Dynamics in the C-H insertion reaction of vinyl cations

Dynamics &Houk Steven Bachrach 09 Oct 2018 No Comments

A recent paper by Papov, Shao, Bagdasarian, Benton, Zou, Yang, Houk, and Nelson uncovers a vinyl cation insertion reaction that once again involves dynamic effects.1

They find that vinyl triflates and cyclic vinyl triflates will react with [Ph3C]+[HCB11Cl11] and triethylsilane to generate vinyl cations that can then be trapped through a C-H insertion reaction. For example, cyclohexenyl triflate 1 reacts in a cyclohexane solvent to give the insertion product 2.

The reactions of isomers 3 and 4 give different ratios of the two products 5 and 6. In both cases, the cyclohexyl is trapped predominantly at the site of the triflate substituent. This means that the mechanism cannot involve a cyclohexene intermediate, since then the two ratios should be identical.

They performed molecular dynamic trajectory analysis at the M062X/6-311+G(d,p) level, starting with the two transition states leading from 3 (TS3) and 4 (TS4), the only transition states located for the insertion reaction. The structures of these TSs are shown in Figure 1.


TS3


TS4

Figure 1. M062X/6-311+G(d,p) optimized geometries of TS3 and TS4.

The trajectories end up in two product basins associated with 5 and 6 starting with either TS3 or TS4. Thus, these transition states are ambimodal, and typical of reactions where dynamic effects dominate. For the reaction of 3, the majority of the trajectories starting at TS3 end up as 5, consistent with the experiments. Similarly, for the trajectories that start at TS4, the majority end up as 6, consistent with experiments.

Once again, we see that relatively simple organic reactions do not follow simple reaction mechanisms, that a single transition state leads to two different products and the product distributions are dependent on reaction dynamics. This may not be too surprising for the vinyl cation insertions given the many examples provide by the Tantillo group of cation rearrangements that are controlled by reaction dynamics (see for examples, this post and this post).

References

1. Popov, S.; Shao, B.; Bagdasarian, A. L.; Benton, T. R.; Zou, L.; Yang, Z.; Houk, K. N.; Nelson, H. M., "Teaching an old carbocation new tricks: Intermolecular C–H insertion reactions of vinyl cations." Science 2018, 361, 381-387, DOI: 10.1126/science.aat5440.

InChIs

1: InChI=1S/C7H10F3O3S/c8-7(9,10)14(11,12,13)6-4-2-1-3-5-6/h4H,1-3,5H2,(H,11,12,13)
InChIKey=CMPVYBNXADJVOM-UHFFFAOYSA-N

2: InChI<=1S/C12H22/c1-3-7-11(8-4-1)12-9-5-2-6-10-12/h11-12H,1-10H2
InChIKey=WVIIMZNLDWSIRH-UHFFFAOYSA-N

3: InChI=1S/C9H14F3O3S/c1-8(2)5-3-7(4-6-8)16(13,14,15)9(10,11)12/h3H,4-6H2,1-2H3,(H,13,14,15)
InChIKey=XDWBLRRAHKBZJR-UHFFFAOYSA-N

4: InChI=1S/C9H14F3O3S/c1-8(2)5-3-4-7(6-8)16(13,14,15)9(10,11)12/h4H,3,5-6H2,1-2H3,(H,13,14,15)
InChIKey=YHVCPSRICQJFDT-UHFFFAOYSA-N

5: InChI=1S/C14H26/c1-14(2)10-8-13(9-11-14)12-6-4-3-5-7-12/h12-13H,3-11H2,1-2H3
InChIKey=BZQBWUOXOYWYJC-UHFFFAOYSA-N

6: InChI=1S/C14H26/c1-14(2)10-6-9-13(11-14)12-7-4-3-5-8-12/h12-13H,3-11H2,1-2H3
InChIKey=AENMAOBTECURBO-UHFFFAOYSA-N

Curved Aromatic molecules – 4 new examples

Aromaticity Steven Bachrach 24 Sep 2018 No Comments

I have recently been interested in curved aromatic systems – see my own paper on double helicenes.1 In this post, I cover four recent papers that discuss non-planar aromatic molecules.

The first paper2 discusses the warped aromatic 1 built off of the scaffold of depleiadene 3. The crystal structure of 1 shows the molecule to be a saddle with near C2v symmetry. B3LYP/6-31G computations indicate that the saddle isomer is 10.5 kcal mol-1 more stable than the twisted isomer, and the barrier between them is 16.0 kcal mol-1, with a twisted saddle intermediate as well.

The PES is significantly simpler for the structure lacking the t-butyl groups, 2. The B3LYP/6-31G PES of 2 has the saddle as the transition state interconverting mirror images of the twisted saddle isomer, and this barrier is only 1.8 kcal mol-1. Figure 1 displays the twisted saddle and the saddle transition state. Clearly, the t-butyl groups significantly alter the flexibility of this C86 aromatic surface. One should be somewhat concerned about the small basis set employed here, especially lacking polarization functions, and a functional that lacks dispersion correction. However, the computed geometry of 1 is quite similar to that of the x-ray structure.


2 twisted saddle (ground state)


2 saddle (transition state)

Figure 1. B3LYP/6-31G optimized geometries of the isomer of 2.

The second paper presents 4, a non-planar aromatic based on [8]circulene 6.3 (See this post for a general study of circulenes.) [8]circulene has a tub-shape, but is flexible and can undergo tub-to-tub inversion. The expanded aromatic 4 is found to have a twisted shape in the x-ray crystal structure. A simplified model 5 was computed at B3LYP/6-31G(d) and the twisted isomer is 4.1 kcal mol-1 lower in energy than the saddle (tub) isomer (see Figure 2). The barrier for interconversion of the two isomers is only 6.2 kcal mol-1, indicating a quite labile structure.


5 twisted
0.0


5 TS
6.2


5 saddle
4.1

Figure 2. B3LYP/6-31G(d) optimized geometries and relative energies (kcal mol-1) of the isomers of 5.

The third paper presents a geodesic molecule based on 1,3,5-trisubstitued phenyl repeat units.4 The authors prepared 7, and its x-ray structure shows a saddle-shape. The NMR indicate a molecule that undergoes considerable conformational dynamics. To address this, they did some computations on the methyl analogue 8. The D7h structure is 309 kcal mol-1 above the local energy minimum structure, which is way too high to be accessed at room temperature. PM6 computations identified a TS only 0.6 kcal mol-1 above the saddle ground state. (I performed a PM6 optimization starting from the x-ray structure, which is highly disordered, and the structure obtained is shown in Figure 3. Unfortunately, the authors did not report the optimized coordinates of any structure!)

Figure 3. PM6 optimized structure of 8.

The fourth and last paper describes the aza-buckybowl 9.5 The x-ray crystal structure shows a curved bowl shape with Cs symmetry. NICS(0) values were computed for the parent molecule 10 B3LYP/6-31G(d). These values are shown in Scheme 1 and the geometry is shown in Figure 4. The 6-member rings that surround the azacylopentadienyl ring all have NICS(0) near zero, which suggests significant bond localization.

Scheme 1. NICS(0) values of 10

Figure 4. B3LYP/6-31G(d) optimized structure of 10.

Our understanding of what aromaticity really means is constantly being challenged!

References

1. Bachrach, S. M., "Double helicenes." Chem. Phys. Lett. 2016, 666, 13-18, DOI: 10.1016/j.cplett.2016.10.070.

2. Ho, P. S.; Kit, C. C.; Jiye, L.; Zhifeng, L.; Qian, M., "A Dipleiadiene-Embedded Aromatic Saddle Consisting
of 86 Carbon Atoms." Angew. Chem. Int. Ed. 2018, 57, 1581-1586, DOI: 10.1002/anie.201711437.

3. Yin, C. K.; Kit, C. C.; Zhifeng, L.; Qian, M., "A Twisted Nanographene Consisting of 96 Carbon Atoms." Angew. Chem. Int. Ed. 2017, 56, 9003-9007, DOI: 10.1002/anie.201703754.

4. Koki, I.; Jennie, L.; Ryo, K.; Sota, S.; Hiroyuki, I., "Fluctuating Carbonaceous Networks with a Persistent
Molecular Shape: A Saddle-Shaped Geodesic Framework of 1,3,5-Trisubstituted Benzene (Phenine)." Angew. Chem. Int. Ed. 2018, 57, 8555-8559, DOI: 10.1002/anie.201803984.

5. Yuki, T.; Shingo, I.; Kyoko, N., "A Hybrid of Corannulene and Azacorannulene: Synthesis of a Highly Curved Nitrogen-Containing Buckybowl." Angew. Chem. Int. Ed. 2018, 57, 9818-9822, DOI: 10.1002/anie.201805678.

InChIs

1: InChI=1S/C134H128/c1-123(2,3)57-37-65-66-38-58(124(4,5)6)42-70-74-46-62(128(16,17)18)50-82-94(74)110-106(90(66)70)105-89(65)69(41-57)73-45-61(127(13,14)15)49-81-93(73)109(105)119-113-97(81)85(131(25,26)27)53-77-78-54-87(133(31,32)33)99-83-51-63(129(19,20)21)47-75-71-43-59(125(7,8)9)39-67-68-40-60(126(10,11)12)44-72-76-48-64(130(22,23)24)52-84-96(76)112-108(92(68)72)107(91(67)71)111(95(75)83)121-115(99)103(78)118-104-80(56-88(134(34,35)36)100(84)116(104)122(112)121)79-55-86(132(28,29)30)98(82)114(120(110)119)102(79)117(118)101(77)113/h37-56H,1-36H3
InChIKey=GKUTUWMASUJSFD-UHFFFAOYSA-N

2: InChI=1S/C86H32/c1-9-33-34-10-2-14-38-42-18-6-22-46-50-26-30-55-56-32-28-52-48-24-8-20-44-40-16-4-12-36-35-11-3-15-39-43-19-7-23-47-51-27-31-54-53-29-25-49-45-21-5-17-41-37(13-1)57(33)73-74(58(34)38)78(62(42)46)84-70(50)66(55)81(65(53)69(49)83(84)77(73)61(41)45)82-67(54)71(51)85-79(63(43)47)75(59(35)39)76(60(36)40)80(64(44)48)86(85)72(52)68(56)82/h1-32H
InChIKey=MXCDWJZMTKLBDM-UHFFFAOYSA-N

3: InChI=1S/C18H12/c1-2-6-14-11-12-16-8-4-3-7-15-10-9-13(5-1)17(14)18(15)16/h1-12H
InChIKey=KVJJNMIHWIRGRP-UHFFFAOYSA-N

4: InChI=1S/C132H108O4/c1-125(2,3)53-29-65-66-30-54(126(4,5)6)34-70-74-38-58(130(16,17)18)42-78-86-46-82-63-51-91(135-27)92(136-28)52-64(63)84-48-88-80-44-60(132(22,23)24)40-76-72-36-56(128(10,11)12)32-68-67-31-55(127(7,8)9)35-71-75-39-59(131(19,20)21)43-79-87-47-83-62-50-90(134-26)89(133-25)49-61(62)81-45-85-77-41-57(129(13,14)15)37-73-69(33-53)93(65)109-110(94(66)70)114(98(74)78)122-106(86)118-103(82)104(84)120-108(88)124-116(100(76)80)112(96(68)72)111(95(67)71)115(99(75)79)123(124)107(87)119(120)102(83)101(81)117(118)105(85)121(122)113(109)97(73)77/h29-52H,1-28H3
InChIKey=ZLPRACZKLACDHX-UHFFFAOYSA-N

5: InChI=1S/C108H60O4/c1-37-13-49-50-14-38(2)18-54-58-22-42(6)26-62-70-30-66-47-35-75(111-11)76(112-12)36-48(47)68-32-72-64-28-44(8)24-60-56-20-40(4)16-52-51-15-39(3)19-55-59-23-43(7)27-63-71-31-67-46-34-74(110-10)73(109-9)33-45(46)65-29-69-61-25-41(5)21-57-53(17-37)77(49)93-94(78(50)54)98(82(58)62)106-90(70)102-87(66)88(68)104-92(72)108-100(84(60)64)96(80(52)56)95(79(51)55)99(83(59)63)107(108)91(71)103(104)86(67)85(65)101(102)89(69)105(106)97(93)81(57)61/h13-36H,1-12H3
InChIKey=ZSIVUKSPPZUSQL-UHFFFAOYSA-N

6: 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

7: InChI=1S/C224H210/c1-211(2,3)197-99-169-85-183(113-197)184-86-170(100-198(114-184)212(4,5)6)157-66-149-67-158(79-157)172-88-187(117-200(102-172)214(10,11)12)188-90-174(104-202(118-188)216(16,17)18)161-70-151-71-162(81-161)176-92-191(121-204(106-176)218(22,23)24)193-95-179(109-207(123-193)221(31,32)33)165-74-153-75-166(83-165)180-96-195(125-208(110-180)222(34,35)36)196-98-182(112-210(126-196)224(40,41)42)168-77-154-76-167(84-168)181-97-194(124-209(111-181)223(37,38)39)192-94-178(108-206(122-192)220(28,29)30)164-73-152-72-163(82-164)177-93-190(120-205(107-177)219(25,26)27)189-91-175(105-203(119-189)217(19,20)21)160-69-150-68-159(80-160)173-89-186(116-201(103-173)215(13,14)15)185-87-171(101-199(115-185)213(7,8)9)156-65-148(64-155(169)78-156)141-50-127-43-128(51-141)130-45-132(55-143(150)53-130)134-47-136(59-145(152)57-134)138-49-140(63-147(154)61-138)139-48-137(60-146(153)62-139)135-46-133(56-144(151)58-135)131-44-129(127)52-142(149)54-131/h43-126H,1-42H3
InChIKey=ZDDKJXIESSWTIA-UHFFFAOYSA-N

8: InChI=1S/C182H126/c1-99-15-113-43-127(29-99)141-57-142-65-155(64-141)162-78-169-92-170(79-162)172-82-164-83-174(94-172)176-85-166-87-178(96-176)180-89-168-91-182(98-180)181-90-167-88-179(97-181)177-86-165-84-175(95-177)173-81-163(80-171(169)93-173)156-66-143(128-30-100(2)16-114(113)44-128)58-144(67-156)130-32-103(5)19-117(47-130)118-20-104(6)34-132(48-118)147-60-148(71-158(165)70-147)134-36-107(9)23-121(51-134)123-25-109(11)39-137(53-123)151-62-152(75-160(167)74-151)138-40-111(13)27-125(55-138)126-28-112(14)42-140(56-126)154-63-153(76-161(168)77-154)139-41-110(12)26-124(54-139)122-24-108(10)38-136(52-122)150-61-149(72-159(166)73-150)135-37-106(8)22-120(50-135)119-21-105(7)35-133(49-119)146-59-145(68-157(164)69-146)131-33-102(4)18-116(46-131)115-17-101(3)31-129(142)45-115/h15-98H,1-14H3
InChIKey=FJHGGHOTCCNJNI-UHFFFAOYSA-N

9: InChI=1S/C44H23N/c1-44(2,3)21-16-28-24-8-4-6-22-26-14-19-12-10-18-11-13-20-15-27-23-7-5-9-25-29(17-21)41(28)45-42(33(22)24)39-35(26)37-31(19)30(18)32(20)38(37)36(27)40(39)43(45)34(23)25/h4-17H,1-3H3
InChIKey=QHBWEZKXFSKCSM-UHFFFAOYSA-N

10: InChI=1S/C40H15N/c1-4-19-23-8-3-9-24-20-5-2-7-22-26-15-18-13-11-16-10-12-17-14-25-21(6-1)30(19)39-36-32(25)34-28(17)27(16)29(18)35(34)33(26)37(36)40(31(20)22)41(39)38(23)24/h1-15H
InChIKey=XWSUADIIRLXSBY-UHFFFAOYSA-N

Dynamics in a terpene cation rearrangement

Dynamics Steven Bachrach 10 Sep 2018 1 Comment

Sarpong and Tantillo have examined the acid-catalyzed Prins/semipinacol rearrangement of hydroxylated pinenes, such as Reaction 1.1

Rxn 1

Interestingly, only the fenchone scaffold products, like 1, are observed and the camphor scaffold products, like 2, are not observed. Cation intermediates are likely, and this means that a primary alkyl shift is taking place in preference to a tertiary alkyl shift, see Scheme 1.

Scheme 1.


Primary alkyl shift


Tertiary alkyl shift

They proposed the following key steps in the reaction mechanism:

ωB97X-D/6-31+G(d,p) computations find a flat surface around cation intermediate 4: the TS leading to 5 and 6 are only 1.3 and 3.3 kcal mol-1, respectively. Since these small barriers are quite susceptible to changes in basis set and functional, and since Tantillo has found many examples of post-transition state bifurcations in cation systems, the authors reasonably decided to conduct molecular dynamics trajectories originating at the TS connecting 3 and 4. The geometries of the critical points are shown in Figure 1.

The trajectory study shows all the usual characteristics of reactions that are under dynamic control. A third of the trajectories show recrossing of the barrier, typical of very flat surfaces. Nearly all of the remaining trajectories led to 5, with only 2 trajectories (~1%) leading to 6. The dynamics are understandable in terms of favoring the primary alkyl shift over the tertiary since a significantly smaller mass needs to move in the former case.


TS 3 → 4


4


TS 4 → 5


TS 4 → 6

Figure 1. ωB97X-D/6-31+G(d,p) optimized geometries.

This is yet another study that implicates dynamic effects in routine reactions, one of many I have discussed over the years.

References

1. Blümel, M.; Nagasawa, S.; Blackford, K.; Hare, S. R.; Tantillo, D. J.; Sarpong, R., "Rearrangement of Hydroxylated Pinene Derivatives to Fenchone-Type Frameworks: Computational Evidence for Dynamically-Controlled Selectivity." J. Am. Chem. Soc. 2018, 140, 9291-9298, DOI: 10.1021/jacs.8b05804.

InChIs

1: InChI=1S/C17H20O2/c1-16-9-12-8-13(16)14(11-6-4-3-5-7-11)19-10-17(12,2)15(16)18/h3-7,12-14H,8-10H2,1-2H3/t12?,13?,14-,16?,17?/m0/s1
InChIKey=LTTUIPPXEHHMJS-XWTIBIIYSA-N

2: InChI=1S/C17H20O2/c1-16-10-19-15(11-6-4-3-5-7-11)13-8-12(16)9-14(18)17(13,16)2/h3-7,12-13,15H,8-10H2,1-2H3/t12?,13?,15-,16?,17?/m0/s1
InChIKey=GCKIOHNLJYVWKL-CMESGNGWSA-N

nano-Saturn

Aromaticity &host-guest Steven Bachrach 28 Aug 2018 No Comments

It never hurts to promote one’s science through clever names – think cubane, buckminsterfullerene, bullvalene, etc. Host-guest chemistry is not immune to this cliché too, and this post discusses the latest synthesis and computations of a nano-Saturn; nano-Saturns are a spherical guest molecule captured inside a ring host molecule. I discussed an example of this a number of years ago – the nano-Saturn comprised of C60 fullerene surrounded by [10]cycloparaphenylene.

Yamamoto, Tsurumaki, Wakamatsu, and Toyota have prepared a nano-Saturn complex with the goal of making a flatter ring component.1 The inner planet is modeled again by C60 and the ring is the [24]circulene analogue 1. The x-ray crystal structure of this nano-Saturn complex is shown in Figure 1.


1: R = 2,4,6-tri-iso-propylphenyl
2: R = H

Figure 1. X-ray crystal structure of the nano-Saturn complex of 1 with C60.

Variable temperature NMR experiments gave the binding values of ΔH = -18.1 ± 2.3 kJ mol-1 and TΔS = 0.8 ± 2.2 kJ mol-1 at 298 K. To gauge this binding energy, they computed the complex of C60 with the parent compound 2 at B3LYP/6-1G(d)//M05-2X/6-31G(d), unfortunately without publishing the coordinates in the supporting materials. The computed binding enthalpy is ΔH = -50.6 kJ mol-1, but this computation is for the gas phase. The computed structure shows close contacts of 0.29 nm between the fullerene and the C9-proton of the anthracenyl groups, in excellent agreement with the x-ray structure. These weak C-Hπ interactions undoubtedly help stabilize the complex, especially given that the fullerene carries a very tiny Mulliken charge of +0.08 e.

References

1) Yuta, Y.; Eiji, T.; Kan, W.; Shinji, T., "Nano-Saturn: Experimental Evidence of Complex Formation of an Anthracene Cyclic Ring with C60." Angew. Chem. Int. Ed. 2018, 57, 8199-8202, DOI: 10.1002/anie.201804430.

InChIs

1: InChI=1S/C174H180/c1-91(2)121-78-150(97(13)14)164(151(79-121)98(15)16)163-90-128-71-139-70-127-59-109(37-38-120(127)77-162(139)163)110-39-49-140-129(60-110)72-130-61-111(40-50-141(130)165(140)170-152(99(17)18)80-122(92(3)4)81-153(170)100(19)20)112-41-51-142-131(62-112)73-132-63-113(42-52-143(132)166(142)171-154(101(21)22)82-123(93(5)6)83-155(171)102(23)24)114-43-53-144-133(64-114)74-134-65-115(44-54-145(134)167(144)172-156(103(25)26)84-124(94(7)8)85-157(172)104(27)28)116-45-55-146-135(66-116)75-136-67-117(46-56-147(136)168(146)173-158(105(29)30)86-125(95(9)10)87-159(173)106(31)32)118-47-57-148-137(68-118)76-138-69-119(128)48-58-149(138)169(148)174-160(107(33)34)88-126(96(11)12)89-161(174)108(35)36/h37-108H,1-36H3
InChIKey=AMDNULXMAMDTMX-UHFFFAOYSA-N

2: InChI=1S/C84H48/c1-13-61-25-62-15-3-51-33-75(62)43-73(61)31-49(1)50-2-14-63-26-64-16-4-52(34-76(64)44-74(63)32-50)54-6-18-66-28-68-20-8-56(38-80(68)46-78(66)36-54)58-10-22-70-30-72-24-12-60(42-84(72)48-82(70)40-58)59-11-23-71-29-69-21-9-57(39-81(69)47-83(71)41-59)55-7-19-67-27-65-17-5-53(51)35-77(65)45-79(67)37-55/h1-48H
InChIKey=ZYXXLAYETADMDM-UHFFFAOYSA-N

An ambiphilic diene for bioorthogonal labeling

Diels-Alder &Houk Steven Bachrach 06 Aug 2018 No Comments

I recently posted on a paper proposing 1,2-benzoquinone and related compounds as the diene component for bioorthogonal labeling. Levandowski, Gamache, Murphy, and Houk report on tetrachlorocyclopentadiene ketal 1 as an active ambiphilic diene component.1

1 is sterically congested to diminish self-dimerization and will react with both electron-rich and electron-poor dienes. To test it as an active diene in bioorthogonal labeling applications, they optimized the structures of the transition states at CPCM(water)/M06-2X/6-311+G(d,p)//CPCM(water)/M06-2X/6-31G(d) for the Diels-Alder reaction of 1 with a variety of dienophiles including trans-cyclooctene 2 and endo-bicyclononyne 3. These transition states are shown in Figure 1. The activation free energy is quite low for each: 18.1 kcal mol-1 with 2 and 18.9 kcal mol-1 with 3.


TS(1+2)


TS(1+3)

Figure 1. CPCM(water)/M06-2X/6-31G(d) optimized geometries for the TSs of the reaction of 1 with 2 and 3.

Experiments were successfully run using 1 as a label on a neuropeptide.

References

1) Levandowski, B. J.; Gamache, R. F.; Murphy, J. M.; Houk, K. N., "Readily Accessible Ambiphilic Cyclopentadienes for Bioorthogonal Labeling." J. Am. Chem. Soc. 2018, 140, 6426-6431, DOI: 10.1021/jacs.8b02978.

InChIs

1:InChI=1S/C7H4Cl4O2/c8-3-4(9)6(11)7(5(3)10)12-1-2-13-7/h1-2H2
InChIkey=DXQQKKGWMVTLOJ-UHFFFAOYSA-N

Aminomethylene carbene does not rearrange by tunneling

Schreiner &Tunneling Steven Bachrach 23 Jul 2018 1 Comment

Eckhardt and Schreiner have spectroscopically characterized the aminomethylene carbene 1.1 Their characterization rests on IR spectra, with comparison to the computed AE-CCSD(T)/cc-pCVQZ anharmonic vibrational frequencies, and the UV-Vis spectra, with comparison to the computed B3LYP/6–311++G(2d,2p) transitions.

1 can be converted to 2 by photolysis. Interestingly, 1 does not convert to 2 after 5 days on the matrix in the dark. This is in distinct contrast to hydroxycarbene and related other carbene which undergo quantum mechanical tunneling (see this post and this post). Examination of the potential energy surface for the reaction of 1 to 2 at AE-CCSD(T)/cc-pCVQZ (see Figure 1) identifies that the lowest barrier is 45.8 kcal mol-1, about 15 kcal mol-1 larger than the barrier for the hydroxycarbene rearrangement. Additionally, the barrier width for 12 is 25% larger than for the hydroxycarbenes. Both of these suggest substantially reduced tunneling, and WKB analysis predicts a tunneling half-life of more than a billion years. The stability of 1 is attributed to the strong π-donor ability of nitrogen to the electron-poor carbene. This is reflected in a very short C-N bond (1.27 Å).

Figure 1. Structures and energies of 1 and 2 and the transition states that connect them. The relative energies (kcal mol-1) are computed at AE-CCSD(T)/cc-pCVQZ.

References

1) Eckhardt, A. K.; Schreiner, P. R., "Spectroscopic Evidence for Aminomethylene (H−C̈−NH2)—The
Simplest Amino Carbene." Angew. Chem. Int. Ed. 2018, 57, 5248-5252, DOI: 10.1002/anie.201800679.

InChIs

1: InChI=1S/CH3N/c1-2/h1H,2H2
InChIKey=KASBEVXLSPWGFS-UHFFFAOYSA-N

2: InChI=1S/CH3N/c1-2/h2H,1H2
InChIKey=WDWDWGRYHDPSDS-UHFFFAOYSA-N

Another long C-C bond

Uncategorized Steven Bachrach 10 Jul 2018 No Comments

This is a third post in a series dealing with very short or very long distances between atoms. Ishigaki, Shimajiri, Takeda, Katoono, and Suzuki have prepared three related analogues of hexaphenylethane that all have long C-C bonds.1 The idea is to create a core by fusing two adjacent phenyls into a naphylene, and then protect the long C-C bond through a shell made up of large aryl groups, 1. Fusing another 5-member ring opposite to the stretched C-C bond (2) creates a scissor effect that should stretch that bond further, even more so in the unsaturated version 3.

Their M062-x/6-31G* computations predict an increasing longer C-C bond (highlighted in blue in the above drawing): 1.730 Å in 1, 1.767 Å in 2, and 1.771 Å in 3. The structure of 3 is shown in Figure 3.

Figure 1. M06-2x/6-31G(d) optimized structure of 3.

These three compounds were synthesized, and characterized by IR and Raman spectroscopy. Their x-ray crystal structures at 200 K and 400K were also determined. The C-C distances are 1.742 Å (1), 1.773 Å (2) and 1.798 Å (3) with distances slightly longer at 400 K. These rank as the longest C-C bonds recorded.

References

1) Ishigaki, Y.; Shimajiri, T.; Takeda, T.; Katoono, R.; Suzuki, T., "Longest C–C Single Bond among Neutral Hydrocarbons with a Bond Length beyond 1.8 Å." Chem 2018, 4, 795-806, DOI: 10.1016/j.chempr.2018.01.011.

InChIs

1: InChI=1S/C40H26/c1-5-17-32-27(11-1)23-24-28-12-2-6-18-33(28)39(32)36-21-9-15-31-16-10-22-37(38(31)36)40(39)34-19-7-3-13-29(34)25-26-30-14-4-8-20-35(30)40/h1-26H
InChIKey=IFIFQLGAOZULMX-UHFFFAOYSA-N

2: InChI=1S/C42H28/c1-5-13-33-27(9-1)17-18-28-10-2-6-14-34(28)41(33)37-25-23-31-21-22-32-24-26-38(40(37)39(31)32)42(41)35-15-7-3-11-29(35)19-20-30-12-4-8-16-36(30)42/h1-20,23-26H,21-22H2
InChIKey=HSJDZFLRPWJAGF-UHFFFAOYSA-N

3: InChI=1S/C42H26/c1-5-13-33-27(9-1)17-18-28-10-2-6-14-34(28)41(33)37-25-23-31-21-22-32-24-26-38(40(37)39(31)32)42(41)35-15-7-3-11-29(35)19-20-30-12-4-8-16-36(30)42/h1-26H
InChIKey=QQYNKBIOZSXWGD-UHFFFAOYSA-N

Long C-C bonds are not caused by crystal packing forces

adamantane &DFT &Grimme &MP &Schreiner Steven Bachrach 25 Jun 2018 No Comments

Schreiner and Grimme have examined a few compounds (see these previous posts) with long C-C bonds that are found in congested systems where dispersion greatly aids in stabilizing the stretched bond. Their new paper1 continues this theme by examining 1 (again) and 2, using computations, and x-ray crystallography and gas-phase rotational spectroscopy and electron diffraction to establish the long C-C bond.

The distance of the long central bond in 1 is 1.647 Å (x-ray) and 1.630 Å (electron diffraction). Similarly, this distance in 2 is 1.642 Å (x-ray) and 1.632 Å (ED). These experiments discount any role for crystal packing forces in leading to the long bond.

A very nice result from the computations is that most functionals that include some dispersion correction predict the C-C distance in the optimized structures with an error of no more than 0.01 Å. (PW6B95-D3/DEF2-QZVP structures are shown in Figure 1.) Not surprisingly, HF and B3LYP without a dispersion correction predict a bond that is too long.) MP2 predicts a distance that is too short, but SCS-MP2 does a very good job.


1


2

Figure 1. PW6B95-D3/DEF2-QZVP optimized structures of 1 and 2.

References

1) Fokin, A. A.; Zhuk, T. S.; Blomeyer, S.; Pérez, C.; Chernish, L. V.; Pashenko, A. E.; Antony, J.; Vishnevskiy, Y. V.; Berger, R. J. F.; Grimme, S.; Logemann, C.; Schnell, M.; Mitzel, N. W.; Schreiner, P. R., "Intramolecular London Dispersion Interaction Effects on Gas-Phase and Solid-State Structures of Diamondoid Dimers." J. Am. Chem. Soc. 2017, 139, 16696-16707, DOI: 10.1021/jacs.7b07884.

InChIs

1: InChI=1S/C28H38/c1-13-7-23-19-3-15-4-20(17(1)19)24(8-13)27(23,11-15)28-12-16-5-21-18-2-14(9-25(21)28)10-26(28)22(18)6-16/h13-26H,1-12H2
InChIKey=MMYAZLNWLGPULP-UHFFFAOYSA-N

2: InChI=1S/C26H34O2/c1-11-3-19-15-7-13-9-25(19,21(5-11)23(27-13)17(1)15)26-10-14-8-16-18-2-12(4-20(16)26)6-22(26)24(18)28-14/h11-24H,1-10H2
InChIKey=VPBJYHMTINJMAE-UHFFFAOYSA-N

An even shorter non-bonding HH distance

Uncategorized Steven Bachrach 22 May 2018 1 Comment

The competition for finding molecules with ever-closer non-bonding HH interactions is heating up. I have previously blogged about 1, a in,in-Bis(hydrosilane) designed by Pascal,1 with an HH distance of 1.57 Å, and also blogged about 2, the dimer of tri(di-t-butylphenyl)methane,2 where the distance between methine hydrogens on adjacent molecules is 1.566 Å.

Now Pascal reports on 3, which shows an even closer HH approach.3

The x-ray structure of 3 shows the in,in relationship of the two critical hydrogens, HA and HB. Though the positions of these hydrogens were refined, the C-H distance are artificially foreshortened. A variety of computed structures are reported, and these all support a very short HH non-bonding distance of about 1.52 Å. The B3PW91-D3/cc-pVTZ optimized structure is shown in Figure 1.

Figure 1. B3PW91-D3/cc-pVTZ optimized structure of 3.

The authors also note an unusual feature of the 1H NMR spectrum of 3: the HB signal appears as a double with JAB= 2.0 Hz. B3LYP/6–311++G(2df,2pd) NMR computations indicated a coupling of 3.1 Hz. This is the largest through-space coupling recorded.

References

1. Zong, J.; Mague, J. T.; Pascal, R. A., "Exceptional Steric Congestion in an in,in-Bis(hydrosilane)." J. Am. Chem. Soc. 2013, 135, 13235-13237, DOI: 10.1021/ja407398w.

2. Rösel, S.; Quanz, H.; Logemann, C.; Becker, J.; Mossou, E.; Cañadillas-Delgado, L.; Caldeweyher, E.; Grimme, S.; Schreiner, P. R., "London Dispersion Enables the Shortest Intermolecular Hydrocarbon H···H Contact." J. Am. Chem. Soc. 2017, 139, 7428–7431, DOI: 10.1021/jacs.7b01879.

3. Xiao, Y.; Mague, J. T.; Pascal, R. A., "An Exceptionally Close, Non-Bonded Hydrogen–Hydrogen Contact with Strong Through-Space Spin–Spin Coupling." Angew. Chem. Int. Ed. 2018, 57, 2244-2247, DOI: 10.1002/anie.201712304.

InChI

3: InChI=1S/C27H24S3/c1-4-17-13-28-10-16-11-29-14-18-5-2-8-21-24(18)27-23(17)20(7-1)26(21)22-9-3-6-19(25(22)27)15-30-12-16/h1-9,16,26-27H,10-15H2
InChIKey=NJBHGDPNFALCTL-UHFFFAOYSA-N

MD studies of simple pericyclic reactions

Cope Rearrangement &Diels-Alder &Dynamics &Houk Steven Bachrach 07 May 2018 No Comments

At the recent ACS meeting in New Orleans, Ken Houk spoke at the Dreyfus award session in honor of Michele Parrinello. Ken’s talk included discussion of some recent molecular dynamics studies of pericyclic reactions. Because of their similarities in approaches and observations, I will discuss three recent papers from his group (which Ken discussed in New Orleans) in this post.

The Cope rearrangement, a fundamental organic reaction, has been studied extensively by computational means (see Chapter 4.2 of my book). Mackey, Yang, and Houk examine the degenerate Cope rearrangement of 1,5-hexadiene with molecular dynamics at the (U)B3LYP/6-31G(d) level.1 They examined 230 trajectories, and find that of the 95% of them that are reactive, 94% are trajectories that directly cross through the transition zone. By this, Houk means that the time gap between the breaking and forming C-C bonds is less than 60 fs, the time for one C-C bond vibration. The average time in the transition zone is 35 fs. This can be thought of as “dynamically concerted”. For the other few trajectories, a transient diradical with lifetime of about 100 fs is found.

The dimerization of cyclopentadiene finds the two [4+2] pathways merging into a single bispericylic transition state. 2 Only a small minority (13%) of the trajectories sample the region about the Cope rearrangement that interconverts the two mirror image dimers. These trajectories average about 60 fs in this space, which comes from the time separation between the formation of the two new C-C bonds. The majority of the trajectories quickly pass through the dimerization transition zone in about 18 fs, and avoid the Cope TS region entirely. These paths can be thought of as “dynamically concerted”, while the other set of trajectories are “dynamically stepwise”. It should be noted however that the value of S2 in the Cope transition zone are zero and so no radicals are being formed.

Finally, Yang, Dong, Yu, Yu, Li, Jamieson, and Houk examined 15 different reactions that involve ambimodal (i.e. bispericyclic) transition states.3 They find a strong correlation between the differences in the bond lengths of the two possible new bond vs. their product distribution. So for example, in the reaction shown in Scheme 1, bond a is the one farthest along to forming. Bond b is slightly shorter than bond c. Which of these two is formed next is dependent on the dynamics, and it turns out the Pab is formed from 73% of the trajectories while Pac is formed only 23% of the time. This trend is seen across the 15 reaction, namely the shorter of bond b or c in the transition state leads to the larger product formation. When competing reactions involve bonds with differing elements, then a correlation can be found with bond order instead of with bond length.

Scheme 1

References

1) Mackey, J. L.; Yang, Z.; Houk, K. N., "Dynamically concerted and stepwise trajectories of the Cope rearrangement of 1,5-hexadiene." Chem. Phys. Lett. 2017, 683, 253-257, DOI: 10.1016/j.cplett.2017.03.011.

2) Yang, Z.; Zou, L.; Yu, Y.; Liu, F.; Dong, X.; Houk, K. N., "Molecular dynamics of the two-stage mechanism of cyclopentadiene dimerization: concerted or stepwise?" Chem. Phys. 2018, in press, DOI: 10.1016/j.chemphys.2018.02.020.

3) Yang, Z.; Dong, X.; Yu, Y.; Yu, P.; Li, Y.; Jamieson, C.; Houk, K. N., "Relationships between Product Ratios in Ambimodal Pericyclic Reactions and Bond Lengths in Transition Structures." J. Am. Chem. Soc. 2018, 140, 3061-3067, DOI: 10.1021/jacs.7b13562.

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