Archive for the 'Aromaticity' Category

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

Chiral aromatics

Naphthalene, phenanthrene and pyrene are all planar aromatic compounds. How can substituted version be chiral, with the chirality present in the aromatic portion of the molecule? The answer is provided by Yamaguchi and Kwon.1 They prepared peri-substituted analogues with the bulky adamantly group as the substituents. This bulky requires one adamantyl group to be position above the aromatic plane and the other below the plane, as in 1 and 2.


1


2

These molecules and two other examples were prepared in their optically pure form. B3LYP/6-31G(d) computations were performed on both of these structures (shown in Figure 1), but computations are a minor component of the work. These structures do show the out-of-plane distortions at C1 and C8, also apparent in the crystal structures. Computations of naphthalene and 1,8-dimethylnaphthalene show a planar naphthalene backbone, but -propyl substitution does force the substituents out of plane.

1

2

Figure 1. B3LYP/6-31G(d) optimized structures of 1 and 2.

These types of systems continue to subject the notion of “aromaticity” to serious scrutiny.

References

(1) Yamamoto, K.; Oyamada, N.; Xia, S.; Kobayashi, Y.; Yamaguchi, M.; Maeda, H.; Nishihara, H.; Uchimaru, T.; Kwon, E. "Equatorenes: Synthesis and Properties of Chiral Naphthalene, Phenanthrene, Chrysene, and Pyrene Possessing Bis(1-adamantyl) Groups at the Peri-position," J. Am. Chem. Soc. 2013, 135, 16526-16532, DOI: 10.1021/ja407800e.

InChIs

1: InChI=1S/C30H36/c1-3-25-4-2-6-27(30-16-22-10-23(17-30)12-24(11-22)18-30)28(25)26(5-1)29-13-19-7-20(14-29)9-21(8-19)15-29/h1-6,19-24H,7-18H2
InChIKey=QNPJKZPPLCPHSS-UHFFFAOYSA-N

2: InChI=1S/C36H38/c1-2-27-4-5-28-6-7-30(35-15-21-8-22(16-35)10-23(9-21)17-35)34-31(14-29(3-1)32(27)33(28)34)36-18-24-11-25(19-36)13-26(12-24)20-36/h1-7,14,21-26H,8-13,15-20H2
InChIKey=DKRBDGNWYTWNHL-UHFFFAOYSA-N

Aromaticity Steven Bachrach 06 Jan 2014 5 Comments

Acene dimers – open or closed?

The role of dispersion in large systems is increasingly recognized as critical towards understanding molecular geometry. An interesting example is this study of acene dimers by Grimme.1 The heptacene and nonacene dimers (1 and 2) were investigated with an eye towards the separation between the “butterfly wings” – is there a “stacked” conformation where the wings are close together, along with the “open” conformer?


1


2

The LPNO-CEPA/CBS potential energy surface of 1 shows only a single local energy minima, corresponding to the open conformer. B3LYP-D3 and B3LYP-NL, two different variations of dealing with dispersion (see this post), do a reasonable job at mimicking the LPNO-CEPA results, while MP2 indicates the stacked conformer is lower in energy than the open conformer.

B3LYP-D3 predicts both conformers for the nonacene dimer 2, and the optimized structures are shown in Figure 2. The stacked conformer is slightly lower in energy than the open one, with a barrier of about 3.5 kcal mol-1. However in benzene solution, the open conformer is expected to dominate due to favorable solvation with both the interior and exterior sides of the wings.

open

stacked

Figure 1. B3LYP-D3/ef2-TZVP optimized structures of the open and stacked conformations of 2.

References

(1) Ehrlich, S.; Bettinger, H. F.; Grimme, S. "Dispersion-Driven Conformational Isomerism in σ-Bonded Dimers of Larger Acenes," Angew. Chem. Int. Ed. 2013, 41, 10892–10895, DOI: 10.1002/anie.201304674.

InChIs

1: InChI=1S/C60H36/c1-2-10-34-18-42-26-50-49(25-41(42)17-33(34)9-1)57-51-27-43-19-35-11-3-4-12-36(35)20-44(43)28-52(51)58(50)60-55-31-47-23-39-15-7-5-13-37(39)21-45(47)29-53(55)59(57)54-30-46-22-38-14-6-8-16-40(38)24-48(46)32-56(54)60/h1-32,57-60H
InChIKey=OYVUURMCCBPDLI-UHFFFAOYSA-N

2: InChI=1S/C76H44/c1-2-10-42-18-50-26-58-34-66-65(33-57(58)25-49(50)17-41(42)9-1)73-67-35-59-27-51-19-43-11-3-4-12-44(43)20-52(51)28-60(59)36-68(67)74(66)76-71-39-63-31-55-23-47-15-7-5-13-45(47)21-53(55)29-61(63)37-69(71)75(73)70-38-62-30-54-22-46-14-6-8-16-48(46)24-56(54)32-64(62)40-72(70)76/h1-40,73-76H
InChIKey=FTSMWBVFVPAXOB-UHFFFAOYSA-N

Aromaticity &Grimme Steven Bachrach 28 Oct 2013 1 Comment

[8]circulene

Circulenes are molecules where a central ring is composed of fused benzenoids. Corranulene can also be named [5]circulene and coronene is [6]circulene. In a previous post I discussed the topology of the circulenes. This earlier work suggested that [8]annulene 1 would have a saddle-shape. This hypothesis has now been confirmed with the synthesis of the substituted [8]circulene 2 by Wu and co-workers.1


1


2

The x-ray structure does show a saddle geometry for 2. The central 8-member ring is tub-shaped, even more puckered that cyclooctatetraene (COT) itself, though the bonds in 2 are nearly of equal length. The bond lengths involving the central carbon atoms appear consistent with an [8]radialene-type structure.

The ωB97X-D/6-31G** optimized geometries of the parent compound 1 and the synthesized compound 2 are shown in Figure 1. These computed structures are very similar to each other, along with being very similar to the x-ray structure of 2.

1

2

Figure 1. ωB97X-D/6-31G** optimized geometries of 1 and 2.
(Don’t forget that you can click on these structures – and any other structure on my blog – to interactively manipulate and visualize them, something worth doing here!)

The computed NICS(0) (at HF/6-31+G* – I would really rather have seen these computed with some density functional, preferably at ωB97X-D/6-31G**) values for the six-member rings of both 1 and 2 are negative, ranging from -8.9 ppm to -4.0 ppm, indicating aromatic character. The NICS(0) value at the center of the 8-member ring is +9.8 ppm in 1 and +12.2 ppm in 2. The authors argue that this value cannot discriminate the 8-member ring from that in COT (NICS(0) = 1.98 ppm, the expected value for a non-aromatic ring) and [8]radialene (NICS(0) = -1.2 ppm, also an expected value for a non-aromatic ring). However, they are silent on whether this might actually imply some antiaromatic character to the 8-member ring, which would be consistent with the equivalent bond lengths around the ring.

The authors note that there should be a second isomer of 2 resulting from a flip of the tub. Variable temperature NMR does not show any change in the spectrum, though with a different substituted [8]circulene they do see some coalescence, suggesting a large flipping barrier of at least 20 kcal mol-1. A computational search for this flipping/inversion might be interesting as the transition state is likely to not be planar.

References

(1) Feng, C.-N.; Kuo, M.-Y.; Wu, Y.-T. "Synthesis, Structural Analysis, and Properties of [8]Circulenes," Angew. Chem. Int. Ed. 2013, 52, 7791-7794, DOI: 10.1002/anie.201303875.

InChIs

1: InChI=1S/C32H16/c1-2-18-5-6-20-9-11-22-13-15-24-16-14-23-12-10-21-8-7-19-4-3-17(1)25-26(18)28(20)30(22)32(24)31(23)29(21)27(19)25/h1-16H
InChIKey=BASWMOIVIHXTRC-UHFFFAOYSA-N

2: InChI=1S/C96H80/c1-49-17-33-65(34-18-49)81-73-57(9)58(10)75-83(67-37-21-51(3)22-38-67)85(69-41-25-53(5)26-42-69)77-61(13)62(14)79-87(71-45-29-55(7)30-46-71)88(72-47-31-56(8)32-48-72)80-64(16)63(15)78-86(70-43-27-54(6)28-44-70)84(68-39-23-52(4)24-40-68)76-60(12)59(11)74(82(81)66-35-19-50(2)20-36-66)90-89(73)91(75)93(77)95(79)96(80)94(78)92(76)90/h17-48H,1-16H3
InChIKey=DEKWLSGHBADDAQ-UHFFFAOYSA-N

Aromaticity Steven Bachrach 03 Sep 2013 No Comments

Non-planar geometry of C80H30

Scott and Itami report on a graphene fragment that is highly warped.1 They have prepared 1 by three separate procedures, one of which starts with corranulene and in two steps makes the product!


1

The five 7-member rings warp the structure so that it is non-planar. In fact the molecule has negative curvature, reminiscent of a riding saddle. They report the x-ray structure, outside of the fullerenes, the largest hydrocarbon reported by x-ray crystallography. Because of its non-planar geometry, 1 does not pack well and so it is soluble in a variety of solvents.

The authors have obtained the structure of 1 at B3LYP/6-31G(d), shown in Figure 1. The central corranulene component is a shallow bowl, much less shallow than in corranulene itself. This suggests that the compound might flip with a relatively low barrier. The computed barrier is only 1.7 kcal mol-1. Due to the negative curvatures associated with the seven-member rings, 1 is chiral and the ring flipping process leaves the chirality unchanged. A second transition was located that leads to racemization through a transition state of Cs symmetry. The barrier for this racemization is computed to be 18.9 kcal mol-1. Variable temperature 1H NMR analysis does show that at room temperature 1 (substituted with one t-butyl ring on each of the ten exterior phenyl rings) undergoes rapid motion that equilibrates all of the protons. However, at lower temperature the signals for ring protons do separate. This leads to the barrier or the racemization process of 13.6 kcal mol-1. The ring flip is not frozen out at the temperatures explored.

1

1-TSflip

1-TSrac

Figure 1. B3LYP/6-31G(d) optimized structures of 1 and the transition states for flipping and racemization. (Remember that all structures in my blog are active – click on them to run Jmol and manipulate the 3-D structure.)

Compound 1 is an example of a very interesting negative curvature hydrocarbon, especially unusual for what might be considered an aromatic compound.

References

(1) Kawasumi, K.; Zhang, Q.; Segawa, Y.; Scott, L. T.; Itami, K. "A grossly warped nanographene and the consequences of multiple odd-membered-ring defects," Nat Chem 2013, advance online publication, DOI: 10.1038/nchem.1704.

InChIs

1: InChI=1S/C80H30/c1-11-31-32-12-2-23-43-44-24-5-15-35-36-16-6-27-47-48-28-9-19-39-40-20-10-30-50-49-29-8-18-38-37-17-7-26-46-45-25-4-14-34-33-13-3-22-42-41(21-1)51(31)61-62(52(32)43)72-65(55(35)44)66(56(36)47)74-69(59(39)48)70(60(40)50)75-68(58(38)49)67(57(37)46)73-64(54(34)45)63(53(33)42)71(61)76-77(72)79(74)80(75)78(73)76/h1-30H
InChIKey=KMAOOAQTQHCOHV-UHFFFAOYSA-N

Aromaticity Steven Bachrach 20 Aug 2013 No Comments

Triplet state aromaticity

One of the most widely recognized principles within organic chemistry is Hückel’s rule: an aromatic compound possesses 4n+2 π-electrons while an antiaromatic compound possesses 4n π-electrons. Much less well known is Baird’s rule:1 the first excited triplet state will be aromatic if it has 4n π-electrons and antiaromatic if it has 4n+2 π-electrons.2

Schleyer used a number of standard methods for assessing aromatic character of a series of excited state triplets, including NICS values and geometric parameters.3 However, Schleyer has long been a proponent of an energetic assessment of aromaticity and it is only now in this recent paper4 that he and co-workers examine the stabilization energy of excited triplet states. The isomerization
stabilization energy (ISE)5 compares an aromatic (or antiaromatic) compound against a non-aromatic reference, one that typically is made by appending an exo-methylene group to the ring. So, to assess the ISE of the T1 state of benzene, Reaction 1 is used. (Note that the inherent assumption here is that the stabilization energy of benzene is essentially identical to that of toluene.) At B3LYP/6-311++G(d,p) the energy of Reaction 1 is +13.5 kcal mol-1. This reaction should be corrected for non-conservation of s-cis and s-trans conformers by adding on the energy of Reaction 2, which is +3.4 kcal mol-1. So, the ISE of triplet benzene is +16.9 kcal mol-1, indicating that it is antiaromatic. In contrast, the ISE for triplet cyclooctatetraene is -15.6 kcal mol-1, and when corrected its ISE value is -24.7 kcal mol-1, indicating aromatic character. These are completely consistent with Baird’s rule. Schleyer also presents an excellent correlation between the computed ISE values for the triplet state of 9 monocyclic polyenes and their NICS(1)zz values.

Reaction 1

Reaction 2

I want to thank Henrik Ottosson for bringing this paper to my attention and for his excellent seminar on the subject of Baird’s rule on his recent visit to Trinity University.

References

(1) Baird, N. C. "Quantum organic photochemistry. II. Resonance and aromaticity in
the lowest 3ππ* state of cyclic hydrocarbons," J. Am. Chem. Soc. 1972, 94, 4941-4948, DOI: 10.1021/ja00769a025.

(2) Ottosson, H. "Organic photochemistry: Exciting excited-state aromaticity," Nat Chem 2012, 4, 969-971, DOI: 10.1038/nchem.1518.

(3) Gogonea, V.; Schleyer, P. v. R.; Schreiner, P. R. "Consequences of Triplet Aromaticity in 4nπ-Electron Annulenes: Calculation of Magnetic Shieldings for Open-Shell Species," Angew. Chem. Int. Ed. 1998, 37, 1945-1948, DOI: 10.1002/(SICI)1521-3773(19980803)37:13/14<1945::AID-ANIE1945>3.0.CO;2-E.

(4) Zhu, J.; An, K.; Schleyer, P. v. R. "Evaluation of Triplet Aromaticity by the
Isomerization Stabilization Energy," Org. Lett. 2013, 15, 2442-2445, DOI: 10.1021/ol400908z.

(5) Schleyer, P. v. R.; Puhlhofer, F. "Recommendations for the Evaluation of Aromatic Stabilization Energies," Org. Lett. 2002, 4, 2873-2876, DOI: 10.1021/ol0261332.

Aromaticity &Schleyer Steven Bachrach 16 Jul 2013 No Comments

o-phenylene polymers – the unwritten post

I was intending to write a post regarding an interesting paper on o-phenylene polymers. This paper describes experiments and computations on the hexamer, with particular attention paid to arene-arene interactions.1 These compounds fold into a helix, which has obvious application to many biological systems (DNA and the α-helix of peptides).

One of the things I am attempting to convey in this blog is the advantage of electronic communication in the sciences. In particular, I incorporate 3-dimensional structures of molecules in a way that allows the reader to interact with the molecule through a Java applet. (If you haven’t done this yet, any of the 3-D static images in this blog are actually linked to active structures – simply click on them and allow the Java applet to load.)

Now the paper by Hartley and co-workers does include supporting information with the coordinates of the different conformers of the o-phenylene hexamer, and I was all set to create images and incorporate the active molecules within a post. However, the pdf version of the supporting materials, while looking fine when viewed, actually has destroyed the data. I cannot copy-and-paste the coordinates into any program – the coordinates are completely corrupted! This is yet another example of how pdf is perhaps one of the worst choices for data deposition, as Peter Murray-Rust has often noted in his blog.

So until the supporting materials are fixed in some way, I will not, really can not, write up a post on it. Authors please remember to submit useful supporting materials!

References

(1) Mathew, S. M.; Engle, J. T.; Ziegler, C. J.; Hartley, C. S. "The Role of Arene–Arene Interactions in the Folding of ortho-Phenylenes," J. Am. Chem. Soc. 2013, 135, 6714-6722, DOI: 10.1021/ja4026006.

Aromaticity Steven Bachrach 08 May 2013 2 Comments

A new aromatic bowl and synthesis strategy

Myśliwiec and Stępień report on a new method for creating buckybowls.1 The usual way had been to build from the inside outward. They opt instead to build from the outside in and have constructed the heterosubstitued bowl chrysaorole 1.


1

B3LYP/6-31G** optimizations reveal two conformers that are very close in energy: one has the butyl chains outstretched (1a) and one has the butyl arms internal or pendant (1b). These structures are shown in Figure 1. The depth of this bowl (1.96 Å) is quite a bit larger than in corranulene (0.87 Å). The agreement between the computed and experimental 13C and 1H chemical shifts are excellent, supporting the notion that this gas phase geometry is similar to the solution phase structure. Though 1 is strained, 53.4 kcal mol-1 based on B3LYP/6-31G** energies for Reaction 1 (which uses the parent of 1 – replacing the butyl groups with hydrogens), on a per sp2 atom basis, it is no more strained than corranulene.

1a

1b

Figure 1. B3LYP/6-31G** optimized geometries of two conformers of 1.

Reaction 1

This new synthetic strategy is likely to afford access to more unusual aromatic structures.

References

(1) Myśliwiec, D.; Stępień, M. "The Fold-In Approach to Bowl-Shaped Aromatic Compounds: Synthesis of Chrysaoroles," Angew. Chem. Int. Ed. 2013, 52, 1713-1717, DOI:10.1002/anie.201208547.

InChI

1: InChI=1S/C54H45N3/c1-4-7-16-55-49-19-31-10-12-33-21-51-45-27-39(33)37(31)25-43(49)44-26-38-32(20-50(44)55)11-13-34-22-52-46(28-40(34)38)48-30-42-36(24-54(48)57(52)18-9-6-3)15-14-35-23-53(47(45)29-41(35)42)56(51)17-8-5-2/h10-15,19-30H,4-9,16-18H2,1-3H3
InChIKey=VUUJVETWVYQACL-UHFFFAOYSA-N

Aromaticity Steven Bachrach 05 Mar 2013 2 Comments

Bowls derived from C70

I have discussed a few bowl-shaped aromatics in this blog (see for example this and this). Kuo and Wu now report on a few bowls derived from C70-fullerenes.1 The bowl 1 was synthesized (along with a couple of other derivatives) and its x-ray structure obtained. As anticipated this polyclic aromatic is not planar, but rather a definite bowl, with a bowl depth of 2.28 Å. This is less curved than when the fragment is present in C70-fullerene.


1

Interestingly, this bowl does not invert through a planar transition state. The fully planar structure 1pl, shown in Figure 1, is 116 kcal mol-1 above the ground state bowl structure, computed at B3LYP/cc-pVDZ. Rather, the molecule inverts through a twisted S-shaped structure 1TS, also shown in Figure 1. The activation barrier through 1TS is 80 kcal mol-1. This suggests that 1 is static at room temperature, unlike corranulene which has an inversion barrier, through a planar transition state, of only 11 kcal mol-1. The much more concave structure of 1 than corranulene leads to the greatly increased strain in its all-planar TS. This implies that properly substituted analogues of 1 will be chiral and configurationally stable. Not remarked upon is that the inversion pathway, which will interchange enantiomers when 1 is properly substituted, follows a fully chiral path, as discussed in this post.

1

1TS

1pl

Figure 1. B3LYP/cc-pVDZ optimized geometries of 1, 1TS, and 1pl.

Reference

(1) Wu, T.-C.; Chen, M.-K.; Lee, Y.-W.; Kuo, M.-Y.; Wu, Y.-T. "Bowl-Shaped Fragments of C70 or Higher Fullerenes: Synthesis, Structural Analysis, and Inversion Dynamics," Angew. Chem. Int. Ed. 2013, 52, 1289-1293, DOI: 10.1002/anie.201208200.

InChIs

1: InChI=1S/C38H14/c1-3-17-21-11-7-15-9-13-23-19-5-2-6-20-24-14-10-16-8-12-22-18(4-1)27(17)33-35-29(21)25(15)31(23)37(35)34(28(19)20)38-32(24)26(16)30(22)36(33)38/h1-14H
InChIKey=KLCLRPVBVWXTPN-UHFFFAOYSA-N

Aromaticity Steven Bachrach 06 Feb 2013 No Comments

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