Posts Tagged ‘Electrophilic aromatic substitution’

Free energy relationships and their linearity: a test example.

Sunday, January 13th, 2019

Linear free energy relationships (LFER) are associated with the dawn of physical organic chemistry in the late 1930s and its objectives in understanding chemical reactivity as measured by reaction rates and equilibria.

The Hammett equation is the best known of the LFERs, albeit derived “intuitively”. It is normally applied to the kinetics of aromatic electrophilic substitution reactions and is expressed as;

log KR/K0 = σRρ (for equilibria) and extended to log kR/k0 = σRρ for rates.

The equilibrium constants are normally derived from the ionisation of substituted benzoic acids, with Kbeing that for benzoic acid itself and Kthat of a substituted benzoic acid, with σR being known as the substituent constant and ρ the reaction constant. The concept involved obtaining the substituent constants by measuring the ionisation equilibria. The value of σis then assumed to be transferable to the rates of reaction, where the values can be used to obtain reaction constants for a given reaction. The latter would then be assumed to give insight into the electronic nature of the transition state for that reaction.

The term log kR/k(the ratio of rates of reaction) can be related to ΔΔG = -RT ln kR/kand this latter quantity can be readily obtained from quantum calculations, where ΔΔG is the difference in computed reaction activation free energies for two substituents (of which one might be R=H). The most interesting such Hammett plots are the ones where a discontinuity becomes apparent. The plot comprises two separate linear relationships, but with different slopes. This is normally taken to indicate a change of mechanism, on the assumption that the two mechanisms will have different responses to substituents. 

A test of this is available via the calculated activations energies for acid catalyzed cyclocondensation to give furanochromanes[1] which is a two-step reaction involving two transition states TS1 and TS2, either of which could be rate determining. A change from one to the other would constitute a change in mechanism. In this example, TS1 involves creation of a carbocationic centre which can be stabilized by the substituent on the Ar group; TS2 involves the quenching of the carbocation by a nucleophilic oxygen and hence might be expected to respond differently to the substituents on Ar. As it happens, the reaction coordinate for TS2 is not entirely trivial, since it also includes an accompanying proton transfer which might perturb the mechanism.

Fortunately for this reaction we have available full FAIR data (DOI: 10.14469/hpc/3943), which includes not only the computed free energies for both sets of transition states but also the entropy-free enthalpies for comparison. This allows the table below to be generated. For each substituent, the highest energy point is in bold, indicating the rate limiting step. The span of substituents corresponds to a range of rate constants of almost 1010, which in fact is rarely if ever achievable experimentally.

Highest free energy overall route for HCl catalysed mechanism,

trans stereochemistry

Sub ΔH/ΔG Reactant ΔH/ΔG, TS1 ΔH/ΔG, TS2 RDS
p-NH2 0.2/6.36 0.0/0.0 0.15/4.0 0.2/6.4 TS2/TS2
p-OMe 2.7/8.48 0.0/0.0 2.7/8.45 2.1/8.48 TS1/TS2
p-Me 5.5/10.00 0.0/0.0 5.5/9.9 3.9/10.00 TS1/TS2
p-Cl 7.7/12.28 0.0/0.0 7.7/12.28 5.9/11.84 TS1/TS1
p-H 7.6/13.01 0.0/0.0 7.6/13.01 5.5/11.51 TS1/TS1
p-CN 10.6/18.02 0.0/0.0 10.6 /17.61 10.5/18.02 TS1/TS2
p-NO2 12.4/19.85 0.0/0.0 12.4/18.24 12.0/19.85 TS1/TS2

For the free energies, you can see that TS2 is the rate limiting step for the first two electron donating substituents, and the last two electron withdrawing ones, whilst TS1 represents the rate limiting step for the middle substituents. This represents two changes of rate limiting step over the entire range of substituents. A different picture emerges if only the enthalpies are used. Now TS1 is rate limiting for essentially all the substituents. The difference of course arises because of significant changes to the entropy of the transition states. The Hammett equation, and its use of  σconstants to try to infer the electronic response of a reaction mechanism, does not really factor in entropic responses. Nor is it often if at all applied using a really wide range of substituents. So any linearity or indeed non-linearity in Hammett plots may correspond only very loosely to the underlying mechanisms involved.

Starting in the 1940s and lasting perhaps 40-50 years, thousands of different reaction mechanisms were subjected to the Hammett treatment during the golden era of physical organic chemistry, but very few have been followed up by exploring the computed free energies, as set out above. One wonders how many of the original interpretations will fully withstand such new scrutiny and in general how influential the role of entropy is.

References

  1. C.D. Nielsen, W.J. Mooij, D. Sale, H.S. Rzepa, J. Burés, and A.C. Spivey, "Reversibility and reactivity in an acid catalyzed cyclocondensation to give furanochromanes – a reaction at the ‘oxonium-Prins’ <i>vs.</i> ‘<i>ortho</i>-quinone methide cycloaddition’ mechanistic nexus", Chemical Science, vol. 10, pp. 406-412, 2019. https://doi.org/10.1039/c8sc04302g

I’ve started so I’ll finish. The ionisation mechanism and kinetic isotope effects for 1,3-dimethylindolin-2 one

Thursday, January 7th, 2016

This is the third and final study deriving from my Ph.D.[1]. The first two topics dealt with the mechanism of heteroaromatic electrophilic attack using either a diazonium cation or a proton as electrophile, followed by either proton abstraction or carbon dioxide loss from the resulting Wheland intermediate. This final study inverts this sequence by starting with the proton abstraction from an indolinone by a base to create/aromatize to a indole-2-enolate intermediate, which only then is followed by electrophilic attack (by iodine).  Here I explore what light quantum chemical modelling might cast on the mechanism.

Indole diazocoupling

The concentration of I3 is used to follow the reaction, given by the expression:  [I3] = k1[B][indolinone]t – k-1/k2*ln[I3] + const, where  k2* = k2/715[I] + k2' , the latter being the rate coefficient for the reaction between the enolate intermediate and I3. With appropriate least squares analysis of this rate equation, a value for k1 using either 1H or 2H (≡ D) isotopes can be extracted and this gives an isotope effect k1H/k1D of 6.3 ± 0.6. Note that this value does NOT depend on [B]. Here, I am going to try to see if I can construct a quantum mechanical model which reproduces this value.

Indole diazocoupling

  1. Model 1 uses just three water molecules as a proton relay (B3LYP+D3/Def2-TZVP/SCRF=water).
  2. Model 2 uses 2H2O.NaOH solvated by two extra passive water molecules. Since under these conditions, the NaOH is largely ionic, [B] ≡ [OH]
Model ΔG298 (ΔH298) kH/kD (298K) DataDOIs
1 28.0 (22.9) 10.3 [2],[3],[4]
2 2.5 (2.8) 4.4 [5],[6],[7]

The plot of rate vs [B] shows[1] that the uncatalysed (water) rate is very slow (intercept passes more or less through zero) and the calculated free energy barrier (28.0 kcal/mol) confirms a slow rate at ambient temperatures. Note in the final (aromatized) product, there is a noticeable hydrogen bond between the 3-carbon and a water molecule (2.14Å). The calculated kinetic isotope effect[8] is substantially larger than observed experimentally for the base catalysed contribution.

Indolineone ionization using 3 water molecules

In the presence of NaOH (standard state = 1 atm = 0.044M), the enthalpy barrier drops very substantially to 2.8 kcal/mol and the free energy to 2.5 kcal/mol. Similar behaviour was noted previously on this blog for the hydrolysis of thalidomide. Although the magnitude of the reduction in barrier in fact implies an extremely fast reaction, recollect that [B]=[OH] appears in the rate equation  and since its value is very much less than 0.044M, the observed rate is relatively slow.

Indolineone ionization using 3 water molecules + NaOH

The calculated KIE for the hydroxide catalysed mechanism is much smaller that for the water route, but also smaller than is observed. This is a value uncorrected for tunnelling, which given the small barrier might be significant. 

These calculations show how a model for ionization of indolinone can be constructed, and used to e.g. probe the sensitivity of KIE to perturbations induced by ring substituents, which may form the basis of a future post.


This is a non-linear equation with kinetics that straddle zero and first order behaviour. In 1972, it was not easily possible to graph such functions in a manner where the slope of a linear plot would yield the rate constant. It was only computers and languages such as Fortran which allowed such non-linear least squares analysis of the rate. In the event, it turned out that the presence of 50% methanol in the mixed aqueous solutions was the cause; in other solvents the kinetics approximated zero order behavour very well.

References

  1. B.C. Challis, and H.S. Rzepa, "Heteroaromatic hydrogen exchange reactions. Part VIII. The ionisation of 1,3-dimethylindolin-2-one", Journal of the Chemical Society, Perkin Transactions 2, pp. 1822, 1975. https://doi.org/10.1039/p29750001822
  2. H.S. Rzepa, "C 10 H 17 N 1 O 4", 2016. https://doi.org/10.14469/ch/191786
  3. H.S. Rzepa, "C 10 H 17 N 1 O 4", 2016. https://doi.org/10.14469/ch/191765
  4. H.S. Rzepa, "C10H17NO4", 2016. https://doi.org/10.14469/ch/191784
  5. H.S. Rzepa, "C 10 H 20 N 1 Na 1 O 6", 2016. https://doi.org/10.14469/ch/191787
  6. H.S. Rzepa, "C 10 H 20 N 1 Na 1 O 6", 2016. https://doi.org/10.14469/ch/191782
  7. H.S. Rzepa, "C10H20NNaO6", 2016. https://doi.org/10.14469/ch/191785
  8. H. Rzepa, "Mechanisms and kinetic isotope effects for the base catalysed ionisation of 1,3-dimethyl indolinone.", 2016. https://doi.org/10.14469/hpc/202

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