Archive for the 'Aromaticity' Category

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

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.


1


13+

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.

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.

References

(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.

InChIs

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-
InChIKey=UMEHBSBBAUKCTH-UIJINECUSA-N

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.

1

trianion of 1

Figure 2. Optimized structure of 1 and its trianion.

References

(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.

InChIs

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
InChIKey=WOYKPMSXBVTRKZ-UHFFFAOYSA-N

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
InChIKey=IHJVIPHOCKVJDZ-UHFFFAOYSA-N

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.

2

bowl inversion TS

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

References

(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.

InChI

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
InChIKey= JJPREOOFFSVARV-UHFFFAOYSA-N

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
InChIKey= FFFUKUDWQMOFQQ-UHFFFAOYSA-N

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.)

singlet

triplet

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

References

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

InChIs

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
InChIKey=WAKUAPLTIMTENF-UHFFFAOYSA-N

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
InChIKey=UXUXNGMSDNTZEC-UHFFFAOYSA-N

Aromaticity Steven Bachrach 04 May 2015 1 Comment

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