1
$\begingroup$

I am looking for a small molecule where an $\mathrm{sp^3}$ atom from Group 16 (O, S, Se,...) is connected to an $\mathrm{sp^2}$ or resonant atom of another column?

Background: The universal force field defines the above case in its torsion rules and I would like to find an example/application of such a structure to understand it better.

Thanks!

$\endgroup$
  • $\begingroup$ You mean something like phenol? $\endgroup$ – Geoff Hutchison Jan 25 '18 at 0:17
  • $\begingroup$ @GeoffHutchison That was actually my first thought, too. But oxygen within phenol is considered to be $\mathrm{sp^2}$-hybridized, right? The original UFF paper (Rappé et al, 1992) states: "For a single bond involving a sp3 atom of the oxygen column and an sp2 or resonant atom of another column, eq 17 is used directly. For this case the periodicity (n) is 2 and the equilibrium angle do is $90^\circ$." I think that the equilibrium angle $90^\circ$ is wrong and that is why I was looking for an example. $\endgroup$ – Andi Jan 25 '18 at 3:44
  • $\begingroup$ I actually used the implementation in Open Babel to check when this rule is triggered which is not the case for phenol. I could only find the single bond in benzenesulfonic acid which is technically d2sp3?! In the meantime I found that towhee and Gulp are using $180^\circ$. At last, I discovered the deMonNano documentation which explicitly mentions this error. $\endgroup$ – Andi Jan 25 '18 at 3:44
  • $\begingroup$ The examples below by permeakra make sense to me (no chemist), but they are too complex for the SMARTS matching/atom typing in Open Babel and hence don't trigger the rule as well. Moreover, my experiments showed that using $90^\circ$ or $180^\circ$ does not really make a difference, since the torsional barrier height is rather low. So I conclude that it is probably a niche case that was included for completeness. [PS: I plan to submit patches to Open Babel, will take some time to assemble my findings.] $\endgroup$ – Andi Jan 25 '18 at 3:45
  • $\begingroup$ @Andi there is no simple molecules matching your requirements since, indeed, oxygen enters conjugation readily. And honestly, exhaustive enumeration of all possible cases for general use is futile, it would be best to print inferred atom types and let the user to override misdetected types by hand from the command line. $\endgroup$ – permeakra Jan 25 '18 at 6:10
0
$\begingroup$

Out of the blue, consider triphenyloxonium cation. It is non-planar thanks to bulkiness of the phenyl groups.

Another possible example is mono-epoxide of allene. Considering oxygen atom as $sp^2$ here is unconvincing since it would involve huge angular strain, much higher than for a structure with $sp^3$ oxygen.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.