A record short H…H non-bonding interaction

Grimme &Schreiner Steven Bachrach 21 Jun 2017 No Comments

Following on previous work (see these posts on ladderane and hexaphenylethane), Schreiner, Grimme and co-workers have examined the structure of the all-meta tri(di-t-butylphenyl)methane dimer 12.1 In the study of hexaphenylethane,2 Schreiner and Grimme note that t-butyl groups stabilize highly congested structures through dispersion, identifying them as “dispersion energy donors”.3 The idea here is that the dimer of 1 will be stabilized by these many t-butyl groups. In fact, the neutron diffraction study of the crystal structure of 12 shows an extremely close approach of the two methane hydrogens of only 1.566 Å, the record holder for the closest approach of two formally non-bonding hydrogen atoms.

To understand the nature of this dimeric structure, they employed a variety of computational techniques. (Shown in Figure 1 is the B3LYPD3ATM(BJ)/def2-TZVPP optimized geometry of 12.) The HSE-3c (a DFT composite method) optimized crystal structure predicts the HH distance is 1.555 Å. The computed gas phase structure lengthens the distance to 1.634 Å, indicating a small, but essential, role for packing forces. Energy decomposition analysis of 12 at B3LYP-D3ATM(BJ)/def2-TZVPP indicates a dominant role for dispersion in holding the dimer together. While 12 is bound by about 8 kcal mol-1, the analogue of 12 lacking all of the t-butyl groups (the dimer of triphenylmethane 22) is unbound by over 8 kcal mol-1. Topological electron density analysis does show a bond critical point between the two formally unbound hydrogen atoms, and the noncovalent interaction plot shows an attractive region between these two atoms.

Figure 1. ATM(BJ)/def2-TZVPP optimized geometry of 12, with most of the hydrogens suppressed for clarity. (Selecting the molecule will launch Jmol with the full structure, including the hydrogens.)


1) Rösel, S.; Quanz, H.; Logemann, C.; Becker, J.; Mossou, E.; Cañadillas-Delgado, L.; Caldeweyher, E.; Grimme, S.; Schreiner, P. R., "London Dispersion Enables the Shortest Intermolecular Hydrocarbon H···H Contact." J. Am. Chem. Soc. 2017, 139, 7428–7431, DOI: 10.1021/jacs.7b01879.

2) Grimme, S.; Schreiner, P. R., "Steric Crowding Can Stabilize a Labile Molecule: Solving the Hexaphenylethane Riddle." Angew. Chem. Int. Ed. 2011, 50 (52), 12639-12642, DOI: 10.1002/anie.201103615.

3) Grimme, S.; Huenerbein, R.; Ehrlich, S., "On the Importance of the Dispersion Energy for the Thermodynamic Stability of Molecules." ChemPhysChem 2011, 12 (7), 1258-1261, DOI: 10.1002/cphc.201100127.


1: InChI=1S/C43H64/c1-38(2,3)31-19-28(20-32(25-31)39(4,5)6)37(29-21-33(40(7,8)9)26-34(22-29)41(10,11)12)30-23-35(42(13,14)15)27-36(24-30)43(16,17)18/h19-27,37H,1-18H3

Dynamics in a [3,3]-rearrangement

Cope Rearrangement &Dynamics Steven Bachrach 05 Jun 2017 No Comments

Bispericyclic reactions occur when two different pericyclic reactions merge to have a single transition state. An example of this is the joining of two [3,3]-sigmatopic rearrangements of 1 that merge to have a single transition state. Lopez, Faza, and Lopez have examined the dynamics of this reaction.1

Because of the symmetry of the species along this reaction pathway, the products of the two different rearrangements are identical, and will be formed in equal amounts, though they are produced from a single transition state with the reaction pathway bifurcating due to a valley-ridge inflection post TS.

The interesting twist that is explored here is when 1 is substituted in order to break the symmetry. The authors have examined 3x with either fluorine, chlorine, or bromine. The critical points on the reactions surface were optimized at M06-2X/Def2TZVPP. In all three cases a single bispericyclic transition state 3TS1x is found, which leads to products 4a and 4b. A second transition state 4TSx corresponds to the [3,3]-rearrangement that interconverts the two products. The structures of 1TS, 3TS1F, and 3TS1Cl are shown in Figure 1.




Figure 1. M06-2X/Def2TZVPP optimized geometries of 1TS, 3TS1F, and 3TS1Cl.

The halogen substitution breaks the symmetry of the reaction path. This leads to a number of important changes. First, the C4-C5 and C7-C8 distances, which are identical in 1TS, are different in the halogen cases. Interestingly, the distortions are dependent on the halogen: in 3TS1F C4-C5 is 0.2 Å longer than C7-C8, but in 3TS1Cl C7-C8 is much longer (by 0.65 Å) than C4-C5. Second, the products are no longer equivalent with the halogen substitution. Again, this is halogen dependent: 4bF is 4.0 kcal mol-1 lower in energy than 4aF, while 4aCl is 8.2 kcal mol-1 lower than 4bCl.

These difference manifest in very different reaction dynamics. With trajectories initiated at the first (bispericyclic) transiting state, 89% end at 4bF and 9% end at 4aF, a ratio far from unity that might be expected from both products resulting from passage through the same TS. The situation is even more extreme for the chlorine case, where all 200 trajectories end in 4aCl. This is yet another example of the role that dynamics play in reaction outcomes (see these many previous posts).


1) Villar López, R.; Faza, O. N.; Silva López, C., "Dynamic Effects Responsible for High Selectivity in a [3,3] Sigmatropic Rearrangement Featuring a Bispericyclic Transition State." J. Org. Chem. 2017, 82 (9), 4758-4765, DOI: 10.1021/acs.joc.7b00425.


1: InChI=1S/C9H12/c1-3-9-6-4-8(2)5-7-9/h1-2,4-7H2

2: InChI<=1S/C9H12/c1-7-4-5-8(2)9(3)6-7/h1-6H2

3F: InChI=1S/C9H8F4/c1-3-7-5-4-6(2)8(10,11)9(7,12)13/h1-2,4-5H2

3Cl: InChI=1S/C9H8Cl4/c1-3-7-5-4-6(2)8(10,11)9(7,12)13/h1-2,4-5H2

4aF: InChI=1S/C9H8F4/c1-5-4-6(8(10)11)2-3-7(5)9(12)13/h1-4H2

4aCl: InChI=1S/C9H8Cl4/c1-5-4-6(8(10)11)2-3-7(5)9(12)13/h1-4H2

4bF: InChI=1S/C9H8F4/c1-5-4-6(2)8(10,11)9(12,13)7(5)3/h1-4H2

4bCl: InChI=1S/C9H8Cl4/c1-5-4-6(2)8(10,11)9(12,13)7(5)3/h1-4H2


Aromaticity &nanohoops Steven Bachrach 22 May 2017 No Comments

The synthesis of components of nanostructures (like fullerenes and nanotubes) has dramatically matured over the past few years. I have blogged about nanohoops before, and this post presents the recent work of the Itami group in preparing the nanobelt 1.1


The synthesis is accomplished through a series of Wittig reactions with an aryl-aryl coupling to stitch together the final rings. The molecule is characterized by NMR and x-ray crystallography. The authors have also computed the structure of 1 at B3LYP/6-31G(d), shown in Figure 1. The computed C-C distances match up very well with the experimental distances. The strain energy of 1, presumably estimated by Reaction 1,2 is computed to be about 119 kcal mol-1.


Figure 1. B3LYP/6-31G(d) optimized structure of 1.

Rxn 1

NICS(0) values were obtained at B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d); the rings along the middle of the belt have values of -7.44ppm and are indicative of normal aromatic 6-member rings, while the other rings have values of -2.00ppm. This suggests the dominant resonance structure shown below:


1) Povie, G.; Segawa, Y.; Nishihara, T.; Miyauchi, Y.; Itami, K., "Synthesis of a carbon nanobelt." Science 2017, 356, 172-175, DOI: 10.1126/science.aam8158.

2) Segawa, Y.; Yagi, A.; Ito, H.; Itami, K., "A Theoretical Study on the Strain Energy of Carbon Nanobelts." Org. Letters 2016, 18, 1430-1433, DOI: 10.1021/acs.orglett.6b00365.


1: InChI=1S/C48H24/c1-2-26-14-40-28-5-6-31-20-44-32(19-42(31)40)9-10-34-24-48-36(23-46(34)44)12-11-35-21-45-33(22-47(35)48)8-7-30-17-41-29(18-43(30)45)4-3-27-15-37(39(26)16-28)25(1)13-38(27)41/h1-24H

Progress in DFT development and the density they predict

DFT Steven Bachrach 08 May 2017 No Comments

“Getting the right answer for the right reason” – how important is this principle when it comes to computational chemistry? Medvedev and co-workers argue that when it comes to DFT, trends in functional development have overlooked this maxim in favor of utility.1 Specifically, they note that

There exists an exact functional that yields the exact energy of a system from its exact density.

Over the past two decades a great deal of effort has gone into functional development, mostly in an empirical way done usually to improve energy prediction. This approach has a problem:

[It], however, overlooks the fact that the reproduction of exact energy is not a feature of the exact functional, unless the input electron density is exact as well.

So, these authors have studied functional performance with regards to obtaining proper electron densities. Using CCSD/aug-cc-pwCV5Z as the benchmark, they computed the electron density for a number of neutral and cationic atoms having 2, 4, or 10 electrons. Then, they computed the densities with 128 different functionals of all of the rungs of Jacob’s ladder. They find that accuracy was increasing as new functionals were developed from the 1970s to the early 2000s. Since then, however, newer functionals have tended towards poorer electron densities, even though energy prediction has continued to improve. Medvedev et al argue that the recent trend in DFT development has been towards functionals that are highly parameterized to fit energies with no consideration given to other aspects including the density or constraints of the exact functional.

In the same issue of Science, Hammes-Schiffer comments about this paper.2 She notes some technical issues, most importantly that the benchmark study is for atoms and that molecular densities might be a different issue. But more philosophically (and practically), she points out that for many chemical and biological systems, the energy and structure are of more interest than the density. Depending on where the errors in density occur, these errors may not be of particular relevance in understanding reactivity; i.e., if the errors are largely near the nuclei but the valence region is well described then reactions (transition states) might be treated reasonably well. She proposes that future development of functionals, likely still to be driven by empirical fitting, might include other data to fit to that may better reflect the density, such as dipole moments. This seems like a quite logical and rational step to take next.

A commentary by Korth3 summarizes a number of additional concerns regarding the Medvedev paper. The last concern is the one I find most striking:

Even if there really are (new) problems, it is as unclear as before how they can be overcome…With this in mind, it does not seem unreasonable to compromise on the quality of the atomic densities to improve the description of more relevant properties, such as the energetics of molecules.

Korth concludes with

In the meantime, while theoreticians should not rest until they have the right answer for the right reason, computational chemists and experimentalists will most likely continue to be happy with helpful answers for good reasons.

I do really think this is the correct take-away message: DFT does appear to provide good predictions of a variety of chemical and physical properties, and it will remain a widely utilized tool even if the density that underpins the theory is incorrect. Functional development must continue, and Medvedev et al. remind us of this need.


1) Medvedev, M. G.; Bushmarinov, I. S.; Sun, J.; Perdew, J. P.; Lyssenko, K. A., "Density functional theory is straying from the path toward the exact functional." Science 2017, 355, 49-52, DOI: 10.1126/science.aah5975.

2) Hammes-Schiffer, S., "A conundrum for density functional theory." Science 2017, 355, 28-29, DOI: 10.1126/science.aal3442.

3) Korth, M., "Density Functional Theory: Not Quite the Right Answer for the Right Reason Yet." Angew. Chem. Int. Ed. 2017, 56, 5396-5398, DOI: 10.1002/anie.201701894.


Aromaticity Steven Bachrach 01 May 2017 No Comments

I have discussed the circulenes in a few previous posts. Depending on their size, they can be bowls, flat disks, or saddles. A computational study of [7]circulene noted that C2 structure is slightly higher in energy than the Cs form,1 though the C2 form is found in the x-ray structure.2

Now, Miao and co-workers have synthesized the tetrabenzo[7]circulene 1 and also examined its structure using DFT.3

As with the parent compound, a C2 and Cs form were located at B3LYP/6-31G(d,p), and are shown in Figure 1. The C2 form is 7.6 kcal mol-1 lower in energy than the Cs structure, and the two are separated by a transition state (also shown in Figure 1) with a barrier of 12.2 kcal mol-1. The interconversion of these conformations takes place without going through a planar form. The x-ray structure contains only the C2 structure. It should be noted that the C2 structure is chiral, and racemization would take place by the path: 1-Cs1-Cs1-C2*, where 1-C2* is the enantiomer of 1-C2.




Figure 1. B3LYP/6-31G(d,p) optimized structures of 1.


1) Hatanaka, M., "Puckering Energetics and Optical Activities of [7]Circulene Conformers." J. Phys. Chem. A 2016, 120 (7), 1074-1083, DOI: 10.1021/acs.jpca.5b10543.

2) Yamamoto, K.; Harada, T.; Okamoto, Y.; Chikamatsu, H.; Nakazaki, M.; Kai, Y.; Nakao, T.; Tanaka, M.; Harada, S.; Kasai, N., "Synthesis and molecular structure of [7]circulene." J. Am. Chem. Soc. 1988, 110 (11), 3578-3584, DOI: 10.1021/ja00219a036.

3) Gu, X.; Li, H.; Shan, B.; Liu, Z.; Miao, Q., "Synthesis, Structure, and Properties of Tetrabenzo[7]circulene." Org. Letters 2017, DOI: 10.1021/acs.orglett.7b00714.


1: InChI=1S/C44H22/c1-5-13-28-24(9-1)32-19-17-23-18-20-33-25-10-2-6-14-29(25)38-31-16-8-4-12-27(31)35-22-21-34-26-11-3-7-15-30(26)37(28)43-39(32)36(23)40(33)44(38)42(35)41(34)43/h1-22H

SpnF revisited

Uncategorized Steven Bachrach 11 Apr 2017 1 Comment

Medvedev, et al. have examined the cyclization step in the formation of Spinosyn A, which is catalyzed by the putative Diels-Alderase enzyme SpnF.1 This work follows on the computational study done by Houk, Singleton and co-workers,2 which I have discussed in this post (Dynamics in a reaction where a [6+4] and [4+2] cycloadditons compete). In fact, I recommend that you read the previous post before continuing on with this one. In summary, Houk, et al. found that a single transition state connects reactant 1 to both 2 and 3. The experimental product with the enzyme SpnF is 3. In the absence of enzyme, Houk, et al. suggest that reactions will cross the bispericyclic transition state TS-BPC (TS1 in the previous post) leading primarily to 2, which then undergoes a Cope rearrangement to get to product 3. Some molecules will follow pathways that go directly to 3.

The PCM(water)/M06-2x/6-31+G(d) study by Medvedev, et al. first identifies 560 conformations of 3. Next, they identified 384 TSs lying within 30 kcal mol-1 from the lowest TS. These can be classified as either TS-DA (leading directly to 3) or TS-BPC (which may lead to 2 by steepest descent, but can bifurcate towards 3). They opt to utilize the Atoms-in-Molecules theory to identify bond critical points to categorize these TS, and find that 144 are TS-BPC and 240 are TS-DA. (The transition state found by Houk, et al. is the second lowest energy TS found in this study, 0.29 kcal mol-1 higher in energy that the lowest TS and also of TS-BPC type.)

They also examined two alternative routes. First, they propose a path that first takes 1 to 4 via an alternative Diels-Alder reaction, and a second Cope rearrangement (TS-Cope2) takes this to 2, which can then convert to 3 via TS-Cope1. The other route involves a biradical pathway to either A or B. These alternatives prove to be non-competitive, with transition state energies significantly higher than either TS-DA or TS-BPC.

Returning to the set of TS-DA and TS-BPC transition states, while the former are more numerous, the latter are lower in energy. In summary, this study further complicates the complex situation presented by Houk, et. al. In the absence of catalyst, 1 can undergo either a Diels-Alder reaction to 3, or pass through a bispericyclic transition state that can lead to 3, but principally to 2 and then undergo a Cope rearrangement to get to 3. The question that ends my previous post on this subject — “ just what role does the enzyme SpnF play?” — remains to be answered.


1) Medvedev, M. G.; Zeifman, A. A.; Novikov, F. N.; Bushmarinov, I. S.; Stroganov, O. V.; Titov, I. Y.; Chilov, G. G.; Svitanko, I. V., "Quantifying Possible Routes for SpnF-Catalyzed Formal Diels–Alder Cycloaddition." J. Am. Chem. Soc. 2017, 139, 3942-3945, DOI: 10.1021/jacs.6b13243.

2) Patel, A.; Chen, Z.; Yang, Z.; Gutiérrez, O.; Liu, H.-w.; Houk, K. N.; Singleton, D. A., "Dynamically Complex [6+4] and [4+2] Cycloadditions in the Biosynthesis of Spinosyn A." J. Am. Chem. Soc. 2016, 138, 3631-3634, DOI: 10.1021/jacs.6b00017.


1: InChI=1S/C24H34O5/c1-3-21-15-12-17-23(27)19(2)22(26)16-10-7-9-14-20(25)13-8-5-4-6-11-18-24(28)29-21/h4-11,16,18-21,23,25,27H,3,12-15,17H2,1-2H3/b6-4+,8-5+,9-7+,16-10+,18-11+/t19-,20+,21-,23-/m0/s1

2: InChI=1S/C24H34O5/c1-3-19-8-6-10-22(26)15(2)23(27)20-12-11-17-14-18(25)13-16(17)7-4-5-9-21(20)24(28)29-19/h4-5,7,9,11-12,15-22,25-26H,3,6,8,10,13-14H2,1-2H3/b7-4-,9-5+,12-11+/t15-,16-,17-,18-,19+,20+,21-,22+/m1/s1

3: InChI=1S/C24H34O5/c1-3-19-5-4-6-22(26)15(2)23(27)11-10-20-16(9-12-24(28)29-19)7-8-17-13-18(25)14-21(17)20/h7-12,15-22,25-26H,3-6,13-14H2,1-2H3/b11-10+,12-9+/t15-,16+,17-,18-,19+,20-,21-,22+/m1/s1

Automated chemical drawings

Uncategorized Steven Bachrach 21 Mar 2017 5 Comments

Making a good drawing of a chemical structure can be a difficult task. One wants to prepare a drawing that provides a variety of different information in a clean and clear way. We tend to want equal bond lengths, angles that are representative of the atom’s hybridization, symmetrical rings, avoided bond crossings, and the absence of overlapping groups. These ideals may be difficult to manage. Sometimes we might also want to represent something about the actual 3-dimensional shape. So for example, the drawing on the left of Figure 1 properly represents the atom connectivity with no bond crossing, but the figure on the right is probably the image all organic chemists would want to see for cubane.

Figure 1. Two drawing of cubane

For another example, the drawing on the left of Figure 2 nicely captures the relative stereo relationships within D-glucose, but the drawing on the right adds in the fact that the cyclohexyl ring is in a chair conformation. Which drawing is better? Well, it likely is in the eye of the beholder, and the context of the chemistry at hand.

Figure 2. Two drawings of D-glucose.

Frączek has reported on an automated procedure for creating aesthetically pleasing 2-D drawings of chemical structures.1 The method involves optimizing distances between atoms projected onto a 2-D plane, along with rules to try to keep atom lengths and angles similar, and symmetrical rings, and minimize overlapping bonds. He shows a number of nice examples, especially of natural products, where his automated procedure PSM (physical simulation method) provides some very nice drawings, often noticeably superior to those generated by previously proposed schemes for preparing drawings.

Using the web site he has developed (http://omnidepict.p.lodz.pl/), I recreated the structures of some of the molecules I have discussed in this blog. In Figure 3, these are shown side-by-side to my drawings. My drawings were generally done with MDL/Isis/Accelrys/Biovia Draw (available for free for academic users) with an eye towards representing what I think is a suitable view of the molecule based on what I am discussing in the blog post. For many molecules, PSM does a very nice job, sometimes better than what I have drawn, but in some cases PSM produces an inferior drawing. Nonetheless, creating nice chemical drawings can be tedious and PSM offers a rapid option, worthy of at least trying out. Ultimately, what we decide to draw and publish is often an aesthetic choice and each individual must decide on one’s own how best to present one’s work.

My Drawing


Figure 3. Comparison of my drawings vs. drawing made by PSM.


1) Frączek, T., "Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram Generation of Complex Molecules and Ligand–Protein Interactions." J. Chem. Inform. Model. 2016, 56, 2320-2335, DOI: 10.1021/acs.jcim.6b00391.

The strongest base?

Acidity Steven Bachrach 21 Feb 2017 1 Comment

The new benchmark has been set for superbases. The previous record holder was LiO, with a computed proton affinity of 424.9 kcal mol-1. A new study by Poad, et al., examines the dianions of the three isomeric phenyldiacetylides: 1o, 1m, and 1p.1 Their computed proton affinities (G4(MP2)-6X) are 440.6, 427.0, and 425.6 kcal mol-1, respectively. The optimized geometries of these dianions are shown in Figure 1.




Figure 1. Optimized geometries of 1o, 1m, and 1p.

The authors also prepared these bases inside a mass spectrometer. All three deprotonate water, but do not deprotonate methane, though that might be a kinetic issue.

The authors speculate that 1o will be hard to beat as a base since loss of an electron is always a concern with small dianions.


1) Poad, B. L. J.; Reed, N. D.; Hansen, C. S.; Trevitt, A. J.; Blanksby, S. J.; Mackay, E. G.; Sherburn, M. S.; Chan, B.; Radom, L., "Preparation of an ion with the highest calculated proton affinity: ortho-diethynylbenzene dianion." Chem. Sci. 2016, 7, 6245-6250, DOI: 10.1039/C6SC01726F.


1o: InChI=1S/C10H4/c1-3-9-7-5-6-8-10(9)4-2/h5-8H/q-2

1m: InChI=1S/C10H4/c1-3-9-6-5-7-10(4-2)8-9/h5-8H/q-2

1p: InChI=1S/C10H4/c1-3-9-5-7-10(4-2)8-6-9/h5-8H/q-2

Conformationally selective tunneling

carbenes &Schreiner &Tunneling Steven Bachrach 07 Feb 2017 2 Comments

The Schreiner group has again reported an amazing experimental and computational study demonstrating a fascinating quantum mechanical tunneling effect, this time for the trifluoromethylhydroxycarbene (CF3COH) 2.1 (I have made on a number of posts discussing a series of important studies in this field by Schreiner.) Carbene 2 is formed, in analogy to many other hydroxycarbenes, by flash vapor pyrolysis of the appropriate oxoacid 1 and capturing the products on a noble gas matrix.

Carbene 2t is observed by IR spectroscopy, and its structure is identified by comparison with the computed CCSD(T)/cc-pVTZ frequencies. When 2t is subjected to 465 nm light, the signals for 2t disappear within 30s, and two new species are observed. The first species is the cis conformer 2c, confirmed by comparison with its computed CCSD(T)/cc-pVTZ frequencies. This cis conformer remains even with continued photolysis. The other product is determined to be trifluoroacetaldehyde 3. Perhaps most interesting is that 2t will convert to 3 in the absence of light at temperatures between 3 and 30 K, with a half-life of about 144 h. There is little rate difference at these temperatures. These results are quite indicative of quantum mechanical tunneling.

To aid in confirming tunneling, they computed the potential energy surface at CCSD(T)/cc-pVTZ. The trans isomer is 0.8 kcal mol-1 lower in energy that the cis isomer, and this is much smaller than for other hydroxycarbenes they have examined. The rotational barrier TS1 between the two isomer is quite large, 26.4 kcal mol-1, precluding their interchange by classical means at matrix temperatures. The barrier for conversion of 2t to 3 (TS2) is also quite large, 30.7 kcal mol-1, and insurmountable at 10K by classical means. No transition state connecting 2c to 3 could be located. These geometries and energies are shown in Figure 1.






Figure 1. Optimized geometries at CCSD(T)/cc-pVTZ. Relative energies (kcal mol-1) of each species are listed as well.

WKB computations at M06-2X/6-311++G(d,p) predict a half-life of 172 h, in nice agreement with experiment. The computed half-life for deuterated 2t is 106 years, and the experiment on the deuterated analogue revealed no formation of deuterated 3.

The novel component of this study is that tunneling is conformationally selective. The CF3 group stabilizes the cis form probably through some weak HF interaction, so that the cis isomer can be observed, but no tunneling is observed from this isomer. Only the trans isomer has the migrating hydrogen atom properly arranged for a short hop over to the carbon, allowing the tunneling process to take place.


1) Mardyukov, A.; Quanz, H.; Schreiner, P. R., "Conformer-specific hydrogen atom tunnelling in trifluoromethylhydroxycarbene." Nat. Chem. 2017, 9, 71–76, DOI: 10.1038/nchem.2609.


1: =1S/C3HF3O3/c4-3(5,6)1(7)2(8)9/h(H,8,9)

2: InChI=1S/C2HF3O/c3-2(4,5)1-6/h6H

3: InChI=1S/C2HF3O/c3-2(4,5)1-6/h1H

A six-coordinate carbon atom

Aromaticity Steven Bachrach 17 Jan 2017 2 Comments

Hypercoordinated carbon has fascinated chemists since the development of the concept of the tetravalent carbon. The advent of superacids has opened up the world of hypercoordinated species and now a crystal structure of a hexacoordinated carbon has been reported for the C6(CH3)62+ species 1.1

The molecule is prepared by first epoxidation of hexamethyl Dewar benzene, followed by reaction with Magic acid, and crystallized by the addition of HF. The crystal structure shows a pentamethylcyclopentadienyl base capped by a carbon with a methyl group. The x-ray structure is well reproduced by the B3LYP/def2-TZVP structure shown in Figure 1. (While this DFT method predicts a six-member isomer to be slightly lower in energy, MP2 does predict the cage as the lowest energy isomer.)


Figure 1. B3LYP/def2-TZVP optimized geometry of 1.

The Wiberg bond order for the bond between the capping carbon and each carbon of the five-member base is about 0.54, so the sum of the bond orders to the apical carbon is less than 4. The carbon is therefore not hypervalent, but it appears to truly be hypercoordinate. (A topological electron density analysis (AIM) study would have been interesting here.) NICS analysis indicates the cage formed by the apical carbon and the five-member ring expresses 3-D aromaticity. This can be thought of as coming from the C5(CH3)5+ fragment with its 4 electrons and the CCH3+ fragment with two electrons, providing 4n + 2 = 6 electrons for the aromatic cage.


1) Malischewski, M.; Seppelt, K., "Crystal Structure Determination of the Pentagonal-Pyramidal Hexamethylbenzene Dication C6(CH3)62+" Angew. Chem. Int. Ed. 2017, 56, 368-370, DOI: 10.1002/anie.201608795.

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