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

History of the development of ChemDraw

Uncategorized Steven Bachrach 08 Oct 2014 3 Comments

I suspect that the majority of my readers have no experience in drawing chemical structures by hand for publication purposes. That’s because of one software product: ChemDraw. I remember using the Fieser triangle (unfortunately no longer sold by Aldrich – click to see a pic and product description!), a plastic template that had standard-sized rings, like nice pentagons and hexagons, and chair and boat conformations of cyclohaxane, and you’d take your fancy ink pen and careful follow the template. Then you moved the template to draw say a bond off of the ring and hoped to god that the ink didn’t smudge. There were other templates for drawing letters and numbers – or you used scratch-off transfer decals. (By this point all of you under 40 are thinking “what the hell is he talking about?”)

Well all of that changed with three seminal events for organic chemists: the introduction of the original Macintosh computer, the introduction of the Apple LaserWriter and the introduction of ChemDraw. The Mac allowed one to sketch in a much more intuitive way – again for those less than 50, computers use to come without a mouse! Imagine trying to draw a chemical structure using a keyboard. That’s why there were no structure drawing tools prior to the Mac. The LaserWriter meant that you could print an output that looked as good as what you had on the screen, and could thus be submitted for publication. And ChemDraw – well this was just astonishing! I still remember the day during my post-doc when the Mac and LaserWriter arrived and we launched ChemDraw and were able to quickly draw molecules – steroid, and conformations, and stereoisomers and they all looked beautiful and we could get them done in a flash!

When I started my first academic position at Northern Illinois University in August 1987 I purchased a Mac and a LaserWriter and ChemDraw as part of my start-up – and I was the first in the department to have a Mac – but that changed rapidly!

So, why all of the teary reminiscences? Well David Evans has just published1 a nice romp through the mid-1980s recalling how Stewart Rubinstein, aided by Evans and his wife, developed ChemDraw and started CambridgeSoft, and as Stuart Schreiber says “ChemDraw changed the field in a way that has not been replicated since.”

Today, there are other chemical structure drawing tools available, and in fact I no longer use ChemDraw, but it is still a wonder to be able to create drawings so easily and so nicely. Maybe one day I’ll reminisce about the day I got EndNote and my life changed again!

References

1) Evans, D. A. “History of the Harvard ChemDraw Project,” Angew. Chem. Int. Ed. 2014, 53, 1521-3773, DOI 10.1002/anie.201405820.

Dynamics in a photorearrangement

Dynamics Steven Bachrach 06 Oct 2014 No Comments

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

Diels-Alder reactions of Fullerene

Diels-Alder &fullerene &Houk Steven Bachrach 29 Sep 2014 No Comments

Diels-Alder reaction involving fullerenes have been known for some time. They occur across the [6,6] double bond of C60, the one between two fused 6-member rings. Houk and Briseno report on the Diels-Alder reaction of C60 with pentacene 1 and bistetracene 2 and compare their computations with experiments.1


Pentacene and bistetracene ring numbering convention

Computations were performed for the reaction of 1 and 2 with C60 at M06-2x/6-31G(d)//M062x-3-21G*. The reaction can occur with the dienophile being either ring 1, 2, or 3 of pentacene and ring 1, 2, 3, or 4 of bistetracene. They located TSs and products for all of these possibilities. Select TSs and products are shown in Figure 1.

For the reaction of 1a, the lowest energy TS is for the reaction at the central ring (ring 3), and the resulting product is the lowest energy product. The transition state (PT_TS3) is shown in Figure 1. This TS has the least distortion energy of the three possibilities, because reacting at this central ring destroys the least amount of aromaticity of pentacene. For the reaction of 1b, the lowest barrier is again for reaction of ring 3 (through TMSPT_TS3). However, the product from the reaction with ring 2 (TMSPT_P2) is lower in free energy than TMSPT­_P3, likely caused by steric interactions with the silyl substituents. This actually matches up with experiments which indicate that an analogue of TMSPT_P2 is the kinetic product but TMSPT_P3 is the thermodynamic product.

PT_TS3

TMSPT_­TS3

TMSPT_P2

TMSPT_P3

BT_TS2

BT_P2

Figure 1. M06-2x/3-21G* optimized geometries.
(Once again a reminder that clicking on any of these structures will launch JMol and you’ll be able to visualize and manipulate this structure in 3-D.)

The computations involving the Diels-Alder reaction of C60 with either 2a or 2b come to the same conclusion. In both cases, the lowest barrier is for the reaction at ring 2, and the product of the reaction at this same ring is the only one that is endoergonic. The geometries of BT_TS2 and BT_P2 are shown in Figure 1. More importantly, the barrier for the Diels-Alder reaction involving 2a and 2b are at least 6 kcal mol-1 higher than the barriers for the reaction of 1a and 1b, in complete agreement with experiments that show little reaction involving analogues of 2b with C60, while analogues of 1b are reasonably rapid.

References

(1) Cao, Y.; Liang, Y.; Zhang, L.; Osuna, S.; Hoyt, A.-L. M.; Briseno, A. L.; Houk, K. N. "Why Bistetracenes Are Much Less Reactive Than Pentacenes in Diels–Alder Reactions with Fullerenes," J. Am. Chem. Soc. 2014, 136, 10743-10751, DOI: 10.1021/ja505240e.

Becke’s Perspective on DFT

DFT Steven Bachrach 24 Sep 2014 No Comments

The Journal of Chemical Physics has produced a Special Topics issue on Advances in Density Functional Theory. I want to call to your attention the Perspective article by Becke titled “Perspective: Fifty years of density-functional theory in chemical physics”.1 Becke writes a personal account of the history of DFT and makes a number of interesting points and observations. He rightly notes that DFT is exact and we should more properly refer to our actual implementations as Density Functional Approximations (DFA). He also notes that use of the term ab initio as a synonym for wavefunction theory is inappropriate as DFT is just as ab initio as HF and post-HF theories.

A common perception about DFT (well, DFA) is that there is no way to systematically improve functionals. Becke exposes a true underlying logic that has driven much of DFA development.

Lastly, Becke is discouraged by the more recent developments that have included virtual orbitals, such as double hybrid methods. His approach is that true DFT is occupied orbitals only (for which he pointedly does not want to adopt the acronym OOO), and that developments that include the virtual orbitals might toll the “death knell” for DFT.

For those interested in a pretty accessible account of the history of DFT, Becke’s Perspective is an excellent place to get started.

References

(1) Becke, A. D. "Perspective: Fifty years of density-functional theory in chemical physics," J. Chem. Phys. 2014, 140, 18A301 DOI: 10.1063/1.4869598.

Looking at “stability” – the role of tunneling

Tunneling Steven Bachrach 22 Sep 2014 No Comments

1 is notable for its very short central C-C bond, computed at B1B95/6-31G(d) to be only 1.30 Å. Also notable is that 1 can rearrange to the carbene 2 with a release of considerable energy (ΔE=-105.4 kcal mol-1). Nonetheless, the barrier for this rearrangement is 6.7 kcal mol-1 suggesting that 1 might be stable and isolable at low temperatures. (See this previous post for more discussion on this rearrangement, including interactive molecules.)

Kozuch has now examined this rearrangement in more detail, to see if 1 is really stable.1 The issue he raises is the role of quantum mechanical tunneling – since the distance that the carbon atoms need to move in reaching the TS is rather small, perhaps heavy atom tunneling might manifest. In the absence of tunneling, conventional variation transition state theory (CVT) predicts that the half-life of 1 is 170 s at 75 K, and longer still at even lower temperatures. However, the situation is radically different when tunneling is included. Accounting for tunneling using the small curvature tunneling (SCT) approximation predicts a half-life of 1.6 x 10-3 s at 75 K and only a minimally longer half-life of 4.6 x 10-3s at 10 K. Thus, Kozuch concludes that 1 is not stable at any temperature! One should thus be cautious in applying the term “stable” to a compound that might be quite strained and susceptible to tunneling.

(As an aside, Kozuch also notes that 2 can rearrange into 3 and this rearrangement also has a very short half-life on the order of milliseconds at cryogenic temperatures. The structure of 3 is shown in Figure 1.)

Figure 1. B1B95/6-31G(d) optimized structure of 3.

References

1) Kozuch, S. “A Quantum Mechanical “Jack in the Box”: Rapid Rearrangement of a Tetrahedryl-Tetrahedrane via Heavy Atom Tunneling,” Org. Lett., 2014, 16, 4102-4105, DOI: 10.1021/ol5017977.

InChIs

1: InChI=1S/C14H12/c1-2-8-11-5-3-9-7(1)10(9)4-6-12(8,11)14(8,11)13(7,9)10/h1-6H2
InChIKey=LNBZAENQMFDBJW-UHFFFAOYSA-N

2: InChI=1S/C14H12/c1-3-11-12-4-2-9-7-8(1,9)10(9)5-6-13(11,12)14(10,11)12/h1-6H2
InChIKey=UKVODHRLGFPZPT-UHFFFAOYSA-N

3: InChI=1S/C14H12/c1-2-10-8-12(10)4-3-11-7-9(1,11)13(11)5-6-14(10,12)13/h1-6H2
InChIKey=AATRYSJRWFKWAY-UHFFFAOYSA-N

Data emancipation

E-publishing Steven Bachrach 17 Sep 2014 No Comments

Readers of my blog know that I am an advocate for Open Data, whereby scientists permit the widespread distribution of data without restrictions. Data should be available to anyone at any time at no cost without any legal (i.e., copyright or IP) restrictions. This will enhance our abilities to follow up on research and reuse the data in whatever way we wish. In particular, reuse of data should be seamless and lossless.

I have noted many times that Supporting Materials in today’s journals is far from ideal. Often authors do not include data at all! Sometimes the data is corrupted, especially if data is being deposited solely through pdf, which involves the loss of almost all semantic information about the data. Unfortunately, very rarely is data deposited in a form that is readily reusable. For example, I make use of 3-D coordinates of molecules for this blog, and these are invariably deposited as simply text within a pdf. I then have to copy-and-paste this data into a new file formatted for use in some molecular viewer of my choice (for me, typically GaussView or Avogadro).

The leader in advocating and demonstrating chemical data reuse is Henry Rzepa (see his blog for many examples). He and his group have published a paper describing a system for separating data from the paper narrative – a process they call data emancipation – as part of the scientific publication process.1 I strongly encourage readers of this blog to take a look at this paper for the publication model they propose that places data at the nexus of the scientific process and makes it available for widespread reuse. Take a look at the web enhanced objects, such as this one (you might need a subscription to access this, but this link takes you to the Figshare site which is open), to see how data can be deposited for search, retrieval, and direct reuse. This is a model I hope many computational chemists will adopt. We also need to advocate with journal editors and publishers to establish similar procedures for all manuscript submissions.

References

(1) Harvey, M. J.; Mason, N. J.; Rzepa, H. S. "Digital Data Repositories in Chemistry and Their Integration with Journals and Electronic Notebooks," J. Chem. Inf. Model. 2014, ASAP, DOI: 10.1021/ci500302p.

Fullerene oligomers as electron traps

fullerene Steven Bachrach 15 Sep 2014 No Comments

Clark and co-workers have examined small fullerene clusters for their ability to capture electrons.1 They first looked at the fullerene dimer, comparing the electron affinity of the dimer having a C-C bond between the two cages (about 1.6-1.7 Å between the two cages) 1 and where the two cages are interacting only through van der Waals attractions (around 2.6 Å) 2. The structures and their radical anions were computed at RI-BP86/TZV. The structures of the two radical anions are shown in Figure 1. Interestingly, the radical anion of 2 is actually lower in energy that the radical anion of 1. Comparisons with some other methods are discussed, including a CASSPT2(5,4)/ANO-L-VDZ, computation, that support this result.

1

2

3

4

Figure 1. RI-BP86/TZV optimized geometries of the radical anions of 1-4.
(Be sure to click on these images to be able to manipulate these structures in 3-D!)

This suggests that the added electron is being held between the cages, in an interstitial region. That suggested looking at the trimer and tetramer structures 3 and 4. The radical anions of these two oligomers are also shown in Figure 1. These oligomers show electron affinities of 1 eV greater than for fullerene itself, along with the ability to stabilize the dianion and even the trianion, what the authors call “deep electron traps”.

References

(1) Shubina, T. E.; Sharapa, D. I.; Schubert, C.; Zahn, D.; Halik, M.; Keller, P. A.; Pyne, S. G.; Jennepalli, S.; Guldi, D. M.; Clark, T. "Fullerene Van der Waals Oligomers as Electron Traps," J. Am. Chem. Soc. 2014, 136, 10890-10893, DOI: 10.1021/ja505949m.

Organocatalytic Enantioselective Michael Addition

Michael addition Steven Bachrach 08 Sep 2014 No Comments

Computational techniques are gaining some traction in helping to understand enantioselective organocatalysis. I talk about a few examples in Chapter 6.3 of my book. Lambert and Vetticatt have now used computations to help understand the role of the catalyst 4 in the Michael addition shown in Scheme 1.1 This reaction proceeds with 99% yield and an ee of 98%.

Scheme 1.

13C kinetic isotope effect studies suggest that the rate determining step is the C-C bond formation (the Michael addition step) which follows the deprotonation of the imine 1 by the catalyst 4.

They performed ONIOM computations to search for transition states of this rate limiting step for the reaction in Scheme 1, using the full molecules. From this ONIOM search, the energies for all transition structures with 5 kcal mol-1 of the lowest energy structure were then obtained at B3LYP/6-31G*. The three lowest energy TS are shown in Figure 1. The two lowest energy structures lead to the major enantiomer, while the third lowest energy structure leads to the minor enantiomer. These energies lead to a prediction of an ee of 92%, in reasonable agreement with the experiment. The computed kinetic isotope effects are in nice agreement with experiment, supporting this step as the overall rate limiting step.

TSs leading to the S isomer

TS1
(0.0)

TS2
(0.9)

TS leading to the R isomer

TS3
(1.7)

Table 1. ONIOM optimized geometries of the three lowest energy TSs. Relative energy (kcal mol-1) in parenthesis.

Analysis of what factors are important in determining the ee is complicated and ultimately the authors are unable to provide a simple explanation. They properly note that

The observation that the major enantiomer (S) is formed from two very geometrically distinct transition structures … suggests that the prediction of enantioselectivity for other reactions … will require a full consideration of all possible transition state assemblies. (emphasis mine)

I agree with this sentiment, pessimistic as it may be. Answering this type of question is likely to remain very challenging for years to come.

References

1) Bandar, J. S.; Sauer, G. S.; Wulff, W. D.; Lambert, T. H.; Vetticatt, M. J. "Transition State Analysis of Enantioselective Brønsted Base Catalysis Chiral Cyclopropenimines," J. Am. Chem. Soc. 2014, 136, 10700-10707, DOI: 10.1021/ja504532d.

InChIs

1: InChI=1S/C20H23NO/c1-20(2,3)14-18(22)15-21-19(16-10-6-4-7-11-16)17-12-8-5-9-13-17/h4-13H,14-15H2,1-3H3
InChIKey=UZCWUGCTNCNJHI-UHFFFAOYSA-N

2: InChI=1S/C4H6O2/c1-3-4(5)6-2/h3H,1H2,2H3
InChIKey=BAPJBEWLBFYGME-UHFFFAOYSA-N

3: InChI=1S/C24H29NO3/c1-24(2,3)17-21(26)20(15-16-22(27)28-4)25-23(18-11-7-5-8-12-18)19-13-9-6-10-14-19/h5-14,20H,15-17H2,1-4H3/t20-/m0/s1
InChIKey=KTASCPHNNZODSX-FQEVSTJZSA-N

4: InChI=1S/C37H57N3/c1-2-30(28-29-18-8-3-9-19-29)38-35-36(39(31-20-10-4-11-21-31)32-22-12-5-13-23-32)37(35)40(33-24-14-6-15-25-33)34-26-16-7-17-27-34/h3,8-9,18-19,30-34H,2,4-7,10-17,20-28H2,1H3/t30-/m1/s1
InChIKey=GEHSIGXXLTVFFG-SSEXGKCCSA-N

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