Archive for the 'adamantane' Category

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 1 Comment

1-Adamantyl cation – Predicting its NMR spectra

What is required in order to compute very accurate NMR chemical shifts? Harding, Gauss and Schleyer take on the interesting spectrum of 1-adamantyl cation to try to discern the important factors in computing its 13C and 1H chemical shifts.1


To start, the chemical shifts of 1-adamtyl cation were computed at B3LYP/def2-QZVPP and
MP2/qz2p//MP2/cc-pVTZ. The root means square error (compared to experiment) for the carbon chemical shifts is large: 12.76 for B3LYP and 6.69 for MP2. The proton shifts are predicted much more accurately with an RMS error of 0.27 and 0.19 ppm, respectively.

The authors speculate that the underlying cause of the poor prediction is the geometry of the molecule. The structure of 1 was optimized at HF/cc-pVTZ, MP2/cc-pVTZ and CCSD(T)/pVTZ and then the chemical shifts were computed using MP2/tzp with each optimized geometry. The RMS error of the 12C chemical shifts are HF/cc-pVTZ: 9.55, MP2/cc-pVTZ: 5.62, and CCSD(T)/pVTZ: 5.06. Similar relationship is seen in the proton chemical shifts. Thus, a better geometry does seem to matter. The CCSD(T)/pVTZ optimized structure of 1 is shown in Figure 1.


Figure 1. CCSD(T)/pVTZ optimized structure of 1.

Unfortunately, the computed chemical shifts at CCSD(T)/qz2p//CCSD(T)/cc-pVTZ are still in error; the RMS is 4.78ppm for the carbon shifts and 0.26ppm for the proton shifts. Including a correction for the zero-point vibrational effects and adjusting to a temperature of 193 K to match the experiment does reduce the error; now the RMS for the carbon shifts is 3.85 ppm, with the maximum error of 6 ppm for C3. The RMS for the proton chemical shifts is 0.21ppm.

The remaining error they attribute to basis set incompleteness in the NMR computation, a low level treatment of the zero-point vibrational effects (which were computed at HF/tz2p), neglect of the solvent, and use of a reference in the experiment that was not dissolved in the same media as the adamantyl cation.

So, to answer our opening question – it appears that a very good geometry and treatment of vibrational effects is critical to accurate NMR shift computation of this intriguing molecule. Let the
computational chemist beware!


(1) Harding, M. E.; Gauss, J.; Schleyer, P. v. R., "Why Benchmark-Quality Computations Are Needed To Reproduce 1-Adamantyl Cation NMR Chemical Shifts Accurately," J. Phys. Chem. A, 2011, 115, 2340-2344, DOI: 10.1021/jp1103356


1: InChI=1/C10H15/c1-7-2-9-4-8(1)5-10(3-7)6-9/h7-9H,1-6H2/q+1

adamantane &NMR &Schleyer Steven Bachrach 18 Jul 2011 4 Comments

Inverted adamantane

There is a mystique surrounding chemical torture. Just how much strain can one subject a poor old carbon atom to? We construct such tortured molecules as cubane and cyclopentyne and trans-fused bicyclo[4.1.0]heptane. Inverted carbons – think of propellanes – are also a fruitful arena for torturing hydrocarbons. Now, Irikura has examined inverted adamantane inv-1.1

The MP2/6-31G(d) optimized geometries of 1 and inv-1 and the transition state separating them are displayed in Figure 1. The inverted structure is a local energy minimum, lying 105 kcal mol-1 above 1.2 The barrier for rearrangement of the inverted adamantane into adamantane, which involved a cleave of a C-C bond, is 17 kcal mol-1, which implies a half-life of 30 ms at 298K and and 2 days at 195 K. The perfluoro isomer has a higher barrier (32 kcal mol-1) and a longer half-life (110 years at 298K).




Table 1. MP2/6-31G(d) optimized geometries of 1, inv-1, and the transition state connecting them.1

So, inv-1 has some kinetic stability. It also has little computed reactivity with water, oxygen, or a second molecule of inv-1. Irikura, however, did not compute reactions that might lead to loss of a hydride from inv-1, which would give a non-classical cation.

As might be expected, the spectroscopic properties of inv-1 are unusual. The C-H vibrational
frequency for the inverted hydrogen is 3490 cm-1 and the C-C-H bend is also 300 cm-1 higher than in 1. The NMR shifts for the inverted methane group are 7.5 ppm for the hydrogen and 21 ppm for the carbon atom.

Irikura ends the article, “Experimental verification (or refutation) of [inv-1] presents a novel synthetic challenge.” Let’s hope someone picks up the gauntlet!


(1) Irikura, K. K., "In-Adamantane, a Small Inside-Out Molecule," J. Org. Chem. 2008, 73, 7906-7908, DOI: 10.1021/jo801806w.

(2) The energies are computed as Eestimate = E[CCSD(T)/6-31G(d)//MP2/6-31G(d)] + E[MP2/aug-cc-pVTZ//MP2/6-31G(d)] – E[MP2/6-31G(d)//MP2/6-31G(d)].


1: InChI=1/C10H16/c1-7-2-9-4-8(1)5-10(3-7)6-9/h7-10H,1-6H2

adamantane Steven Bachrach 17 Nov 2008 1 Comment