Twisting a benzene ring

Aromaticity Steven Bachrach 26 Jan 2015 No Comments

Here’s another cruel and unusual punishment applied to the poor benzene ring. Hashimoto,et al. have created a molecule that is a fused double helicene, where the fusion is about a single phenyl ring.1 Compound 1 has two [5]helicenes oriented in opposite directions. This should provide a twist to the central phenyl ring, and the added methyl groups help to expand that twist.

They prepared 1 and its x-ray crystal structure is reported. The compound exhibits C2 symmetry. The twist (defined as the dihedral of four consecutive carbon atoms of the central ring) is 28.17°, nearly the same twist as in [2]paraphenylene.

The B3LYP/6-31G(d) structure of 1 is shown in Figure 1. This geometry is very similar to the x-ray structure. The calculated NICS value for the central ring is -4.9 (B3LYP/6-311+G(d,p)/B3LYP/6-31G(d)) and -4.3 (B3LYP/6-311+G(d,p)/x-ray structure). This diminished value from either benzene or C6(PSH2)2(CH3)4 indicates reduced aromaticity of this central ring, presumably due to the distortion away from planarity. Nonetheless, the central ring of 1 is not oxidized when subjected to MCPBA to oxidize to the bis phosphine oxides.

1

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

References

(1) Hashimoto, S.; Nakatsuka, S.; Nakamura, M.; Hatakeyama, T. "Construction of a Highly Distorted Benzene Ring in a Double Helicene," Angew. Chem. Int. Ed. 2014, 53, 14074-14076, DOI: 10.1002/anie.201408390.

InChIs

1: InChI=1S/C50H32P2S2/c1-25-17-21-29-9-5-13-33-41(29)37(25)45-46-38-26(2)18-22-30-10-7-15-35(42(30)38)52(54)36-16-8-12-32-24-20-28(4)40(44(32)36)48(50(46)52)47-39-27(3)19-23-31-11-6-14-34(43(31)39)51(33,53)49(45)47/h5-24H,1-4H3

o-Phenylene conformations

Aromaticity Steven Bachrach 21 Jan 2015 No Comments

In solution ortho-phenylenes preferentially coil into a helix with the phenyl rings stacked. However, 25-50% of these chains will typically misfold. Hartley and coworkers have reported the use of substituents to increase the percentage of perfectly folded chains.1

They synthesized two isomeric o-phenylenes, differing in the substitution pattern (1 and 2), with chain length of 6 to 10 phenyl rings. Substituents included methoxy, acetoxy, nitrile, and triflate. They principally employed 1H NMR to assess the conformational distribution, and used computations to confirm the conformation.

Ideally folded conformations of 1 and 2 with eight phenyl rings are shown in Figure 1. The dihedral angle formed by two adjacent phenyl rings are typically about ±55° or ±130°.

1

2

Figure 1. Idealized folding of 1 and 2 with X=OH.
Hydrogens omitted in these images, but full structures available, through Jmol, by clicking on the image.)

Given the size of these systems, and the conformation flexibility not just of the chain but with each substituent, a full search to identify the global minimum was not undertaken. Rather, a library of conformations was generated with MM, the lowest 200 conformations were then reoptimized at PM7 and then the energies were determined at PCM/B97-D/TZV(2d,2p). The lowest energy conformer was then reoptimized at this DFT level. Three conformations of 3 and 4 are shown in Figure 2 with triflate as the substituent with six phenyl rings. The first conformer has optimal stacking (perfect folding), the second conformer as one misfold at the end, and the third conformer has no stacking at all.

3
– ideal fold

3
– one misfold

3 – all misfold

4 – ideal fold

4
– one misfold

4
– all misfold

Figure 2. Optimized geometries of conformers of 3 and 4.
(Remember that clicking on one of these images will bring up the JMol applet allowing you to rotate and visualize the molecule in 3-D – a very useful feature here!)

NMR chemical shifts were then computed using these geometries at PCM/WP04/6-31G(d). In all cases examined, the chemical shifts of the major conformation was confirmed to be the perfect folding one by comparison with the computed chemical shifts. The examined substituents enhanced the proportion of properly folded chains in all cases, often to the extent where no minor conformer was observed at all.

References

(1) Mathew, S.; Crandall, L. A.; Ziegler, C. J.; Hartley, C. S. "Enhanced Helical Folding of ortho-Phenylenes through the Control of Aromatic Stacking Interactions," J. Am. Chem. Soc. 2014, 136, 16666-16675, DOI:10.1021/ja509902m.

InChIs

3: InChI=1S/C42H26F18O18S6/c43-37(44,45)79(61,62,63)23-5-1-21(2-6-23)29-13-9-25(81(67,68,69)39(49,50)51)17-33(29)35-19-27(83(73,74,75)41(55,56)57)11-15-31(35)32-16-12-28(84(76,77,78)42(58,59)60)20-36(32)34-18-26(82(70,71,72)40(52,53)54)10-14-30(34)22-3-7-24(8-4-22)80(64,65,66)38(46,47)48/h1-20H,(H,61,62,63)(H,64,65,66)(H,67,68,69)(H,70,71,72)(H,73,74,75)(H,76,77,78)
InChIKey=BOCNJIZJHQKUNK-UHFFFAOYSA-N

4: InChI=1S/C42H26F18O18S6/c43-37(44,45)79(61,62,63)23-6-4-21(5-7-23)33-17-25(81(67,68,69)39(49,50)51)9-13-30(33)35-19-27(83(73,74,75)41(55,56)57)11-15-32(35)36-20-28(84(76,77,78)42(58,59)60)10-14-31(36)34-18-26(82(70,71,72)40(52,53)54)8-12-29(34)22-2-1-3-24(16-22)80(64,65,66)38(46,47)48/h1-20H,(H,61,62,63)(H,64,65,66)(H,67,68,69)(H,70,71,72)(H,73,74,75)(H,76,77,78)
InChIKey=YKSIXAVDGFBUIZ-UHFFFAOYSA-N

Benchmarking π-conjugation

DFT Steven Bachrach 14 Jan 2015 2 Comments

With the proliferation of density functionals, selecting the functional to use in your particular application requires some care. That is why there have been quite a number of benchmark studies (see these posts for some examples). Yu and Karton have now added to our benchmark catalog with a study of π-conjugation.1

They looked at a set of 60 reactions which involve a reactant with π-conjugation and a product which lacks conjugation. A few examples, showing examples involving linear and cyclic systems, are shown in Scheme 1.

Scheme 1.

The reaction energies were evaluated at W2-F12, which should have an error of a fraction of a kcal mol-1. Three of the reactions can be compared with experimental values, and difference in the experimental and computed values are well within the error bars of the experiment. It is too bad that the authors did not also examine 1,3-cyclohexadiene → 1,4-cyclohexadiene, a reaction that is both of broader interest than many of the ones included in the test set and can also be compared with experiment.

These 60 reactions were then evaluated with a slew of functionals from every rung of Jacob’s ladder. The highlights of this benchmark study are that most GGA and meta-GGA and hybrid functionals (like B3LYP) have errors that exceed chemical accuracy (about 1 kcal mol-1). However, the range-separated functionals give very good energies, including ωB97X-D. The best results are provided with double hybrid functionals. Lastly, the D3 dispersion correction does generally improve energies by 10-20%. On the wavefunction side, SCS-MPs gives excellent results, and may be one of the best choices when considering computational resources.

References

(1) Yu, L.-J.; Karton, A. "Assessment of theoretical procedures for a diverse set of isomerization reactions involving double-bond migration in conjugated dienes," Chem. Phys. 2014, 441, 166-177, DOI: 10.1016/j.chemphys.2014.07.015.

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

Dynamics Steven Bachrach 05 Jan 2015 2 Comments

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

Two review articles for the general audience

Houk &Schleyer Steven Bachrach 22 Dec 2014 No Comments

In trying to clean up my in-box of articles for potential posts, I write here about two articles for a more general audience, authored by two of the major leaders in computational organic chemistry.

Ken Houk offers an overview of how computational simulation is a partner with experiment and theory in aiding and guiding our understanding of organic chemistry.1 The article is written for the non-specialist, really even more for the non-scientist. Ken describes how computations have helped understand relatively simple reactions like pericyclic reactions, that then get more subtle when torquoselection is considered, to metal-catalysis, to designed protein catalysts. If you are ever faced with discussing just what you do as a computational chemist at a cocktail party, this article is a great resource of how to explain our science to the interested lay audience.

Paul Schleyer adds a tutorial on transition state aromaticity.2 The authors discusses a variety of aromaticity measures (energetics, geometry, magnetic properties) that can be employed to analyze the nature of transition states, in addition to ground state molecules. This article provides a very clear description of the methods and a few examples. It is written for a more specialized audience than Houk’s article, but is nonetheless completely accessible to any chemist, even those with no computational background.

References

(1) Houk, K. N.; Liu, P. "Using Computational Chemistry to Understand & Discover Chemical Reactions," Daedalus 2014, 143, 49-66, DOI: 10.1162/DAED_a_00305.

(2) Schleyer, P. v. R.; Wu, J. I.; Cossio, F. P.; Fernandez, I. "Aromaticity in transition structures," Chem. Soc. Rev. 2014, 43, 4909-4921, DOI: 10.1039/C4CS00012A.

Hypercubane

Uncategorized Steven Bachrach 15 Dec 2014 1 Comment

Three-dimensional objects can be projected into four-dimensional objects. So for example a cube can be projected into a hypercube, as in Scheme 1.

Scheme 1.

Pichierri proposes a hydrocarbon analogue of the hypercube. The critical decision is the connecting bridge between the outer (exploded) carbons. This distance is too long to be a single carbon-carbon bond. Pichierri opts to use ethynyl bridges, to give the hypercube 1.1

Now, unfortunately he does not supply any supporting materials. So I have reoptimized this Oh geometry at B3LYP/6-31G(d), and show this structure in Figure 1. Pichierri does not report much beyond the geometry of 1 and the perfluoronated analogue. One interesting property that might be of interest is the ring strain energy of 1, which I will not take up here.


1

2

But a question I will take up is just what bridges might serve to create the hydrocarbon hypercube. A more fundamental choice might be ethanyl bridges, to create 2. However, the Oh conformer of 2 has 13 imaginary frequencies at B3LYP/6-31G(d). Lowering the symmetry to D3 give a structure that has only real frequencies, and it’s shown in Figure 1. An interesting exercise is to ponder other choices of bridges, which I will leave for the reader.

1

2

Figure 1. B3LYP/6-31G(d) optimized structures of 1 and 2.
As always, be sure to click on the image to enable Jmol for interactive viewing of these interesting structures!

References

(1) Pichierri, F. "Hypercubane: DFT-based prediction of an Oh-symmetric double-shell hydrocarbon," Chem. Phys. Lett. 2014, 612, 198-202, DOI: j.cplett.2014.08.032.

InChIs

1: InChI=1S/C40H24/c1-2-26-7-9-29-15-11-27-5-3-25(1)4-6-28-12-16-30(10-8-26)20-23-32(22-19-29)24-21-31(17-13-27,18-14-28)39-35(27)33(25)34(26)37(29,35)40(32,39)38(30,34)36(28,33)39/h1-24H
InChIKey=FFMFUIDOGFAUOP-UHFFFAOYSA-N

2: InChI=1S/C40H48/c1-2-26-7-9-29-15-11-27-5-3-25(1)4-6-28-12-16-30(10-8-26)20-23-32(22-19-29)24-21-31(17-13-27,18-14-28)39-35(27)33(25)34(26)37(29,35)40(32,39)38(30,34)36(28,33)39/h1-24H2
InChIKey=MCSZKKKJCDSRIV-UHFFFAOYSA-N

Structure of carbonic acid

Schreiner Steven Bachrach 09 Dec 2014 No Comments

I remain amazed at how regularly I read reports of structure determinations of what seem to be simple molecules, yet these structures have eluded determination for decades if not centuries. An example is the recently determined x-ray crystal structure of L-phenylalanine;1 who knew that growing these crystals would be so difficult?

The paper I want to discuss here is on the gas-phase structure of carbonic acid 1.2 Who would have thought that preparing a pure gas-phase sample would be so difficult? Schreiner and co-workers prepared carbonic acid by high-vacuum flash pyrolysis (HVFP) of di-tert-butyl carbonate, as shown in Scheme 1.

Scheme 1

Carbonic acid can appear in three difference conformations, shown in Figure 1. The two lowest energy conformations are separated by a barrier of 9.5 kcal mol-1 (estimated by focal point energy analysis). These conformations can be interconverted using near IR light. The third conformation is energetically inaccessible.

1cc
(0.0)

1ct
(1.6)

1tt
(10.1)

2cc

2cc

Figure 1. CCSD(T)/cc-pVQZ optimized structures of 1 (and the focal point relative energies in kcal mol-1) and the CCSD(T)/cc-pVTZ optimized structures of 2.

The structures of these two lowest energy conformations were confirmed by comparing their experimental IR spectra with the computed spectra (CCSD(T)/cc-pVTZ) and their experimental and computed rotational constants.

An interesting added component of this paper is that sublimation of the α- and β-polymorphs of carbonic acid do not produce the same compound. Sublimation of the β-isomorph does produce 1, but sublimation of the α-isomorph produces the methylester of 1, compound 2 (see Figure 1). The structure of 2 is again confirmed by comparison of the experimental and computed IR spectra.

References

(1) Ihlefeldt, F. S.; Pettersen, F. B.; von Bonin, A.; Zawadzka, M.; Görbitz, C. H. "The Polymorphs of L-Phenylalanine," Angew. Chem. Int. Ed. 2014, 53, 13600–13604, DOI: 10.1002/anie.201406886.

(2) Reisenauer, H. P.; Wagner, J. P.; Schreiner, P. R. "Gas-Phase Preparation of Carbonic Acid and Its Monomethyl Ester," Angew. Chem. Int. Ed. 2014, 53, 11766-11771, DOI: 10.1002/anie.201406969.>

InChIs

1: InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)
InChIKey=BVKZGUZCCUSVTD-UHFFFAOYSA-N

2: InChI=1S/C2H4O3/c1-5-2(3)4/h1H3,(H,3,4)
InChIKey=CXHHBNMLPJOKQD-UHFFFAOYSA-N

Paul Schleyer: In Memorium

Schleyer Steven Bachrach 02 Dec 2014 2 Comments

Professor Paul von Ragué Schleyer passed away November 21, 2014. Paul was a major force in physical organic and computational organic chemistry. I followed his career closely for the entirety of my own career; my doctoral studies with Andrew Streitwieser involved the analysis of the nature of the C-Li bond and we were in constant communication with Schleyer. Paul’s work on aromaticity greatly informed my thinking and my studies in this area.

I interviewed Paul in his office at the University of Georgia for the first edition of my book Computational Organic Chemistry. This interview was reprinted in the second edition without any changes. In honor of Paul, I am posting this interview here, so that our community can remember this important, inspirational figure.

 


 

Interview: Professor Paul von Ragué Schleyer

Interviewed March 28, 2006

Professor Paul Schleyer is the Graham Perdue Professor of Chemistry at the University of Georgia, where he has been for the past 8 years. Prior to that, he was a professor at the University at Erlangen (co-director of the Organic Institute) and the founding director of its Computer Chemistry Center. Schleyer began his academic career at Princeton University.

Professor Schleyer’s involvement in computational chemistry dates back to the 1960s, when his group was performing MM and semi-empirical computations as an adjunct to his predominantly experimental research program. This situation dramatically changed when Professor John Pople invited Schleyer to visit Carnegie-Mellon University in 1969 as the NSF Center of Excellence Lecturer. From discussions with Dr. Pople, it became clear to Schleyer that “ab initio methods could look at controversial subjects like the nonclassical carbocations. I became hooked on it!” The collaboration between Pople and Schleyer that originated from that visit lasted well over 20 years, and covered such topics as substituent effects, unusual structures that Schleyer terms “rule-breaking”, and organolithium chemistry. This collaboration started while Schleyer was at Princeton but continued after his move to Erlangen, where Pople came to visit many times. The collaboration was certainly of peers. “It would be unfair to say that the ideas came from me, but it’s clear that the projects we worked on would not have been chosen by Pople. Pople added a great deal of insight and he would advise me on what was computationally possible,” Schleyer recalls of this fruitful relationship.

Schleyer quickly became enamored with the power of ab initio computations to tackle interesting organic problems. His enthusiasm for computational chemistry eventually led to his decision to move to Erlangen – they offered unlimited (24/7) computer time, while Princeton’s counteroffer was just 2 hours of computer time per week. He left Erlangen in 1998 due to enforced retirement. However, his adjunct status at the University of Georgia allowed for a smooth transition back to the United States, where he now enjoys a very productive collaborative relationship with Professor Fritz Schaefer.

Perhaps the problem that best represents how Schleyer exploits the power of ab initio computational chemistry is the question of how to define and measure aromaticity. Schleyer’s interest in the concept of aromaticity spans his entire career. He was drawn to this problem because of the pervasive nature of aromaticity across organic chemistry. Schleyer describes his motivation: “Aromaticity is a central theme of organic chemistry. It is re-examined by each generation of chemists. Changing technology permits that re-examination to occur.” His direct involvement came about by Kutzelnigg’s development of a computer code to calculate chemical shifts. Schleyer began use of this program in the 1980s and applied it first to structural problems. His group “discovered in this manner many experimental structures that were incorrect.”

To assess aromaticity, Schleyer first computed the lithium chemical shifts in complexes formed between lithium cation and the hydrocarbon of interest. The lithium cation would typically reside above the aromatic ring and its chemical shift would be affected by the magnetic field of the ring. While this met with some success, Schleyer was frustrated by the fact that lithium was often not positioned especially near the ring, let alone in the center of the ring. This led to the development of nucleus-independent chemical shift (NICS), where the virtual chemical shift can be computed at any point in space. Schleyer advocated using the geometric center of the ring, then later a point 1 Å above the ring center.

Over time, Schleyer came to refine the use of NICS, advocating an examination of NICS values on a grid of points. His most recent paper posits using just the component of the chemical shift tensor perpendicular to the ring evaluated at the center of the ring. This evolution reflects Schleyer’s continuing pursuit of a simple measure of aromaticity. “Our endeavor from the beginning was to select one NICS point that we could say characterizes the compound,” Schleyer says. “The problem is that chemists want a number which they can associate with a phenomenon rather than a picture. The problem with NICS was that it was not soundly based conceptually from the beginning because cyclic electron delocalization-induced ring current was not expressed solely perpendicular to the ring. It’s only that component which is related to aromaticity.”

The majority of our discussion revolved around the definition of aromaticity. Schleyer argues that “aromaticity can be defined perfectly well. It is the manifestation of cyclic electron delocalization which is expressed in various ways. The problem with aromaticity comes in its quantitative definition. How big is the aromaticity of a particular molecule? We can answer this using some properties. One of my objectives is to see whether these various quantities are related to one another. That, I think, is still an open question.”

Schleyer further detailed this thought, “The difficulty in writing about aromaticity is that it is encrusted by two centuries of tradition, which you cannot avoid. You have to stress the interplay of the phenomena. Energetic properties are most important, but you need to keep in mind that aromaticity is only 5% of the total energy. But if you want to get as close to the phenomenon as possible, then one has to go to the property most closely related, which is magnetic properties.” This is why he focuses upon the use of NICS as an aromaticity measure. He is quite confident in his new NICS measure employing the perpendicular component of the chemical shift tensor. “This new criteria is very satisfactory,” he says. “Most people who propose alternative measures do not do the careful step of evaluating them against some basic standard. We evaluate against aromatic stabilization energies.”

Schleyer notes that his evaluation of the aromatic stabilization energy of benzene is larger than many other estimates. This results from the fact that, in his opinion, “all traditional equations for its determination use tainted molecules. Cyclohexene is tainted by hyperconjugation of about 10 kcal mol-1. Even cyclohexane is very tainted, in this case by 1,3-interactions.” An analogous complaint can be made about the methods Schleyer himself employs: NICS is evaluated at some arbitrary point or arbitrary set of points, the block-diagonalized “cyclohexatriene” molecule is a gedanken molecule. When pressed on what then to use as a reference that is not ‘tainted’, Schleyer made this trenchant comment: “What we are trying to measure is virtual. Aromaticity, like almost all concepts in organic chemistry, is virtual. They’re not measurable. You can’t measure atomic charges within a molecule. Hyperconjugation, electronegativity, everything is in this sort of virtual category. Chemists live in a virtual world. But science moves to higher degrees of refinement.” Despite its inherent ‘virtual’ nature, “Aromaticity has this 200 year history. Chemists are interested in the unusual stability and reactivity associated with aromatic molecules. The term survives, and remains an enormously fruitful area of research.”

His interest in the annulenes is a natural extension of the quest for understanding aromaticity. Schleyer was particularly drawn to [18]-annulene because it can express the same D6h symmetry as does benzene. His computed chemical shifts for the D6h structure differed significantly from the experimental values, indicating that the structure was clearly wrong. “It was an amazing computational exercise,” Schleyer mused, “because practically every level you used to optimize the geometry gave a different structure. MP2 overshot the aromaticity, HF and B3LYP undershot it. Empirically, we had to find a level that worked. This was not very intellectually satisfying but was a pragmatic solution.” Schleyer expected a lot of flak from crystallographers about this result, but in fact none occurred. He hopes that the x-ray structure will be re-done at some point.

Reflecting on the progress of computational chemistry, Schleyer recalls that “physical organic chemists were actually antagonistic toward computational chemistry at the beginning. One of my friends said that he thought I had gone mad. In addition, most theoreticians disdained me as a black-box user.” In those early years as a computational chemist, Schleyer felt disenfranchised from the physical organic chemistry community. Only slowly has he felt accepted back into this camp. “Physical organic chemists have adopted computational chemistry; perhaps, I hope to think, due to my example demonstrating what can be done. If you can show people that you can compute chemical properties, like chemical shifts to an accuracy that is useful, computed structures that are better than experiment, then they get the word sooner or later that maybe you’d better do some calculations.” In fact, Schleyer considers this to be his greatest contribution to science – demonstrating by his own example the importance of computational chemistry towards solving relevant chemical problems. He cites his role in helping to establish the Journal of Computational Chemistry in both giving name to the discipline and stature to its practitioners.

Schleyer looks to the future of computational chemistry residing in the breadth of the periodic table. “Computational work has concentrated on one element, namely carbon,” Schleyer says. “The rest of the periodic table is waiting to be explored.” On the other hand, he is dismayed by the state of research at universities. In his opinion, “the function of universities is to do pure research, not to do applied research. Pure research will not be carried out at any other location.” Schleyer sums up his position this way – “Pure research is like putting money in the bank. Applied research is taking the money out.” According to this motto, Schleyer’s account is very much in the black.

Reprinted from Computational Organic Chemistry, Steven M. Bachrach, 2014, Wiley:Hoboken.

 

Structure of Histidine

amino acids Steven Bachrach 01 Dec 2014 No Comments

The Alonso group has yet again (see these posts) determined the gas-phase structure of an important, biologically significant molecule using a combination of exquisite microwave spectroscopy and quantum computations. This time they examine the structure of histidine.1

They optimized four conformations of histidine, as its neutral tautomer, at MP2/6-311++G(d,p). These are schematically drawn in Figure 1. Conformer 1a is the lowest in free energy, likely due to the two internal hydrogen bonds. Its structure is shown in Figure 2.

Figure 1. The four conformers of histidine. The relative free energy (MP2/6-311++G(d,p)) in kcal mol-1 are also indicated.

Figure 2. MP2/6-311++G(d,p) optimized geometry of 1a.

The initial experimental rotation constants were only able to eliminate 1b from consideration. So they then determined the quadrupole coupling constants for the 14N nuclei. These values strongly implicated 1a as the only structure in the gas phase. The agreement between the experimental values and the computed values at MP2/6-311++G(d,p) was a concern, so they rotated the amine group to try to match the experimental values. This lead to a change in the NHCC dihedral value of -16° to -23° Reoptimization of the structure at MP2/cc-pVTZ led to a dihedral of -21° and overall excellent agreement between the experimental spectral parameters and the computed values.

It is somewhat disappointing the supporting materials does not include the structures of the other three isomers, nor the optimized geometry at MP2/cc-pVTZ.

References

1) Bermúdez, C.; Mata, S.; Cabezas, C.; Alonso, J. L. "Tautomerism in Neutral Histidine," Angew. Chem. Int. Ed. 2014, 53, 11015-11018, DOI: 10.1002/anie.201405347.

InChIs

Histidine: InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m0/s1
InChIKey=HNDVDQJCIGZPNO-YFKPBYRVSA-N

Dynamics in the Wittig reaction

Singleton &Wittig Steven Bachrach 18 Nov 2014 No Comments

If you hadn’t noticed, I am a big fan of the work that Dan Singleton is doing concerning the role of dynamics in discerning reaction mechanisms. Dan’s group has reported another outstanding study combining experiments, traditional QM computations, and molecular dynamics – this time on the Wittig reaction.1

The key question concerning the mechanism is whether a betaine intermediate is accessed along the reaction (path A) or whether the reaction proceeds in a concerted manner (path B). Earlier computations had supported the concerted pathway (B).

Experimental determination of the heavy atom kinetic isotope effect was made for Reaction 1.

Reaction 1

Using the 6-31+G(2df,p) basis set, three different density functionals predict three different potential energy surfaces. With M06-2x, the surface indicates path A (stepwise), with the first step rate-limiting. B3P86 also predicts the stepwise reaction, but the second step is rate-limiting. The Lc-wPBE functional predicts a concerted reaction. Using these surfaces, they predicted the carbon isotope effect and compared it to the experimental values. The best agreement is with the M06-2x surface with a weighting of the vibrational energies of the two different TSs. The optimized structures of the two transition states, the betaine intermediate, and the product are shown in Figure 1.

TS1

Betaine

TS2

Product

Figure 1. M06-2x/6-31+G(2df,p) optimized geometry of the critical points of Reaction 1.

The agreement of the predicted and experimental KIE is not ideal. So, they performed molecular dynamics computations with the ONIOM approach using M06-2x/6-31G* for Reaction 1 and 53 THF molecules treated at PM3. 360 trajectories were begun in the region of the first transition state (TS1), and they can be organized into 4 groups. The first group (128 trajectories) are reactions that produce product. The second group (76 cases) form the C-C bond but then it ruptures and returns to reactant. The third group (82 cases) have an immediate recrossing back to reactant, and the last group (16 cases) takes product back to the first TS and then returns to product. The predicted KIE using this weighted MD results gives values in outstanding agreement with the experiments.

Of the first group, about 50% pass from TS1 to TS2 in less than 150 fs, or in other words look like a concerted path. But a good number of trajectories reside in the betaine region for 1-2 ps.

In contrast, trajectories initiated from the betaine with equilibrated THF molecules indicate a median of 600 ps to travel from TS1 to TS2 and do not resemble a concerted path.

They argue that this bimodal distribution is in part associated with a solvent effect. When the first TS is crossed the solvent molecules are not equilibrated about the solute, and 10-20% of the trajectories immediately pass through the betaine region due to “dynamic matching” where the entering motion matches with exiting over the second transition state. The longer trajectories result from improper dynamic matching, but faster motion in the solute than motion amongst the solvent needed to stabilize the betaine. So, not only do we need to be concerned about dynamic effects involving the reactants, we need to be concerned about dynamics associated with the solvent too!

References

(1) Chen, Z.; Nieves-Quinones, Y.; Waas, J. R.; Singleton, D. A. "Isotope Effects, Dynamic Matching, and Solvent Dynamics in a Wittig Reaction. Betaines as Bypassed Intermediates," J. Am. Chem. Soc. 2014, 136, 13122-13125, DOI: 10.1021/ja506497b.

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