Search Results for "long c-c"

Another long C-C bond

This is a third post in a series dealing with very short or very long distances between atoms. Ishigaki, Shimajiri, Takeda, Katoono, and Suzuki have prepared three related analogues of hexaphenylethane that all have long C-C bonds.1 The idea is to create a core by fusing two adjacent phenyls into a naphylene, and then protect the long C-C bond through a shell made up of large aryl groups, 1. Fusing another 5-member ring opposite to the stretched C-C bond (2) creates a scissor effect that should stretch that bond further, even more so in the unsaturated version 3.

Their M062-x/6-31G* computations predict an increasing longer C-C bond (highlighted in blue in the above drawing): 1.730 Å in 1, 1.767 Å in 2, and 1.771 Å in 3. The structure of 3 is shown in Figure 3.

Figure 1. M06-2x/6-31G(d) optimized structure of 3.

These three compounds were synthesized, and characterized by IR and Raman spectroscopy. Their x-ray crystal structures at 200 K and 400K were also determined. The C-C distances are 1.742 Å (1), 1.773 Å (2) and 1.798 Å (3) with distances slightly longer at 400 K. These rank as the longest C-C bonds recorded.


1) Ishigaki, Y.; Shimajiri, T.; Takeda, T.; Katoono, R.; Suzuki, T., "Longest C–C Single Bond among Neutral Hydrocarbons with a Bond Length beyond 1.8 Å." Chem 2018, 4, 795-806, DOI: 10.1016/j.chempr.2018.01.011.


1: InChI=1S/C40H26/c1-5-17-32-27(11-1)23-24-28-12-2-6-18-33(28)39(32)36-21-9-15-31-16-10-22-37(38(31)36)40(39)34-19-7-3-13-29(34)25-26-30-14-4-8-20-35(30)40/h1-26H

2: InChI=1S/C42H28/c1-5-13-33-27(9-1)17-18-28-10-2-6-14-34(28)41(33)37-25-23-31-21-22-32-24-26-38(40(37)39(31)32)42(41)35-15-7-3-11-29(35)19-20-30-12-4-8-16-36(30)42/h1-20,23-26H,21-22H2

3: InChI=1S/C42H26/c1-5-13-33-27(9-1)17-18-28-10-2-6-14-34(28)41(33)37-25-23-31-21-22-32-24-26-38(40(37)39(31)32)42(41)35-15-7-3-11-29(35)19-20-30-12-4-8-16-36(30)42/h1-26H

Uncategorized Steven Bachrach 10 Jul 2018 No Comments

Long C-C bonds are not caused by crystal packing forces

Schreiner and Grimme have examined a few compounds (see these previous posts) with long C-C bonds that are found in congested systems where dispersion greatly aids in stabilizing the stretched bond. Their new paper1 continues this theme by examining 1 (again) and 2, using computations, and x-ray crystallography and gas-phase rotational spectroscopy and electron diffraction to establish the long C-C bond.

The distance of the long central bond in 1 is 1.647 Å (x-ray) and 1.630 Å (electron diffraction). Similarly, this distance in 2 is 1.642 Å (x-ray) and 1.632 Å (ED). These experiments discount any role for crystal packing forces in leading to the long bond.

A very nice result from the computations is that most functionals that include some dispersion correction predict the C-C distance in the optimized structures with an error of no more than 0.01 Å. (PW6B95-D3/DEF2-QZVP structures are shown in Figure 1.) Not surprisingly, HF and B3LYP without a dispersion correction predict a bond that is too long.) MP2 predicts a distance that is too short, but SCS-MP2 does a very good job.



Figure 1. PW6B95-D3/DEF2-QZVP optimized structures of 1 and 2.


1) Fokin, A. A.; Zhuk, T. S.; Blomeyer, S.; Pérez, C.; Chernish, L. V.; Pashenko, A. E.; Antony, J.; Vishnevskiy, Y. V.; Berger, R. J. F.; Grimme, S.; Logemann, C.; Schnell, M.; Mitzel, N. W.; Schreiner, P. R., "Intramolecular London Dispersion Interaction Effects on Gas-Phase and Solid-State Structures of Diamondoid Dimers." J. Am. Chem. Soc. 2017, 139, 16696-16707, DOI: 10.1021/jacs.7b07884.


1: InChI=1S/C28H38/c1-13-7-23-19-3-15-4-20(17(1)19)24(8-13)27(23,11-15)28-12-16-5-21-18-2-14(9-25(21)28)10-26(28)22(18)6-16/h13-26H,1-12H2

2: InChI=1S/C26H34O2/c1-11-3-19-15-7-13-9-25(19,21(5-11)23(27-13)17(1)15)26-10-14-8-16-18-2-12(4-20(16)26)6-22(26)24(18)28-14/h11-24H,1-10H2

adamantane &DFT &Grimme &MP &Schreiner Steven Bachrach 25 Jun 2018 No Comments

Dispersion leads to long C-C bonds

Schreiner has expanded on his previous paper1 regarding alkanes with very long C-C bonds, which I commented upon in this post. He and his colleagues report2 now a series of additional diamond-like and adamantane-like sterically congested alkanes that are stable despite have C-C bonds that are longer that 1.7 Å (such as 1! In addition they examine the structures and rotational barriers using a variety of density functionals.



For 2, the experimental C-C distance is 1.647 Å. A variety of functionals all using the cc-pVDZ basis predict distances that are much too long: B3LYP, B96, B97D, and B3PW91. However, functionals that incorporate some dispersion, either through an explicit dispersion correction (Like B3LYP-D and B2PLYP-D) or with a functional that address mid-range or long range correlation (like M06-2x) or both (like ωB97X-D) all provide very good estimates of this distance.

On the other hand, prediction of the rotational barrier about the central C-C bond of 2 shows different functional performance. The experimental barrier, determined by 1H and 13C NMR is 16.0 ± 1.3 kcal mol-1. M06-2x, ωB97X-D and B3LYP-D, all of which predict the correct C-C distance, overestimate the barrier by 2.5 to 3.5 kcal mol-1, outside of the error range. The functionals that do the best in getting the rotational barrier include B96, B97D and PBE1PBE and B3PW91. Experiments and computations of the rotational barriers of the other sterically congested alkanes reveals some interesting dynamics, particularly that partial rotations are possible by crossing lower barrier and interconverting some conformers, but full rotation requires passage over some very high barriers.

In the closing portion of the paper, they discuss the possibility of very long “bonds”. For example, imagine a large diamond-like fragment. Remove a hydrogen atom from an interior position, forming a radical. Bring two of these radicals together, and their computed attraction is 27 kcal mol-1 despite a separation of the radical centers of more than 4 Å. Is this a “chemical bond”? What else might we want to call it?

A closely related chemical system was the subject of yet another paper3 by Schreiner (this time in collaboration with Grimme) on the hexaphenylethane problem. I missed this paper somehow near
the end of last year, but it is definitely worth taking a look at. (I should point out that this paper was already discussed in a post in the Computational Chemistry Highlights blog, a blog that acts as a journals overlay – and one I participate in as well.)

So, the problem that Grimme and Schreiner3 address is the following: hexaphenylethane 3 is not stable, and 4 is also not stable. The standard argument for their instabilities has been that they are simply too sterically congested about the central C-C bond. However, 5 is stable and its crystal structure has been reported. The central C-C bond length is long: 1.67 Å. But why should 5 exist? It appears to be even more crowded that either 3 or 4. TPSS/TZV(2d,2p) computations on these three compounds indicate that separation into the two radical fragments is very exoergonic. However, when the “D3” dispersion correction is included, 3 and 4 remain unstable relative to their diradical fragments, but 5 is stable by 13.7 kcal mol-1. In fact, when the dispersion correction is left off of the t-butyl groups, 5 becomes unstable. This is a great example of a compound whose stability rests with dispersion attractions.

3: R1 = R2 = H
4: R1 = tBu, R2 = H
5: R1 = H, R2 = tBu


(1) Schreiner, P. R.; Chernish, L. V.; Gunchenko, P. A.; Tikhonchuk, E. Y.; Hausmann, H.; Serafin, M.; Schlecht, S.; Dahl, J. E. P.; Carlson, R. M. K.; Fokin, A. A. "Overcoming lability of extremely long alkane carbon-carbon bonds through dispersion forces," Nature 2011, 477, 308-311, DOI: 10.1038/nature10367

(2) Fokin, A. A.; Chernish, L. V.; Gunchenko, P. A.; Tikhonchuk, E. Y.; Hausmann, H.; Serafin, M.; Dahl, J. E. P.; Carlson, R. M. K.; Schreiner, P. R. "Stable Alkanes Containing Very Long Carbon–Carbon Bonds," J. Am. Chem. Soc., 2012, 134, 13641-13650, DOI: 10.1021/ja302258q

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

Grimme &Schreiner Steven Bachrach 25 Sep 2012 4 Comments

A long C-C bond

Compounds with long C-C bonds have typically been designed by placing large, sterically bulky groups attached to the two carbons. Not only does this lead to a longer bond (like the 1.67 Å C-C bond in 1) but these bulky groups also weaken the bond. This leads to molecules that tend to be difficult to isolate.

1 R = t-But

Schreiner has taken an alternative approach: design a sterically crowded molecules that is stabilized by dispersive forces between the large groups!1 The dimer formed from diamantane 2 was prepared and isolated. The C-C distance is quite long: 1.647 Å. The compound is stable up to at least 300 ° C.


Computations of 2 were performed with a variety of density functional, all of which predict a long C-C bond. The bond dissociation energy of 2 is predicted to be 43.9 kcal mol-1 at B3LYP/6-31G(d,p), a value consistent with the long CC bond. However, B3LYP does not account for dispersion. The HH distances between the two diamantyl groups range from 1.94 – 2.28 Å, suggesting that there could be appreciable dispersion stabilization. In fact, computing the BDE with B3LYP+D (Grimme’s dispersion correction) or B97D or M06-2x (all of which account for dispersion to some extent), predicts a much stronger bond, with the BDE ranging from 65-71 kcal mol-1! Here is a stable molecule with a stroing, yet long C-C bond – where a good deal of the strength results not form the interaction between the two atoms of the formal bond, but rather from the energy associated form interactions across the entire molecule. This is a true delocalization effect!

Figure 1. B3LYP-D/6-31G(d,p) optimized structure of 2.


(1) Schreiner, P. R.; Chernish, L. V.; Gunchenko, P. A.; Tikhonchuk, E. Y.; Hausmann, H.; Serafin, M.; Schlecht, S.; Dahl, J. E. P.; Carlson, R. M. K.; Fokin, A. A., "Overcoming lability of extremely long alkane carbon-carbon bonds through dispersion forces," Nature, 2011, 477, 308-311, DOI: 10.1038/nature10367.


1: InChI=1/C86H126/c1-73(2,3)55-37-56(74(4,5)6)44-67(43-55)85(68-45-57(75(7,8)9)38-58(46-68)76(10,11)12

2: InChI=1/C28H38/c1-13-7-23-19-3-15-4-20(17(1)19)24(8-13)27(23,11-15)28-12-16-5-21-18-2-14(9-25(21)28)

Schreiner Steven Bachrach 01 Nov 2011 9 Comments

Long C-O bonds

I have written a number of posts discussing long C-C bonds (here and here). What about very long bonds between carbon and a heteroatom? Well, Mascal and co-workers1 have computed the structures of some oxonium cations that express some very long C-O bonds. The champion, computed at MP2/6-31+G**, is the oxatriquinane 1, whose C-O bond is predicted to be 1.602 Å! (It is rather disappointing that the optimized structures are not included in the supporting materials!) The long bond is attributed not to dispersion forces, as in the very long C-C bonds (see the other posts), but rather to σ(C-H) or σ(C-C) donation into the σ*(C-O) orbital.


Inspired by these computations, they went ahead and synthesized 1 and some related species. They were able to get crystals of 1 as a (CHB11Cl11) salt. The experimental C-O bond lengths for the x-ray crystal study are 1.591, 1.593, and 1.622 Å, confirming the computational prediction of long C-O bonds.

As an aside, they also noted many examples of very long C-O distances within the Cambridge
Structural database that are erroneous – a cautionary note to anyone making use of this database to identify unusual structures.


(1) Gunbas, G.; Hafezi, N.; Sheppard, W. L.; Olmstead, M. M.; Stoyanova, I. V.; Tham, F. S.; Meyer, M. P.; Mascal, M. "Extreme oxatriquinanes and a record C–O bond length," Nat. Chem. 2012, 4, 1018-1023, DOI: 10.1038/nchem.1502


1: InChI=1S/C21H39O/c1-16(2,3)19-10-12-20(17(4,5)6)14-15-21(13-11-19,22(19)20)18(7,8)9/h10-15H2,1-9H3/q+1/t19-,20+,21-

Uncategorized Steven Bachrach 07 Jan 2013 1 Comment

The longest straight chain alkane

The role of dispersion in understanding organic chemistry, both structure and reactivity, is truly coming into prominence (see for example this blog post for a compound whose stability is the result of dispersion). This has been driven in part by new computational techniques to properly account for dispersion. An interesting recent example is the structure of long chain alkanes, with a question posed and answered by Mata and Suhm:1 What is the largest alkane whose most stable conformation is the extended chain?

The question is attacked by computation and experiment. The computational methodology involves corrections to the local MP2-F12 energy involving the separation of orbital pairs that are treated with a coupled clusters method. The straight chain (having only anti arrangements about the C-C bonds) and the hairpin conformer (having three gauche arrangements) were completely optimized. The C17H36 hairpin isomer is shown in Figure 1. For chains with 16 or fewer carbons, the all-anti straight chain is lower in energy, but for chains with 17 or more carbon atoms, the hairpin is lower in energy. Gas-phase low temperature IR and Raman spectra suggest that dominance of the hairpin occurs when the chain has 18 carbons, though careful analysis suggests that this is likely an upper bound. At least tentatively the answer to the question is that heptadecane is likely the longest alkane with a straight chain, but further lower temperature experiments are needed to see if the C16 chain might fold as well.

Figure 1. Optimized geometry of the hairpin conformation of heptadecane.

(I thank Dr. Peter Schreiner for bringing this paper to my attention.)


(1) Lüttschwager, N. O. B.; Wassermann, T. N.; Mata, R. A.; Suhm, M. A. "The Last Globally Stable Extended Alkane," Angew. Chem. Int. Ed. 2012, ASAP, DOI: 10.1002/anie.201202894.


Heptadecane: InChI=1S/C17H36/c1-3-5-7-9-11-13-15-17-16-14-12-10-8-6-4-2/h3-17H2,1-2H3

Uncategorized Steven Bachrach 10 Sep 2012 3 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

MD studies of simple pericyclic reactions

At the recent ACS meeting in New Orleans, Ken Houk spoke at the Dreyfus award session in honor of Michele Parrinello. Ken’s talk included discussion of some recent molecular dynamics studies of pericyclic reactions. Because of their similarities in approaches and observations, I will discuss three recent papers from his group (which Ken discussed in New Orleans) in this post.

The Cope rearrangement, a fundamental organic reaction, has been studied extensively by computational means (see Chapter 4.2 of my book). Mackey, Yang, and Houk examine the degenerate Cope rearrangement of 1,5-hexadiene with molecular dynamics at the (U)B3LYP/6-31G(d) level.1 They examined 230 trajectories, and find that of the 95% of them that are reactive, 94% are trajectories that directly cross through the transition zone. By this, Houk means that the time gap between the breaking and forming C-C bonds is less than 60 fs, the time for one C-C bond vibration. The average time in the transition zone is 35 fs. This can be thought of as “dynamically concerted”. For the other few trajectories, a transient diradical with lifetime of about 100 fs is found.

The dimerization of cyclopentadiene finds the two [4+2] pathways merging into a single bispericylic transition state. 2 Only a small minority (13%) of the trajectories sample the region about the Cope rearrangement that interconverts the two mirror image dimers. These trajectories average about 60 fs in this space, which comes from the time separation between the formation of the two new C-C bonds. The majority of the trajectories quickly pass through the dimerization transition zone in about 18 fs, and avoid the Cope TS region entirely. These paths can be thought of as “dynamically concerted”, while the other set of trajectories are “dynamically stepwise”. It should be noted however that the value of S2 in the Cope transition zone are zero and so no radicals are being formed.

Finally, Yang, Dong, Yu, Yu, Li, Jamieson, and Houk examined 15 different reactions that involve ambimodal (i.e. bispericyclic) transition states.3 They find a strong correlation between the differences in the bond lengths of the two possible new bond vs. their product distribution. So for example, in the reaction shown in Scheme 1, bond a is the one farthest along to forming. Bond b is slightly shorter than bond c. Which of these two is formed next is dependent on the dynamics, and it turns out the Pab is formed from 73% of the trajectories while Pac is formed only 23% of the time. This trend is seen across the 15 reaction, namely the shorter of bond b or c in the transition state leads to the larger product formation. When competing reactions involve bonds with differing elements, then a correlation can be found with bond order instead of with bond length.

Scheme 1


1) Mackey, J. L.; Yang, Z.; Houk, K. N., "Dynamically concerted and stepwise trajectories of the Cope rearrangement of 1,5-hexadiene." Chem. Phys. Lett. 2017, 683, 253-257, DOI: 10.1016/j.cplett.2017.03.011.

2) Yang, Z.; Zou, L.; Yu, Y.; Liu, F.; Dong, X.; Houk, K. N., "Molecular dynamics of the two-stage mechanism of cyclopentadiene dimerization: concerted or stepwise?" Chem. Phys. 2018, in press, DOI: 10.1016/j.chemphys.2018.02.020.

3) Yang, Z.; Dong, X.; Yu, Y.; Yu, P.; Li, Y.; Jamieson, C.; Houk, K. N., "Relationships between Product Ratios in Ambimodal Pericyclic Reactions and Bond Lengths in Transition Structures." J. Am. Chem. Soc. 2018, 140, 3061-3067, DOI: 10.1021/jacs.7b13562.

Cope Rearrangement &Diels-Alder &Dynamics &Houk Steven Bachrach 07 May 2018 No Comments

Triplet cyclobutadiene

Cyclobutadiene has long fascinated organic chemists. It is the 4e analogue of the 6e benzene molecule, yet it could hardly be more different. Despite nearly a century of effort, cyclobutadiene analogues were only first prepared in the 1970s, reflecting its strong antiaromatic character.

Per-trimethylsilylcyclobutadiene 1 offers opportunities to probe the properties of the cyclobutadiene ring as the bulky substituents diminish dimerization and polymerization of the reactive π-bonds. Kostenko and coworkers have now reported on the triplet state of 1.1 They observe three EPR signals of 1 at temperatures above 350 K, and these signals increase in area with increasing temperature. This is strong evidence for the existence of triplet 1 in equilibrium with the lower energy singlet. Using the variable temperature EPR spectra, the singlet triplet gap is 13.9 ± 0.8 kcal mol-1.

The structures of singlet and triplet 1 were optimized at B3LYP-D3/6-311+G(d,p) and shown in Figure 1. The singlet is the expected rectangle, with distinctly different C-C distance around the ring. The triplet is a square, with equivalent C-C distances. Since both the singlet and triplet states are likely to have multireference character, the energies of both states were obtained at RI-MRDDCI2-CASSCF(4,4)/def2-SVP//B3LYPD3/6-311+G(d,p) and give a singlet-triplet gap of 11.8 kcal mol-1, in quite reasonable agreement with experiment.



Figure 1. Optimized geometries of singlet and triplet 1.


1. Kostenko, A.; Tumanskii, B.; Kobayashi, Y.; Nakamoto, M.; Sekiguchi, A.; Apeloig, Y., "Spectroscopic Observation of the Triplet Diradical State of a Cyclobutadiene." Angew. Chem. Int. Ed. 2017, 56, 10183-10187, DOI: 10.1002/anie.201705228.


1: InChI=1S/C16H36Si4/c1-17(2,3)13-14(18(4,5)6)16(20(10,11)12)15(13)19(7,8)9/h1-12H3

Aromaticity &cyclobutadiene Steven Bachrach 11 Sep 2017 1 Comment


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

Aromaticity &nanohoops Steven Bachrach 22 May 2017 No Comments

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