Archive for the 'non-classical' Category

The complex PES for sesquiterpene formation

Hong and Tantillo1 report a real tour de force computational study of multiple pathways along the routes towards synthesis of a variety of sesquiterpenes. The starting point is the bisabolyl cation 1, and a variety of rearrangements, cyclizations, proton and hydride transfers are examined to convert it into such disparate products as barbatene 2, widdradiene 3, and champinene 4. The pathways are explored at mPW1PW91/6-31+G(d,p)//B3LYP/6-31+G(d,p). Some new pathways are proposed but the main points are the sheer complexity of the C15H25+ potential energy surface and the interconnections between potential intermediates.


(1) Hong, Y. J.; Tantillo, D. J. "Branching Out from the Bisabolyl Cation. Unifying Mechanistic Pathways to Barbatene, Bazzanene, Chamigrene, Chamipinene, Cumacrene, Cuprenene, Dunniene, Isobazzanene, Iso-γ-bisabolene, Isochamigrene, Laurene, Microbiotene, Sesquithujene, Sesquisabinene, Thujopsene, Trichodiene, and Widdradiene Sesquiterpenes," J. Am. Chem. Soc. 2014, 136, 2450-2463, DOI: 10.1021/ja4106489.


1: InChI=1S/C15H25/c1-12(2)6-5-7-14(4)15-10-8-13(3)9-11-15/h6,8,15H,5,7,9-11H2,1-4H3/q+1

2: InChI=1S/C15H24/c1-11-6-9-13(2)10-12(11)14(3)7-5-8-15(13,14)4/h6,12H,5,7-10H2,1-4H3/t12-,13-,14+,15-/m0/s1

3: InChI=1S/C15H24/c1-12-6-7-13-14(2,3)9-5-10-15(13,4)11-8-12/h6-7H,5,8-11H2,1-4H3/t15-/m0/s1

4: InChI=1S/C15H24/c1-11-6-9-15-10-12(11)14(15,4)8-5-7-13(15,2)3/h6,12H,5,7-10H2,1-4H3/t12-,14-,15-/m1/s1

non-classical &terpenes Steven Bachrach 13 Mar 2014 2 Comments

The x-ray structure of norbornyl cation

A long sought-after data point critical to the non-classical cation story has finally been obtained. The elusive x-ray crystal structure of a norbornyl cation was finally solved.1 The [C7H11]+[Al2Br7] salt was crystallized in CH2Br2 at low temperature (40 K). This low temperature was needed to prohibit rotation of the norbornyl cation within the crystal (the cation is near spherical and so subject to relatively easy rotation within the crystal matrix) and hydride scrambling among the three carbons (C1, C2, and C6) involved in the non-classical cation structure.

The authors report a number of different structures, all very similar, depending on slight differences in the crystals used. However, the important features are consistent with all of the structures. The cation is definitely of the non-classical type (see Figure 1) with the basal C1-C2 bond length of 1.39 Å similar that in benzene and long non-classical C1-C6 and C2-C6 distances of 1.80 Å. These distances match very well with the MP2(FC)/def2-QZVPP optimized distances of 1.393 and 1.825 Å, respectively.

Figure 1. X-ray structure of norbornyl cation.


(1) Scholz, F.; Himmel, D.; Heinemann, F. W.; Schleyer, P. v. R.; Meyer, K.; Krossing, I. "Crystal Structure Determination of the Nonclassical 2-Norbornyl Cation," Science 2013, 341, 62-64, DOI: 10.1126/science.1238849.

non-classical &norbornyl cation &Schleyer Steven Bachrach 16 Sep 2013 No Comments

Nonamethylcyclopentyl cation

The nine methyl groups of nonamethylcyclopentyl cation 1 all interconvert with a barrier of 7 kcal mol-1. However, at low temperature only partial scrambling occurs: there are two sets of methyl groups, one containing five groups and the other containing four methyl groups. The barrier for this scrambling is only 2.5 kcal mol-1. While this behavior was found more than 20 years ago, Tantillo and Schleyer1 only now have offered a complete explanation.


The ground state structure of 1 is shown in Figure 1 and has C1 symmetry. The two pseudo-axial methyl groups adjacent to the cationic center show evidence of hyperconjugation: long C-C bonds and Me-C-C+ angles of 100°.

The transition state TS1¸also in Figure 1, is of Cs symmetry. This transition state leads to interchange of the pseudo-axial methyls, and interchange of the pseudo-equatorial methyls, but no exchange between the members of these two groups. The M06-2x/6-31+G(d,p) and mPW1PW91/6-31+G(d,p) estimate of this barrier is 1.5 and 2.5 kcal mol-1, respectively. This agrees well with the experiment.




Figure 1. B3LYP/6-3+G(d,p) optimized geometries.

A second transition state TS2 was found and it corresponds with a twisting motion that interconverts an axial methyl with an equatorial methyl. This TS has Cs symmetry (shown in Figure 1) and the eclipsing interaction give rise to a larger barrier: 7.3 (M06-2x/6-31+G(d,p)) and 6.7 kcal mol-1 (mPW1PW91/6-31+G(d,p)). So twisting through TS2 and scrambling through TS1 allows for complete exchange of all 9 methyl groups.

An interesting point also made by these authors is that these three structures represent the continuum of cationic structure: a classical (localized) cation in TS2, a bridged structure in TS1 and hyperconjugated cation in 1.


(1) Tantillo, D. J.; Schleyer, P. v. R. “Nonamethylcyclopentyl Cation Rearrangement Mysteries Solved,” Org. Lett. 2013, 15, 1725-1727, DOI: 10.1021/ol4005189.


1: InChI=1S/C14H27/c1-10-11(2,3)13(6,7)14(8,9)12(10,4)5/h1-9H3/q+1

non-classical &Schleyer Steven Bachrach 23 Jul 2013 4 Comments

Hexacoordinate carbon

The search for the elusive hypervalent carbon atom took an interesting turn for the positive with the report of the synthesis and characterization of 1 and especially its dication 2.1 The x-ray structure was obtained for both compounds along with computing their B3PW91/6-31G(d) geometries. These computed geometries are shown in Figure 1.





Figure 1. B3PW91/6-31G(d) optimized geometries of 1 and 2.1

The allene fragment is bent in both structures: 168.5° (169.9° at B3PW91) in 1 and 166.8° (172.7° at B3PW91) in 2. The distances between the central carbon atom of the allene and the four oxygen atoms are 2.66 to 2.82 Å, and computed to be a little longer. Interestingly, these distance contract when the dication 2 is created; ranging from 2.64 to 2.75 Å (again computed to be a little longer). These distances, while significantly longer than normal covalent C-O bonds, are less than the sum of the C and O van der Waals radii. But are they really bonds?

This is not a trivial answer to solve. The authors opt to employ topological electron density analysis (Bader’s atoms-in-molecules approach). Using the electron density from both the high resolution x-ray density map and from the DFT computations, bond paths between the central allene carbon and each oxygen are found, though with, as expected, low values of ρ. The Laplacian of the density at the critical point are positive, indicative of ionic interactions. So according to Bader’s model, the existence of a bond path in a ground state molecule is the necessary and sufficient condition for bonding.

The others conclude by proposing that OC intermolecular interactions with separations of around 2.6 to 2.8 Å may also suggest hypervalent cases. They note that about 2000 structures in the Cambridge crystallographic database fit this criterion.


(1) Yamaguchi, T.; Yamamoto, Y.; Kinoshita, D.; Akiba, K.-y.; Zhang, Y.; Reed, C. A.; Hashizume, D.; Iwasaki, F., "Synthesis and Structure of a Hexacoordinate
Carbon Compound," J. Am. Chem. Soc., 2008, 130, 6894-6895, DOI: 10.1021/ja710423d.


1: InChI=1/C31H24O4S2/c1-32-20-9-5-13-24-28(20)18(29-21(33-2)10-6-14-25(29)36-24)17-19-30-22(34-3)11-7-15-26(30)37-27-16-8-12-23(35-4)31(19)27/h5-16H,1-4H3

2: InChI=1/C33H30O4S2/c1-34-22-11-7-15-26-30(22)20(31-23(35-2)12-8-16-27(31)38(26)5)19-21-32-24(36-3)13-9-17-28(32)39(6)29-18-10-14-25(37-4)33(21)29/h7-18H,1-6H3/q+2

DFT &non-classical Steven Bachrach 03 Jun 2008 3 Comments