Hypercubane

Uncategorized Steven Bachrach 15 Dec 2014 No Comments

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.

Oblong molecule stacking

Aromaticity Steven Bachrach 13 Nov 2014 No Comments

π-π-stacking has been a major theme of my blog, and is discussed in Chapter 3.5.4 in the Second Edition of my book. Most examples involved molecules that are nearly circular (like benzene or triphenylene). Hartley and co-workers discuss the π-π-stacking of the oblong molecule 1, comparing its experimental features with computed features of the model compound 2.1

The key spectroscopic feature associated with assembly of 1 are the changes in the 1H chemical shifts with increasing concentration. For example, the chemical shift of the three protons on the triphenylene unit shift upfield by 0.30 to 0.66 ppm as the concentration increases from 10-5 to 10-2 M.

To see if these NMR shift changes are due to association of 1, they employed a computational approach. First they optimized the structure of model compound 2 at B3LYP/6-31G(d) (Shown in Figure 1a). Then using this fixed geometry, they computed the 1H chemical shifts of the dimer of 2. They explored the stacking distance (ranging from 3.2 to 4.0 Å along with varying the displacement of the two molecules along the major axis from 0.0 to 6.0 Å, finding the best fit to the chemical shifts with a separation of 3.6 Å and a displacement along the major axis of 3.5 Å. Using these two fixed values, they explored displacement of the molecules along the minor axis, along with rotation of the two molecules. The best fit to the experimental chemical shifts was with a displacement of 0.5 Å along the short axis and no rotation. This structure is shown in Figure 1b, with a RMS error of only 0.09 ppm from experiment. Models of the trimer show poorer fit to the experimental data.

(a)

2

(b)

2
dimer

Figure 1. B3LYP/6-31G(d) (a) optimized structure of 2 and the (b) structure of the best fit of the dimer of 2. (As always, clicking on these images will allow you to manipulate the 3-D structure using JMol – highly recommended for the dimer.)

Using some smaller models and the B97-D functional, they argue that the displacement, which is substantially larger than the displacement found in stacked triphenylene, results from the need to minimize the steric interactions between the alkoxyl chains.

References

(1) Chu, M.; Scioneaux, A. N.; Hartley, C. S. "Solution-Phase Dimerization of an Oblong Shape-Persistent Macrocycle," J. Org. Chem. 2014, 79, 9009–9017; DOI: 10.1021/jo501260c.

InChIs:

1: InChI=1S/C116H148O10/c1-11-21-31-41-59-117-95-71-87-51-55-91-75-97-99(103-81-111(121-63-45-35-25-15-5)115(125-67-49-39-29-19-9)85-107(103)105-83-113(123-65-47-37-27-17-7)109(79-101(97)105)119-61-43-33-23-13-3)77-93(91)57-53-89-70-90(74-96(73-89)118-60-42-32-22-12-2)54-58-94-78-100-98(76-92(94)56-52-88(69-87)72-95)102-80-110(120-62-44-34-24-14-4)114(124-66-48-38-28-18-8)84-106(102)108-86-116(126-68-50-40-30-20-10)112(82-104(100)108)122-64-46-36-26-16-6/h69-86H,11-50,59-68H2,1-10H3
InChIKey=UUKOQEVXPHHWBJ-UHFFFAOYSA-N

2: InChI=1S/C76H68O10/c1-11-77-55-31-47-21-25-51-35-57-59(63-41-71(81-15-5)75(85-19-9)45-67(63)65-43-73(83-17-7)69(79-13-3)39-61(57)65)37-53(51)27-23-49-30-50(34-56(33-49)78-12-2)24-28-54-38-60-58(36-52(54)26-22-48(29-47)32-55)62-40-70(80-14-4)74(84-18-8)44-66(62)68-46-76(86-20-10)72(82-16-6)42-64(60)68/h29-46H,11-20H2,1-10H3
InChIKey=NGTKTKCZPONPTB-UHFFFAOYSA-N

Computationally handling ion pairs

Ion Pairs &Solvation &sugars Steven Bachrach 04 Nov 2014 5 Comments

Comparing SN2 and SN1 reactions using computational methods is often quite difficult. The problem is that the heterolytic cleavage in the SN1 reaction leads to an ion pair, and in the gas phase this is a highly endothermic process. Optimization of the ion pair in the gas phase invariably leads to recombination. This is disturbingly the result even when one uses PCM to mimic the solvent, which one might have hoped would be sufficient to stabilize the ions.

The computational study of the glycoside cleavage by Hosoya and colleagues offers some guidance towards dealing with this problem.1 They examined the cleavage of triflate from 2,3,4,6-tetra-O-methyl-α-D-glucopyranosyl triflate 1.

Benchmarking the dissociation energy for the cleavage of 1 and considering computational performance, they settled on M06-2X/BS-III//M06-2X/BS-I, where BS-III is aug-cc-pVTZ basis set for O, F, and Cl and cc-pVTZ for H, C, and S and BS-I is 6-31G(d,p) basis sets were employed for H, C, and S, and 6-31+G(d) for O, F, and Cl. Solvent (dichloromethane) was included through PCM.

Attempted optimization of the contact ion pair formed from cleavage of 1 invariably led back to the covalent bound 1. PCM is not capable of properly stabilizing these types of ions in proximity. To solve this problem, they incorporated four explicit dichloromethane molecules. A minor drawback to their approach is that they did not sample much of configuration space and so their best geometries may not be the lowest energy configurations. Nonetheless, with four solvent molecules, they were able to locate contact ion pairs and solvent-separated ion pairs. Representative examples are shown in Figure 1. This method of explicit incorporation of a few solvent molecules seems to be the direction we must take to treat ions or even highly polar molecules in solution.

1
0.0

1-CIP
8.5

1-SSIPa
8.4




1-SSIPb
11.1

Figure 1. Representative examples of microsolvated 1, its contact ion pair (CIP) and solvent separated ion pair (SSIP) computed at M06-2X/BS-III//M06-2X/BS-I, and relative energies (kcal mol-1)

References

(1) Hosoya, T.; Takano, T.; Kosma, P.; Rosenau, T. "Theoretical Foundation for the Presence of Oxacarbenium Ions in Chemical Glycoside Synthesis," J. Org. Chem. 2014, 79, 7889-7894, DOI: 10.1021/jo501012s.

InChIs

1: InChI=1S/C11H19F3O8S/c1-17-5-6-7(18-2)8(19-3)9(20-4)10(21-6)22-23(15,16)11(12,13)14/h6-10H,5H2,1-4H3/t6-,7-,8+,9-,10-/m1/s1
InChIKey=RPZNYYCDDYUPJR-HOTMZDKISA-N

QM reflection off a barrier

Tunneling Steven Bachrach 27 Oct 2014 No Comments

Organic chemists are beginning to recognize that tunneling may be more pervasive than previously thought. This blog has noted a number of interesting occurrences of tunneling, and here’s one more, by Karmakar and Datta.1

The barrier for the intramolecular earrangement (Reaction 1) taking the carbene 1 into 2 is estimated to be 44.1 kcal mol-1 at M06-2X/6-31+G(d,p), prohibitively large. However, the intermolecular rearrangement (Reaction 2) has a much smaller barrier of 11.4 kcal mol-1. The structures of the transition states for these two reactions are shown in Figure 1.

TSintra

TSinter

Figure 1. M06-2X/6-31+G(d,p) optimized transition states for Reactions 1 and 2.

Given that the barrier width is likely to be very small for the intramolecular route, perhaps tunneling may play a role. The rate predicted with canonical variational transition-state theory (CVT) and small curvature tunneling (SCT) at 298K is negligible. However, for the intermolecular process, the rate at 298K including tunneling is 3.56 x 104 s-1, more than 10 times great than predicted with CVT alone, and tunneling makes a dramatically larger difference at lower temperatures.

The intermolecular barrier for the rearrangement of 3 into 4 is very small, only 1.6 kcal mol-1.
This manifests in a very interesting rate prediction: the reaction is actually predicted to be slower at temperatures above 150K when tunneling is included than when tunneling is omitted. This is a result of quantum mechanical reflection off of the barrier, and this becomes noticeable with the very small barrier. In addition, the kinetic isotope effects are smaller than expected when D is substituted in for H. These predictions await experimental confirmation.

References

(1) Karmakar, S.; Datta, A. "Tunneling Assists the 1,2-Hydrogen Shift in N-Heterocyclic Carbenes," Angew. Chem. Int. Ed. 2014, 53, 9587-9591, DOI: 10.1002/anie.201404368.

InChIs:

1: InChI=1S/C3H6N2/c1-2-5-3-4-1/h4-5H,1-2H2
InChIKey=JKQUEGZDRZXJNY-UHFFFAOYSA-N

2: InChI=1S/C3H6N2/c1-2-5-3-4-1/h3H,1-2H2,(H,4,5)
InChIKey=MTNDZQHUAFNZQY-UHFFFAOYSA-N

3: InChI=1S/C3H2F2N2/c4-2-3(5)7-1-6-2/h6-7H
InChIKey=LHUPDFSUHVZFPD-UHFFFAOYSA-N

4: InChI=1S/C3H2F2N2/c4-2-3(5)7-1-6-2/h1H,(H,6,7)
InChIKey=KXXZDIFMEWOLPE-UHFFFAOYSA-N

The unusual PES of (CO)3

Borden Steven Bachrach 21 Oct 2014 No Comments

As recently explicated by Wang and Borden using NIPE spectroscopy and computations, the potential energy surface of cyclopropyl-1,2,3-trione 1 is remarkably complex.1 (U)CCSD(T)//aug-cc-pVTZ computations of the D3h singlet (the 1A1’ state shown in Figure 1) is actually a hilltop, possessing two imaginary frequencies. Distorting the structure as indicated by these imaginary frequencies and then optimizing the structure leads directly to dissociation to three CO molecules. Thus, (CO)3 does not exist as a stable minima on the singlet surface.

The D3h triplet (the 3E” state shown in Figure 1) is not a critical point on the surface; due to the Jahn-Teller effect is distorts into two different states: the 3B1 state which is a local energy minimum, and the 3A2 state which is a transition state between the symmetry-related 3B1 states.

So, this implies the possibility of a very interesting NIPE experiment. If the radical anion (CO)3-.
loses an electron and goes to the singlet surface, it lands at a hilltop(!) and should have a very short lifetime. If it goes to the triplet surface, it lands at either a transition state (3A2) and again should have a short lifetime, or it can land at the 3B1 state and perhaps have some lifetime before it dissociates by losing one CO molecule.

1-.

1A1’

3E”

3B1

3A2

Figure 1. (U)CCSD(T)//aug-cc-pVTZ optimized geometries of 1 and its radical anion.

The NIPE spectrum identifies three transitions. By comparing the energies of the electron loss seen in the experiment with the computations, along with calculating the Franck-Condon factors using the computed geometries and vibrational frequencies, the lowest energy transition is to the 1A1’ state, and the second transition is part of the vibrational progression also to the 1A1’ state. This is the first identification of vibrational frequencies associated with a hilltop structure. The third transition is to the 3A2 state. No transition to the 3B1 state is found due to the large geometric difference between the radical anion and the 3B1 state; the Franck-Condon factors are zero due to no overlap of their wavefunctions.

Once again, the power of the symbiotic relationship between experiment and computation is amply demonstrated in this paper.

References

(1) Chen, B.; Hrovat, D. A.; West, R.; Deng, S. H. M.; Wang, X.-B.; Borden, W. T. "The Negative Ion Photoelectron Spectrum of Cyclopropane-1,2,3-Trione Radical Anion, (CO)3•– — A Joint Experimental and Computational Study," J. Am. Chem. Soc. 2014, 136, 12345-12354, DOI: 10.1021/ja505582k.

InChIs

1: InChI=1S/C3O3/c4-1-2(5)3(1)6
InChIKey=RONYDRNIQQTADL-UHFFFAOYSA-N

A Triple-Möbius Aromatic Molecule

Aromaticity Steven Bachrach 13 Oct 2014 6 Comments

Herges and co-workers have prepared a triply-twisted Möbius molecule. 1 The key element is recognizing that most of the “twisting” needs to be accomplished through writhe, a twisting that produces figure-8-like crossing, the way an old-school phone cord twists about itself or the way a pretzel is formed. Herges employs three bi-naphthelene subunits to provide the template for the writhe needed. The prepared compound is 1. A clever, relatively straightforword synthesis produces this amazing molecule, along with the single-twisted 2.

The B3LYP/6-31G* optimized geometries of 1 and the single-twisted analogue 2 are shown in Figure 1. Table 1 presents the key topological parameters of 1 and 2, comparing the computed and X-ray crystal structure. The absolute value of the linking number Lk is 3, indicating the three twists, and the reason that this highly twisted molecule can be made is that half of the twist actually results from writhe.

1

2

Figure 1. B3LYP/6-31G* optimized geometries of the two diastereomers if 1. (Be sure to click on these images to launch JMol and interactively manipulate the structures!)

Table 1. Topological parameters of 1. a

 

|Lk|

|Tw|

|Wr|

X-ray, 1

3.0

1.42

1.58

Comp, 1

3.0

1.33

1.67

Comp, 2

1.0

0.37

0.63

aLk is the linking number, Tw is the twist number, and Wr is the writhe number, with the condition that Tk + Wr = Lk.

References

(1) Schaller, G. R.; Topić, F.; Rissanen, K.; Okamoto, Y.; Shen, J.; Herges, R. "Design and synthesis of the first triply twisted Möbius annulene," Nat. Chem. 2014, 6, 608-613, DOI: 10.1038/nchem.1955.

InChIs

1: InChI=1S/C72H36/c1-2-26-56-44-38-50-20-8-14-32-62(50)68(56)70-58(46-40-52-22-10-16-34-64(52)70)28-5-6-30-60-48-42-54-24-12-18-36-66(54)72(60)71-59(47-41-53-23-11-17-35-65(53)71)29-4-3-27-57-45-39-51-21-9-15-33-63(51)69(57)67-55(25-1)43-37-49-19-7-13-31-61(49)67/h7-24,31-48H/b69-67-,70-68-,72-71-
InChIkey=ICOGWBLQQNBWJA-UWFYZODKSA-N

Next Page »