Rotatable bond count in JChem for Excel

Hi,

I am working with JChem for Excel (version 5.11.5.906) and I have a used the chemical function "JCRotatableBondCount" to evaluate a series of compounds (such as the one attached).

I
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.

Rosa.

 

Hi Rosa,

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

Viktor

 

Hi Rosa,

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

• not in a ring: there are 4 of them: 2 C-O bonds, 1 C-C bond and one C-N bond connecting the rings


• bond to nonterminal heavy atom: C-N bond connecting the rings (the others are bound to a terminal heavy atom)

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!

Regards
Attila

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

 

Rosa.