Posts Tagged ‘above search’

A new way of exploring the directing influence of (electron donating) substituents on benzene.

Friday, April 17th, 2015

The knowledge that substituents on a benzene ring direct an electrophile engaged in a ring substitution reaction according to whether they withdraw or donate electrons is very old.[1] Introductory organic chemistry tells us that electron donating substituents promote the ortho and para positions over the meta. Here I try to recover some of this information by searching crystal structures.

I conducted the following search:
xray

  1. Any electron donating group as a ring substituent, defined by any of the elements N, O, F, S, Cl, Br.
  2. A distance from the H of an OH fragment (as a hydrogen bonder to the aryl ring) to the ortho position relative to the electron donating group.
  3. A similar distance to the meta position.
  4. The |torsion angle| between the aryl plane and the C…H axis to be constrained to 90° ± 20.
  5. Restricting the H…C contact distance to the van der Waals sum of the radii -0.3Å (to capture only the stronger interactions)
  6. The usual crystallographic requirements of R < 0.1, no disorder, no errors and normalised H positions.

The result of such a search is seen below. The red line indicates those hits where the distance from the H to the ortho and meta positions is equal. In the top left triangle, the distance to ortho is shorter than to meta (and the converse in the bottom right triangle). You can see that both the red hot-spot and indeed the majority of the structures conform to ortho direction (of π-facial ) hydrogen bonding.

benzene-xrayHere is a little calculation, optimising the position that HBr adopts with respect to bromobenzene. You can see that the distance discrimination towards ortho is ~ 0.17Å, a very similar value to the “hot-spot” in the diagram above.

benzene-HBr

This little search of course has hardly scratched the surface of what could be done. Changing eg the OH acceptor to other electronegative groups. Restricting the wide span of N, O, F, S, Cl, Br. Probing rings bearing two substituents. What of the minority of points in the bottom right triangle; are they true exceptions or does each have extenuating circumstances? Why do many points actually lie on the diagonal? Can one correlate the distances with the substituent? Is there a difference between intra and intermolecular H-bonds? What of electron withdrawing groups?

The above search took perhaps 20 minutes to define and optimise, and it gives a good statistical overview of this age-old effect. It is something every new student of organic chemistry can try for themselves! If you run an introductory course in organic aromatic chemistry, or indeed a laboratory, try to see what your students come up with!

References

  1. H.E. Armstrong, "XXVIII.—An explanation of the laws which govern substitution in the case of benzenoid compounds", J. Chem. Soc., Trans., vol. 51, pp. 258-268, 1887. https://doi.org/10.1039/ct8875100258

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σ-π-Conjugation: seeking evidence by a survey of crystal structures.

Sunday, February 3rd, 2013

The electronic interaction between a single bond and an adjacent double bond is often called σ-π-conjugation (an older term for this is hyperconjugation), and the effect is often used to e.g. explain why more highly substituted carbocations are more stable than less substituted ones. This conjugation is more subtle in neutral molecules, but following my use of crystal structures to explore the so-called gauche effect (which originates from σ-σ-conjugation), I thought I would have a go here at seeing what the crystallographic evidence actually is for the σ-π-type.

sigma-pi-conjugation

The basic two molecules are shown above; in effect propene 1 and butene 2. The latter was in fact the topic of another post, in which I attempted to show that the close H…H contact in cis-butene (2.1Å) was in effect an unwelcome consequence of the σ-π-conjugation of any of the four “outward leaning” C-H bonds of the methyl groups acting as donors (red-blue below) overlapping with the similarly “outward leaning” π* orbital of the alkene (purple-orange below; blue and purple overlap positively).

C-H/alkene interaction. Click for 3D.

NBO orbitals for C-H/alkene interaction. Click for 3D.

So how general might this be? To find out, I performed the following search on the Cambridge crystal database: cis-butene-search

  1. The search defines an alkene, bearing two cis-substituents each with at least one C-H bond. The substituents are both sp3 carbon, and the attachment bond to the alkene is defined as acyclic
  2. The H…H distance uses normalised terminal hydrogen positions (to try to correct for the normally over-short C-H bond lengths found by X-ray).
  3. Other constraints were R factor < 0.05, no disorder, no errors and (perhaps most importantly) T < 150K to try to reduce thermal libration.

I should qualify all of this by reminding that hydrogen positions in crystal structures are notoriously prone to errors. Nevertheless, with 624 hits using the above search, one might hope for statistical significance of a real effect.

Search result for close H...H contacts in cis-butenes.

Search result for close H…H contacts in cis-butenes.

For this sample, the most frequent H…H distance emerged as 2.1Å. This can only result from having the C-H bonds lie coplanar with the C=C alkene, as is shown above. The value is also remarkably close to the H…H distance for cis-butene itself (both computationally and as determined using electron diffraction). This does I feel provide a strong indication that σ-π-conjugation is manifesting in these systems.

Re-defining the search for propenes 1 as above gives 1656 hits, with a maximum in the distribution at 2.35Å corresponding to a syn-orientation of the C=C and the C-H bonds. The smaller maximum at about 2.75Å arises from a gauche-orientation between the C=C and C-H (in effect you have to halve this number, since there are twice as many possibilities for this to occur than for the syn). The “inward leaning” gauche C-H bond overlaps less well with the “outward leaning” π* orbital of the alkene.

Propene.

Search result for close H…H contacts in propenes.

These aspects are perhaps better seen in the orbital overlaps shown below.

Click for 3D.

Click for 3D.

I will follow-up this theme with esters and amides next.

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