Archive for the 'Dynamics' Category

Bispericyclic reaction involving two [6+4] cycloadditions

Bispericyclic transition states arise when two pericyclic reactions merge to a common transition state. This leads to a potential energy surface with a bifurcation such that reactions that traverse this type of transition state will head towards two different products. The classic example is the dimerization of cyclopentadiene, involving two [4+2] Diels-Alder reactions. Unusual PESs are discussed in my book and in past blog posts.

Houk and coworkers have now identified a bispericyclic transition state involving two [6+4] cycloadditions.1 Reaching back to work Houk pursued as a graduate student with Woodward for inspiration, these authors examined the reaction of tropone 1 with dimethylfulvene 2. Each moiety can act as the diene or triene component of a [6+4] allowed cycloaddition:

The product with fulvene 2 as the 6 π-e component and tropone as the 4 π-e component [6F+4T] is 3, while reversing their participation in the [6T+4F] cycloaddition leads to 4. A variety of [4+2] reactions are also possible. All of these reactions were investigated at PCM/M06-2X/6-311+G(d,p)//B3LYP-D3/6-31G(d). The reaction leading to 3 is exothermic by 3.0 kcal mol-1, while the reaction to 4 endothermic by 1.3 kcal mol-1.

Interestingly, there is only one transition state that leads to both 3 and 4, the first known bispericyclic transition state for two conjoined [6+4] cycloadditions. The barrier is 27.9 kcal mol-1. The structures of the two products and the transition state leading to them are shown in Figure 1. 3 and 4 can interconvert through a Cope transition state, also shown in Figure 1, with a barrier of 26.3 kcal mol-1 (for 43).

3

4

TS [6+4]

TS Cope

Figure 1. B3LYP-D3/6-31G(d) optimized geometries.

Given that a single transition leads to two products, the product distribution is dependent on the molecular dynamics. A molecular dynamics simulation at B3LYP-D3/6-31G(d) with 117 trajectories indicates that 4 is formed 91% while 3 is formed only 9%. Once again, we are faced with the reality of much more complex reaction mechanisms/processes than simple models would suggest.

References

1) Yu, P.; Chen, T. Q.; Yang, Z.; He, C. Q.; Patel, A.; Lam, Y.-h.; Liu, C.-Y.; Houk, K. N., "Mechanisms and Origins of Periselectivity of the Ambimodal [6 + 4] Cycloadditions of Tropone to Dimethylfulvene." J. Am. Chem. Soc. 2017, 139 (24), 8251-8258, DOI: 10.1021/jacs.7b02966.

InChIs

1: InChI=1S/C7H6O/c8-7-5-3-1-2-4-6-7/h1-6H
InChIKey=QVWDCTQRORVHHT-UHFFFAOYSA-N

2: InChI=1S/C8H10/c1-7(2)8-5-3-4-6-8/h3-6H,1-2H3
InChIKey=WXACXMWYHXOSIX-UHFFFAOYSA-N

3:InChI=1S/C15H16O/c1-15(2)10-6-8-12(14(16)9-7-10)11-4-3-5-13(11)15/h3-12H,1-2H3
InChIKey=SEKRUGIZAIQCDA-UHFFFAOYSA-N

4: InChI=1S/C15H16O/c1-9(2)14-10-7-8-11(14)13-6-4-3-5-12(10)15(13)16/h3-8,10-13H,1-2H3
InChIKey=AQQAMUGJSGJKLC-UHFFFAOYSA-N

cycloadditions &Dynamics &Houk Steven Bachrach 07 Aug 2017 No Comments

A few review articles

A few nice review/opinion pieces have been piling up in my folder of papers of interest for this Blog. So, this post provides a short summary of a number of review articles that computationally-oriented chemists may find of interest.

Holy Grails in computational chemistry

Houk and Liu present a short list of “Holy Grails” in computationally chemistry.1 They begin by pointing out a few technical innovations that must occur for the Grails to be found: development of a universal density functional; an accurate, generic force field; improved sampling for MD; and dealing with the combinatorial explosion with regards to conformations and configurations. Their list of Grails includes predicting crystal structures and structure of amorphous materials, catalyst design, reaction design, and device design. These Grails overlap with the challenges I laid out in my similarly-themed article in 2014.2

Post-transition state bifurcations and dynamics

Hare and Tantillo review the current understanding of post-transition state bifurcations (PTSB).3 This type of potential energy surface has been the subject of much of Chapter 8 of my book and many of my blog posts. What is becoming clear is the possibility of a transition state followed by a valley-ridge inflection leads to reaction dynamics where trajectories cross a single transition state but lead to two different products. This new review updates the state-of-the-art from Houk’s review4 of 2008 (see this post). Mentioned are a number of studies that I have included in this Blog, along with reactions involving metals, and biochemical systems (many of these examples come from the Tantillo lab). They close with the hope that their review might “inspire future studies aimed at controlling selectivity for reactions with PTSBs” (italics theirs). I might offer that controlling selectivity in these types of dynamical systems is another chemical Grail!

The Hase group has a long review of direct dynamics simulations.5 They describe a number of important dynamics studies that provide important new insight to reaction mechanism, such as bimolecular SN2 reactions (including the roundabout mechanism) and unimolecular dissociation. They write a long section on post-transition state bifurcations, and other dynamic effects that cannot be interpreted using transition state theory or RRKM. This section is a nice complement to the Tantillo review.

Benchmarking quantum chemical methods

Mata and Suhm look at our process of benchmarking computational methods.6 They point out the growing use of high-level quantum computations as the reference for benchmarking new methods, often with no mention of any comparison to experiment. In defense of theoreticians, they do note the paucity of useful experimental data that may exist for making suitable comparisons. They detail a long list of better practices that both experimentalists and theoreticians can take to bolster both efforts, leading to stronger computational tools that are more robust at helping to understand and discriminate difficult experimental findings.

References

1) Houk, K. N.; Liu, F., "Holy Grails for Computational Organic Chemistry and Biochemistry." Acc. Chem. Res. 2017, 50 (3), 539-543, DOI: 10.1021/acs.accounts.6b00532.

2) Bachrach, S. M., "Challenges in computational organic chemistry." WIRES: Comput. Mol. Sci. 2014, 4, 482-487, DOI: 10.1002/wcms.1185.

3) Hare, S. R.; Tantillo, D. J., "Post-transition state bifurcations gain momentum – current state of the field." Pure Appl. Chem. 2017, 89, 679-698, DOI: 0.1515/pac-2017-0104.

4) Ess, D. H.; Wheeler, S. E.; Iafe, R. G.; Xu, L.; Çelebi-Ölçüm, N.; Houk, K. N., "Bifurcations on Potential Energy Surfaces of Organic Reactions." Angew. Chem. Int. Ed. 2008, 47, 7592-7601, DOI: 10.1002/anie.200800918

5) Pratihar, S.; Ma, X.; Homayoon, Z.; Barnes, G. L.; Hase, W. L., "Direct Chemical Dynamics Simulations." J. Am. Chem. Soc. 2017, 139, 3570-3590, DOI: 10.1021/jacs.6b12017.

6) Mata, R. A.; Suhm, M. A., "Benchmarking Quantum Chemical Methods: Are We Heading in the Right Direction?" Angew. Chem. Int. Ed. 2017, ASAP, DOI: 10.1002/anie.201611308.

Dynamics &Houk Steven Bachrach 25 Jul 2017 No Comments

Dynamics in a [3,3]-rearrangement

Bispericyclic reactions occur when two different pericyclic reactions merge to have a single transition state. An example of this is the joining of two [3,3]-sigmatopic rearrangements of 1 that merge to have a single transition state. Lopez, Faza, and Lopez have examined the dynamics of this reaction.1

Because of the symmetry of the species along this reaction pathway, the products of the two different rearrangements are identical, and will be formed in equal amounts, though they are produced from a single transition state with the reaction pathway bifurcating due to a valley-ridge inflection post TS.

The interesting twist that is explored here is when 1 is substituted in order to break the symmetry. The authors have examined 3x with either fluorine, chlorine, or bromine. The critical points on the reactions surface were optimized at M06-2X/Def2TZVPP. In all three cases a single bispericyclic transition state 3TS1x is found, which leads to products 4a and 4b. A second transition state 4TSx corresponds to the [3,3]-rearrangement that interconverts the two products. The structures of 1TS, 3TS1F, and 3TS1Cl are shown in Figure 1.

1TS

3TS1F

3TS1Cl

Figure 1. M06-2X/Def2TZVPP optimized geometries of 1TS, 3TS1F, and 3TS1Cl.

The halogen substitution breaks the symmetry of the reaction path. This leads to a number of important changes. First, the C4-C5 and C7-C8 distances, which are identical in 1TS, are different in the halogen cases. Interestingly, the distortions are dependent on the halogen: in 3TS1F C4-C5 is 0.2 Å longer than C7-C8, but in 3TS1Cl C7-C8 is much longer (by 0.65 Å) than C4-C5. Second, the products are no longer equivalent with the halogen substitution. Again, this is halogen dependent: 4bF is 4.0 kcal mol-1 lower in energy than 4aF, while 4aCl is 8.2 kcal mol-1 lower than 4bCl.

These difference manifest in very different reaction dynamics. With trajectories initiated at the first (bispericyclic) transiting state, 89% end at 4bF and 9% end at 4aF, a ratio far from unity that might be expected from both products resulting from passage through the same TS. The situation is even more extreme for the chlorine case, where all 200 trajectories end in 4aCl. This is yet another example of the role that dynamics play in reaction outcomes (see these many previous posts).

References

1) Villar López, R.; Faza, O. N.; Silva López, C., "Dynamic Effects Responsible for High Selectivity in a [3,3] Sigmatropic Rearrangement Featuring a Bispericyclic Transition State." J. Org. Chem. 2017, 82 (9), 4758-4765, DOI: 10.1021/acs.joc.7b00425.

InChIs

1: InChI=1S/C9H12/c1-3-9-6-4-8(2)5-7-9/h1-2,4-7H2
InChIKey=RRXCPJIEZVQPSZ-UHFFFAOYSA-N

2: InChI<=1S/C9H12/c1-7-4-5-8(2)9(3)6-7/h1-6H2
InChIKey=AMBNQWVPTPHADI-UHFFFAOYSA-N

3F: InChI=1S/C9H8F4/c1-3-7-5-4-6(2)8(10,11)9(7,12)13/h1-2,4-5H2
InChIKey=VZFAQFJKHDWJDN-UHFFFAOYSA-N

3Cl: InChI=1S/C9H8Cl4/c1-3-7-5-4-6(2)8(10,11)9(7,12)13/h1-2,4-5H2
InChIKey=AIVUHFMHIMNOJB-UHFFFAOYSA-N

4aF: InChI=1S/C9H8F4/c1-5-4-6(8(10)11)2-3-7(5)9(12)13/h1-4H2
InChIKey=NAUUHIHYMAOMIF-UHFFFAOYSA-N

4aCl: InChI=1S/C9H8Cl4/c1-5-4-6(8(10)11)2-3-7(5)9(12)13/h1-4H2
InChIKey=MMCKDJXQYSGQEH-UHFFFAOYSA-N

4bF: InChI=1S/C9H8F4/c1-5-4-6(2)8(10,11)9(12,13)7(5)3/h1-4H2
InChIKey=LMFNAIRCNARWSX-UHFFFAOYSA-N

4bCl: InChI=1S/C9H8Cl4/c1-5-4-6(2)8(10,11)9(12,13)7(5)3/h1-4H2
InChIKey=NOFFASDSCUGRTP-UHFFFAOYSA-N

Cope Rearrangement &Dynamics Steven Bachrach 05 Jun 2017 No Comments

Dynamics in a reaction where a [6+4] and [4+2] cycloadditons compete

Enzyme SpnF is implicated in catalyzing the putative [4+2] cycloaddition taking 1 into 3. Houk, Singleton and co-workers have now examined the mechanism of this transformation in aqueous solution but without the enzyme.1 As might be expected, this mechanism is not straightforward.

Reactant 1, transition states, and products 2 and 3 were optimized at SMD(H2O)/M06-2X/def2-TZVPP//B3LYP-D3(BJ)//6-31+G(d,p). Geometries and relative energies are shown in Figure 1. The reaction 12 is a formal [6+4] cycloaddition, and the reaction 13 is a formal [4+2] cycloaddition. Interestingly, only a single transition state could be located TS1. It is a bispericyclic TS (see Chapter 4 of my book), where these two pericyclic reaction sort of merge together. After TS1 is traversed the potential energy surface bifurcates, leading to 2 or 3. This is yet again an example of a single TS leading to two different products. (See the many posts I have written on this topic.) The barrier height is 27.6 kcal mol-1, with 2 lying 13.1 kcal mol-1 above 3. However, the steepest descent pathway from TS1 leads to 2. There is a second transition state TScope that describes a Cope rearrangement between 2 and 3. Using the more traditional TS theory description, 1 undergoes a [6+4] cycloaddition to form 2 which then crosses a lower barrier (TScope) to form the thermodynamically favored 3, which is the product observed in the enzymatically catalyzed reaction.

1 (0.0)

TS1 (27.6)

2 (4.0)

3 (-9.1)

(24.7)

Figure 1. B3LYP-D3(BJ)//6-31+G(d,p) optimized geometries and relative energies in kcal mol-1.

Molecular dynamics computations were performed on this system by tracking trajectories starting in the neighborhood of TS1 on a B3LYP-D2/6-31G(d) PES. The results are that 63% of the trajectories end at 2, 25% end at 3, and 12% recross back to reactant 1, suggesting an initial formation ratio for 2:3 of 2.5:1. The reactions are very slow to cross through the “transition zone”, typically 2-3 times longer than for a usual Diels-Alder reaction (see this post).

Once again, we see an example of dynamic effects dictating a reaction mechanism. The authors pose a tantalizing question: Can an enzyme control the outcome of an ambimodal reaction by altering the energy surface such that the steepest downhill path from the transition state leads to the “desired” product(s)? The answer to this question awaits further study.

References

(1) Patel, A; Chen, Z. Yang, Z; Gutierrez, O.; Liu, H.-W.; Houk, K. N.; Singleton, D. A. “Dynamically
Complex [6+4] and [4+2] Cycloadditions in the Biosynthesis of Spinosyn A,” J. Amer. Chem. Soc. 2016, 138, 3631-3634, DOI: 10.1021/jacs.6b00017.

InChIs

1: InChI=1S/C24H34O5/c1-3-21-15-12-17-23(27)19(2)22(26)16-10-7-9-14-20(25)13-8-5-4-6-11-18-24(28)29-21/h4-11,16,18-21,23,25,27H,3,12-15,17H2,1-2H3/b6-4+,8-5+,9-7+,16-10+,18-11+/t19-,20+,21-,23-/m0/s1
InChIKey=JEKALMRMHDPSQK-ZTRRSECRSA-N

2: InChI=1S/C24H34O5/c1-3-19-8-6-10-22(26)15(2)23(27)20-12-11-17-14-18(25)13-16(17)7-4-5-9-21(20)24(28)29-19/h4-5,7,9,11-12,15-22,25-26H,3,6,8,10,13-14H2,1-2H3/b7-4-,9-5+,12-11+/t15-,16-,17-,18-,19+,20+,21-,22+/m1/s1
InChIKey=AVLPWIGYFVTVTB-PTACFXJJSA-N

3: InChI=1S/C24H34O5/c1-3-19-5-4-6-22(26)15(2)23(27)11-10-20-16(9-12-24(28)29-19)7-8-17-13-18(25)14-21(17)20/h7-12,15-22,25-26H,3-6,13-14H2,1-2H3/b11-10+,12-9+/t15-,16+,17-,18-,19+,20-,21-,22+/m1/s1
InChIKey=BINMOURRBYQUKD-MBPIVLONSA-N

cycloadditions &Diels-Alder &Dynamics &Houk &Singleton Steven Bachrach 30 Aug 2016 1 Comment

Dynamics in the reaction of tetrazine with cyclopropene

Houk and Doubleday report yet another example of dynamic effects in reactions that appear to be simple, ordinary organic reactions.1 Here they look at the Diels-Alder reaction of tetrazine 1 with cyclopropene 2. The reaction proceeds by first crossing the Diels-Alder transition state 3 to form the intermediate 4. This intermediate can then lose the anti or syn N2, through 5a or 5s, to form the product 6. The structures and relative energies, computed at M06-2X/6-31G(d), of these species are shown in Figure 1.

3
17.4

4
-33.2

5a
-28.9

5s
-20.0

6
-86.2

Figure 1. M06-2X/6-31G(d) optimized geometries and energies (relative to 1 + 2) of the critical points along the reaction of tetrazine with cyclopropene.

The large difference in the activation barriers between crossing 5a and 5s (nearly 9 kcal mol-1) suggests, by transition state theory, a preference of more than a million for loss of the anti N2 over the syn N2. However, quasiclassical trajectory studies, using B3LYP/6-31G(d), finds a different situation. The anti pathway is preferred, but only by a 4:1 ratio! This dynamic effect arises from a coupling of the v3 mode which involves a rocking of the cyclopropane ring that brings a proton near the syn N2 functionality, promoting its ejection. In addition, the trajectory studies find short residence times within the intermediate neighborhood for the trajectories that lead to the anti product and longer residence times for the trajectories that lead to the syn product. All together, a very nice example of dynamic effects playing a significant role in a seemingly straightforward organic reaction.

References

(1) Törk, L.; Jiménez-Osés, G.; Doubleday, C.; Liu, F.; Houk, K. N. "Molecular Dynamics of the Diels–Alder Reactions of Tetrazines with Alkenes and N2 Extrusions from Adducts," J. Am. Chem. Soc. 2015, 137, 4749-4758, DOI: 10.1021/jacs.5b00014.

InChIs

1: InChI=1S/C2H2N4/c1-3-5-2-6-4-1/h1-2H
InChIKey=HTJMXYRLEDBSLT-UHFFFAOYSA-N

2: InChI=1S/C3H4/c1-2-3-1/h1-2H,3H2
InChIKey=OOXWYYGXTJLWHA-UHFFFAOYSA-N

4: InChI=1S/C5H6N4/c1-2-3(1)5-8-6-4(2)7-9-5/h2-5H,1H2
InChIKey=JGSMBFYJCNPYDM-UHFFFAOYSA-N

6: InChI=1S/C5H6N2/c1-4-2-6-7-3-5(1)4/h2-5H,1H2
InChIKey=RYJFHKGQZKUXEH-UHFFFAOYSA-N

Diels-Alder &Dynamics &Houk Steven Bachrach 09 Nov 2015 No Comments

Dynamic effects in the Garratt-Braverman/[1,5]-H migration

Schmittel has examined the thermolysis of 1, which undergoes a Garratt-Braverman rearrangement followed by a [1,5]-H migration to produce 3.1 The product 3 is formed in a 10.3:1 ratio of E to Z consistently over the temperature range of 60 – 140 °C. This non-changing ratio is unusual. The difference in the computed (UB3LYP/6-31g(d)) free energy of activation for the step 23 ranges from 2.35 to 2.56 kcal mol-1 for this temperature range, manifesting in a predicted E:Z ratio of 24.9 at 60 °C to 22.7 at 140 °C.

The computed structures of 1-3 along with the transition states are shown in Figure 1. The activation free energy for the first step (Garrat-Braverman) is 30.9 kcal mol-1. This is about 30 kcal mol-1 larger than the barrier for the second step. Schmittel suggests that a non-statistical effect is manifesting here. The molecule crosses the first TS and then follows a downhill path directly over TS2E without spending any time in the region of the intermediate 2. A few computed trajectories all indicate that it takes less than 50 fs from the time the reaction crosses TS1 until the hydrogen migrates, supporting the notion that vibrational relaxation within the intermediate 2 is not occurring. This reaction is yet another example of dynamic effects dictating product distributions.

1a
0.0

1b
12.3

TS1
30.9

2
-14.6

TS2E
0.5

TS2Z
2.8

3E
-50.5

3Z
-46.1

Figure 1. UB3LYP/6-31G(d) optimized structures and relative free energies (kcal mol-1) for the reaction 13. (Note that a conformational change must first take 1a into 1b before the reaction can take place.)

References

1) Samanta, D.; Rana, A.; Schmittel, M. “Nonstatistical Dynamics in the Thermal Garratt−Braverman/[1,5]‑H Shift of One Ene−diallene: An Experimental and Computational Study,” J. Org. Chem. 2014, 79, 8435–8439, DOI: 10.1021/jo501324w.

InChIs

1: InChI=1S/C24H34/c1-5-11-21(12-6-2)17-19-23-15-9-10-16-24(23)20-18-22(13-7-3)14-8-4/h9-10,15-16,19-20H,5-8,11-14H2,1-4H3
InChIKey=RVCDLAOAATXCKZ-UHFFFAOYSA-N

2: InChI=1S/C24H34/c1-5-11-19(12-6-2)23-17-21-15-9-10-16-22(21)18-24(23)20(13-7-3)14-8-4/h9-10,15-18H,5-8,11-14H2,1-4H3
InChIKey=QCHALYJSTFUUQF-UHFFFAOYSA-N

3E; InChI=1S/C24H34/c1-5-11-19(12-6-2)23-17-21-15-9-10-16-22(21)18-24(23)20(13-7-3)14-8-4/h9-11,15-18,23H,5-8,12-14H2,1-4H3/b19-11-
InChIKey=XWILUXHXXNRMRE-ODLFYWEKSA-N

3Z: InChI=1S/C24H34/c1-5-11-19(12-6-2)23-17-21-15-9-10-16-22(21)18-24(23)20(13-7-3)14-8-4/h9-11,15-18,23H,5-8,12-14H2,1-4H3/b19-11+
InChIKey=XWILUXHXXNRMRE-YBFXNURJSA-N

Dynamics Steven Bachrach 05 Jan 2015 2 Comments

Dynamics in a photorearrangement

The di-π-methane photorearrangement has been known for many years, first studied by Zimmerman.1,2 The triplet photorearrangement gives an interesting rearranged product; and the mechanism of this photorearrangement of 1 into 2 has now been examined by the Houk group using computational techniques, including trajectory analysis. The proposed mechanism is that excitation to the triplet state 1* is followed by rearrangement to the triplet intermediate INT1* which then rearranges to the triplet INT2*. Intersystem crossing then leads to the singlet product 2.

The PES for this rearrangement was explored3 at CASMP2(10,10)/6-31G(d)//CASSCF(10,10)/6-31G(d), with geometries and relative energies shown in Figure 1, as well as at (U)M06-2x/6-31G(d) and (U)B3LYP/6-31G(d); they all give qualitatively the same result. The first TS is the rate limiting step, and the second TS lies only 1-2 kcal mol-1 above the intermediate INT1. So, the reaction appears to be two steps, but with such a low barrier for the second step, dynamic effects might be important as trajectories might cross INT1* and go over TS2* without residing in the intermediate well for any appreciable time – a seemingly one step reaction. Note than no TS for directly traversing from 1* to INT2* was found.

1*
0.0

TS1*
12.9

INT1*
7.1

TS2*
8.2

INT2*
-15.4

Figure 1. CASSCF(10,10)/6-31G(d) geometries and CASMP2 energies in kcal mol-1.

Now in a follow-up study, Houk and co-workers4 performed trajectories analysis on the M06-2x/6-31G(d) PES. A total of 256 trajectories were initiated at TS1* and 241 ended at INT2* within 1500fs. Of these, 24 trajectories resided for less than 60fs within the region of INT1, a time less than a C-C vibration. Furthermore, the lifetime of INT1 that is predicted by RRKM is much longer (about 500fs) than what is observed in the trajectories (about 200 fs). Thus, there is significant dynamic effects in this excited state rearrangement, though INT1 is always sampled.

References

(1) Zimmerman, H. E.; Grunewald, G. L. "The Chemistry of Barrelene. III. A Unique Photoisomerization to Semibullvalene," J. Am. Chem. Soc. 1966, 88, 183-184, DOI: 10.1021/ja00953a045.

(2) Zimmerman, H. E.; Binkley, R. W.; Givens, R. S.; Sherwin, M. A. "Mechanistic organic photochemistry. XXIV. The mechanism of the conversion of barrelene to semibullvalene. A general photochemical process," J. Am. Chem. Soc. 1967, 89, 3932-3933, DOI: 10.1021/ja00991a064.

(3)  Matute, R. A.; Houk, K. N. "The Triplet Surface of the Zimmerman Di-π-Methane Rearrangement of Dibenzobarrelene," Angew. Chem. Int. Ed. 2012, 51, 13097-13100, DOI: 10.1002/anie.201208002.

(4) Jiménez-Osés, G.; Liu, P.; Matute, R. A.; Houk, K. N. "Competition Between Concerted and Stepwise Dynamics in the Triplet Di-π-Methane Rearrangement," Angew. Chem. Int. Ed. 2014,
53, 8664-8667, DOI: 10.1002/anie.201310237.

InChIs

1: InChI=1S/C16H12/c1-2-6-12-11(5-1)15-9-10-16(12)14-8-4-3-7-13(14)15/h1-10,15-16H
InChIKey=VWDKVBGOVYWYFZ-UHFFFAOYSA-N

2: InChI=1S/C16H12/c1-3-7-11-9(5-1)13-10-6-2-4-8-12(10)15-14(11)16(13)15/h1-8,13-16H
InChIKey=RATAQXOLJVRERC-UHFFFAOYSA-N

Dynamics Steven Bachrach 06 Oct 2014 1 Comment

An approach towards identifying dynamic effect without trajectories

Demonstrating the occurrence of non-statistical dynamics generally has been accomplished through trajectory studies. These trajectory studies are often quite computationally demanding, requiring many trajectories, often of long duration, with molecules that are typically not small! Schmittel and co-workers present a case where their evidence for non-statistical dynamics rests not on trajectory studies but a combination of experimental product distributions and free energy of activation computations.1

For the Schmittel C2-C6 cyclization taking 1 into 5¸Schmittel has located no concerted transition state, but rather two different transition states 2 and 2’, leading to a common intermediate diradical 3. Then there are two different transition states 4 and 4’ leading to the two regioisomeric products 5 and 5’. The BLYP/6-31G* structures and relative free energies are shown in Figure 1.

1
0.0

2
19.4

2’
20.2

3
13.3

4
16.5

4’
15.4

5
-6.3

5’
-14.3

Figure 1. BLYP/6-31G*geometries and relative free energies (kcal mol-1) of the critical points along the reaction 15.

If transition state theory (TST) holds here, the rate limiting step is the first set of transition states, and the product distribution should be dictated by the second set of transition states. Since 4’ is lower in energy than 4, TST predicts that 5’ should be the major product. However, the experiments show that the ratio 5:5’ ranges from 1.48 at 30 °C to 1.65 at 60 °C, with the ratio decreasing a bit at higher temperatures still.

Examination of the potential energy surfaces in the neighborhoods of the transition states and the intermediate show a couple of interesting features. First, there is a large barrier separating 2 and 2’ and this precludes the concerted pathway. Second, the minimum energy path forward from 2 requires a sharp turn to proceed to the intermediate 3. Schmittel suggests that this surface supports the notion of some direct reaction paths from 2 avoiding the intermediate 3 and directly over transition state 4’. Schmittel offers a simple formula for predicting the percentage of the products formed from a non-statistical pathway:

XNSQ1 + XSQ2 = Qexp

where XNS is the mole fraction following non-statistical pathways and XS is the fraction following a statistical pathway and Qexp is the experimental mole ratio and Q1 is the partitioning at the first set of TSs and Q2 is the partitioning at the second set of TSs. While this approach is certainly much simpler than performing molecular dynamics, it does require experimental values. According to this model, the above reaction follows non-statistical dynamics about 75% of the time.

References

(1) Samanta, D.; Rana, A.; Schmittel, M. "Quantification of Nonstatistical Dynamics in an Intramolecular Diels–Alder Cyclization without Trajectory Computation," J. Org. Chem. 2014, 79, 2368-2376, DOI: 10.1021/jo500035b.

InChIs

1: InChI=1S/C28H29NSi/c1-29(2)27-17-11-16-26(22-27)28(30(3,4)5)21-20-25-15-10-9-14-24(25)19-18-23-12-7-6-8-13-23/h6-17,20,22H,1-5H3
InChIKey=CKQXQJAGCGSOOP-UHFFFAOYSA-N

5: InChI=1S/C28H29NSi/c1-29(2)24-17-11-16-22-27(24)25(19-12-7-6-8-13-19)26-21-15-10-9-14-20(21)18-23(26)28(22)30(3,4)5/h6-17H,18H2,1-5H3
InChIKey=OFALZDSJOVLMHZ-UHFFFAOYSA-N

5′: InChI=1S/C28H29NSi/c1-29(2)21-15-16-23-24(18-21)28(30(3,4)5)25-17-20-13-9-10-14-22(20)27(25)26(23)19-11-7-6-8-12-19/h6-16,18H,17H2,1-5H3
InChIKey=UQRNTADMKHTLNR-UHFFFAOYSA-N

Dynamics Steven Bachrach 12 May 2014 No Comments

Dynamic effects in [1,2]- and [2,3]-sigmatropic rearrangements

While the [2-3]-sigmatropic rearrangement is well known and understood as allowed under the Woodward-Hoffmann rules, [1,2]-sigmatropic are much more rare, perhaps because they are forbidden by the same orbital symmetry arguments. It is perhaps surprising that these two rearrangements may sometimes be found in competition. Singleton has applied many of his tried-and-true techniques, namely, careful normal abundance kinetic isotope effect (KIE) analysis and molecular dynamics computations, to this problem.1

Reaction 1 takes place exclusively through a [2,3]-rearrangement; the principle evidence is the lack of any crossover reaction. However, the slightly more substituted analogue shown in Reaction 2 gives rise to two products: that obtained from a [2,3]-rearrangement 6 and that obtained from a [1,2]-rearrangement 7.

The KIE for the rearrangement of 2 is large for the carbon breaking the bond with nitrogen, while it is small at the carbons that are forming the new bond. This becomes a metric for judging the transition state obtained with computations. With the computed TS and canonical variational transition state theory (VTST) including small curvature tunneling, the KIE can be computed from a computed structures and frequencies. This imposes a range of reasonable distances for the forming C-C bond of 2.6-2.9 Å – much longer that a typical distance in the TS of similar pericyclic reactions.

Crossover experiments for Reaction 2 are understood in terms of a reaction model whereby some fraction of the reactants undergo a concerted rearrangement to form 6, and 7 is formed by first breaking the C-N bond, forming two radicals, that either recombine right away or form isolated radicals that then collapse to product.

The interesting twist here is that one would expect two different transition states, one for the concerted process 8 and one to cleave the bond 9. Both do exist and are shown in Figure 1. However, VTST predicts that the concerted process should be 25-50 times faster than cleavage, and that does not match up with experiments. Amazingly, molecular dynamics trajectories started from the concerted TS 8 leads to cleavage about 20% of the time using UMO6-2X with a variety of basis sets. Thus, as Singleton has noted many times before, a single TS is crossed that leads to two different products! An argument based on entropy helps explain why the second (cleavage) pathway is viable.

8

9

Figure 1. UMO6-2x/6-31G* optimized structures of TS 8 and 9.

References

(1) Biswas, B.; Collins, S. C.; Singleton, D. A. "Dynamics and a Unified Understanding of Competitive [2,3]- and [1,2]-Sigmatropic Rearrangements Based on a Study of Ammonium Ylides," J. Am. Chem. Soc. 2014, 136, 3740-3743, DOI: 10.1021/ja4128289.

Dynamics &Singleton Steven Bachrach 29 Apr 2014 No Comments

Dynamic effects in nucleophilic substitution

I think most organic chemists hold dear to their hearts the notion that selectivity is due to crossing over different transition states. Readers of my book and this blog know of the many examples where this notion simply is not true (see here). This post discusses yet another example taking place in a seemingly simple reaction.

Singleton has examined the nucleophilic substitution reaction of 1 with sodium tolylsulfide.1 The mono substitution gives potentially two different stereoproducts 2 and 3. The experimental ratio of these products 2:3 is 81:19. (Note that things are a bit more complicated because disubstitution can also occur, but this has been factored into the product ratio.)

Based on previous literature, this reaction is likely to proceed in a concerted fashion, and so one might anticipate running computations to locate a transition state leading to 2 and a transition state leading to 3. In fact, Singleton finds six different TSs (the lowest energy TS 4 is shown in Figure 1), all within 2 kcal mol-1 of each other at PCM(ethanol)/B3LYP/6-31+G**. However, the intrinsic reaction coordinate going forward from each of these six TSs leads solely to 2; no TS could be located that connects to 3! (Computations were also performed at PCM(ethanol)/M06-2x/6-31+G** which give very similar results.) Classical transition state theory would lead
one to conclude that only 2 should be formed, inconsistent with experiment.

4

5

Figure 1. PCM/B3LYP/6-31+G** optimized structures of TSs 4 and 5.

Furthermore, no intermediate could be located. This is consistent with a concerted mechanism. A second transition state was located which interconverts 2 and 3 with the involvement of a chloride – a sort of addition/rotation/elimination process. This TS 5 is also shown in Figure 1.

A direct dynamics study was performed, and 197 trajectories were computed. Of these, 185 trajectories went to product: 156 to 2 and 29 to 3, for a ratio of 84:16 – in amazing agreement with experiment! The product selectivity is due entirely to dynamic effects. In fact, it is one vibrational mode that dictates the product distribution. Essentially, the nature of the rotation about the C=C bond differentiates the eventual route, with a clockwise rotation leading always to 2 and a counterclockwise rotation leading about a third of the time to 3.

References

(1) Bogle, X. S.; Singleton, D. A. "Dynamic Origin of the Stereoselectivity of a Nucleophilic Substitution Reaction," Org. Lett., 2012, 14, 2528-2531, DOI: 10.1021/ol300817a.

InChIs

1: InChI=1S/C4H4Cl2O/c1-3(7)2-4(5)6/h2H,1H3
InChIKey=NXDUHPYJFYSBCT-UHFFFAOYSA-N

2: InChI=1S/C11H11ClOS/c1-8-3-5-10(6-4-8)14-11(12)7-9(2)13/h3-7H,1-2H3/b11-7-
InChIKey=NCXXSKTZGJETLW-XFFZJAGNSA-N

3: InChI=1S/C11H11ClOS/c1-8-3-5-10(6-4-8)14-11(12)7-9(2)13/h3-7H,1-2H3/b11-7+
InChIKey=NCXXSKTZGJETLW-YRNVUSSQSA-N

Dynamics &Singleton &Substitution Steven Bachrach 03 Jul 2012 12 Comments

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