Archive for the 'Aromaticity' Category

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


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.

x-ray

1a

1b

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.

References

(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.

InChIs

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
InChIKey=CXZHCTLIHKZRMW-UHFFFAOYSA-N

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.

1

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

References

(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.

InChIs

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°.

1

2

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.

3
– ideal fold

3
– one misfold

3 – all misfold

4 – ideal fold

4
– one misfold

4
– 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.

References

(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.

InChIs

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)
InChIKey=BOCNJIZJHQKUNK-UHFFFAOYSA-N

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)
InChIKey=YKSIXAVDGFBUIZ-UHFFFAOYSA-N

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.

(a)

2

(b)

2
dimer

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.

References

(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.

InChIs:

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
InChIKey=UUKOQEVXPHHWBJ-UHFFFAOYSA-N

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
InChIKey=NGTKTKCZPONPTB-UHFFFAOYSA-N

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.

1

2

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

 

|Lk|

|Tw|

|Wr|

X-ray, 1

3.0

1.42

1.58

Comp, 1

3.0

1.33

1.67

Comp, 2

1.0

0.37

0.63

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

References

(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.

InChIs

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-
InChIkey=ICOGWBLQQNBWJA-UWFYZODKSA-N

Aromaticity Steven Bachrach 13 Oct 2014 6 Comments

18π-electron tautomers

Muranaka and Uchiyama have prepared an 18π-electron system that exhibits variable aromaticity in its tautomeric forms.1 The synthesized benziphthalacyanine 1 shows upfield resonances in the 1H NMR for the internal hydrogens: 1.89 ppm for the C-H proton and 4.67 ppm for the N-H proton. This indicates some weak diatropicity.

To address this interesting magnetic property, they reported B3LYP/6-31+G(d) computations on the model system 2 in its phenol 2p and quinoidal 2q tautomeric forms.

The optimized structures are shown in Figure 1. The phenol form 2p has NICS(0) and NICS(1) values of -6.77 and -6.04 ppm, respectively, indicating only modest aromaticity. However, the NICS values for the quinoidal from 2q are much more negative, -11.43 (NICS(0)) and -10.10 (NICS(1)) ppm, indicating a more significant aromatic character. The calculated chemical shift of the internal C-H is most telling: for 2q it is -4.55ppm but for 2p it is 0.97 ppm, in good agreement with experiment. Thus, 1 has an 18π-electron modestly aromatic periphery, with the phenol form dominant. There is no evidence of a 20π-electron periphery.

2p

2q

Figure 1. B3LYP/6-31+G(d) optimized geometries of 2p and 2q.

(Note that the supporting materials have a missing carbon in 2q and I have made a guess at its proper location – so this is not quite the optimized structure! Once again, a statement about the quality of SI!)

References

(1) Toriumi, N.; Muranaka, A.; Hirano, K.; Yoshida, K.; Hashizume, D.; Uchiyama, M. "18π-Electron Tautomeric Benziphthalocyanine: A Functional Near-Infrared Dye with Tunable Aromaticity," Angew. Chem. Int. Ed. 2014, 53, 7814-7818, DOI: 10.1002/anie.201404020.

InChIs

1: InChI=1S/C108H125N7O2/c1-57(2)75-31-25-32-76(58(3)4)87(75)43-69-49-93-95(51-71(69)45-89-79(61(9)10)35-27-36-80(89)62(11)12)105-111-103(93)109-99-55-100(102(117)56-101(99)116)110-104-94-50-70(44-88-77(59(5)6)33-26-34-78(88)60(7)8)72(46-90-81(63(13)14)37-28-38-82(90)64(15)16)52-96(94)106(112-104)114-108-98-54-74(48-92-85(67(21)22)41-30-42-86(92)68(23)24)73(53-97(98)107(113-105)115-108)47-91-83(65(17)18)39-29-40-84(91)66(19)20/h25-42,49-68,116-117H,43-48H2,1-24H3,(H,109,110,111,112,113,114,115)
InChIKey=LCYQUXHUTZWPDZ-UHFFFAOYSA-N

2p: InChI=1S/C30H17N7O2/c38-23-14-24(39)22-13-21(23)31-25-15-7-1-3-9-17(15)27(33-25)35-29-19-11-5-6-12-20(19)30(37-29)36-28-18-10-4-2-8-16(18)26(32-22)34-28/h1-14,38-39H,(H,31,32,33,34,35,36,37)
InChIKey=JBKUPBCBFUTSRM-UHFFFAOYSA-N

2q: InChI=1S/C30H17N7O2/c38-23-14-24(39)22-13-21(23)31-25-15-7-1-3-9-17(15)27(33-25)35-29-19-11-5-6-12-20(19)30(37-29)36-28-18-10-4-2-8-16(18)26(32-22)34-28/h1-14H,(H3,31,32,33,34,35,36,37,38,39)
InChIKey=PSSSGMKTDQVWLR-UHFFFAOYSA-N

Aromaticity Steven Bachrach 02 Sep 2014 No Comments

Fused aromatic ring effect on electrocyclization reactions

Aromaticity and orbital symmetry rules, though seemingly of ancient origin, remain areas of active interest. This paper by Fukazawa, et al combine both issues.1 The multiple-step electrocyclization of 1 gives 2 in a reaction that takes 9 days at 80 °C. What would be the effect of diminishing the aromatic character of the fused rings of 1? Would the reaction be faster or slower?

Before discussing the experimental results, let’s examine the B3LYP/6-31G(d) results for the reaction of 1’, 3 and 5. (Note that a slightly smaller pendant substituent is used in the computations than in the experiment.) The optimized geometries of the critical points along the reaction pathway for the cyclization of 3 are shown in Figure 1.

3
(0.0)

3-TS1
(17.9)

3-INT
(10.4)

3-TS2
(13.3)

4
(-60.7)

Figure 1. B3LYP/6-31G(d) optimized geometries and relative energies (kcal mol-1) for the critical points along the reaction 34.
Remember that all structures on my blog can be viewed interactively by clicking on the image of the molecule.

For 1’, the first barrier (for the 8π cyclization) has a barrier of about 23 kcal mol-1, but the second step (the 4π cyclization) has an even larger barrier of 28 kcal mol-1. However, reducing the aromaticity of one of the fused rings (compound 3) leads to lower barriers of 18 and 13 kcal mol-1. For the cyclization of 5, only a single transition state was found – no intermediate and no second TS – with a barrier of 12 kcal mol-1. Thus, removing these external aromatic rings reduces the barrier of the reaction, and that is exactly what is found experimentally!

References

(1) Fukazawa, A.; Oshima, H.; Shimizu, S.; Kobayashi, N.; Yamaguchi, S. "Dearomatization-Induced Transannular Cyclization: Synthesis of Electron-Accepting Thiophene-S,S-Dioxide-Fused Biphenylene," J. Am. Chem. Soc. 2014, 136, 8738-8745, DOI: 10.1021/ja503499n.

InChIs:

1: InChI=1S/C44H64S4Si4/c1-41(2,3)49(13,14)37-25-29-30-26-38(50(15,16)42(4,5)6)46-34(30)23-24-36-32(28-40(48-36)52(19,20)44(10,11)12)31-27-39(51(17,18)43(7,8)9)47-35(31)22-21-33(29)45-37/h25-28H,1-20H3/b30-29-,32-31-
InChIKey=OCNQBMWQONUVNH-IOYDOZLVSA-N

1’:InChI=1S/C32H40S4Si4/c1-37(2,3)29-17-21-22-18-30(38(4,5)6)34-26(22)15-16-28-24(20-32(36-28)40(10,11)12)23-19-31(39(7,8)9)35-27(23)14-13-25(21)33-29/h17-20H,1-12H3/b22-21-,24-23-
InChIKey=GTFPBRMBCLREPG-ICHHBZPXSA-N

2: InChI=1S/C44H64S4Si4/c1-41(2,3)49(13,14)29-21-25-26-22-30(50(15,16)42(4,5)6)46-38(26)34-33(37(25)45-29)35-36(34)40-28(24-32(48-40)52(19,20)44(10,11)12)27-23-31(47-39(27)35)51(17,18)43(7,8)9/h21-24H,1-20H3
InChIKey=OTDXAOVIIQYYNV-UHFFFAOYSA-N

2’: InChI=1S/C32H40S4Si4/c1-37(2,3)21-13-17-18-14-22(38(4,5)6)34-30(18)26-25(29(17)33-21)27-28(26)32-20(16-24(36-32)40(10,11)12)19-15-23(35-31(19)27)39(7,8)9/h13-16H,1-12H3
InChIKey=IYZNCPPDTHWWCO-UHFFFAOYSA-N

3: InChI=1S/C32H40O2S4Si4/c1-39(2,3)29-17-21-22-18-30(40(4,5)6)37-27(22)15-16-28-24(20-32(38(28,33)34)42(10,11)12)23-19-31(41(7,8)9)36-26(23)14-13-25(21)35-29/h17-20H,1-12H3/b22-21-,24-23-
InChIKey=ZJBDGDJVLGNVOD-ICHHBZPXSA-N

4: InChI=1S/C32H40O2S4Si4/c1-39(2,3)21-13-17-18-14-22(40(4,5)6)36-30(18)26-25(29(17)35-21)27-28(26)32-20(16-24(38(32,33)34)42(10,11)12)19-15-23(37-31(19)27)41(7,8)9/h13-16H,1-12H3
InChIKey=QUSJUOMZBJUGON-UHFFFAOYSA-N

5: InChI=1S/C32H40O8S4Si4/c1-45(2,3)29-17-21-22-18-30(46(4,5)6)42(35,36)26(22)15-16-28-24(20-32(44(28,39)40)48(10,11)12)23-19-31(47(7,8)9)43(37,38)27(23)14-13-25(21)41(29,33)34/h17-20H,1-12H3/b22-21-,24-23-
InChIKey=NNZTUSIYEPMHMP-ICHHBZPXSA-N

6: InChI=1S/C32H40O8S4Si4/c1-45(2,3)21-13-17-18-14-22(46(4,5)6)42(35,36)30(18)26-25(29(17)41(21,33)34)27-28(26)32-20(16-24(44(32,39)40)48(10,11)12)19-15-23(47(7,8)9)43(37,38)31(19)27/h13-16H,1-12H3
InChIKey=JZHQQYXUIQXWLQ-UHFFFAOYSA-N

Aromaticity &electrocyclization Steven Bachrach 22 Jul 2014 1 Comment

[4]Cyclo-2,7-pyrenylene

Macrocycles composed of aromatic subunits, like polycycloparaphenylenes, are of interest as components of nanotubes and for possible interesting optical properties. Tremendous advances have occurred over the past decade in preparing these rings ; see for examples these posts. Yamago now reports on the synthesis, optical properties and structure of [4]cyclo-2,7-pyrenylene 1, made by joining four pyrene units together.1

B3LYP/6-31G(d) optimization of the structure of 1 reveals a D2 geometry (Figure 1). This structure shows a very distorted pyrene unit. The strain energy of 1 is estimated as 392 kJ mol-1 (though how this was arrived at is not mentioned!), which is much larger than the strain energy of [8]-cycloparaphenylene.

Figure 1. B3LYP/6-31G(d) optimized structure of 1
This is another molecule to be sure to click on and rotate using JMol.

The nature of the HOMO and LUMO of 1 is very different than that of linear tetra-2,7-pyrene. The degenerate HOMOs and degenerate LUMOs of the linear compound have a node at the 2 and 7 positions and are localized to the terminal and central pyrene units, respectively. The HOMO and LUMO of 1 are fully delocalized. The implications of this are seen in the spectroscopy and electrochemistry of 1.

References

(1) Iwamoto, T.; Kayahara, E.; Yasuda, N.; Suzuki, T.; Yamago, S. "Synthesis, Characterization, and Properties of [4]Cyclo-2,7-pyrenylene: Effects of Cyclic Structure on the Electronic Properties of Pyrene Oligomers," Angew. Chem. Int. Ed. 2014, 53, 6430-6434, DOI: http://dx.doi.org/10.1002/anie.201403624.

InChIs

1: InChI=1S/C64H32/c1-2-34-18-50-20-36-4-3-35-19-49(17-33(1)57(35)58(34)36)51-21-37-5-7-41-25-53(26-42-8-6-38(22-51)59(37)61(41)42)55-29-45-13-15-47-31-56(32-48-16-14-46(30-55)63(45)64(47)48)54-27-43-11-9-39-23-52(50)24-40-10-12-44(28-54)62(43)60(39)40/h1-32H/b51-49-,52-50-,55-53-,56-54-
InChIKey=AWPUJIHMRRFHHU-GYSOBDCPSA-N

Aromaticity Steven Bachrach 09 Jul 2014 No Comments

Structure of benzene dication

Benzene is certainly one of the most iconic chemical compounds – its planar hexagonal structure is represented often in popular images involving chemists, and its alternating single and double bonds the source of one of chemistry’s most mythic stories: Kekule’s dream of a snake biting its own tail. So while the structure of benzene is well-worn territory, what of the structure of the benzene dication? Jasik, Gerlich and Rithova probe that question using a combined experimental and computational approach.1

The experiment involves generation of the benzene dication at low temperature and complexed
to helium. Then, using infrared predissociation spectroscopy (IRPD), they obtained a spectrum that suggested two different structures.

Next, employing MP2/aug-cc-pVTZ computations, they identified a number of possible geometries, and the two lowest energy singlet dications have the geometries shown in Figure 1. The first structure (1) has a six member ring, but the molecule is no longer planar. Lying a bit lower in energy is 2, having a pentagonal pyramid form. The combination of the computed IR spectra of each of these two structures matches up extremely well with the experimental spectrum.

1

2

Figure 1. MP2/aug-cc-pVTZ geometries of benzene dication 1 and 2.

References

(1) Jašík, J.; Gerlich, D.; Roithová, J. "Probing Isomers of the Benzene Dication in a Low-Temperature Trap," J. Am. Chem. Soc. 2014, 136, 2960-2962, DOI: 10.1021/ja412109h.

Aromaticity &MP Steven Bachrach 08 Apr 2014 2 Comments

Is the cyclopropenyl anion antiaromatic?

The concept of antiaromaticity is an outgrowth of the well-entrenched notion or aromaticity. While 4n+2 π-electron systems are aromatic, 4n π-electron systems should be antiaromatic. That should mean that antiaromatic systems are unstable. The cyclopropenyl anion 1a has 4 π-electrons and should be antiaromatic. Kass has provided computational results that strongly indicate it is not antiaromatic!1

Let’s first look at the 3-cyclopropenyl cation 1c. Kass has computed (at both G3 and W1) the hydride affinity of 1c-4c. The hydride affinities of the latter three compounds plotted against the C=C-C+ angle is linear. The hydride affinity of 1c however falls way below the line, indicative of 1c being very stable – it is aromatic having just 2 π-electrons.

A similar plot of the deprotonation enthalpies leading to 1a-4d vs. C=C-C- angle is linear including all four compounds. If 1a where antiaromatic, one would anticipate that the deprotonation energy to form 1a would be much greater than expected simply from the effect of the smaller angle. Kass suggests that this indicates that 1a is not antiaromatic, but just a regular run-of-the-mill (very) reactive anion.

A hint at what’s going on is provided by the geometry of the lowest energy structure of 1a, shown in Figure 1. The molecule is non-planar, having Cs symmetry. A truly antiaromatic structure should be planar, really of D3h symmetry. The distortion from this symmetry reduces the antiaromatic character, in the same way that cyclobutadiene is not a perfect square and that cyclooctatraene is tub-shaped and not planar. So perhaps it is more fair to say that 1a has a distorted structure to avoid antiaromaticity, and that the idealized D3h structure, does not exist because of its antiaromatic character.





Figure 1. G3 optimized geometry of 1a.

References

(1) Kass, S. R. "Cyclopropenyl Anion: An Energetically Nonaromatic Ion," J. Org. Chem. 2013, 78, 7370-7372, DOI: 10.1021/jo401350m.

InChIs

1a: InChI=1S/C3H3/c1-2-3-1/h1-3H/q-1
InChIKey=IBTMQWIWZUYLHW-UHFFFAOYSA-N

1c: InChI=1S/C3H3/c1-2-3-1/h1-3H/q+1
InChIKey=IPKCFGQXHZKYLH-UHFFFAOYSA-N

Aromaticity &Kass Steven Bachrach 20 Jan 2014 2 Comments

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