemAxon bd13b5bd77

11-02-2013 19:06:08

Hi Rosa,

we are investigating the issue. Attila will be back to you soon.



ChemAxon 7fa93bc77d

12-02-2013 09:58:14

Hi Rosa,

I tried to apply the Veber rules to your structure. It says count only single bonds  as rotatable which are:

So, there is only one bond fulfils Veber's rotatable bond definition which is the C-N bond connecting the two rings.
I attached a structure in which I removed all aliphatic single bonds except the C-N one. Here you get 1 rotatable bond too.

I hope it helps!


User d190c185e7

12-02-2013 10:41:03

Thanks Attila and Viktor! Now I've realized the reason why I was confused...