Diels-Alder of yne-diyne species

Cramer &Diels-Alder &diradicals Steven Bachrach 05 Oct 2015 No Comments

Cramer, Hoye, Kuwata and coworkers have examined the intramolecular cyclization of an alkyne with a diyne.1 Their model system is 1, which can cyclize through a concerted transition state TSC togive the benzyne product 2, or it can proceed through a stepwise pathway, first going through TS1 to form the intermediate INT¸ before traversing through a second transition state TS2 and on to product 2. Using both computations and experiments, they examined a series of compounds with
differing substituents at the ends of the two yne moieties.

The experiments show almost the exact same rate of reaction regardless of the terminal substituents. This includes the parent case where the terminal substituents are hydrogens and also the case where the terminal substituents (which end up on adjacent centers on the benzyne ring) are bulky TMS groups. And though there is no real rate effect due to changes in solvent or the presence of light or triplet oxygen, which suggest a concerted reaction, these substituent effects argue for a step wise reaction.

computations help explain these observations. Shown in Figure 1 are the optimized geometries and relative energies of the critical points on the reaction surface for the conversion of 1 into 2, and these results are similar with the other substituents as well.









Figure 1. SMD(o-dichlorobenzene)/B3LYP-D3BJ/6-311+G-(d,p)//M06-2X/6-311+G(d,p) optimized geometries and relative energies (kcal mol-1).

The first thing to note is that the concerted TSC is higher in energy than the stepwise TS1. The wavefunction for TSC unstable towards moving from a restricted to unrestricted formalism. Reoptimization of some of these concerted TSs actually led to the stepwise TS.

The next item of note is that TS2 for this case is actually lower in energy than the intermediate (this is a true TS on the energy surface, but when zero-point energy and other thermal corrections are included, it becomes lower in energy than INT). For some of the cases the second TS lies above the intermediate, but typically by a small amount.

Therefore, the mechanism of this reaction is stepwise, but the second step might have such a small barrier (or even no barrier) that one might consider this to be concerted, though highly asymmetric and really bearing little resemblance to more traditional concerted pericyclic reactions.

The authors obliquely hinted at some potential interesting dynamics. I suspect that molecular dynamics calculations will show no effect of that second TS, and one might observe some interesting dynamics, which could be seen in kinetic isotope experiments.


(1)  Marell, D. J.; Furan, L. R.; Woods, B. P.; Lei, X.; Bendelsmith, A. J.; Cramer, C. J.; Hoye, T. R.; Kuwata, K. T. "Mechanism of the Intramolecular Hexadehydro-Diels–Alder Reaction," J. Org. Chem. 2015 ASAP, DOI: 10.1021/acs.joc.5b01356.


1: InChI=1S/C8H4O2/c1-3-5-6-7-10-8(9)4-2/h1-2H,7H2

2: InChI=1S/C8H4O2/c9-8-7-4-2-1-3-6(7)5-10-8/h2,4H,5H2

Triprotonated rosarin: singlet or triplet?

Aromaticity &Borden Steven Bachrach 22 Sep 2015 No Comments

What is the spin state of the ground state of an aromatic species? Can this be spin state be manipulated by charge? These questions are addressed by Borden, Kim, Sessler and coworkers1 for the hexaphyrin 1. B3LYP/6-31G(d) optimization of 1 shows it to be a ground state singlet. This structure is shown in Figure 1.



Protonation of the three pyrrole nitrogens creates 13+, which has interesting frontier orbitals. The HOMO of 13+, of a1” symmetry, has nodes running through all six nitrogens. The next higher energy orbital, of a2” symmetry, has a small π-contribution on each nitrogen. Protonation will therefore have no effect on the energy of the a1” orbital, but the charge will stabilize the a2” orbital. This will lower the energy gap between the two orbitals, suggesting that a ground state triplet might be possible. The lowest singlet and triplet states of 13+ are also shown in Figure 1.


Singlet 13+

Triplet 13+

Figure 1. (U)B3LYP/6-31G(d) optimized structures of 1 and singlet and triplet 13+.

This spin state change upon protonation was experimentally verified by synthesis of two analogues of 1, shown below. The triprotonated versions of both are observed to have triplet character in their EPR spectrum.


(1) Fukuzumi, S.; Ohkubo, K.; Ishida, M.; Preihs, C.; Chen, B.; Borden, W. T.; Kim, D.; Sessler, J. L. "Formation of Ground State Triplet Diradicals from Annulated Rosarin Derivatives by Triprotonation," J. Am. Chem. Soc. 2015, 137, 9780-9783, DOI: 10.1021/jacs.5b05309.


1: InChI=1S/C45H24N6/c1-2-8-29-28(7-1)34-16-22-13-24-18-36-30-9-3-4-10-31(30)38-20-26(50-43(38)42(36)48-24)15-27-21-39-33-12-6-5-11-32(33)37-19-25(49-44(37)45(39)51-27)14-23-17-35(29)41(47-23)40(34)46-22/h1-21,46,49-50H/b22-13-,23-14-,24-13-,25-14-,26-15-,27-15-

Sumanene anions

Aromaticity Steven Bachrach 14 Sep 2015 1 Comment

Spisak, et al. treated sumanene 1 with excess potassium in THF.1

They obtained an interesting structure, characterized by x-ray crystallography: a mixture of the dianion and trianion of 1 (well these are really conjugate di- and tribases of 1, but we’ll call them di- and trianions for simplicity’s sake). A fragment of the x-ray structure is shown in Figure 1, showing that there is one potassium cation on the concave face and six potassium ions on the convex face.

Figure 1. X-ray structure of 1 surrounded by six K+ ions on the convex face and one K+ on the concave face.

To help understand this structure, they performed RIJCOSX-PBE0/cc-pVTZ computations on the mono-, di-, and trianion of 1. The structure of 1 (which I optimized at ωB97X-D/6-311G(d)) and the trianion are displayed in Figure 2. The molecular electrostatic potential of the trianion shows highly negative regions in the 5-member ring regions, symmetrically distributed and prime for coordination with 6 cations.


trianion of 1

Figure 2. Optimized structure of 1 and its trianion.


(1) Spisak, S. N.; Wei, Z.; O’Neil, N. J.; Rogachev, A. Y.; Amaya, T.; Hirao, T.; Petrukhina, M. A. "Convex and Concave Encapsulation of Multiple Potassium Ions by Sumanenyl Anions," J. Am. Chem. Soc. 2015, 137, 9768-9771, DOI: 10.1021/jacs.5b06662.


1: InChI=1S/C21H12/c1-2-11-8-13-5-6-15-9-14-4-3-12-7-10(1)16-17(11)19(13)21(15)20(14)18(12)16/h1-6H,7-9H2

Trianion of 1: InChI=1S/C21H9/c1-2-11-8-13-5-6-15-9-14-4-3-12-7-10(1)16-17(11)19(13)21(15)20(14)18(12)16/h1-5,7-8H,9H2/q-3

Review of planar hypercoordinate atoms

Schleyer Steven Bachrach 26 Aug 2015 6 Comments

Yang, Ganz, Chen, Wang, and Schleyer have published a very interesting and comprehensive review of planar hypercoordinate compounds, with a particular emphasis on planar tetracoordinate carbon compounds.1 A good deal of this review covers computational results.

There are two major motifs for constructing planar tetracoordinate carbon compounds. The first involves some structural constraints that hold (or force) the carbon into planarity. A fascinating example is 1 computed by Rasmussen and Radom in 1999.2 This molecule taxed their computational resources, and as was probably quite typical for that time, there is no supplementary materials. But since this compound has high symmetry (D2h) I reoptimized its structure at ω-B97X-D/6-311+G(d) and computed its frequencies in just a few hours. This structure is shown in Figure 1. However, it should be noted that at this computational level, 1 possesses a single imaginary frequency corresponding to breaking the planarity of the central carbon atom. Rasmussen and Radom computed the structure of 1 at MP2/6-31G(d) with numerical frequencies all being positive. They also note that the B3LYP/6-311+G(3df,2p) structure also has a single imaginary frequency.

A second approach toward planar tetracoordinate carbon compounds is electronic: having π-acceptor ligands to stabilize the p-lone pair on carbon and σ-donating ligands to help supply sufficient electrons to cover the four bonds. Perhaps the premier simple example of this is the dication 2¸ whose ω-B97X-D/6-311+G(d,p) structure is also shown in Figure 1.

The review covers heteroatom planar hypercoordinate species as well. It also provides brief coverage of some synthesized examples.



Figure 1. Optimized structures of 1 and 2.


(1) Yang, L.-M.; Ganz, E.; Chen, Z.; Wang, Z.-X.; Schleyer, P. v. R. "Four Decades of the Chemistry of Planar Hypercoordinate Compounds," Angew. Chem. Int. Ed. 2015, 54, 9468-9501, DOI: 10.1002/anie.201410407.

(2) Rasmussen, D. R.; Radom, L. "Planar-Tetracoordinate Carbon in a Neutral Saturated Hydrocarbon: Theoretical Design and Characterization," Angew. Chem. Int. Ed. 1999, 38, 2875-2878, DOI: 10.1002/(SICI)1521-3773(19991004)38:19<2875::AID-ANIE2875>3.0.CO;2-D.


1: InChI=1S/C23H24/c1-7-11-3-15-9-2-10-17-5-13-8(1)14-6-18(10)22-16(9)4-12(7)20(14,22)23(22)19(11,13)21(15,17)23/h7-18H,1-6H2

2: InChI=1S/C5H4/c1-2-5(1)3-4-5/h1-4H/q+2


benzynes &Schaefer Steven Bachrach 18 Aug 2015 No Comments

I want to update my discussion of m-benzyne, which I present in my book in Chapter 5.5.3. The interesting question concerning m-benzyne concerns its structure: is it a single ring structure 1a or a bicyclic structure 1b? Single configuration methods including closed-shell DFT methods predict the bicylic structure, but multi-configuration methods and unrestricted DFT predict it to be 1a. Experiments support the single ring structure 1a.

The key measurement distinguishing these two structure type is the C1-C3 distance. Table 1 updates Table 5.11 from my book with the computed value of this distance using some new methods. In particular, the state-specific multireference coupled cluster Mk-MRCCSD method1 with the cc-pCVTZ basis set indicates a distance of 2.014 Å.2 The density cumulant functional theory3 ODC-124 with the cc-pCVTZ basis set also predicts the single ring structure with a distance of 2.101 Å.5

Table 1. C1-C3 distance (Å) with different computational methods using the cc-pCVTZ basis set












(1) Evangelista, F. A.; Allen, W. D.; Schaefer III, H. F. "Coupling term derivation and general implementation of state-specific multireference coupled cluster theories," J. Chem. Phys 2007, 127, 024102-024117, DOI: 10.1063/1.2743014.

(2) Jagau, T.-C.; Prochnow, E.; Evangelista, F. A.; Gauss, J. "Analytic gradients for Mukherjee’s multireference coupled-cluster method using two-configurational self-consistent-field orbitals," J. Chem. Phys. 2010, 132, 144110, DOI: 10.1063/1.3370847.

(3) Kutzelnigg, W. "Density-cumulant functional theory," J. Chem. Phys. 2006, 125, 171101, DOI: 10.1063/1.2387955.

(4) Sokolov, A. Y.; Schaefer, H. F. "Orbital-optimized density cumulant functional theory," J. Chem. Phys. 2013, 139, 204110, DOI: 10.1063/1.4833138.

(5) Mullinax, J. W.; Sokolov, A. Y.; Schaefer, H. F. "Can Density Cumulant Functional Theory Describe Static Correlation Effects?," J. Chem. Theor. Comput. 2015, 11, 2487-2495, DOI: 10.1021/acs.jctc.5b00346.


1a: InChI=1S/C6H4/c1-2-4-6-5-3-1/h1-3,6H

Domino Tunneling

focal point &Schreiner &Tunneling Steven Bachrach 11 Aug 2015 1 Comment

A 2013 study of oxalic acid 1 failed to uncover any tunneling between its conformations,1 despite observation of tunneling in other carboxylic acids (see this post). This was rationalized by computations which suggested rather high rearrangement barriers. Schreiner, Csaszar, and Allen have now re-examined oxalic acid using both experiments and computations and find what they call domino tunneling.2

First, they determined the structures of the three conformations of 1 along with the two transition states interconnecting them using the focal point method. These geometries and relative energies are shown in Figure 1. The barrier for the two rearrangement steps are smaller than previous computations suggest, which suggests that tunneling may be possible.






Figure 1. Geometries of the conformers of 1 and the TS for rearrangement and relative energies (kcal mol-1)

Placing oxalic acid in a neon matrix at 3 K and then exposing it to IR radiation populates the excited 1tTt conformation. This state then decays to both 1cTt and 1cTc, which can only happen through a tunneling process at this very cold temperature. Kinetic analysis indicates that there are two different rates for decay from both 1tTt and 1cTc, with the two rates associated with different types of sites within the matrix.

The intrinsic reaction paths for the two rearrangements: 1tTt1cTt and → 1cTc were obtained at MP2/aug-cc-pVTZ. Numerical integration and the WKB method yield similar half-lives: about 42 h for the first reaction and 23 h for the second reaction. These match up very well with the experimental half-lives from the fast matrix sites of 43 ± 4 h and 30 ± 20 h, respectively. Thus, the two steps take place sequentially via tunneling, like dominos falling over.


(1) Olbert-Majkut, A.; Ahokas, J.; Pettersson, M.; Lundell, J. "Visible Light-Driven Chemistry of Oxalic Acid in Solid Argon, Probed by Raman Spectroscopy," J. Phys. Chem. A 2013, 117, 1492-1502, DOI: 10.1021/jp311749z.

(2) Schreiner, P. R.; Wagner, J. P.; Reisenauer, H. P.; Gerbig, D.; Ley, D.; Sarka, J.; Császár, A. G.; Vaughn, A.; Allen, W. D. "Domino Tunneling," J. Am. Chem. Soc. 2015, 137, 7828-7834, DOI: 10.1021/jacs.5b03322.


1: InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)

An amazing barrel structure

Uncategorized Steven Bachrach 04 Aug 2015 1 Comment

I don’t really have anything to say about this recent paper by Anderson, et al.1 They have simply prepared a very beautiful structure, an aryllated analogue of 1. They even optimized the structure of 1 at BLYP/6-31G(d) and it’s shown in Figure 1. That must have taken some time!

Figure 1. BLYP/6-31G(d) optimized structure of 1.
(Remember that you can manipulate this structure by simply clicking on in, which will launch the JMol app.)


(1) Neuhaus, P.; Cnossen, A.; Gong, J. Q.; Herz, L. M.; Anderson, H. L. "A Molecular Nanotube with Three-Dimensional π-Conjugation," Angew. Chem. Int. Ed. 2015, 54, 7344-7348, DOI: 10.1002/anie.201502735.

Hetero-substituted corranulene

Aromaticity Steven Bachrach 20 Jul 2015 2 Comments

A heterosubstituted corranulene analogue has now been prepared. Ito, Tokimaru, and Nozaki report the synthesis of 1 and compare it with corranulene.1 The x-ray structure of 1 shows it to be a deeper bowl than corranulene, and the bond distances suggest the Kekule structure with a central pyrrole and five Clar-type phenyl rings.

The B3LYP/6-311+G(2d,p) optimized structure of 2, then analogue of 1 missing the t-butyl group, is shown in Figure 1. Its geometry is very similar to that of 1 observed in the crystal structure. The NICS(0) values are shown in Scheme 1. These values support the notion of a central (aromatic) pyrrole surrounded by a periphery of five aromatic phenyl rings.

Scheme 1. NICS(0) values

An interesting feature of bowl compounds is their inversion. The inversion barrier, through the planar TS shown in Figure 2, is computed to be 17.0 kcal mol-1 at B3LYP/6-311+G(2d,p). This is 6-7 kcal mol-1 larger than the inversion barrier of corranulene, which is not surprising given the additional phenyl groups about the periphery.


bowl inversion TS

Figure 1. B3LYP/6-311+G(2d,p) optimized geometry of 2.


(1) Ito, S.; Tokimaru, Y.; Nozaki, K. "Benzene-Fused Azacorannulene Bearing an Internal Nitrogen Atom," Angew. Chem. Int. Ed. 2015, 54, 7256-7260, DOI: 10.1002/anie.201502599.


1: InChI=1S/C38H23N/c1-38(2,3)18-16-27-25-14-6-12-23-21-10-4-8-19-20-9-5-11-22-24-13-7-15-26-28(17-18)35(27)39-36(31(23)25)33(29(19)21)34(30(20)22)37(39)32(24)26/h4-17H,1-3H3

2: InChI=1S/C34H15N/c1-6-16-17-7-2-9-19-21-11-4-13-23-25-15-5-14-24-22-12-3-10-20-18(8-1)26(16)30-31(27(17)19)34(29(21)23)35(32(24)25)33(30)28(20)22/h1-15H

Hypercoordinated carbon revisited

Isotope Effects &Tunneling Steven Bachrach 14 Jul 2015 No Comments

Last year I wrote a post on the possibility of a stable hypercoordinated carbon in the C(CH3)5+ molecule as proposed by Schleyer and Schaefer.1 Kozuch has re-examined this molecule with an eye towards examining the lifetime of this proposed “fleeting” molecule.2

The computed barriers for either (1) loss of a methane molecule leaving behind the (CH3)2C+CH2CH3 cation or (2) loss of an ethane molecule leaving behind the t-butyl cation are small: 1.65 and 1.37 kcal mol-1, respectively. Kozuch employed canonical variational theory with and without small curvature tunneling (SCT). Without the tunneling correction, the pentamethylmethyl cation is predicted to have a long (millennia) lifetime at very low temperatures (<20 K). However, when tunneling is included, the half-life is reduced to 6 and 40 μs for degradation along the two pathways. Clearly, this is not a fleeting molecule – its lifetime is really too short to consider it as anything.

Interestingly, perdeuterating the molecule ((CD3)5C+) substantially increases the half-life to 4 ms, a thousand-fold increase. Tritium substitution would further increase the half-life to 0.2 s – a long enough time to really identify it and perhaps justify the name “molecule”. What is perhaps the most interesting aspect here is that H/D substitution has such a large effect on the tunneling rate even though no C-H bond is broken in the TS! This results from a mass effect (a CH3 vs. a CD3 group is migrating) along with a zero-point vibrational energy effect.


(1) McKee, W. C.; Agarwal, J.; Schaefer, H. F.; Schleyer, P. v. R. "Covalent Hypercoordination: Can Carbon Bind Five Methyl Ligands?," Angew. Chem. Int. Ed. 2014, 53, 7875-7878, DOI: 10.1002/anie.201403314.

(2) Kozuch, S. "On the tunneling instability of a hypercoordinated carbocation," Phys. Chem. Chem. Phys. 2015, 17, 16688-16691, DOI: 10.1039/C5CP02080H.


C(CH3)5+: InChI=1S/C6H15/c1-6(2,3,4)5/h1-5H3/q+1

Inverted Carbon Atoms

Schreiner Steven Bachrach 06 Jul 2015 8 Comments

Inverted carbon atoms, where the bonds from a single carbon atom are made to four other atoms which all on one side of a plane, remain a subject of fascination for organic chemists. We simply like to put carbon into unusual environments! Bremer, Fokin, and Schreiner have examined a selection of molecules possessing inverted carbon atoms and highlights some problems both with experiments and computations.1

The prototype of the inverted carbon is propellane 1. The ­Cinv-Cinv bond distance is 1.594 Å as determined in a gas-phase electron diffraction experiment.2 A selection of bond distance computed with various methods is shown in Figure 1. Note that CASPT2/6-31G(d), CCSD(t)/cc-pVTZ and MP2 does a very fine job in predicting the structure. However, a selection of DFT methods predict a distance that is too short, and these methods include functionals that include dispersion corrections or have been designed to account for medium-range electron correlation.















Figure 1. Optimized Structure of 1 at MP2/cc-pVTZ, along with Cinv-Cinv distances (Å) computed with different methods.

Propellanes without an inverted carbon, like 2, are properly described by these DFT methods; the C-C distance predicted by the DFT methods is close to that predicted by the post-HF methods.

The propellane 3 has been referred to many times for its seemingly very long Cinv-Cinv bond: an x-ray study from 1973 indicates it is 1.643 Å.3 However, this distance is computed at MP2/cc-pVTZ to be considerably shorter: 1.571 Å (Figure 2). Bremer, Fokin, and Schreiner resynthesized 3 and conducted a new x-ray study, and find that the Cinv-Cinv distance is 1.5838 Å, in reasonable agreement with the computation. This is yet another example of where computation has pointed towards experimental errors in chemical structure.

Figure 2. MP2/cc-pVTZ optimized structure of 3.

However, DFT methods fail to properly predict the Cinv-Cinv distance in 3. The functionals B3LYP, B3LYP-D3BJ and M06-2x (with the cc-pVTZ basis set) predict a distance of 1.560, 1.555, and 1.545 Å, respectively. Bremer, Folkin and Schreiner did not consider the ωB97X-D functional, so I optimized the structure of 3 at ωB97X-D/cc-pVTZ and the distance is 1.546 Å.

Inverted carbon atoms appear to be a significant challenge for DFT methods.


(1) Bremer, M.; Untenecker, H.; Gunchenko, P. A.; Fokin, A. A.; Schreiner, P. R. "Inverted Carbon Geometries: Challenges to Experiment and Theory," J. Org. Chem. 2015, 80, 6520–6524, DOI: 10.1021/acs.joc.5b00845.

(2) Hedberg, L.; Hedberg, K. "The molecular structure of gaseous [1.1.1]propellane: an electron-diffraction investigation," J. Am. Chem. Soc. 1985, 107, 7257-7260, DOI: 10.1021/ja00311a004.

(3) Gibbons, C. S.; Trotter, J. "Crystal Structure of 1-Cyanotetracyclo[,7.03,7]decane," Can. J. Chem. 1973, 51, 87-91, DOI: 10.1139/v73-012.


1: InChI=1S/C5H6/c1-4-2-5(1,4)3-4/h1-3H2

3: InChI=1S/C11H13N/c12-7-9-1-8-2-10(4-9)6-11(10,3-8)5-9/h8H,1-6H2

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