Archive for June, 2011

Aromaticity of Perylene Diimide

Changing the number of π-electrons in a molecule should alter its aromaticity and antiaromaticity – if the Hückel rule holds! Iron, Cohen and Rybtchinski1 look at an interesting polycyclic aromatic perylene diimide 1 and its dianion and evaluate the aromaticity and reactivity of these species, using both experiment and computation.


The M06-2x/6-31++G** geometries of 1 and its dianion 12- are shown in Figure 1. 1 can be thought of as two naphthalenyl groups joined together by single bond (their distance is 1.479 Å). In the dianion, the bond distance between the two naphthyl groups (making the central 6-member ring) is shorter, 1.425 Å. In addition the C-C(O) bond of the imide ring shortens from 1.485 to 1.441 Å in going from the neutral to the dianion, with the C=O bond also lengthening, from 1.214 to 1.243 Å. These geometric changes suggest the formation of an aromatic central six-member ring, and perhaps some aromaticity in the diimide rings, too.



Figure 1. M06-2x optimized structures of 1 and 12-.

The changes are reflected in the NICS(1) values. In 1, the NICS values for each ring of the naphthyl group is -9.31, as expected for an aromatic 6-member ring. The diimide has a NICS value of -0.01, indicating a non-aromatic ring, and the central ring has a NICS value of +1.78, suggesting some slight antiaromatic character. Significant changes come about with the reduction to the dianion. The central ring now has a NICS value of -9.10, indicating an aromatic ring. The naphthyl rings have NICS values of -3.94 and the diimide ring has a value of -4.53.

So, the dianion 12- species appears to be more aromatic than the neutral 1. This is reflected in its chemistry. The dianion of pegylated 1 is actually stable in water, though it is readily oxidized by air. Its stability in water is understood in terms of the computed reaction energy with water, which is quite positive due to that aromatic stabilization of 12-. This is compared with the computed negative free energies for the reaction of other dianions with water, such as the anthracenyl, and perylenyl dianions.


1) Iron, M. A.; Cohen, R.; Rybtchinski, B., "On the Unexpected Stability of the Dianion of Perylene Diimide in Water – A Computational Study," J. Phys. Chem. A, 2011, 115, 2047-2056, DOI: 10.1021/jp1107284


1: InChI=1/C24H10N2O4/c27-21-13-5-1-9-10-2-6-15-20-16(24(30)26-23(15)29)8-4-12(18(10)20)11-3-7-14(22(28)25-21)19(13)17(9)11/h1-8H,(H,25,27,28)(H,26,29,30)/f/h25-26H

Aromaticity Steven Bachrach 28 Jun 2011 2 Comments

Not a Penrose Stair – but still interesting!

Henry Rzepa brought this interesting paper to my attention via his blog post. I have a few comments too.

Isobe and co-workers prepared the interesting polycyclic aromatic compound 1, which they represent with the picture given below.1 The molecule is non-planar due to the clash of the interior hydrogens. If you stare at this picture long enough you might decide that something looks amiss. If you start at the lower left phenyl ring of the top segment and move counterclockwise you would move upwards, out of the plane of the page. Then you cross into the lower half and continue the counter clockwise motion, again you climb upwards out of the page. And then you cross back over to the top half and your back where you started – but you’ve been climbing uphill all the time! This might remind you of the famous Escher drawing Ascending and Descending.


So, what’s the catch? Well, the molecule does exist and its crystal structure shows the key. The molecule is in fact of D2 symmetry, so the upper and lower halves of the molecule are twisted in and out of the plane. B3LYP/6-31G(d,p) computations on the parent compound 2 indicate the D2 symmetry of the ground state (see Figure 1). (Don’t forget to click on the structure to be able to manipulate the structure!) This is a chiral species. Racemization occurs through a barrier of 10.1 kcal mol-1 (3) which connects to the meso structure 4, Passing then through the mirror image of 3 completes the process, joining to the mirror image of 2.




I think the title is a bit misleading here – the molecular expression is misleading as its drawn in 1, but the full 3D structure shows no such illusion; the molecule is in fact not a Penrose Stair. But 1 certainly possesses a structure of interesting shape and topology!


(1) Nakanishi, W.; Matsuno, T.; Ichikawa, J.; Isobe, H., "Illusory Molecular Expression of “Penrose Stairs” by an Aromatic Hydrocarbon," Angew. Chem. Int. Ed., 2011, ASAP, DOI: 10.1002/anie.201102210


1: InChI=1/C52H52/c1-5-9-13-37-25-41-26-38(14-10-6-2)44-22-19-35-30-48(44)51(41)47-29-33(17-21-43(37)47)34-18-23-45-39(15-11-7-3)27-42-28-40(16-12-8-4)46-24-20-36(35)32-50(46)52(42)49(45)31-34/h17-32H,5-16H2,1-4H3

2: InChI=1/C36H20/c1-9-25-10-2-22-6-15-29-18-32(22)35(25)31-17-27(13-5-21(1)31)28-14-7-23-3-11-26-12-4-24-8-16-30(29)20-34(24)36(26)33(23)19-28/h1-20H

Aromaticity Steven Bachrach 20 Jun 2011 No Comments

Methylhydroxycarbene and tunelling control

Another remarkable piece of science from the Schreiner and Allen groups has appeared demonstrating the critical importance of combining experiment with computations.1 (This one will surely be in the running for computational chemistry paper of the year.) Once again they examine tunneling from a carbene intermediate, but this time with an amazing conclusion that will have impact on chemistry textbooks!

Schreiner and Allen have previously examined a number of hydroxycarbenes (see these posts: A, B, C) and have found tunneling to be the main exit channel from these carbenes. The tunneling passes through barriers that are as large as 30 kcal mol-1, and as expected, the deuterium labeled analogues have tunneling half lives that are exceptionally long, like 4000 years.

Now they examine methylhydroxycarbene 1,1 which is interesting because there are two possible exit channels, leading to acetaldehyde 2 or vinyl alcohol 3. Previous gas-phase pyrolysis of pyruvic acid suggested the intermediacy of 1, which rearranges to 2 much more rapidly than to 3. However, G1 computations predict the barrier to 3 is smaller than the barrier to 2,2 which should mean that 2 is the kinetic product!

Methylhydroxycarbene 1 was prepared by flash pyrolysis of pyruvic acid with capture of the products in an argon matrix. The carbene 1 was characterized by IR. The predicted frequencies (CCSD(T)/cc-pCVTZ – with corrections for anharmonicity) of 9 of the 11 bands of 1 are within 8 cm-1 of the experimental frequencies. The OH and OD stretches, the ones not in agreement, are likely to be perturbed by the matrix. The predicted (MRCC/aug-cc-pVTZ) and experimental UV spectrum are also in close agreement.

Holding the matrix at 11 K and following the spectra of 1-3 led to the following important kinetic results: the half-life for formation of 2 is 66 min with no 3 observed to form. In addition, the rate for the deuterium labeled carbene to form 2 was too long for measuring, but was 196 minutes in Kr and 251 minutes in Xe. CCSD(T)/cc-pCVCZ computations followed by focal point methods gives the barrier to form acetaldehyde from 1 as 28.0 kcal mol-1 while that to form vinyl alcohol 3 is much lower: 22.6 kcal mol-1. (The structures of these three molecules and the transition states connecting them are shown in Figure 1.) Apparently, the reaction passes through or over the higher barrier in large preference over passing through or over the lower barrier!






Figure 1. CCSD(T)/cc-pCVTZ optimizes structures of 1-3 and the transition states connecting 1 to 2 and 1 to 3.

Precise mapping of the intrinsic reaction path at CCSD(T)/cc-pCVTZ allows for computing the WKB tunneling probabilities. This leads to the prediction of the half-life for the reaction 12 as 71 minutes, in excellent agreement with experiment. The computed half-life for the deuterium labeled reaction of 400 years and the computed half-life for 13 of 190 days are both in fine agreement with experiment.

Why does the reaction preferentially tunnel through the higher barrier? Well, the tunneling rate is dependent on the square root of the barrier height and linearly on the barrier width. The width is much smaller for the rearrangement to 2. The hydrogen needs to move a shorter amount in proceeding from 1to 2 than to 3, and in the rearrangement to vinyl alcohol a second hydrogen must migrate downwards to form the planar vinyl group. Basically, width beats out the height.

The important conclusion from this paper is the following: in addition to reactions being under kinetic or thermodynamic control, we must now consider a third options – a reaction under tunneling control!

A nice perspective on this paper and its implications has been written by Carpenter, who points out how this adds to our general notion of significant limitations to transition state theory.3


(1) Schreiner, P. R.; Reisenauer, H. P.; Ley, D.; Gerbig, D.; Wu, C.-H.; Allen, W. D., "Methylhydroxycarbene: Tunneling Control of a Chemical Reaction," Science, 2011, 332, 1300-1303, DOI: 10.1126/science.1203761.

(2) Smith, B. J.; Nguyen Minh, T.; Bouma, W. J.; Radom, L., "Unimolecular rearrangements connecting hydroxyethylidene (CH3-C-OH), acetaldehyde (CH3-CH:O), and vinyl alcohol (CH2:CH-OH)," J. Am. Chem. Soc., 1991, 113, 6452-6458, DOI: 10.1021/ja00017a015

(3) Carpenter, B. K., “Taking the High Road and Getting There Before You,” Science, 2011, 332, 1269-1270, DOI: 10.1126/science.1206693.


1: InChI=1/C2H4O/c1-2-3/h3H,1H3

2: InChI=1/C2H4O/c1-2-3/h2H,1H3

3: InChI=1/C2H4O/c1-2-3/h2-3H,1H2

focal point &Schreiner &Tunneling Steven Bachrach 14 Jun 2011 3 Comments

Conformation of propyphenazone

Compounds like antipyrine 1 might be expected to have two pyramidal nitrogens with their substituents on opposite sides of the ring. Interestingly, a new polymorph of propyphenazone 2 has both N-methyl and N-phenyl groups on the same side of the ring. Just how unusual is this?



Roumanos and Kertesz1 have sampled the crystallographic database and found 334 structures with the antipyrine backbone. The vast majority of them have the nitrogen substituents on opposite sides, and a few structures have these groups essential co-planar with the ring. The new propyphenazone structure does seem to be unusual. However, they also performed a BLYP/DNP scan of the potential energy surface of 2. When this surface is overlayed on the distribution of the x-ray structures, one sees that most structures are within 3 kcal mol-1 of the energy minimum (with the nitrogen groups on opposite sides). However, the structure with both groups on the same side is about 4 kcal mol-1 higher in energy than the minimum energy structure, and the nearly planar structures are higher in energy still. Thus, the authors conclude that while this new structure is unusual, it is not an outlier.


(1) Roumanos, M.; Kertesz, M., "Conformations of Antipyrines," J. Phys. Chem.A, 2011, ASAP, DOI: 10.1021/jp201510w


1: InChI=1/C11H12N2O/c1-9-8-11(14)13(12(9)2)10-6-4-3-5-7-10/h3-8H,1-2H3

2: InChI=1/C14H18N2O/c1-10(2)13-11(3)15(4)16(14(13)17)12-8-6-5-7-9-12/h5-10H,1-4H3

Uncategorized Steven Bachrach 08 Jun 2011 1 Comment