Archive for the 'Aromaticity' Category

Triprotonated rosarin: singlet or triplet?

What is the spin state of the ground state of an aromatic species? Can this be spin state be manipulated by charge? These questions are addressed by Borden, Kim, Sessler and coworkers1 for the hexaphyrin 1. B3LYP/6-31G(d) optimization of 1 shows it to be a ground state singlet. This structure is shown in Figure 1.



Protonation of the three pyrrole nitrogens creates 13+, which has interesting frontier orbitals. The HOMO of 13+, of a1” symmetry, has nodes running through all six nitrogens. The next higher energy orbital, of a2” symmetry, has a small π-contribution on each nitrogen. Protonation will therefore have no effect on the energy of the a1” orbital, but the charge will stabilize the a2” orbital. This will lower the energy gap between the two orbitals, suggesting that a ground state triplet might be possible. The lowest singlet and triplet states of 13+ are also shown in Figure 1.


Singlet 13+

Triplet 13+

Figure 1. (U)B3LYP/6-31G(d) optimized structures of 1 and singlet and triplet 13+.

This spin state change upon protonation was experimentally verified by synthesis of two analogues of 1, shown below. The triprotonated versions of both are observed to have triplet character in their EPR spectrum.


(1) Fukuzumi, S.; Ohkubo, K.; Ishida, M.; Preihs, C.; Chen, B.; Borden, W. T.; Kim, D.; Sessler, J. L. "Formation of Ground State Triplet Diradicals from Annulated Rosarin Derivatives by Triprotonation," J. Am. Chem. Soc. 2015, 137, 9780-9783, DOI: 10.1021/jacs.5b05309.


1: InChI=1S/C45H24N6/c1-2-8-29-28(7-1)34-16-22-13-24-18-36-30-9-3-4-10-31(30)38-20-26(50-43(38)42(36)48-24)15-27-21-39-33-12-6-5-11-32(33)37-19-25(49-44(37)45(39)51-27)14-23-17-35(29)41(47-23)40(34)46-22/h1-21,46,49-50H/b22-13-,23-14-,24-13-,25-14-,26-15-,27-15-

Aromaticity &Borden Steven Bachrach 22 Sep 2015 No Comments

Sumanene anions

Spisak, et al. treated sumanene 1 with excess potassium in THF.1

They obtained an interesting structure, characterized by x-ray crystallography: a mixture of the dianion and trianion of 1 (well these are really conjugate di- and tribases of 1, but we’ll call them di- and trianions for simplicity’s sake). A fragment of the x-ray structure is shown in Figure 1, showing that there is one potassium cation on the concave face and six potassium ions on the convex face.

Figure 1. X-ray structure of 1 surrounded by six K+ ions on the convex face and one K+ on the concave face.

To help understand this structure, they performed RIJCOSX-PBE0/cc-pVTZ computations on the mono-, di-, and trianion of 1. The structure of 1 (which I optimized at ωB97X-D/6-311G(d)) and the trianion are displayed in Figure 2. The molecular electrostatic potential of the trianion shows highly negative regions in the 5-member ring regions, symmetrically distributed and prime for coordination with 6 cations.


trianion of 1

Figure 2. Optimized structure of 1 and its trianion.


(1) Spisak, S. N.; Wei, Z.; O’Neil, N. J.; Rogachev, A. Y.; Amaya, T.; Hirao, T.; Petrukhina, M. A. "Convex and Concave Encapsulation of Multiple Potassium Ions by Sumanenyl Anions," J. Am. Chem. Soc. 2015, 137, 9768-9771, DOI: 10.1021/jacs.5b06662.


1: InChI=1S/C21H12/c1-2-11-8-13-5-6-15-9-14-4-3-12-7-10(1)16-17(11)19(13)21(15)20(14)18(12)16/h1-6H,7-9H2

Trianion of 1: InChI=1S/C21H9/c1-2-11-8-13-5-6-15-9-14-4-3-12-7-10(1)16-17(11)19(13)21(15)20(14)18(12)16/h1-5,7-8H,9H2/q-3

Aromaticity Steven Bachrach 14 Sep 2015 1 Comment

Hetero-substituted corranulene

A heterosubstituted corranulene analogue has now been prepared. Ito, Tokimaru, and Nozaki report the synthesis of 1 and compare it with corranulene.1 The x-ray structure of 1 shows it to be a deeper bowl than corranulene, and the bond distances suggest the Kekule structure with a central pyrrole and five Clar-type phenyl rings.

The B3LYP/6-311+G(2d,p) optimized structure of 2, then analogue of 1 missing the t-butyl group, is shown in Figure 1. Its geometry is very similar to that of 1 observed in the crystal structure. The NICS(0) values are shown in Scheme 1. These values support the notion of a central (aromatic) pyrrole surrounded by a periphery of five aromatic phenyl rings.

Scheme 1. NICS(0) values

An interesting feature of bowl compounds is their inversion. The inversion barrier, through the planar TS shown in Figure 2, is computed to be 17.0 kcal mol-1 at B3LYP/6-311+G(2d,p). This is 6-7 kcal mol-1 larger than the inversion barrier of corranulene, which is not surprising given the additional phenyl groups about the periphery.


bowl inversion TS

Figure 1. B3LYP/6-311+G(2d,p) optimized geometry of 2.


(1) Ito, S.; Tokimaru, Y.; Nozaki, K. "Benzene-Fused Azacorannulene Bearing an Internal Nitrogen Atom," Angew. Chem. Int. Ed. 2015, 54, 7256-7260, DOI: 10.1002/anie.201502599.


1: InChI=1S/C38H23N/c1-38(2,3)18-16-27-25-14-6-12-23-21-10-4-8-19-20-9-5-11-22-24-13-7-15-26-28(17-18)35(27)39-36(31(23)25)33(29(19)21)34(30(20)22)37(39)32(24)26/h4-17H,1-3H3

2: InChI=1S/C34H15N/c1-6-16-17-7-2-9-19-21-11-4-13-23-25-15-5-14-24-22-12-3-10-20-18(8-1)26(16)30-31(27(17)19)34(29(21)23)35(32(24)25)33(30)28(20)22/h1-15H

Aromaticity Steven Bachrach 20 Jul 2015 2 Comments

Uthrene, the smallest diradical graphene fragment

Uthrene 1 is the smallest formally diradical fragment of graphene; it cannot be expressed in a closed shell, fully electron-paired Kekule form. Its isomer zethrene 2 on the other hand, can be expressed in closed shell form.

Melle-Franco has examined these, and related, polycyclic aromatic hydrocarbons with DFT.1 The optimized structure of singlet and triplet 1 at CAM-B3LYP/6-31g(d,p) are shown in Figure 1. The singlet-triplet energy gap of 2 is 16.5 kcal mol-1 with a ground state singlet. However, for 1 the triplet is predicted to be lower in energy than the singlet by 7.7 kcal mol-1. And this gap increases to 10.9 kcal mol-1 at CASSCF(14,14)/6-31g(d,p)//CAM-B3LYP/6-31g(d,p). Natural orbital population analysis of the singlet of 1 at CASSCF identifies two orbitals with populations around 1 e.

Interestingly, both the singlet and triplet of 1 are not planar, exhibiting a twist to avoid the clashing of the hydrogens in the bay region. (This twisting is best seen by clicking on the structures in Figure 1, and viewing the molecules interactively through Jmol.)



Figure 1. CAM-B3LYP/6-31g(d,p) optimized geometries of the singlet and triplet of 1.


(1) Melle-Franco, M. "Uthrene, a radically new molecule?," Chem. Commun. 2015, 51, 5387-5390, DOI: 10.1039/C5CC01276G.


1: InChI=1S/C24H14/c1-5-15-7-3-11-20-22(15)17(9-1)13-19-14-18-10-2-6-16-8-4-12-21(23(16)18)24(19)20/h1-14H

2: InChI=1S/C24H14/c1-5-15-7-3-11-19-22-14-18-10-2-6-16-8-4-12-20(24(16)18)21(22)13-17(9-1)23(15)19/h1-14H

Aromaticity Steven Bachrach 04 May 2015 1 Comment

Fluorenyl cation

Is the fluorenyl cation 1 antiaromatic or non-aromatic? This is still an open question. But the recent paper by Costa, et al. provides a new path towards potentially answering this question; they have finally synthesized this molecule.1

By photolizing 2 in low-density amorphous ice (LDA ice) and in deuterated ice at 8 K, they have identified a new IR spectrum.

To identify the origin of these spectra, they optimized the geometry of the fluorenyl cation 1 at B3LYP-D3/def2-TZVP (see Figure 1) and computed its IR spectra. These computed IR frequencies were then scaled by 0.97. The agreement between the computed and experimental frequencies is quite reasonable, and the isotopic shifts are also reasonably well reproduced. The agreement is not perfect, as seen in Table 1. Hopefully, further experiments will now be carried out to try to answer the lead question of this post.

Figure 1. B3LYP-D3/def2-TZVP optimized geometry of 1.

Table 1. Experimental and computed IR frequencies (cm-1)
and isotopic shift (in parentheses) of 1.





1106.8 (+2.1)

1076.8 (+1.7)







1373.4 (-16.4)



1469.0 (-7.3)

1530.7 (-3.2)

1490.5 (-1.0)



1640.9 (0.0)

1601.2 (-4.0)


(1) Costa, P.; Trosien, I.; Fernandez-Oliva, M.; Sanchez-Garcia, E.; Sander, W. "The Fluorenyl Cation," Angew. Chem. Int. Ed. 2015, 54, 2656-2660, DOI: 10.1002/anie.201411234.


1: InChI=1S/C13H9/c1-3-7-12-10(5-1)9-11-6-2-4-8-13(11)12/h1-9H/q+1

Aromaticity Steven Bachrach 13 Apr 2015 1 Comment

Molecular rotor and C-Hπ interaction

Molecular rotors remain a fascinating topic – the idea of creating a miniature motor just seems to capture the imagination of scientists. Garcia-Garibay and his group have synthesized the interesting rotor 1, and in collaboration with the Houk group, they have utilized computations to help understand the dynamics of this rotor.1


The x-ray structure of this compound, shown in Figure 1, displays two close interactions of a hydrogen on the central phenyl ring with the face of one of the steroidal phenyl rings. Rotation of the central phenyl ring is expected to then “turn off” one or both of these C-Hπ interactions. The authors argue this as a competition between the molecule sampling an enthalpic region, where the molecule has one or two favorable C-Hπ interactions, and the large entropic region where these C-Hπ interactions do not occur, but this space is expected to have a large quantity of energetically similar conformations.




Figure 1. X-ray and M06-2x/6-31G(d) optimized structures of 1.

Variable temperature NMR finds the central phenyl hydrogen with a chemical shift of 6.55ppm at 295 K but at 6.32 ppm at 222 K. This suggest as freezing of the conformations at low temperature favoring those conformations possessing the internal C-Hπ interactions. M06-2X/6-31G(d) optimization finds two low-energy conformations with a single C-Hπ interaction. These are shown in Figure 1. No competing conformation was found to have two such interactions. Computations of the chemical shifts of these conformations show the upfield shift of the central phenyl hydrogens. Fitting these chemical shifts to the temperature data gives ΔH = -1.74 kcal mol-1, ΔS = -5.12 esu and ΔG = -0.21 kcal mol-1 for the enthalpic region to entropic region transition.


(1) Pérez-Estrada, S.; Rodrı́guez-Molina, B.; Xiao, L.; Santillan, R.; Jiménez-Osés, G.; Houk, K. N.; Garcia-Garibay, M. A. "Thermodynamic Evaluation of Aromatic CH/π Interactions and Rotational Entropy in a Molecular Rotor," J. Am. Chem. Soc. 2015, 137, 2175-2178, DOI: 10.1021/ja512053t.


1: InChI=1S/C48H54O4/c1-45-23-19-39-37-15-11-35(51-3)29-33(37)9-13-41(39)43(45)21-27-47(45,49)25-17-31-5-7-32(8-6-31)18-26-48(50)28-22-44-42-14-10-34-30-36(52-4)12-16-38(34)40(42)20-24-46(44,48)2/h5-8,11-12,15-16,29-30,39-44,49-50H,9-10,13-14,19-24,27-28H2,1-4H3

Aromaticity &Houk &Hydrogen bond Steven Bachrach 23 Mar 2015 No Comments

Twisting a benzene ring

Here’s another cruel and unusual punishment applied to the poor benzene ring. Hashimoto,et al. have created a molecule that is a fused double helicene, where the fusion is about a single phenyl ring.1 Compound 1 has two [5]helicenes oriented in opposite directions. This should provide a twist to the central phenyl ring, and the added methyl groups help to expand that twist.

They prepared 1 and its x-ray crystal structure is reported. The compound exhibits C2 symmetry. The twist (defined as the dihedral of four consecutive carbon atoms of the central ring) is 28.17°, nearly the same twist as in [2]paraphenylene.

The B3LYP/6-31G(d) structure of 1 is shown in Figure 1. This geometry is very similar to the x-ray structure. The calculated NICS value for the central ring is -4.9 (B3LYP/6-311+G(d,p)/B3LYP/6-31G(d)) and -4.3 (B3LYP/6-311+G(d,p)/x-ray structure). This diminished value from either benzene or C6(PSH2)2(CH3)4 indicates reduced aromaticity of this central ring, presumably due to the distortion away from planarity. Nonetheless, the central ring of 1 is not oxidized when subjected to MCPBA to oxidize to the bis phosphine oxides.


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


(1) Hashimoto, S.; Nakatsuka, S.; Nakamura, M.; Hatakeyama, T. "Construction of a Highly Distorted Benzene Ring in a Double Helicene," Angew. Chem. Int. Ed. 2014, 53, 14074-14076, DOI: 10.1002/anie.201408390.


1: InChI=1S/C50H32P2S2/c1-25-17-21-29-9-5-13-33-41(29)37(25)45-46-38-26(2)18-22-30-10-7-15-35(42(30)38)52(54)36-16-8-12-32-24-20-28(4)40(44(32)36)48(50(46)52)47-39-27(3)19-23-31-11-6-14-34(43(31)39)51(33,53)49(45)47/h5-24H,1-4H3

Aromaticity Steven Bachrach 26 Jan 2015 No Comments

o-Phenylene conformations

In solution ortho-phenylenes preferentially coil into a helix with the phenyl rings stacked. However, 25-50% of these chains will typically misfold. Hartley and coworkers have reported the use of substituents to increase the percentage of perfectly folded chains.1

They synthesized two isomeric o-phenylenes, differing in the substitution pattern (1 and 2), with chain length of 6 to 10 phenyl rings. Substituents included methoxy, acetoxy, nitrile, and triflate. They principally employed 1H NMR to assess the conformational distribution, and used computations to confirm the conformation.

Ideally folded conformations of 1 and 2 with eight phenyl rings are shown in Figure 1. The dihedral angle formed by two adjacent phenyl rings are typically about ±55° or ±130°.



Figure 1. Idealized folding of 1 and 2 with X=OH.
Hydrogens omitted in these images, but full structures available, through Jmol, by clicking on the image.)

Given the size of these systems, and the conformation flexibility not just of the chain but with each substituent, a full search to identify the global minimum was not undertaken. Rather, a library of conformations was generated with MM, the lowest 200 conformations were then reoptimized at PM7 and then the energies were determined at PCM/B97-D/TZV(2d,2p). The lowest energy conformer was then reoptimized at this DFT level. Three conformations of 3 and 4 are shown in Figure 2 with triflate as the substituent with six phenyl rings. The first conformer has optimal stacking (perfect folding), the second conformer as one misfold at the end, and the third conformer has no stacking at all.

– ideal fold

– one misfold

3 – all misfold

4 – ideal fold

– one misfold

– all misfold

Figure 2. Optimized geometries of conformers of 3 and 4.
(Remember that clicking on one of these images will bring up the JMol applet allowing you to rotate and visualize the molecule in 3-D – a very useful feature here!)

NMR chemical shifts were then computed using these geometries at PCM/WP04/6-31G(d). In all cases examined, the chemical shifts of the major conformation was confirmed to be the perfect folding one by comparison with the computed chemical shifts. The examined substituents enhanced the proportion of properly folded chains in all cases, often to the extent where no minor conformer was observed at all.


(1) Mathew, S.; Crandall, L. A.; Ziegler, C. J.; Hartley, C. S. "Enhanced Helical Folding of ortho-Phenylenes through the Control of Aromatic Stacking Interactions," J. Am. Chem. Soc. 2014, 136, 16666-16675, DOI:10.1021/ja509902m.


3: InChI=1S/C42H26F18O18S6/c43-37(44,45)79(61,62,63)23-5-1-21(2-6-23)29-13-9-25(81(67,68,69)39(49,50)51)17-33(29)35-19-27(83(73,74,75)41(55,56)57)11-15-31(35)32-16-12-28(84(76,77,78)42(58,59)60)20-36(32)34-18-26(82(70,71,72)40(52,53)54)10-14-30(34)22-3-7-24(8-4-22)80(64,65,66)38(46,47)48/h1-20H,(H,61,62,63)(H,64,65,66)(H,67,68,69)(H,70,71,72)(H,73,74,75)(H,76,77,78)

4: InChI=1S/C42H26F18O18S6/c43-37(44,45)79(61,62,63)23-6-4-21(5-7-23)33-17-25(81(67,68,69)39(49,50)51)9-13-30(33)35-19-27(83(73,74,75)41(55,56)57)11-15-32(35)36-20-28(84(76,77,78)42(58,59)60)10-14-31(36)34-18-26(82(70,71,72)40(52,53)54)8-12-29(34)22-2-1-3-24(16-22)80(64,65,66)38(46,47)48/h1-20H,(H,61,62,63)(H,64,65,66)(H,67,68,69)(H,70,71,72)(H,73,74,75)(H,76,77,78)

Aromaticity Steven Bachrach 21 Jan 2015 No Comments

Oblong molecule stacking

π-π-stacking has been a major theme of my blog, and is discussed in Chapter 3.5.4 in the Second Edition of my book. Most examples involved molecules that are nearly circular (like benzene or triphenylene). Hartley and co-workers discuss the π-π-stacking of the oblong molecule 1, comparing its experimental features with computed features of the model compound 2.1

The key spectroscopic feature associated with assembly of 1 are the changes in the 1H chemical shifts with increasing concentration. For example, the chemical shift of the three protons on the triphenylene unit shift upfield by 0.30 to 0.66 ppm as the concentration increases from 10-5 to 10-2 M.

To see if these NMR shift changes are due to association of 1, they employed a computational approach. First they optimized the structure of model compound 2 at B3LYP/6-31G(d) (Shown in Figure 1a). Then using this fixed geometry, they computed the 1H chemical shifts of the dimer of 2. They explored the stacking distance (ranging from 3.2 to 4.0 Å along with varying the displacement of the two molecules along the major axis from 0.0 to 6.0 Å, finding the best fit to the chemical shifts with a separation of 3.6 Å and a displacement along the major axis of 3.5 Å. Using these two fixed values, they explored displacement of the molecules along the minor axis, along with rotation of the two molecules. The best fit to the experimental chemical shifts was with a displacement of 0.5 Å along the short axis and no rotation. This structure is shown in Figure 1b, with a RMS error of only 0.09 ppm from experiment. Models of the trimer show poorer fit to the experimental data.





Figure 1. B3LYP/6-31G(d) (a) optimized structure of 2 and the (b) structure of the best fit of the dimer of 2. (As always, clicking on these images will allow you to manipulate the 3-D structure using JMol – highly recommended for the dimer.)

Using some smaller models and the B97-D functional, they argue that the displacement, which is substantially larger than the displacement found in stacked triphenylene, results from the need to minimize the steric interactions between the alkoxyl chains.


(1) Chu, M.; Scioneaux, A. N.; Hartley, C. S. "Solution-Phase Dimerization of an Oblong Shape-Persistent Macrocycle," J. Org. Chem. 2014, 79, 9009–9017; DOI: 10.1021/jo501260c.


1: InChI=1S/C116H148O10/c1-11-21-31-41-59-117-95-71-87-51-55-91-75-97-99(103-81-111(121-63-45-35-25-15-5)115(125-67-49-39-29-19-9)85-107(103)105-83-113(123-65-47-37-27-17-7)109(79-101(97)105)119-61-43-33-23-13-3)77-93(91)57-53-89-70-90(74-96(73-89)118-60-42-32-22-12-2)54-58-94-78-100-98(76-92(94)56-52-88(69-87)72-95)102-80-110(120-62-44-34-24-14-4)114(124-66-48-38-28-18-8)84-106(102)108-86-116(126-68-50-40-30-20-10)112(82-104(100)108)122-64-46-36-26-16-6/h69-86H,11-50,59-68H2,1-10H3

2: InChI=1S/C76H68O10/c1-11-77-55-31-47-21-25-51-35-57-59(63-41-71(81-15-5)75(85-19-9)45-67(63)65-43-73(83-17-7)69(79-13-3)39-61(57)65)37-53(51)27-23-49-30-50(34-56(33-49)78-12-2)24-28-54-38-60-58(36-52(54)26-22-48(29-47)32-55)62-40-70(80-14-4)74(84-18-8)44-66(62)68-46-76(86-20-10)72(82-16-6)42-64(60)68/h29-46H,11-20H2,1-10H3

Aromaticity Steven Bachrach 13 Nov 2014 No Comments

A Triple-Möbius Aromatic Molecule

Herges and co-workers have prepared a triply-twisted Möbius molecule. 1 The key element is recognizing that most of the “twisting” needs to be accomplished through writhe, a twisting that produces figure-8-like crossing, the way an old-school phone cord twists about itself or the way a pretzel is formed. Herges employs three bi-naphthelene subunits to provide the template for the writhe needed. The prepared compound is 1. A clever, relatively straightforword synthesis produces this amazing molecule, along with the single-twisted 2.

The B3LYP/6-31G* optimized geometries of 1 and the single-twisted analogue 2 are shown in Figure 1. Table 1 presents the key topological parameters of 1 and 2, comparing the computed and X-ray crystal structure. The absolute value of the linking number Lk is 3, indicating the three twists, and the reason that this highly twisted molecule can be made is that half of the twist actually results from writhe.



Figure 1. B3LYP/6-31G* optimized geometries of the two diastereomers if 1. (Be sure to click on these images to launch JMol and interactively manipulate the structures!)

Table 1. Topological parameters of 1. a





X-ray, 1




Comp, 1




Comp, 2




aLk is the linking number, Tw is the twist number, and Wr is the writhe number, with the condition that Tk + Wr = Lk.


(1) Schaller, G. R.; Topić, F.; Rissanen, K.; Okamoto, Y.; Shen, J.; Herges, R. "Design and synthesis of the first triply twisted Möbius annulene," Nat. Chem. 2014, 6, 608-613, DOI: 10.1038/nchem.1955.


1: InChI=1S/C72H36/c1-2-26-56-44-38-50-20-8-14-32-62(50)68(56)70-58(46-40-52-22-10-16-34-64(52)70)28-5-6-30-60-48-42-54-24-12-18-36-66(54)72(60)71-59(47-41-53-23-11-17-35-65(53)71)29-4-3-27-57-45-39-51-21-9-15-33-63(51)69(57)67-55(25-1)43-37-49-19-7-13-31-61(49)67/h7-24,31-48H/b69-67-,70-68-,72-71-

Aromaticity Steven Bachrach 13 Oct 2014 6 Comments

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