Search Results for "dispersion"

Dispersion in organic chemistry – a review and another example

The role of dispersion in organic chemistry has been slowly recognized as being quite critical in a variety of systems. I have blogged on this subject many times, discussing new methods for properly treating dispersion within quantum computations along with a variety of molecular systems where dispersion plays a critical role. Schreiner1 has recently published a very nice review of molecular systems where dispersion is a key component towards understanding structure and/or properties.

In a similar vein, Wegner and coworkers have examined the Z to E transition of azobenzene systems (1a-g2a-g) using both experiment and computation.2 They excited the azobenzenes to the Z conformation and then monitored the rate for conversion to the E conformation. In addition they optimized the geometries of the two conformers and the transition state for their interconversion at both B3LYP/6-311G(d,p) and B3LYP-D3/6-311G(d,p). The optimized structure of the t-butyl-substituted system is shown in Figure 1.


a: R=H; b: R=tBu; c: R=Me; d: R=iPr; e: R=Cyclohexyl; f: R=Adamantyl; g: R=Ph

1b

1b-TS-2b

2b

Figure 1. B3LYP-D3/6-311G(d,p) optimized geometries of 1a, 2a, and the TS connecting them.

The experiment finds that the largest activation barriers are for the adamantly 1f and t-butyl 1b azobenzenes, while the lowest barriers are for the parent 1a and methylated 1c azobenzenes.

The trends in these barriers are not reproduced at B3LYP but are reproduced at B3LYP-D3. This suggests that dispersion is playing a role. In the Z conformations, the two phenyl groups are close together, and if appropriately substituted with bulky substituents, contrary to what might be traditionally thought, the steric bulk does not destabilize the Z form but actually serves to increase the dispersion stabilization between these groups. This leads to a higher barrier for conversion from the Z conformer to the E conformer with increasing steric bulk.

References

(1) Wagner, J. P.; Schreiner, P. R. "London Dispersion in Molecular Chemistry—Reconsidering Steric Effects," Angew. Chem. Int. Ed. 2015, 54, 12274-12296, DOI: 10.1002/anie.201503476.

(2) Schweighauser, L.; Strauss, M. A.; Bellotto, S.; Wegner, H. A. "Attraction or Repulsion? London Dispersion Forces Control Azobenzene Switches," Angew. Chem. Int. Ed. 2015, 54, 13436-13439, DOI: 10.1002/anie.201506126.

InChIs

1b: InChI=1S/C28H42N2/c1-25(2,3)19-13-20(26(4,5)6)16-23(15-19)29-30-24-17-21(27(7,8)9)14-22(18-24)28(10,11)12/h13-18H,1-12H3/b30-29-
InChIKey=SOCNVTNVHBWFKC-FLWNBWAVSA-N

2b: InChI=1S/C28H42N2/c1-25(2,3)19-13-20(26(4,5)6)16-23(15-19)29-30-24-17-21(27(7,8)9)14-22(18-24)28(10,11)12/h13-18H,1-12H3/b30-29+
InChIKey=SOCNVTNVHBWFKC-QVIHXGFCSA-N

DFT &Schreiner Steven Bachrach 04 Jan 2016 No Comments

Dispersion – application to cellular membranes

Schreiner provides another beautiful example of the important role that dispersion plays, this time in a biological system.1 The microbe Candidatus Brocadia Anammoxidans oxidizes ammonia with nitrite. This unusual process must be done anaerobically and without allowing toxic side products, like hydrazine to migrate into the cellular environment. So this cell has a very dense membrane surrounding the enzymes that perform the oxidation. This dense membrane is home to some very unusual lipids, such as 1. These lipids contain the ladderane core, a highly strained unit. Schreiner hypothesized that these ladderane groups might pack very well and very tightly due to dispersion.


1

The geometries of the [2]- through [5]-ladderanes and their dimers were optimized at MP2/aug-cc-pVDZ, and the binding energies corrected for larger basis sets and higher correlation effects. The dimers were oriented in their face-to-face orientation (parallel-displaced dimer, PDD) or edge-to-edge (side-on dimer, SD). Figure 1 shows the optimized structures of the two dimeric forms of [4]-ladderane.

[4]-PDD

[4]-SD

Figure 1. MP2/aug-cc-pVDZ optimized geometries of the dimers of [4]-ladderane in the PDD and SD orientations.

The binding energies of the ladderane dimers, using the extrapolated energies and at B3LYP-D3/6-311+G(d,p), are listed in Table 1. (The performance of the B3LYP-D3 functional is excellent, by the way.)The binding is quite appreciable, greater than 6 kcal mol-1 for both the [4]- and [5]-ladderanes. Interestingly, these binding energies far exceed the binding energies of similarly long alkanes. So, very long alkyl lipid chains would be needed to duplicate the strong binding. Nature appears to have devised a rather remarkable solution to its cellular isolation problem!

 

Eextrapolated

EB3LYP-D3

[2]-PDD

-27.

-3.2

[3]-PDD

-4.2

-4.1

[4]-PDD

-5.5

-5.3

[5]-PDD

-6.6

-6.5

[2]-SD

-3.3

-3.1

[3}-SD

-4.1

-4.4

[4]-SD

-6.5

-5.7

[5]-SD

-7.5

-7.0

References

(1) Wagner, J. P.; Schreiner, P. R. "Nature Utilizes Unusual High London Dispersion
Interactions for Compact Membranes Composed of Molecular Ladders," J. Chem. Theor. Comput. 2014, 10, 1353-1358, DOI: 10.1021/ct5000499.

InChIs

1: InChI=InChI=1S/C20H30O2/c21-15(22)7-5-3-1-2-4-6-11-10-14-16(11)20-18-13-9-8-12(13)17(18)19(14)20/h11-14,16-20H,1-10H2,(H,21,22)/t11-,12-,13+,14-,16+,17+,18-,19-,20+/m0/s1
InChIKey=ZKKJRZDMLYQUNK-QIPWGTBCSA-N

[2]-ladderane: InChI=1S/C6H10/c1-2-6-4-3-5(1)6/h5-6H,1-4H2/t5-,6+
InChIKey=YZLCEXRVQZNGEK-OLQVQODUSA-N

[3]-ladderane: InChI=1S/C8H12/c1-2-6-5(1)7-3-4-8(6)7/h5-8H,1-4H2/t5-,6+,7+,8-
InChIKey=YTZCZYFFHKYOBJ-SOSBWXJGSA-N

[4]-ladderane: InChI=1S/C10H14/c1-2-6-5(1)9-7-3-4-8(7)10(6)9/h5-10H,1-4H2/t5-,6+,7+,8-,9-,10+
InChIKey=VZHFDSXKIJOCAY-UXAOAXNSSA-N

[5]-ladderane: InChI=1S/C12H16/c1-2-6-5(1)9-10(6)12-8-4-3-7(8)11(9)12/h5-12H,1-4H2/t5-,6+,7-,8+,9+,10-,11-,12+
InChIKey=CWUAAECPDWVJSU-SBBGGFAWSA-N

Schreiner Steven Bachrach 22 Apr 2014 1 Comment

Benchmarked Dispersion corrected DFT and SM12

This is a short post mainly to bring to the reader’s attention a couple of recent JCTC papers.

The first is a benchmark study by Hujo and Grimme of the geometries produced by DFT computations that are corrected for dispersion.1 They use the S22 and S66 test sets that span a range of compounds expressing weak interactions. Of particular note is that the B3LYP-D3 method provided the best geometries, suggesting that this much (and justly) maligned functional can be significantly improved with just the simple D3 fix.

The second paper entails the description of Truhlar and Cramer’s latest iteration on their solvation model, namely SM12.2 The main change here is the use of Hirshfeld-based charges, which comprise their Charge Model 5 (CM5). The training set used to obtain the needed parameters is much larger than with previous versions and allows for treating a very broad set of solvents. Performance of the model is excellent.

References

(1) Hujo, W.; Grimme, S. "Performance of Non-Local and Atom-Pairwise Dispersion Corrections to DFT for Structural Parameters of Molecules with Noncovalent Interactions," J. Chem. Theor. Comput. 2013, 9, 308-315, DOI: 10.1021/ct300813c

(2) Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. "Generalized Born Solvation Model SM12," J. Chem. Theor. Comput. 2013, 9, 609-620, DOI: 10.1021/ct300900e

Cramer &DFT &Grimme &Solvation &Truhlar Steven Bachrach 14 Jan 2013 No Comments

Dispersion leads to long C-C bonds

Schreiner has expanded on his previous paper1 regarding alkanes with very long C-C bonds, which I commented upon in this post. He and his colleagues report2 now a series of additional diamond-like and adamantane-like sterically congested alkanes that are stable despite have C-C bonds that are longer that 1.7 Å (such as 1! In addition they examine the structures and rotational barriers using a variety of density functionals.


1


2

For 2, the experimental C-C distance is 1.647 Å. A variety of functionals all using the cc-pVDZ basis predict distances that are much too long: B3LYP, B96, B97D, and B3PW91. However, functionals that incorporate some dispersion, either through an explicit dispersion correction (Like B3LYP-D and B2PLYP-D) or with a functional that address mid-range or long range correlation (like M06-2x) or both (like ωB97X-D) all provide very good estimates of this distance.

On the other hand, prediction of the rotational barrier about the central C-C bond of 2 shows different functional performance. The experimental barrier, determined by 1H and 13C NMR is 16.0 ± 1.3 kcal mol-1. M06-2x, ωB97X-D and B3LYP-D, all of which predict the correct C-C distance, overestimate the barrier by 2.5 to 3.5 kcal mol-1, outside of the error range. The functionals that do the best in getting the rotational barrier include B96, B97D and PBE1PBE and B3PW91. Experiments and computations of the rotational barriers of the other sterically congested alkanes reveals some interesting dynamics, particularly that partial rotations are possible by crossing lower barrier and interconverting some conformers, but full rotation requires passage over some very high barriers.

In the closing portion of the paper, they discuss the possibility of very long “bonds”. For example, imagine a large diamond-like fragment. Remove a hydrogen atom from an interior position, forming a radical. Bring two of these radicals together, and their computed attraction is 27 kcal mol-1 despite a separation of the radical centers of more than 4 Å. Is this a “chemical bond”? What else might we want to call it?

A closely related chemical system was the subject of yet another paper3 by Schreiner (this time in collaboration with Grimme) on the hexaphenylethane problem. I missed this paper somehow near
the end of last year, but it is definitely worth taking a look at. (I should point out that this paper was already discussed in a post in the Computational Chemistry Highlights blog, a blog that acts as a journals overlay – and one I participate in as well.)

So, the problem that Grimme and Schreiner3 address is the following: hexaphenylethane 3 is not stable, and 4 is also not stable. The standard argument for their instabilities has been that they are simply too sterically congested about the central C-C bond. However, 5 is stable and its crystal structure has been reported. The central C-C bond length is long: 1.67 Å. But why should 5 exist? It appears to be even more crowded that either 3 or 4. TPSS/TZV(2d,2p) computations on these three compounds indicate that separation into the two radical fragments is very exoergonic. However, when the “D3” dispersion correction is included, 3 and 4 remain unstable relative to their diradical fragments, but 5 is stable by 13.7 kcal mol-1. In fact, when the dispersion correction is left off of the t-butyl groups, 5 becomes unstable. This is a great example of a compound whose stability rests with dispersion attractions.


3: R1 = R2 = H
4: R1 = tBu, R2 = H
5: R1 = H, R2 = tBu

References

(1) Schreiner, P. R.; Chernish, L. V.; Gunchenko, P. A.; Tikhonchuk, E. Y.; Hausmann, H.; Serafin, M.; Schlecht, S.; Dahl, J. E. P.; Carlson, R. M. K.; Fokin, A. A. "Overcoming lability of extremely long alkane carbon-carbon bonds through dispersion forces," Nature 2011, 477, 308-311, DOI: 10.1038/nature10367

(2) Fokin, A. A.; Chernish, L. V.; Gunchenko, P. A.; Tikhonchuk, E. Y.; Hausmann, H.; Serafin, M.; Dahl, J. E. P.; Carlson, R. M. K.; Schreiner, P. R. "Stable Alkanes Containing Very Long Carbon–Carbon Bonds," J. Am. Chem. Soc., 2012, 134, 13641-13650, DOI: 10.1021/ja302258q

(3) Grimme, S.; Schreiner, P. R. "Steric Crowding Can tabilize a Labile Molecule: Solving the Hexaphenylethane Riddle," Angew. Chem. Int. Ed., 2011, 50, 12639-12642, DOI: 10.1002/anie.201103615

Grimme &Schreiner Steven Bachrach 25 Sep 2012 4 Comments

Review of DFT with dispersion corrections

For those of you interested in learning about dispersion corrections for density functional theory, I recommend Grimme’s latest review article.1 He discusses four different approaches to dealing with dispersion: (a) vdW-DF methods whereby a non-local dispersion term is included explicitly in the functional, (b) parameterized functional which account for some dispersion (like the M06-2x functional), (c) semiclassical corrections, labeled typically as DFT-D, which add an atom-pair term that typically has an r-6 form, and (d) one-electron corrections.

The heart of the review is the comparison of the effect of including dispersion on thermochemistry. Grimme nicely points out that reaction energies and activation barriers typically are predicted with errors of 6-8 kcal mol-1 with conventional DFT, and these errors are reduced by up to 1.5 kcal mol-1 with the inclusion fo the “-D3” correction. Even double hybrid methods, whose mean errors are much smaller (about 3 kcal mol-1), can be improved by over 0.5 kcal mol-1 with the inclusion of the “-D3” correction. The same is also true for conformational energies.

Since the added expense of including the “-D3” correction is small, there is really no good reason for not including it routinely in all types of computations.

(As an aside, the article cited here is available for free through the end of this year. This new journal WIREs Computational Molecular Science has many review articles that will be of interest to readers of this blog.)

References

(1) Grimme, S., "Density functional theory with London dispersion corrections," WIREs Comput. Mol. Sci., 2011, 1, 211-228, DOI: 10.1002/wcms.30

DFT &Grimme Steven Bachrach 06 Dec 2011 20 Comments

Using vibrational frequencies to identify stereoisomers

Can vibrational spectroscopy be used to identify stereoisomers? Medel, Stelbrink, and Suhm have examined the vibrational spectra of (+)- and (-)-α-pinene, (±)-1, in the presence of four different chiral terpenes 2-5.1 They recorded gas phase spectra by thermal expansion of a chiral α-pinene with each chiral terpene.

For the complex of 4 with (+)-1 or (-)-1 and 5 with (+)-1 or (-)-1, the OH vibrational frequency is identical for the two different stereoisomers. However, the OH vibrational frequencies differ by 2 cm-1 with 3, and the complex of 3/(+)-1 displays two different OH stretches that differ by 11 cm-1. And in the case of the complex of α-pinene with 2, the OH vibrational frequencies of the two different stereoisomers differ by 11 cm-1!

The B3LYP-D3(BJ)/def2-TZVP optimized geometry of the 2/(+)-1 and 2/(-)-1 complexes are shown in Figure 2, and some subtle differences in sterics and dispersion give rise to the different vibrational frequencies.


2/(+)-1


2/(-)-1

Figure 2. B3LYP-D3(BJ)/def2-TZVP optimized geometry of the 2/(+)-1 and 2/(-)-1

Of interest to readers of this blog will be the DFT study of these complexes. The authors used three different well-known methods – B3LYP-D3(BJ)/def2-TZVP, M06-2x/def2-TZVP, and ωB97X-D/def2-TZVP – to compute structures and (most importantly) predict the vibrational frequencies. Interestingly, M06-2x/def2-TZVP and ωB97X-D/ def2-TZVP both failed to predict the vibrational frequency difference between the complexes with the two stereoisomers of α-pinene. However, B3LYP-D3(BJ)/def2-TZVP performed extremely well, with a mean average error (MAE) of only 1.9 cm-1 for the four different terpenes. Using this functional and the larger may-cc-pvtz basis set reduced the MAE to 1.5 cm-1 with the largest error of only 2.5 cm-1.

As the authors note, these complexes provide some fertile ground for further experimental and computational study and benchmarking.

Reference

1. Medel, R.; Stelbrink, C.; Suhm, M. A., “Vibrational Signatures of Chirality Recognition Between α-Pinene and Alcohols for Theory Benchmarking.” Angew. Chem. Int. Ed. 2019, 58, 8177-8181, DOI: 10.1002/anie.201901687.

InChIs

(-)-1, (-)-α-pinene: InChI=1S/C10H16/c1-7-4-5-8-6-9(7)10(8,2)3/h4,8-9H,5-6H2,1-3H3/t8-,9-/m0/s1
InChIKey=GRWFGVWFFZKLTI-IUCAKERBSA-N

(+)-1, (-)-α-pinene: InChI=1S/C10H16/c1-7-4-5-8-6-9(7)10(8,2)3/h4,8-9H,5-6H2,1-3H3/t8-,9-/m1/s1
InChIKey=GRWFGVWFFZKLTI-RKDXNWHRSA-N

2, (-)borneol: InChI=1S/C10H18O/c1-9(2)7-4-5-10(9,3)8(11)6-7/h7-8,11H,4-6H2,1-3H3/t7-,8+,10+/m0/s1
InChiKey=DTGKSKDOIYIVQL-QXFUBDJGSA-N

3, (+)-fenchol: InChI=1S/C10H18O/c1-9(2)7-4-5-10(3,6-7)8(9)11/h7-8,11H,4-6H2,1-3H3/t7-,8-,10+/m0/s1
InChIKey=IAIHUHQCLTYTSF-OYNCUSHFSA-N

4, (-1)-isopinocampheol: InChI=1S/C10H18O/c1-6-8-4-7(5-9(6)11)10(8,2)3/h6-9,11H,4-5H2,1-3H3/t6-,7+,8-,9-/m1/s1
InChIKey=REPVLJRCJUVQFA-BZNPZCIMSA-N

5, (1S)-1-phenylethanol: InChI=1S/C8H10O/c1-7(9)8-5-3-2-4-6-8/h2-7,9H,1H3/t7-/m0/s1
InChIKey=WAPNOHKVXSQRPX-ZETCQYMHSA-N

DFT &vibrational frequencies Steven Bachrach 10 Jun 2019 No Comments

Planar ring in a nano-Saturn

For the past twelve years, I have avoided posting on any of my own papers, but I will stoop to some shameless promotion to mention my latest paper,1 since it touches on some themes I have discussed in the past.

Back in 2011, Iwamoto, et al. prepared the complex of C60 1 surrounded by [10]cycloparaphenylene 2 to make the Saturn-like system 3.2 Just last year, Yamamoto, et al prepared the Nano-Saturn 5a as the complex of 1 with the macrocycle 4a.3 The principle idea driving their synthesis was to utilize a ring that is flatter than 2. The structures of 3 and 5b (made with the parent macrocycle 4b) are shown in side view in Figure 1, and clearly seen is the achievement of the flatter ring.


3

5b

7

Figure 1. Computed structures of 3, 5, and 7.

However, the encompassing ring is not flat, with dihedral angles between the anthrenyl groups of 35°. This twisting is due to the steric interactions of the ortho-ortho’ hydrogens. A few years ago, my undergraduate student David Stück and I suggested that selective substitution of a nitrogen for one of the C-H groups would remove the steric interaction,4 leading to a planar poly-aryl system, such as making twisted biphenyl into the planar 2-(2-pyridyl)-pyridine (Scheme 1)

Scheme 1.

Following this idea leads to four symmetrical nitrogen-substituted analogues of 4b; and I’ll mention just one of them here, 6.

As expected, 6 is perfectly flat. The ring remains flat even when complexed with 1 (as per B3LYP-D3(BJ)/6-31G(d) computations), see the structure of 7 in Figure 1.

I also examined the complex of the flat macrocycle 6 (and its isomers) with a [5,5]-nanotube, 7. The tube bends over to create better dispersion interaction with the ring, which also become somewhat non-planar to accommodate the tube. Though not mentioned in the paper, I like to refer to 7 as Beyoncene, in tribute to All the Single Ladies.

Figure 2. Computed structure of 7.

My sister is a graphic designer and she made this terrific image for this work:

References

1. Bachrach, S. M., “Planar rings in nano-Saturns and related complexes.” Chem. Commun. 2019, 55, 3650-3653, DOI: 10.1039/C9CC01234F.

2. Iwamoto, T.; Watanabe, Y.; Sadahiro, T.; Haino, T.; Yamago, S., “Size-Selective Encapsulation of C60 by [10]Cycloparaphenylene: Formation of the Shortest Fullerene-Peapod.” Angew. Chem. Int. Ed. 2011, 50, 8342-8344, DOI: 10.1002/anie.201102302

3. Yamamoto, Y.; Tsurumaki, E.; Wakamatsu, K.; Toyota, S., “Nano-Saturn: Experimental Evidence of Complex Formation of an Anthracene Cyclic Ring with C60.” Angew. Chem. Int. Ed. 2018 , 57, 8199-8202, DOI: 10.1002/anie.201804430.

4. Bachrach, S. M.; Stück, D., “DFT Study of Cycloparaphenylenes and Heteroatom-Substituted Nanohoops.” J. Org. Chem. 2010, 75, 6595-6604, DOI: 10.1021/jo101371m

InChIs

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

6: InChI=1S/C72H36N12/c1-2-38-14-44-20-45-25-67(73-31-50(45)13-37(1)44)57-9-4-39-15-51-32-74-68(26-46(51)21-61(39)80-57)58-10-5-40-16-52-33-75-69(27-47(52)22-62(40)81-58)59-11-6-41-17-53-34-76-70(28-48(53)23-63(41)82-59)60-12-7-42-18-54-35-77-71(29-49(54)24-64(42)83-60)72-78-36-55-19-43-3-8-56(38)79-65(43)30-66(55)84-72/h1-36H
InChIKey=NSSCKPFBHGOOIJ-UHFFFAOYSA-N

Aromaticity &host-guest Steven Bachrach 26 Mar 2019 2 Comments

More DFT benchmarking

Selecting the appropriate density functional for one’s molecular system at hand is often a very confounding problem, especially for non-expert or first-time users of computational chemistry. The DFT zoo is vast and confusing, and perhaps what makes the situation worse is that there is no lack of benchmarking studies. For example, I have made more than 30 posts on benchmark studies, and I made no attempt to be comprehensive over the past dozen years!

One such benchmark study that I missed was presented by Mardirossian and Head-Gordon in 2017.1 They evaluated 200 density functional using the MGCDB84 database, a combination of data from a number of different groups. They make a series of recommendations for local GGA, local meta-GGA, hybrid GGA, and hybrid meta-GGA functionals. And when pressed to choose just one functional overall, they opt for ωB97M-V, a range-separated hybrid meta-GGA with VV10 nonlocal correlation.

Georigk and Mehta2 just recently offer a review of the density functional zoo. Leaning heavily on benchmark studies using the GMTKN553 database, they report a number of observations. Of no surprise to readers of this blog, their main conclusion is that accounting for London dispersion is essential, usually through some type of correction like those proposed by Grimme.

These authors also note the general disparity between the most accurate, best performing functional per the benchmark studies and the results of the DFT poll conducted for many years by Swart, Bickelhaupt and Duran. It is somewhat remarkable that PBE or PBE0 have topped the poll for many years, despite the fact that many newer functionals perform better. As always, when choosing a functional caveat emptor.

References

1.  Mardirossian, N.; Head-Gordon, M., “Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals.” Mol. Phys. 2017, 115, 2315-2372, DOI: 10.1080/00268976.2017.1333644.

2. Goerigk, L.; Mehta, N., “A Trip to the Density Functional Theory Zoo: Warnings and Recommendations for the User.” Aust. J. Chem. 2019, ASAP, DOI: 10.1071/CH19023.

3. Goerigk, L.; Hansen, A.; Bauer, C.; Ehrlich, S.; Najibi, A.; Grimme, S., “A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions.” Phys. Chem. Chem. Phys. 2017, 19, 32184-32215, DOI: 10.1039/C7CP04913G.

DFT Steven Bachrach 18 Mar 2019 No Comments

Curved Aromatic molecules – 4 new examples

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

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

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


2 twisted saddle (ground state)


2 saddle (transition state)

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

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


5 twisted
0.0


5 TS
6.2


5 saddle
4.1

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

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

Figure 3. PM6 optimized structure of 8.

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

Scheme 1. NICS(0) values of 10

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

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

References

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

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

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

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

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

InChIs

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

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

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

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

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

6: InChI=1S/C32H16/c1-2-18-5-6-20-9-11-22-13-15-24-16-14-23-12-10-21-8-7-19-4-3-17(1)25-26(18)28(20)30(22)32(24)31(23)29(21)27(19)25/h1-16H
InChIkey=BASWMOIVIHXTRC-UHFFFAOYSA-N

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

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

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

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

Aromaticity Steven Bachrach 24 Sep 2018 No Comments

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

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

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

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


1


2

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

References

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

InChIs

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

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

adamantane &DFT &Grimme &MP &Schreiner Steven Bachrach 25 Jun 2018 1 Comment

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