Archive for the 'polycyclic aromatics' Category

Planar cyclooctatetraene?

Here’s another attempt (almost successful!) in creating a planar cyclooctatetraene. Nishininaga and Iyoda have fused silicon and sulfur bridges to the COT framework, hoping to force the 8-member ring out of its preferred tub-shape into a planar structure.1 They report the synthesis of 1, 2, and 3b along with their x-ray structures. They also calculated the structures at B3LYP/6-31G(d,p) for 1-4 , and these optimized structures are shown in Figure 1.



7.0° (for 3b)
3.2° (for 3a)


Figure 1. B3LYP/6-31G(d,p) optimized geometries of 1-4. The experimental (top) and computed (Bottom in italics) value of α are listed for each compound.1

The bent angle α is defined at the angle between the two planes that define the bottom of the tub and one of the sides. For COT itself, this angle is 40°, decidedly non-planar – as expected for a molecule avoiding the antiaromatic character it would have in its planar conformation. The computed and experimental values of α are shown in Figure 1. 4 is tub shaped. The value of α for 1 is about 18° – still tub shaped but flattened. But 2 and 3 are nearly planar, with experimental values of α about 3° and the computed values are similar.

So what is the character of the 8-member ring in these compounds. The computed NICS(0) values are 3.8 ppm for 4, the expected small value for a non-aromatic compound. (Note that the NICS value for COT is 2.9 ppm.) The values are much more positive for the other compounds: 12.7 ppm for 1, 17.4 ppm for 2, and 15.4 ppm for 3a. These compounds therefore display antiaromatic character yet they are isolable compounds!


(1) Ohmae, T.; Nishinaga, T.; Wu, M.; Iyoda, M., "Cyclic Tetrathiophenes Planarized by Silicon and Sulfur Bridges Bearing Antiaromatic Cyclooctatetraene Core: Syntheses, Structures, and Properties," J. Am. Chem. Soc., 2009, 132, 1066-1074, DOI: 10.1021/ja908161r


1: InChI=1/C20H16S4Si2/c1-25(2)9-5-21-17-13(9)14-10(25)6-22-18(14)20-16-12(8-24-20)26(3,4)11-7-23-19(17)15(11)16/h5-8H,1-4H3/b19-17-,20-18-


3a: InChI=1/C16H4O4S6/c17-25(18)5-1-21-13-9(5)10-6(25)2-23-15(10)16-12-8(4-24-16)26(19,20)7-3-22-14(13)11(7)12/h1-4H/b14-13-,16-15-

3b: InChI=1/C28H36O4S6Si4/c1-39(2,3)25-21-13-14-19(35-26(40(4,5)6)22(14)37(21,29)30)20-16-15-18(17(13)33-25)34-27(41(7,8)9)23(15)38(31,32)24(16)28(36-20)42(10,11)12/h1-12H3/b18-17-,20-19-

4: InChI=1/C16H8S4/c1-5-17-13-9(1)10-2-6-18-14(10)16-12(4-8-20-16)11-3-7-19-15(11)13/h1-8H/b10-9-,12-11-,15-13-,16-14-

Aromaticity &polycyclic aromatics Steven Bachrach 15 Mar 2010 3 Comments

No HH bonding in phenanthrene despite a bond path

I blogged on Bickelhaput’s examination of the stability of kinked vs. linear polycyclic aromatics1 in this post. Bickelhaupt argued against any HH stabilization across the bay region, a stabilization that Matta and Bader2 argued is present based on the fact that there is a bond path linking the two hydrogens.

Grimme and Erker have now added to this story.3 They prepared the dideuterated phenanthrene 1 and obtained its IR and Raman spectra. The splitting of the symmetric (a1) and asymmetric (b1) vibrational frequencies is very small 9-12 cm-1. The computed splitting are in the same range, with very small variation with the computational methodology employed. The small splitting argues against any significant interaction between the two hydrogen (deuterium) atoms. Further, the sign of the coupling between the two vibrations indicates a repulsive interaction between the two atoms. These authors argue that the vibrational splitting is almost entirely due to conventional weak van der Waals interactions, and that there is no “bond” between the two atoms, despite the fact that a bond path connects them. This bond path results simply from two (electron density) basins forced to butt against each other by the geometry of the molecule as a whole.



(1) Poater, J.; Visser, R.; Sola, M.; Bickelhaupt, F. M., "Polycyclic Benzenoids: Why Kinked is More Stable than Straight," J. Org. Chem. 2007, 72, 1134-1142, DOI: 10.1021/jo061637p

(2) Matta, C. F.; Hernández-Trujillo, J.; Tang, T.-H.; Bader, R. F. W., "Hydrogen-Hydrogen Bonding: A Stabilizing Interaction in Molecules and Crystals," Chem. Eur. J. 2003, 9, 1940-1951, DOI: 10.1002/chem.200204626

(3) Grimme, S.; Mück-Lichtenfeld, C.; Erker, G.; Kehr, G.; Wang, H.; Beckers, H. W., H., "When Do Interacting Atoms Form a Chemical Bond? Spectroscopic Measurements and Theoretical Analyses of Dideuteriophenanthrene," Angew. Chem. Int. Ed. 2009, 48, 2592-2595, DOI: 10.1002/anie.200805751


1: InChI=1/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H/i7D,8D

Grimme &polycyclic aromatics Steven Bachrach 12 May 2009 2 Comments

Strain and aromaticity in the [n](2,7)pyrenophanes

Once again into the breach – how much strain can an aromatic species withstand and remain aromatic? Cyranski, Bodwell and Schleyer employ the [n](2,7)pyrenophanes 1 to explore this question.1 As the tethering bridge gets shorter, the pyrene framework must pucker, presumably reducing its aromatic character. Systematic shrinking allows one to examine the loss of aromaticity as defined by aromatic stabilization energy (ASE), magnetic susceptibility exaltation (Λ) and NICS, among other measures.

They examined the series of pyrenophanes where the tethering chain has 6 to 12 carbon atoms. I have shown the structures of three of these compounds in Figure 1. The bend angle α is defined as the angle made between the outside ring plane and the horizon. Relative ASE is computed using Reaction 1, which cleverly avoids the complication of exactly (a) what is the ASE of pyrene itself and (b) what is the strain energy in these compounds.




Figure 1. B3LYP/6-311G** optimized geometries of 1a, 1d, and 1g.1

Reaction 1

The results of the computations for this series of pyrenophanes is given in Table 1. The bending angle smoothly increases with decreasing length of the tether. The ASE decreases in the same manner. The ASE correlates quite well with the bending angle, as does the relative magnetic susceptibility exaltation. The NICS(1) values become less negative with decreasing tether length.

Table 1. Computed values for the pyrenophanes.




Rel. Λc


6(2,7)pyrenophane 1a




-7.8, -4.1

7(2,7)pyrenophane 1b




-8.7, -4.5

8(2,7)pyrenophane 1c




-9.6, -5.2

9(2,7)pyrenophane 1d




-10.6, -5.5

10(2,7)pyrenophane 1e




-11.3, -6.2

11(2,7)pyrenophane 1f




-12.0, -6.4

12(2,7)pyrenophane 1g




-12.6, -7.0





-13.9, -7.8

ain degrees.bin kcal mol-1, from Reaction 1.
cin cgs.ppm. din ppm, for the outer and inner rings.

All of these trends are consistent with reduced aromaticity with increased out-of-plane distortion of the pyrene framework. What may be surprising is the relatively small loss of aromaticity in this sequence. Even though the bend angle is as large as almost 40°, the loss of ASE is only 16 kcal mol-1, only about a quarter of the ASE of pyrene itself. Apparently, aromatic systems are fairly robust!


(1) Dobrowolski, M. A.; Cyranski, M. K.; Merner, B. L.; Bodwell, G. J.; Wu, J. I.; Schleyer, P. v. R.,
"Interplay of π-Electron Delocalization and Strain in [n](2,7)Pyrenophanes," J. Org. Chem., 2008, 73, 8001-8009, DOI: 10.1021/jo8014159


1a: InChI=1/C22H20/c1-2-4-6-16-13-19-9-7-17-11-15(5-3-1)12-18-8-10-20(14-16)22(19)21(17)18/h7-14H,1-6H2

1b: InChI=1/C23H22/c1-2-4-6-16-12-18-8-10-20-14-17(7-5-3-1)15-21-11-9-19(13-16)22(18)23(20)21/h8-15H,1-7H2

1c: InChI=1/C24H24/c1-2-4-6-8-18-15-21-11-9-19-13-17(7-5-3-1)14-20-10-12-22(16-18)24(21)23(19)20/h9-16H,1-8H2

1d: InChI=1/C25H26/c1-2-4-6-8-18-14-20-10-12-22-16-19(9-7-5-3-1)17-23-13-11-21(15-18)24(20)25(22)23/h10-17H,1-9H2

1e: InChI=1/C26H28/c1-2-4-6-8-10-20-17-23-13-11-21-15-19(9-7-5-3-1)16-22-12-14-24(18-20)26(23)25(21)22/h11-18H,1-10H2

1f: InChI=1/C27H30/c1-2-4-6-8-10-20-16-22-12-14-24-18-21(11-9-7-5-3-1)19-25-15-13-23(17-20)26(22)27(24)25/h12-19H,1-11H2

1g: InChI=1/C28H32/c1-2-4-6-8-10-12-22-19-25-15-13-23-17-21(11-9-7-5-3-1)18-24-14-16-26(20-22)28(25)27(23)24/h13-20H,1-12H2

Pyrene: InChI=1/C16H10/c1-3-11-7-9-13-5-2-6-14-10-8-12(4-1)15(11)16(13)14/h1-10H

4,9-dimethylenepyrene: InChI=1/C18H12/c1-11-9-13-5-4-8-16-12(2)10-14-6-3-7-15(11)17(14)18(13)16/h3-10H,1-2H2

Aromaticity &polycyclic aromatics &Schleyer Steven Bachrach 11 Dec 2008 No Comments

Dihydrodiazatetracene: is it antiaromatic?

Schleyer continues his study of aromaticity with a paper1 that picks up on the theme presented in one2 I have previously blogged on – the relationship between a formally aromatic pyrazine and formally antiaromatic dihydropyrazine. He now examines the diazotetracene 1 and it dihydro analogue 2.1 In terms of formal electron count, 1 should be aromatic, just like the all carbon analogue tetracene 3, and 2 should be antiaromatic.

Schleyer used the NICSπzz values obtained in the center of each ring to evaluate the aromatic/antiaromatic character of these three molecules. These calculations were performed using canonical molecular orbitals and repeated using localized molecular orbitals. The results are similar for each method, and the canonical MO values are presented in Table 1. As expected for an aromatic compound, each ring of tetracene 3 has large negative NICS values, indicating that each ring is locally aromatic and the molecule as a whole is aromatic. The same is true for the diazotetracene 1. (In fact the NICS values for 1 and 3 are remarkably similar.) However, for 2, the dihydropyrazine ring has a positive NICS values, indicative of a locally antiaromatic ring. While the three phenyl rings have negative NICS values, these absolute values are smaller than for the rings of 1 or 3, indicating an attenuation of their aromaticity. Nonetheless, the sum of the NICS values of 2 is negative, suggesting that the molecule is globally aromatic, though only marginally so. This is due to the antiaromaticity of the dihydropyrazine ring being delocalized to some extent over the entire molecule. Schleyer, concludes that “large 4n π compounds […] are not appreciably destabilized relative to their 4n+2 π congeners.”

Table 1 NICSπzz (ppm) for each ring of 1-3 and their sum.1






sum = -144.0






sum = -25.9






Sum = -143.4


(1) Miao, S.; Brombosz, S. M.; Schleyer, P. v. R.; Wu, J. I.; Barlow, S.; Marder, S. R.; Hardcastle, K. I.; Bunz, U. H. F., "Are N,N-Dihydrodiazatetracene Derivatives Antiaromatic?," J. Am. Chem. Soc., 2008, 130, 7339-7344, DOI: 10.1021/ja077614p.

(2) Miao, S.; Schleyer, P. v. R.; Wu, J. I.; Hardcastle, K. I.; Bunz, U. H. F., "A Thiadiazole-Fused N,N-Dihydroquinoxaline: Antiaromatic but Isolable," Org. Lett. 2007, 9, 1073-1076, DOI: 10.1021/ol070013i


1: InChI=1/C18H12/c1-2-6-14-10-18-12-16-8-4-3-7-15(16)11-17(18)9-13(14)5-1/h1-12H

2: InChI=1/C16H10N2/c1-2-6-12-10-16-15(9-11(12)5-1)17-13-7-3-4-8-14(13)18-16/h1-10H

3: InChI=1/C16H12N2/c1-2-6-12-10-16-15(9-11(12)5-1)17-13-7-3-4-8-14(13)18-16/h1-10,17-18H

Aromaticity &polycyclic aromatics &Schleyer Steven Bachrach 15 Jul 2008 No Comments

Bergman cyclization and [10]annulenes

In their continuing efforts to build novel aromatic systems, Siegel and Baldridge report the preparation of the decapropyl analogue of the per-ethynylated corrannulene 1.1 They were hoping that this might cyclize to the bowl 2. It is however stable up to 100 °C, however, the analogue 3 was obtained in the initial preparation of decapropyl-1.

The B3LYP/cc-pVDZ optimized structures of 1 and 3 are shown in Figure 1. 1 is bowl-shaped, reflecting the property of corranulene, but interestingly 3 is planar. The geometry of the {10]annulene is interesting as it is more consistent with the alkynyl resonance form B.



Figure 1. B3LYP/cc-pVDZ optimized structures of 1 and 3.1

Siegel and Baldridge speculate that the conversion of 1 → 3 occurs by first undergoing the Bergman cyclization to give 4, which then opens to give 3. Unfortunately, they did not compute the activation barrier for this process. They do suggest that further cyclization to give the hoped for 2 might be precluded by the long distances between radical center and neighboring alkynes in 4, but the radicals are too protected to allowing trapping by the solvent, allowing for the formation of 3.


(1) Hayama, T.; Wu, Y. T.; Linden, A.; Baldridge, K. K.; Siegel, J. S., "Synthesis, Structure, and Isomerization of Decapentynylcorannulene: Enediyne Cyclization/Interconversion of C40R10 Isomers," J. Am. Chem. Soc., 2007, 129, 12612-12613 DOI: 10.1021/ja074403b.


1: InChI=1/C40H10/c1-11-21-22(12-2)32-25(15-5)26(16-6)34-29(19-9)30(20-10)35-28(18-8)27(17-7)33-24(14-4)23(13-3)31(21)36-37(32)39(34)40(35)38(33)36/h1-10H

2: InChI=1/C40H10/c1-2-12-14-5-6-16-18-9-10-20-19-8-7-17-15-4-3-13-11(1)21-22(12)32-24(14)26(16)34-29(18)30(20)35-28(19)27(17)33-25(15)23(13)31(21)36-37(32)39(34)40(35)38(33)36/h1-10H

3: InChI=1/C40H12/c1-9-23-25(11-3)33-27(13-5)29(15-7)35-30(16-8)28(14-6)34-26(12-4)24(10-2)32-22-20-18-17-19-21-31(23)36-37(32)39(34)40(35)38(33)36/h1-8,17-18,31-32H/b18-17-

annulenes &Bergman cyclization &DFT &polycyclic aromatics Steven Bachrach 05 Nov 2007 No Comments

Kinked vs. Straight Polycyclic Benzenoids

Kinked polycyclic benzoids are more stable that their straight chain analogues. For example, the gaseous heat of formation of phenanthrene 1 is 49.6 kcal mol-1 while that of anthracene 2 is 55.2 kcal mol-1.1 This stability of the kinked over the straight chain is reproduced by computation: 1 is 4.24 kcal mol-1 lower in energy than 2 at BLYP/TZ2P.href="#phenanref2">2 The standard explanation for this has been better resonance in 1 than in 2, leading to 1 being more aromatic than 2.

Bader has recently offered at alternative explanation. Topological electron density analysis3 (also referred to as Atoms-In-Molecules, or AIM) examines the electron density distribution to uncover chemically-relevant information. The bond path traces out the ridge of maximum electron density between two atoms, passing through the bond critical point. Bader has argued that the existence of the bond path is the necessary and sufficient condition for a chemical bond. In the AIM analysis of 1, he noted a bond path connecting the hydrogen atoms on C4 and C5.4 These are the hydrogen atoms in the bay region, labeled explicitly in the sketch above. Based on this bond path, and the fact that the bay region hydrogen atoms are stabilized due to charge transfer from carbon, Bader argued that H-H bonding in 1 stabilizes this molecule, accounting for its lower heat of formation than 2.

In a 2007 JOC paper, Bickelhaupt directly attacked this contention.2 The BLYP/TZ2P geometries of 1 and 2 are shown in Figure 1.



Figure 1. BLYP/TZ2P optimized geometries of 1 and 2.2

He approached the problem by examining the reaction of two 2-methtriylphenyl moieties combining to form either 1 or 2 (Scheme 1). The binding energy ΔE is then decomposed into two terms, ΔEprep which is the energy required to deform the triradical fragment 3 from its optimum geometry into the geometry within either 1 or 2, designated as 3(1) or 3(2), and ΔEint which is the interaction energy of the deformed fragments.

Scheme 1.

The deformation energy of the triradical fragment is nearly identical for 1 and 2. Therefore, the interaction energy to from 1 is more negative (stabilizing) than to form 2. The interaction energy for 1 was also obtained in two other ways. First, 3 was fixed to its geometry in 2 (i.e., 3(2)) with the distance of the two forming C-C bonds also that of 2. The interaction energy defined this way is -0.69 kcal mol-1, indicating a preference for aligning the fragments in the orientation of phenanthrene. Bickelhaupt further partitions the interaction energy to σ- and π-components, and finds the stabilization of the model interaction energy is dominated by π-interactions, not the σ-interactions one would expect from Bader’s model of H-H stabilization. Allowing the C-C distances between the two 3(2) fragments to adjust to those in 1 further strengthens the interaction energy to -2.49 kcal mol-1. The geometrical changes allow for the p-bonds to strengthen (by shortening the C9-C10 distance), and the repulsion between the bay area hydrogen atoms to diminish (by lengthening the C4a-C4b distance).

Bickelhaupt argues that the presence of a bond path may simply be due to two atomic basins being forced to bump into each other, whether these contacts be stabilizing or destabilizing. For example, two benzene molecules arranged such that a C-H bond points toward the C-H bond of another (see 4), a bond path will connect the two hydrogen atoms and the AIM energies of these two hydrogen atoms will indicate a net stabilization. He concludes by calling into question the basis for the claim that a bond path is the necessary and sufficient conditions for a chemical bond.


1: InChI=1/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H

2: InChI=1/C14H10/c1-2-6-12-10-14-8-4-3-7-13(14)9-11(12)5-1/h1-10H


(1) Cox, J. D.; Pilcher, G. Thermochemistry of Organic and Organometallic Compounds; Academic Press: New York, 1970.

(2) Poater, J.; Visser, R.; Sola, M.; Bickelhaupt, F. M., "Polycyclic Benzenoids: Why Kinked is More Stable than Straight," J. Org.Chem. 2007, 72, 1134-1142, DOI: 10.1021/jo061637p

(3) Bader, R. F. W. Atoms in Molecules: A Quantum Theory; Clarendon Press: Oxford, UK, 1990.

(4) Matta, C. F.; Hernández-Trujillo, J.; Tang, T.-H.; Bader, R. F. W., "Hydrogen-Hydrogen Bonding: A Stabilizing Interaction in Molecules and Crystals," Chem. Eur. J. 2003, 9, 1940-1951, DOI: 10.1002/chem.200204626

polycyclic aromatics Steven Bachrach 27 Jul 2007 1 Comment

Antiaromatic but Isolable

In the pursuit of further elucidation of just what the concepts “aromatic” and “antiaromatic” mean, Schleyer and Bunz reported the preparation and characterization of a novel antiaromatic compound that is isolable.1

Bunz synthesized the redox pair of compounds 1 and 2 that differ in the electron count in the pi-system. The former (1) has 14 π electrons and should be aromatic, while the latter (5) has 16 π electrons and should be antiaromatic. The NMR spectrum of both compounds was measured and compared to the computed signals of the parent compounds 3 and 4. The signals match very nicely. The structures of 1 and 2 were further confirmed by x-ray crystallography. 1 and 2 can be interconverted by redox reactions and 2 is stable in air, only slowly oxidizing to 1.

The NICS(0)πizz values computed for 3 and 4 are shown in Figure 1. (See ref 2 for a discussion on this NICS method and also Chapter 2 of my book.) These values are quite negative for each ring of 3, consistent with its expected aromatic character. On the other hand, the NICS value for each ring of 4 is more positive than the corresponding ring of 3, with the value in the center of the pyrazine ring being positive. These NICS values indicate that 4 is certainly less aromatic than 3, and perhaps even expresses antiaromatic character.

Figure 1. NICS(0)πzz values for 3 and 4 computed at PW91/6-311G**.

Interestingly, hydrogenation of 3 to give 4 is -14.0, indicating that while 3 appears to be a normal aromatic compound, 4, if it is antiaromatic, exhibits some energetic stabilization. They identify this stabilization as a result of the interaction between the dihydropyrazine ring and the thidiazole ring, evidenced in the exothermicity of the isodemic reaction:

So while 4 may be antiaromatic, it appears to be energetically reasonably stable. It is important to keep in mind though that 4 is not the most stable tricycle isomer; in fact, 5 is 7 kcal mol-1 lower in energy than 4.

Schleyer and Bunz conclude that antiaromaticity may “not result in a prohibitive energetic penalty.”


(1) Miao, S.; Schleyer, P. v. R.; Wu, J. I.; Hardcastle, K. I.; Bunz, U. H. F., "A Thiadiazole-Fused N,N-Dihydroquinoxaline: Antiaromatic but Isolable," Org. Lett. 2007, 9, 1073-1076, DOI: 10.1021/ol070013i

(2) Fallah-Bagher-Shaidaei, H.; Wannere, C. S.; Corminboeuf, C.; Puchta, R.; Schleyer, P. v. R., "Which NICS Aromaticity Index for Planar π Rings Is Best?," Org. Lett., 2006, 8, 863-866, DOI: 10.1021/ol0529546.


3: InChI=1/C8H4N4S/c1-2-10-6-4-8-7(11-13-12-8)3-5(6)9-1/h1-4H
4: InChI=1/C8H6N4S/c1-2-10-6-4-8-7(11-13-12-8)3-5(6)9-1/h1-4,9-10H
5: InChI=1/C8H6N4S/c1-2-10-6-4-8-7(11-13-12-8)3-5(6)9-1/h1-2H,3-4H2

Aromaticity &DFT &polycyclic aromatics &Schleyer Steven Bachrach 25 Jul 2007 2 Comments