Archive for July, 2010

Thorpe-Ingold Effect

Often gem-dialkyl substitution accelerates a reaction, for example in the formation of an epoxide via reaction 1. Here the relative rates are 1:21:252 in going from 1 to 2 to 3.1 This acceleration is the Thorpe-Ingold effect and had been suggested to arise from a steric reaction: that the methyl groups contract the angle and bring the terminal groups closer together.

1: R1 = R2 = H
2: R1 = Me, R2 = H
3: R1 = R2 = Me

Kostal and Jorgensen2 have examined the reaction of the 2-chloroethoxides 1-3 using computations, especially to look at the effect of solvent. At MP2/6-311+G(d,p) and CBS-Q, the relative rates (based on the activation free energy ΔG) are 1:2.8:17 and 1:0.7:3.7, respectively. Evidently there is no significant rate enhancement afforded by gem-substitution in the gas phase.

However, solution computations give a very different result. Using PCM along with the MP2 method, the computed relative rates are 1:5.8:1100 and with the Monte Carlo-Free Energy Perturbation method, the relative rates for aqueous solution are 1:30:773. Thus, the Thorpe-Ingold acceleration is due to solvent. Analysis of the hydrogen bonded structures and the solute-water pair distributions suggest that increasing alkyl substitution reduces the strength of solvation of the reactant, leading to the lower activation barrier.


(1) Jung, M. E.; Piizzi, G., "gem-Disubstituent Effect:Theoretical Basis and Synthetic Applications," Chem. Rev., 2005, 105, 1735-1766, DOI: 10.1021/cr940337h

(2) Kostal, J.; Jorgensen, W. L., "Thorpe-Ingold Acceleration of Oxirane Formation Is Mostly a Solvent Effect," J. Am. Chem. Soc., 2010, 132, 8766-8773, DOI: 10.1021/ja1023755

Jorgensen &Solvation Steven Bachrach 27 Jul 2010 2 Comments

[6+4] and [4+2] cycloadditions: Unusual potential energy surfaces

Alder and co-workers have published a substantial theoretical study of potential [6+4]-cycloaddition reactions.1 There is much too much to summarize from this study, but I highlight here an interesting result that is consistent with one of the themes of the book and blog: unusual potential energy surfaces.

They examined two [6+4]-cycloadditon routes involving 1,3,5-hexatriene with 1,3-butadiene to give 1 and 2. These products are shown in Figure 1. A competing [4+2]-cycloaddition is also possible, giving rise to 3 and 4. Interestingly, only one TS is found leading to 1/3 and one TS leading to 2/4. (These TSs are also shown in Figure 1.) This is reminiscent of many examples from the book and blog where a single TS seems to lead to 2 different products. A valley-ridge inflection point divides the surface between 1 and 3 (VRI-1), and a second valley-ridge inflection point separates 2 from 4 (VRI-2). In addition a Cope transition state (CTS1) takes 1 into 3, and a second TS (CTS2) takes 2 into 4.







Figure 1. B3LYP/6-31G* optimized structures of the TSs and products of the reaction of 1,3,5-hexadiene with 1,3-butadiene.1

This type of surface requires study of the dynamics to truly predict what the outcome will be of the reaction. Unfortunately, the low barriers for the Cope rearrangements along with 3 and 4 being much more stable than 1 and 2 indicates that the [6+4] product is unlikely to be observed. Nonetheless, this is yet another example of an unexpected PES.


(1) Alder, R. W.; Harvey, J. N.; Lloyd-Jones, G. C.; Oliva, J. M., "Can π6 + π4 = 10? Exploring Cycloaddition Routes to Highly Unsaturated 10-Membered Rings," J. Am. Chem. Soc. 2010, 132, 8325-8337, DOI: 10.1021/ja1008135


1: InChI=1/C10H14/c1-2-4-6-8-10-9-7-5-3-1/h1-4,9-10H,5-8H2/b3-1-,4-2+,10-9+

2: InChI=1/C10H14/c1-2-4-6-8-10-9-7-5-3-1/h1-4,9-10H,5-8H2/b3-1-,4-2-,10-9+

3: InChI=1/C10H14/c1-3-9-7-5-6-8-10(9)4-2/h3-5,7,9-10H,1-2,6,8H2/t9-,10-/m0/s1

4: InChI=1/C10H14/c1-3-9-7-5-6-8-10(9)4-2/h3-5,7,9-10H,1-2,6,8H2/t9-,10+/m1/s1

cycloadditions &Dynamics Steven Bachrach 20 Jul 2010 1 Comment

Racemization of imidazolines

Grinberg and colleagues have published a combination of VCD and computation to understand the racemization of imidazoline 1 when exposed to base.1 Experimental VCD performed at various temperatures indicates first-order kinetics with a barrier of about 24 kcal mol-1.

The mechanism for this racemization was proposed and supported with B3LYP/6-31G(d) computations. The anion of 1 can undergo a disrotatory ring opening to form 2, passing through TS1 with a barrier of about 21 kcal mol-1. Since 2 is chiral with the phenyl groups oriented in non-equivalent positions, ring closure of 2 will go back to 1 and not on to its racemate. In order to racemize, 2 must convert to 3, which can invert to 3’ and then on to 1’. While the barrier for ring opening is likely to be rate limiting, and it does match up reasonably well with the experimental value, the authors have not optimized the transition state that take 2 into 3 or the TS that interconverts 3 with 3’. It’s the former TS that may be pretty large as it requires disruption of the conjugation. Unfortunately, not only have the authors not computed these other TSs, the supplementary materials include only the optimized structure of 1 and not TS1, 2, or 3!

The authors do note that the ring opening is facilitated by the phenyl group on the chiral carbons of 1. They replaced the phenyls with cyclohexyl or cyclohexenyl groups and racemization is no longer observed. Strangely, the authors include in the supporting materials the optimized structures of these variants, but not the TSs for ring opening. Thus, the confirming evidence of a very high barrier for ring opening that would really nail down the mechanism is missing!


1) Ma, S.; Busacca, C. A.; Fandrick, K. R.; Bartholomeyzik, T.; Haddad, N.; Shen, S.; Lee, H.; Saha, A.; Yee, N.; Senanayake, C.; Grinberg, N., "Directly Probing the Racemization of Imidazolines by Vibrational Circular Dichroism: Kinetics and Mechanism," Org. Lett., 2010, 12, 2782–2785, DOI: 10.1021/ol100734t


1: InChI=1/C21H18N2/c1-4-10-16(11-5-1)19-20(17-12-6-2-7-13-17)23-21(22-19)18-14-8-3-9-15-18/h1-15,19-20H,(H,22,23)/t19-,20-/m0/s1/f/h22H

cycloadditions Steven Bachrach 13 Jul 2010 No Comments

Understanding 1,3-dipole cycloaddition reactions

A couple of years ago Ess and Houk described computations on the cycloaddition reactions of ethene and ethyne with 9 different 1,3-dipoles 1-9.1,2 Two interesting results were noted: (a) though barrier heights systematically decreased with the decreasing HOMO-LUMO gap of the 1,3-dipole, the reaction barriers are the same for a given dipole with either ethane or ethyne; (b) The TS geometries about the ethane and ethyne fragments are similar, even though the reactions are quite different in overall reaction energies. This implies a violation of the Hammond Postulate.

Diazonium betaines

Nitrilium betaines

Azomethine betaines

Ess and Houk suggested that what dictated these reactions were the energies of distortion of the 1,3-dipole. This is the energy needed to distort the 1,3-dipole into its geometry in the TS. This is typically associated with the bending about the central atom, but rehybridization at the
terminal positions is also needed in many cases. A plot of the distortion energy against the activation barrier gives a line with an R2 value of 0.97.

Now Braida, Hiberty and coworkers have employed valence bond computations to interpret these findings.3 The 1,3-dipoles are composed of three valence bond structures a, b and c (shown for 1 below). The last structure (c) is the one associated with the cycloaddition reaction, as it is set up for making the two new bonds at the terminal positions.

The coefficients associated with these VB structures are given in Table 1. It is readily apparent that the degree of diradical character varies considerably among these compounds. Furthermore, for each set of 1,3-dipoles, increasing diradical content correlates with a decreased activation barrier. They also note a strong correlation of decreasing energy needed to excite the ground state 1,3-dipole to the diradical structure (of either the ground state geometry or in the TS geometry) with decreasing activation barrier. Thus, they conclude that it is the diradical character of the 1,3-dipole that controls the reaction – greater diradical character translates into a lower barrier. They argues that the concerted reaction proceeds in two phases, the first phase is distortion of the 1,3-dipole to create sufficient diradical character, and a second phase where the new bonds are made to the dipolarophile, independent of just what that dipolarophile happens to be.

Table 1. Coefficients of the 3 valence bond structures a-c for the ground state 1,3-dipoles 1-9.










































(1) Ess, D. H.; Houk, K. N., "Distortion/Interaction Energy Control of 1,3-Dipolar
Cycloaddition Reactivity," J. Am. Chem. Soc., 2007, 129, 10646-10647, DOI: 10.1021/ja0734086

(2) Ess, D. H.; Houk, K. N., "Theory of 1,3-Dipolar Cycloadditions: Distortion/Interaction and Frontier Molecular Orbital Models," J. Am. Chem. Soc., 2008, 130, 10187-10198, DOI: 10.1021/ja800009z

(3) Braida, B.; Walter, C.; Engels, B.; Hiberty, P. C., "A Clear Correlation between the Diradical Character of 1,3-Dipoles and Their Reactivity toward Ethylene or Acetylene," J. Am. Chem. Soc., 2010, 132, 7631-7637, DOI: 10.1021/ja100512d


1: InChI=1/N2O/c1-2-3

2: InChI=1/HN3/c1-3-2/h1H

3: InChI=1/CH2N2/c1-3-2/h1H2

4: InChI=1/CHNO/c1-2-3/h1H

5: InChI=1/CH2N2/c1-3-2/h1-2H

6: InChI=1/C2H3N/c1-3-2/h1H,2H2

7: InChI<=1/CH3NO/c1-2-3/h2H,1H2

8: InChI=1/CH4N2/c1-3-2/h2-3H,1H2

9: InChI=1/C2H5N/c1-3-2/h3H,1-2H2

cycloadditions Steven Bachrach 06 Jul 2010 1 Comment