Archive for the 'Aromaticity' Category

Nanobelt

The synthesis of components of nanostructures (like fullerenes and nanotubes) has dramatically matured over the past few years. I have blogged about nanohoops before, and this post presents the recent work of the Itami group in preparing the nanobelt 1.1


1

The synthesis is accomplished through a series of Wittig reactions with an aryl-aryl coupling to stitch together the final rings. The molecule is characterized by NMR and x-ray crystallography. The authors have also computed the structure of 1 at B3LYP/6-31G(d), shown in Figure 1. The computed C-C distances match up very well with the experimental distances. The strain energy of 1, presumably estimated by Reaction 1,2 is computed to be about 119 kcal mol-1.

1

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

Rxn 1

NICS(0) values were obtained at B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d); the rings along the middle of the belt have values of -7.44ppm and are indicative of normal aromatic 6-member rings, while the other rings have values of -2.00ppm. This suggests the dominant resonance structure shown below:

References

1) Povie, G.; Segawa, Y.; Nishihara, T.; Miyauchi, Y.; Itami, K., "Synthesis of a carbon nanobelt." Science 2017, 356, 172-175, DOI: 10.1126/science.aam8158.

2) Segawa, Y.; Yagi, A.; Ito, H.; Itami, K., "A Theoretical Study on the Strain Energy of Carbon Nanobelts." Org. Letters 2016, 18, 1430-1433, DOI: 10.1021/acs.orglett.6b00365.

InChIs:

1: InChI=1S/C48H24/c1-2-26-14-40-28-5-6-31-20-44-32(19-42(31)40)9-10-34-24-48-36(23-46(34)44)12-11-35-21-45-33(22-47(35)48)8-7-30-17-41-29(18-43(30)45)4-3-27-15-37(39(26)16-28)25(1)13-38(27)41/h1-24H
InChIKey=KJWRWEMHJRCQKK-UHFFFAOYSA-N

Aromaticity &nanohoops Steven Bachrach 22 May 2017 No Comments

Tetrabenzo[7]circulene

I have discussed the circulenes in a few previous posts. Depending on their size, they can be bowls, flat disks, or saddles. A computational study of [7]circulene noted that C2 structure is slightly higher in energy than the Cs form,1 though the C2 form is found in the x-ray structure.2

Now, Miao and co-workers have synthesized the tetrabenzo[7]circulene 1 and also examined its structure using DFT.3

As with the parent compound, a C2 and Cs form were located at B3LYP/6-31G(d,p), and are shown in Figure 1. The C2 form is 7.6 kcal mol-1 lower in energy than the Cs structure, and the two are separated by a transition state (also shown in Figure 1) with a barrier of 12.2 kcal mol-1. The interconversion of these conformations takes place without going through a planar form. The x-ray structure contains only the C2 structure. It should be noted that the C2 structure is chiral, and racemization would take place by the path: 1-Cs1-Cs1-C2*, where 1-C2* is the enantiomer of 1-C2.

1-C2

1-TS

1-Cs

Figure 1. B3LYP/6-31G(d,p) optimized structures of 1.

References

1) Hatanaka, M., "Puckering Energetics and Optical Activities of [7]Circulene Conformers." J. Phys. Chem. A 2016, 120 (7), 1074-1083, DOI: 10.1021/acs.jpca.5b10543.

2) Yamamoto, K.; Harada, T.; Okamoto, Y.; Chikamatsu, H.; Nakazaki, M.; Kai, Y.; Nakao, T.; Tanaka, M.; Harada, S.; Kasai, N., "Synthesis and molecular structure of [7]circulene." J. Am. Chem. Soc. 1988, 110 (11), 3578-3584, DOI: 10.1021/ja00219a036.

3) Gu, X.; Li, H.; Shan, B.; Liu, Z.; Miao, Q., "Synthesis, Structure, and Properties of Tetrabenzo[7]circulene." Org. Letters 2017, DOI: 10.1021/acs.orglett.7b00714.

InChIs

1: InChI=1S/C44H22/c1-5-13-28-24(9-1)32-19-17-23-18-20-33-25-10-2-6-14-29(25)38-31-16-8-4-12-27(31)35-22-21-34-26-11-3-7-15-30(26)37(28)43-39(32)36(23)40(33)44(38)42(35)41(34)43/h1-22H
InChIKey=KVMXYGAVHDZMNP-UHFFFAOYSA-N

Aromaticity Steven Bachrach 01 May 2017 No Comments

A six-coordinate carbon atom

Hypercoordinated carbon has fascinated chemists since the development of the concept of the tetravalent carbon. The advent of superacids has opened up the world of hypercoordinated species and now a crystal structure of a hexacoordinated carbon has been reported for the C6(CH3)62+ species 1.1

The molecule is prepared by first epoxidation of hexamethyl Dewar benzene, followed by reaction with Magic acid, and crystallized by the addition of HF. The crystal structure shows a pentamethylcyclopentadienyl base capped by a carbon with a methyl group. The x-ray structure is well reproduced by the B3LYP/def2-TZVP structure shown in Figure 1. (While this DFT method predicts a six-member isomer to be slightly lower in energy, MP2 does predict the cage as the lowest energy isomer.)

1

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

The Wiberg bond order for the bond between the capping carbon and each carbon of the five-member base is about 0.54, so the sum of the bond orders to the apical carbon is less than 4. The carbon is therefore not hypervalent, but it appears to truly be hypercoordinate. (A topological electron density analysis (AIM) study would have been interesting here.) NICS analysis indicates the cage formed by the apical carbon and the five-member ring expresses 3-D aromaticity. This can be thought of as coming from the C5(CH3)5+ fragment with its 4 electrons and the CCH3+ fragment with two electrons, providing 4n + 2 = 6 electrons for the aromatic cage.

References

1) Malischewski, M.; Seppelt, K., "Crystal Structure Determination of the Pentagonal-Pyramidal Hexamethylbenzene Dication C6(CH3)62+" Angew. Chem. Int. Ed. 2017, 56, 368-370, DOI: 10.1002/anie.201608795.

Aromaticity Steven Bachrach 17 Jan 2017 2 Comments

A Twisted Aromatic Makes for an Accessible Triplet State

Wentrup and co-workers examined the strained, non-planar aromatic 1.1

The UKS-BP86-D3BJ/def2-TZVP optimized geometry of the singlet 1 is shown in Figure 1. The molecule is decidedly twisted, with an angle of about 52°. This large twist, weakening the π-bond between the two aromatic fragments, suggests that the triplet state of 1 might be easily accessible. The geometry of 31 is also shown in Figure 1, and the two aromatic portions are orthogonal.

11

31

Figure 1. UKS-BP86-D3BJ/def2-TZVP optimized geometries of 11 and 31.

The proton and 13C NMR studies of 1 show increasing paramagnetism, observed as line broadening, with increasing temperature. Confirming this is ESR which shows increasing signal with increasing temperature. The triplet state is clearly present. The experimental ΔEST=9.6 kcal mol-1 and the computed singlet-triplet gap is 9.3 kcal mol-1. This is in excellent agreement, and much better than previous computations which predict a gap of 3.4 kcal mol-1, but omitted the D3 correction. This dispersion correction stabilizes the singlet state over the triplet state, as might be expected. (The triplet has the two aromatic components orthogonal and so they have minimal dispersion interactions, while the aromatic planes are much closer in the singlet state.)

For comparison, the computed ΔEST of isomer 2 is much larger: 17.9 kcal mol-1. The energies of the triplet states of 1 and 2 are nearly identical. Both of these structures have orthogonal, non-interacting aromatic moieties. However, the energy of 12 with the twist angles of 11 is 8.2 kcal mol-1 lower than that of 11. This the twisting causes a significant strain to the singlet state, but not to the triplet, and that gives rise to its small singlet-triplet gap.

References

1) Wentrup, C.; Regimbald-Krnel, M. J.; Müller, D.; Comba, P., "A Thermally Populated, Perpendicularly Twisted Alkene Triplet Diradical." Angew. Chem. Int. Ed. 2016, 55, 14600-14605, DOI: 10.1002/anie.201607415.

InChIs

1: InChI=1S/C42H24/c1-5-13-29-25(9-1)17-21-33-34-22-18-26-10-2-6-14-30(26)38(34)41(37(29)33)42-39-31-15-7-3-11-27(31)19-23-35(39)36-24-20-28-12-4-8-16-32(28)40(36)42/h1-24H
InChIKey=YEHKZURNXPRJHP-UHFFFAOYSA-N

2: InChI=1S/C42H24/c1-5-13-29-21-37-33(17-25(29)9-1)34-18-26-10-2-6-14-30(26)22-38(34)41(37)42-39-23-31-15-7-3-11-27(31)19-35(39)36-20-28-12-4-8-16-32(28)24-40(36)42/h1-24H
InChIKey=PKXAAFWZKNGAED-UHFFFAOYSA-N

Aromaticity Steven Bachrach 03 Jan 2017 No Comments

Redox switching

In searching for a redox switch, Matsuda, Ishikawa and co-workers1 landed on 13,14-picenedione 1, which could, at least in principle, be reduced by reacting with H2 to form the diol 2. The back reaction could then occur via the reaction with oxygen gas.

They first optimized the geometries of both compounds at B3PW91/6-311+G(2d), and these geometries are shown in Figure 1. TD-DFT computations then predicted that 1 would be yellow (maximum absorption at 412nm) and 2 would be colorless (maximum absorption at 378nm). Furthermore, 1 should have no fluorescence while 2 should fluoresce at 464nm and be blue.

1

2

Figure 1. B3PW91/6-311+G(2d) optimized geometries of 1 and 2.

Of particular note is that the geometry of 1 is twisted, with the O-C-C-O dihedral angle being 34.9°, while there is essentially no such twisting in 2 (its O-C-C-O dihedral angle is 0.7°). The twisting in 1 manifests in antiaromatic character of the central ring, with NICS(0)=+13.2ppm, while the central ring of 2 is aromatic, with NICS(0)=-10.0. The redox properties therefore reflect the change in the aromatic character.

They next synthesized 2 and reduced it with hydrogen gas to 1. The x-ray crystal structure of 1 shows a twisted structure (O-C-C-O dihedral of 28.87°). As predicted, 1 is yellow and 2 is colorless, and 1 has no fluorescence while 2 fluoresces blue.

References

(1) Urakawa, K.; Sumimoto, M.; Arisawa, M.; Matsuda, M.; Ishikawa, H. "Redox Switching of Orthoquinone-Containing Aromatic Compounds with Hydrogen and Oxygen Gas," Angew. Chem. Int. Ed. 2016, 55, 7432-7436, DOI: 10.1002/anie.201601906.

InChIs

1: InChI=1S/C22H12O2/c23-21-19-15-7-3-1-5-13(15)9-11-17(19)18-12-10-14-6-2-4-8-16(14)20(18)22(21)24/h1-12H
InChIKey=ASVNSCAISPNPGI-UHFFFAOYSA-N

2: InChI=InChI=1S/C22H14O2/c23-21-19-15-7-3-1-5-13(15)9-11-17(19)18-12-10-14-6-2-4-8-16(14)20(18)22(21)24/h1-12,23-24H
InChIKey=KZHNWJFXGDGIDE-UHFFFAOYSA-N

Aromaticity Steven Bachrach 06 Jul 2016 No Comments

Diels-Alder reactions of some arenes

Houk has examined the Diels-Alder reaction involving ethene with benzene 1 and all of its aza-substituted isomers having four or fewer nitrogen atoms 2-11.1 The reactions were computed at M06-2X/6-311+G(d,p).

All of the possible Diels-Alder reactions were examined, and they can be classified in terms of whether two new C-C bonds are formed, one new C-C and one new C-N bond are formed, or two new C-N bonds are formed. Representative transition states of these three reaction types are shown in Figure 1, using the reaction of 7 with ethene.

Figure 1. M06-2X/6-311+G(d,p) optimized transition states for the Diels-Alders reactions of 7 with ethene.

A number of interesting trends are revealed. For a given type of reaction (as defined above), as more nitrogens are introduced into the ring, the activation energy decreases. Forming two C-C bonds has a lower barrier than forming a C-C and a C-N, which has a lower barrier than forming two C-N bonds. The activation barriers are linearly related to the aromaticity of the ring defined by either NICS(0) or aromatic stabilization energy, with the barrier decreasing with decreasing aromaticity. The barrier is also linearly related to the exothermicity of the reaction.

The activation barrier is also linearly related to the distortion energy. With increasing nitrogen substitution, the ring becomes less aromatic, and therefore more readily distorted from planarity to adopt the transition state structure.

References

(1) Yang, Y.-F.; Liang, Y.; Liu, F.; Houk, K. N. "Diels–Alder Reactivities of Benzene, Pyridine, and Di-, Tri-, and Tetrazines: The Roles of Geometrical Distortions and Orbital Interactions," J. Am. Chem. Soc. 2016, 138, 1660-1667, DOI: 10.1021/jacs.5b12054.

Aromaticity &Diels-Alder &Houk Steven Bachrach 26 Apr 2016 No Comments

A linear acene with 13 rings

Bunz and co-workers have synthesized the novel aromatic compound 1 that contains 13 acenes in a row.1

They optimized the geometry of 1 at B3LYP/6-311G*, and its geometry is shown in Figure 1. Even though this compound has quite an extensive π-system, an unrestricted computations collapses to the closed-shell wavefunction.

1

Figure 1. B3LYP/6-311G* optimized geometry of 1. (As always, don’t forget to click on this image to launch JMol and visualize the molecule in 3-D.)

NICS(1)πzz values for the rings are given in Table 1. Interestingly, the aromaticity of the coronene moiety is reduced; in fact the central ring (ring A, with rings labeled sequentially working towards either end from the center) has a very small NICS value of only -3.77.

Table 1. NICS(1)πzz values for the rings of 1.

Ring

NICS(1)πzz

A
B
C
D
E
F
G
H

-3.7
-12.2
-27.7
-28.7
-35.8
-36.1
-40.5
-29.8

References

(1) Endres, A. H.; Schaffroth, M.; Paulus, F.; Reiss, H.; Wadepohl, H.; Rominger, F.; Krämer, R.; Bunz, U. H. F. "Coronene-Containing N-Heteroarenes: 13 Rings in a Row," J. Am. Chem. Soc. 2016, 138, 1792-1795, DOI: 10.1021/jacs.5b12642.

InChIs

1: InChI=1S/C100H76N8O4Si4/c1-49(2)56-31-24-32-57(50(3)4)75(56)84-95(111)72-47-68-80-78-66(89-91(68)107-99-97(105-89)101-85-58(33-37-113(5,6)7)62-41-52-27-20-22-29-54(52)43-64(62)60(87(85)103-99)35-39-115(11,12)13)45-70-76-71(94(110)74(93(70)109)51-25-18-17-19-26-51)46-67-79(82(76)78)81-69(48-73(96(84)112)77(72)83(80)81)92-90(67)106-98-100(108-92)104-88-61(36-40-116(14,15)16)65-44-55-30-23-21-28-53(55)42-63(65)59(86(88)102-98)34-38-114(8,9)10/h17-32,41-50,74,84H,1-16H3
InChIKey=GNQHLGPUXJMSCH-UHFFFAOYSA-N

Aromaticity Steven Bachrach 04 Apr 2016 No Comments

Highly efficient Buckycatchers

Capturing buckyballs involves molecular design based on non-covalent interactions. This poses interesting challenges for both the designer and the computational chemist. The curved surface of the buckyball demands a sequestering agent with a complementary curved surface, likely an aromatic curved surface to facilitate π-π stacking interactions. For the computational chemist, weak interactions, like dispersion and π-π stacking demand special attention, particularly density functionals designed to account for these interactions.

Two very intriguing new buckycatchers were recently prepared in the Sygula lab, and also examined by DFT.1 Compounds 1 and 2 make use of the scaffold developed by Klärner.2 In these two buckycatchers, the tongs are corranulenes, providing a curved aromatic surface to match the C60 and C70 surface. They differ in the length of the connector unit.

B97-D/TZVP computations of the complex of 1 and 2 with C60 were carried out. The optimized structures are shown in Figure 1. The binding energies (computed at B97-D/QZVP*//B97-D/TZVP) of these two complexes are really quite large. The binding energy for 1:C60 is 33.6 kcal mol-1, comparable to some previous Buckycatchers, but the binding energy of 2:C60 is 50.0 kcal mol-1, larger than any predicted before.

1

2

Figure 1. B97-D/TZVP optimized geometries of 1:C60and 2:C60.

Measurement of the binding energy using NMR was complicated by a competition for one or two molecules of 2 binding to buckyballs. Nonetheless, the experimental data show 2 binds to C60 and C70 more effectively than any previous host. They were also able to obtain a crystal structure of 2:C60.

References

(1) Abeyratne Kuragama, P. L.; Fronczek, F. R.; Sygula, A. "Bis-corannulene Receptors for Fullerenes Based on Klärner’s Tethers: Reaching the Affinity Limits," Org. Lett. 2015, ASAP, DOI: 10.1021/acs.orglett.5b02666.

(2) Klärner, F.-G.; Schrader, T. "Aromatic Interactions by Molecular Tweezers and Clips in Chemical and Biological Systems," Acc. Chem. Res. 2013, 46, 967-978, DOI: 10.1021/ar300061c.

InChIs

1: InChI=1S/C62H34O2/c1-63-61-57-43-23-45(41-21-37-33-17-13-29-9-5-25-3-7-27-11-15-31(35(37)19-39(41)43)53-49(27)47(25)51(29)55(33)53)59(57)62(64-2)60-46-24-44(58(60)61)40-20-36-32-16-12-28-8-4-26-6-10-30-14-18-34(38(36)22-42(40)46)56-52(30)48(26)50(28)54(32)56/h3-22,43-46H,23-24H2,1-2H3/t43-,44+,45+,46-
InChIKey=RLOJCVYXCBOUQB-RYSLUOGPSA-N

2: InChI=1S/C66H36O2/c1-67-65-51-24-45-43-23-44(42-20-38-34-16-12-30-8-4-27-3-7-29-11-15-33(37(38)19-41(42)43)59-55(29)53(27)56(30)60(34)59)46(45)25-52(51)66(68-2)64-50-26-49(63(64)65)47-21-39-35-17-13-31-9-5-28-6-10-32-14-18-36(40(39)22-48(47)50)62-58(32)54(28)57(31)61(35)62/h3-22,24-25,43-44,49-50H,23,26H2,1-2H3/t43-,44+,49+,50-
InChIKey=JAUUHTKCNSNBMD-NETXOKAWSA-N

Aromaticity &fullerene &host-guest Steven Bachrach 30 Nov 2015 No Comments

Bistetracene is a biradical singlet

Feng, Müller and co-workers have prepared a bistetracene analogue 1.1 This molecule displays some interesting features. While a closed shell Kekule structure can be written, a biradical structure results in more closed Clar rings, suggesting that perhaps the molecule is a ground state singlet biradical. The loss of NMR signals with increasing temperature along with an EPR signal that increases with temperature both support the notion of a ground state singlet biradical with a triplet excited state. The EPR measurement suggest as singlet-triplet gap of 3.4 kcal mol-1.

The optimized B3LYP/6-31G(d,p) geometries of the biradical singlet and triplet states are shown in Figure 1. The singlet is lower in energy by 6.7 kcal mol-1. The largest spin densities are on the carbons that carry the lone electron within the diradical-type Kekule structures.

singlet 1

triplet 1

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

References

(1) Liu, J.; Ravat, P.; Wagner, M.; Baumgarten, M.; Feng, X.; Müllen, K. "Tetrabenzo[a,f,j,o]perylene: A Polycyclic Aromatic Hydrocarbon With An Open-Shell Singlet Biradical Ground State," Angew. Chem. Int. Ed. 2015, 54, 12442-12446, DOI: 10.1002/anie.201502657.

InChIs

1: InChI=1S/C62H56/c1-33-25-35(3)51(36(4)26-33)53-45-17-13-15-19-47(45)57-56-44-24-22-42(62(10,11)12)30-40(44)32-50-54(52-37(5)27-34(2)28-38(52)6)46-18-14-16-20-48(46)58(60(50)56)55-43-23-21-41(61(7,8)9)29-39(43)31-49(53)59(55)57/h13-32H,1-12H3
InChIKey=LPRMROONCKWUEJ-UHFFFAOYSA-N

Aromaticity &diradicals Steven Bachrach 16 Nov 2015 No Comments

Ground and excited state (anti)aromaticity

What is the relationship between a ground state and the first excited triplet (or first excited singlet) state regarding aromaticity? Baird1 argued that there is a reversal, meaning that a ground state aromatic compound is antiaromatic in its lowest triplet state, and vice versa. It is suggested that the same reversal is also true for the second singlet (excited singlet) state.

Osuka, Sim and coworkers have examined the geometrically constrained hexphyrins 1 and 2.2 1 has 26 electrons in the annulene system and thus should be aromatic in the ground state, while 2, with 28 electrons in its annulene system should be antiaromatic. The ground state and lowest triplet structures, optimized at B3LYP/6-31G(d,p), of each of them are shown in Figure 1.


1


2

11

12

31

32

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

NICS computations where made in the centers of each of the two rings formed by the large macrocycle and the bridging phenyl group (sort of in the centers of the two lenses of the eyeglass). The NICS values for 1 are about -15ppm, indicative of aromatic character, while they are about +15ppm for 2, indicative of antiaromatic character. However, for the triplet states, the NICS values change sign, showing the aromatic character reversal between the ground and excited triplet state. The aromatic states are also closer to planarity than the antiaromatic states (which can be seen by clicking on the images in Figure 1, which will launch the JMol applet so that you can rotate the molecular images).

They also performed some spectroscopic studies that support the notion of aromatic character reversal in the excited singlet state.

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) Sung, Y. M.; Oh, J.; Kim, W.; Mori, H.; Osuka, A.; Kim, D. quot;Switching between Aromatic and Antiaromatic 1,3-Phenylene-Strapped [26]- and [28]Hexaphyrins upon Passage to the Singlet Excited State," J. Am. Chem. Soc. 2015, 137, 11856-11859, DOI: 10.1021/jacs.5b04047.

InChIs

1: InChI=1S/C60H18F20N6/c61-41-37(42(62)50(70)57(77)49(41)69)33-23-8-4-19(81-23)31-17-2-1-3-18(16-17)32(21-6-10-25(83-21)35(29-14-12-27(33)85-29)39-45(65)53(73)59(79)54(74)46(39)66)22-7-11-26(84-22)36(40-47(67)55(75)60(80)56(76)48(40)68)30-15-13-28(86-30)34(24-9-5-20(31)82-24)38-43(63)51(71)58(78)52(72)44(38)64/h1-16,85-86H/b31-19+,31-20+,32-21+,32-22+,33-23+,33-27+,34-24+,34-28+,35-25+,35-29+,36-26+,36-30+
InChIKey=TUOMWLSCXXODFY-CQGNQUHXSA-N

2: InChI=1S/C60H20F20N6/c61-41-37(42(62)50(70)57(77)49(41)69)33-23-8-4-19(81-23)31-17-2-1-3-18(16-17)32(21-6-10-25(83-21)35(29-14-12-27(33)85-29)39-45(65)53(73)59(79)54(74)46(39)66)22-7-11-26(84-22)36(40-47(67)55(75)60(80)56(76)48(40)68)30-15-13-28(86-30)34(24-9-5-20(31)82-24)38-43(63)51(71)58(78)52(72)44(38)64/h1-16,81-84H/b31-19+,31-20+,32-21+,32-22+,33-23+,33-27+,34-24+,34-28+,35-25+,35-29+,36-26+,36-30+
InChIKey=KTIAGNMFTAGKFJ-CQGNQUHXSA-N

Aromaticity Steven Bachrach 26 Oct 2015 3 Comments

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