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.


(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.





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”.


(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



TS leading to the R isomer


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.


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.


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

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

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

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

18π-electron tautomers

Aromaticity Steven Bachrach 02 Sep 2014 No Comments

Muranaka and Uchiyama have prepared an 18π-electron system that exhibits variable aromaticity in its tautomeric forms.1 The synthesized benziphthalacyanine 1 shows upfield resonances in the 1H NMR for the internal hydrogens: 1.89 ppm for the C-H proton and 4.67 ppm for the N-H proton. This indicates some weak diatropicity.

To address this interesting magnetic property, they reported B3LYP/6-31+G(d) computations on the model system 2 in its phenol 2p and quinoidal 2q tautomeric forms.

The optimized structures are shown in Figure 1. The phenol form 2p has NICS(0) and NICS(1) values of -6.77 and -6.04 ppm, respectively, indicating only modest aromaticity. However, the NICS values for the quinoidal from 2q are much more negative, -11.43 (NICS(0)) and -10.10 (NICS(1)) ppm, indicating a more significant aromatic character. The calculated chemical shift of the internal C-H is most telling: for 2q it is -4.55ppm but for 2p it is 0.97 ppm, in good agreement with experiment. Thus, 1 has an 18π-electron modestly aromatic periphery, with the phenol form dominant. There is no evidence of a 20π-electron periphery.



Figure 1. B3LYP/6-31+G(d) optimized geometries of 2p and 2q.

(Note that the supporting materials have a missing carbon in 2q and I have made a guess at its proper location – so this is not quite the optimized structure! Once again, a statement about the quality of SI!)


(1) Toriumi, N.; Muranaka, A.; Hirano, K.; Yoshida, K.; Hashizume, D.; Uchiyama, M. "18π-Electron Tautomeric Benziphthalocyanine: A Functional Near-Infrared Dye with Tunable Aromaticity," Angew. Chem. Int. Ed. 2014, 53, 7814-7818, DOI: 10.1002/anie.201404020.


1: InChI=1S/C108H125N7O2/c1-57(2)75-31-25-32-76(58(3)4)87(75)43-69-49-93-95(51-71(69)45-89-79(61(9)10)35-27-36-80(89)62(11)12)105-111-103(93)109-99-55-100(102(117)56-101(99)116)110-104-94-50-70(44-88-77(59(5)6)33-26-34-78(88)60(7)8)72(46-90-81(63(13)14)37-28-38-82(90)64(15)16)52-96(94)106(112-104)114-108-98-54-74(48-92-85(67(21)22)41-30-42-86(92)68(23)24)73(53-97(98)107(113-105)115-108)47-91-83(65(17)18)39-29-40-84(91)66(19)20/h25-42,49-68,116-117H,43-48H2,1-24H3,(H,109,110,111,112,113,114,115)

2p: InChI=1S/C30H17N7O2/c38-23-14-24(39)22-13-21(23)31-25-15-7-1-3-9-17(15)27(33-25)35-29-19-11-5-6-12-20(19)30(37-29)36-28-18-10-4-2-8-16(18)26(32-22)34-28/h1-14,38-39H,(H,31,32,33,34,35,36,37)

2q: InChI=1S/C30H17N7O2/c38-23-14-24(39)22-13-21(23)31-25-15-7-1-3-9-17(15)27(33-25)35-29-19-11-5-6-12-20(19)30(37-29)36-28-18-10-4-2-8-16(18)26(32-22)34-28/h1-14H,(H3,31,32,33,34,35,36,37,38,39)

A pentacoordinate carbon

Schaefer &Schleyer Steven Bachrach 25 Aug 2014 No Comments

Trying to get carbon to bond in unnatural ways seems to be a passion for many organic chemists! Schleyer has been interested in unusual carbon structures for decades and he and Schaefer now report a molecule with a pentacoordinate carbon bound to five other carbon atoms. Their proposed target is pentamethylmethane cation C(CH3)5+ 1.1 The optimized geometry of 1, which has C3h symmetry, at MP2/cc-pVTZ is shown in Figure 1. The bonds from the central carbon to the equatorial carbon are a rather long 1.612 Å, but the bonds to the axial carbon are even longer, namely 1.736 Å. Bader analysis shows five bond critical points, each connecting the central carbon to one of the methyl carbons. Wiberg bond index and MO analysis suggests that the central carbon is tetravalent, with a 2-electron-3-center bond involving the central and axial carbons.




Figure 1. MP2/cc-pVTZ optimized geometries of 1 and dissociation transition states.

So while 1 is a local energy minimum, it sits in a very shallow well. One computed dissociation path, which passes through TS1 (Figure 1) on its way to 2-methyl-butyl cation and methane has a barrier of only 1.65 kcal mol-1 (CCSD(T)/CBS + ZPE). A second dissociation pathway goes through TS2 to t-butyl cation and ethane with a barrier of only 1.34 kcal mol-1. Worse still is that the free energy estimates suggest “spontaneous dissociation … through both pathways”.

Undoubtedly, this will not be the last word on trying to torture a poor carbon atom.


(1) McKee, W. C.; Agarwal, J.; Schaefer, H. F.; Schleyer, P. v. R. "Covalent Hypercoordination: Can Carbon Bind Five Methyl Ligands?," Angew. Chem. Int. Ed. 2014, 53, 7875-7878, DOI: 10.1002/anie.201403314.


1: InChI=1S/C6H15/c1-6(2,3,4)5/h1-5H3/q+1

Torqoselectivity in forming a Cis,Trans-Cyclooctadienone

Houk Steven Bachrach 11 Aug 2014 No Comments

Houk’s theory of torquoselectivity is a great achievement of computational chemistry, as told in Chapter 4.6 of the second edition of my book. Houk, in a collaboration with Krenske and Hsung, now report on an application of torquoselectivity in the formation of a cis-trans-cyclooctadienone intermediate.1

The proposed reaction is shown in Scheme 1, where the bicyclic compound undergoes a conrotatory ring opening in just one orientation to form the E,E-cyclooctadienone, which can then ring close to product.

Scheme 1.

Houk ran M06-2x//6-311+G(d,p)//B3LYP/6-31G(d) computations on the model system 1, passing over the two torquodistinctive transition states TSEE and TSZZ, and on to produce the two cyclooctadienones 2EE and 2ZZ, respectively. As seen in Figure 1, the barrier through TSEE is favored by 9.8 kcal mol-1, and leads to the much more favorable cycloocatadienone 2EE.







Figure 1. B3LYP/6-31G(d) optimized structures and relative free energies (kcal mol-1) at M06-2x//6-311+G(d,p)//B3LYP/6-31G(d).

Ring closure taking TSEE to product goes through TS2 (Figure 1), with a very high barrier, 47.5 kcal mol-1 above reactant, suggesting that this path is not likely to occur. Instead, they propose that 2EE is first protonated (2EEH+) and then cyclizes through TS2H+ (Figure 2). This barrier is only 6.2 kcal mol-1, some 44 kcal mol-1 lower than the neutral process through TS2.



Figure 2. B3LYP/6-31G(d) optimized structures


(1) Wang, X.-N.; Krenske, E. H.; Johnston, R. C.; Houk, K. N.; Hsung, R. P. "Torquoselective Ring Opening of Fused Cyclobutenamides: Evidence for a Cis,Trans-Cyclooctadienone Intermediate," J. Am. Chem. Soc. 2014, 136, 9802-9805, DOI: 10.1021/ja502252t.

Splitting CO2 with a two-coordinate boron cation

Uncategorized Steven Bachrach 04 Aug 2014 1 Comment

This paper is a bit afield from the usual material I cover but this is an interesting reaction. Shoji and coworkers have prepared the two-coordinate boron species 1,1 and confirmed its geometry by an x-ray crystal structure. What I find interesting is its reaction with CO2, which gives 2 and organoboranes that are not identified, though presumably derived from 3.

M06-2x/6-311+G(d,p) computations support a hypothetical mechanism whereby first a complex between 1 and CO2 is formed (CP1), that is 4.4 kcal mol-1 above isolated reactants. Then passing through TS1, which is 4.2 kcal mol-1 above CP1, an intermediate is formed (INT), which is almost 6 kcal mol-1 below starting materials. A second transition state is then traversed (about 1 kcal mol-1 below starting materials), to form an exit complex between 2 and 3, which can then separate to the final products with an overall exothermicity of 10.6 kcal mol-1. The structures of these critical points are shown in Figure 1.







Figure 1. M06-2x/6-311+G(d,p) optimized structures. Relative energy in kcal mol-1.


(1) Shoji, Y.; Tanaka, N.; Mikami, K.; Uchiyama, M.; Fukushima, T. "A two-coordinate boron cation featuring C–B+–C bonding," Nat. Chem. 2014, 6, 498-503, DOI: 10.1038/nchem.1948.


1: InChI=1S/C18H22B/c1-11-7-13(3)17(14(4)8-11)19-18-15(5)9-12(2)10-16(18)6/h7-10H,1-6H3/q+1

2: InChI=1S/C10H11O/c1-7-4-8(2)10(6-11)9(3)5-7/h4-5H,1-3H3/q+1

3: InChI=1S/C9H11BO/c1-6-4-7(2)9(10-11)8(3)5-6/h4-5H,1-3H3

New policy regarding articles I will blog

E-publishing Steven Bachrach 28 Jul 2014 6 Comments

I was all set to write a review of an interesting study of bowtiene 1: its rearrangement to other C10H6 isomers and its dimerization. But as I was gathering my information, I wanted to prepare the images of the optimized geometries, and so I went to get the supplementary materials.

The author has a section on the supplementary materials that indicates it contains Cartesian coordinates – just what I need. (This section ends with the curious line “This material is available for free of charge via the internet at”; it’s curious because the article is in a journal not published by ACS. I’ll leave for speculation just what happened here, but clearly the copy-editing done by the Canadian Journal of Chemistry is not quite up to snuff!)

So, I went to the website and clicked on the link for the supplementary material and was then told that I did not have access to this material and that either I had to become a subscriber or I had to purchase access to the article. (I should point out here that I received this article through interlibrary loan.) This is the first time that I have run into a paywall to get supporting materials! I know I am probably lucky that it took 7 years before running into this problem. But that makes this situation so frustrating – just why is the Canadian Journal of Chemistry placing supplementary material behind a paywall, especially when so few other publishers are doing this?

Well, until I get the supplementary materials, I will not write a post about this article.

New policy: I will not blog about an article unless (a) there is information on the 3-D structure of the molecules, typically in supporting materials, and (b) this information is available for free. This requirement should really be the minimum for publishing computational chemistry results. Now, I would also hope that the coordinates are readily reusable – see Henry Rzepa’s post about recent problems he’s run into!

Fused aromatic ring effect on electrocyclization reactions

Aromaticity &electrocyclization Steven Bachrach 22 Jul 2014 1 Comment

Aromaticity and orbital symmetry rules, though seemingly of ancient origin, remain areas of active interest. This paper by Fukazawa, et al combine both issues.1 The multiple-step electrocyclization of 1 gives 2 in a reaction that takes 9 days at 80 °C. What would be the effect of diminishing the aromatic character of the fused rings of 1? Would the reaction be faster or slower?

Before discussing the experimental results, let’s examine the B3LYP/6-31G(d) results for the reaction of 1’, 3 and 5. (Note that a slightly smaller pendant substituent is used in the computations than in the experiment.) The optimized geometries of the critical points along the reaction pathway for the cyclization of 3 are shown in Figure 1.






Figure 1. B3LYP/6-31G(d) optimized geometries and relative energies (kcal mol-1) for the critical points along the reaction 34.
Remember that all structures on my blog can be viewed interactively by clicking on the image of the molecule.

For 1’, the first barrier (for the 8π cyclization) has a barrier of about 23 kcal mol-1, but the second step (the 4π cyclization) has an even larger barrier of 28 kcal mol-1. However, reducing the aromaticity of one of the fused rings (compound 3) leads to lower barriers of 18 and 13 kcal mol-1. For the cyclization of 5, only a single transition state was found – no intermediate and no second TS – with a barrier of 12 kcal mol-1. Thus, removing these external aromatic rings reduces the barrier of the reaction, and that is exactly what is found experimentally!


(1) Fukazawa, A.; Oshima, H.; Shimizu, S.; Kobayashi, N.; Yamaguchi, S. "Dearomatization-Induced Transannular Cyclization: Synthesis of Electron-Accepting Thiophene-S,S-Dioxide-Fused Biphenylene," J. Am. Chem. Soc. 2014, 136, 8738-8745, DOI: 10.1021/ja503499n.


1: InChI=1S/C44H64S4Si4/c1-41(2,3)49(13,14)37-25-29-30-26-38(50(15,16)42(4,5)6)46-34(30)23-24-36-32(28-40(48-36)52(19,20)44(10,11)12)31-27-39(51(17,18)43(7,8)9)47-35(31)22-21-33(29)45-37/h25-28H,1-20H3/b30-29-,32-31-


2: InChI=1S/C44H64S4Si4/c1-41(2,3)49(13,14)29-21-25-26-22-30(50(15,16)42(4,5)6)46-38(26)34-33(37(25)45-29)35-36(34)40-28(24-32(48-40)52(19,20)44(10,11)12)27-23-31(47-39(27)35)51(17,18)43(7,8)9/h21-24H,1-20H3

2’: InChI=1S/C32H40S4Si4/c1-37(2,3)21-13-17-18-14-22(38(4,5)6)34-30(18)26-25(29(17)33-21)27-28(26)32-20(16-24(36-32)40(10,11)12)19-15-23(35-31(19)27)39(7,8)9/h13-16H,1-12H3

3: InChI=1S/C32H40O2S4Si4/c1-39(2,3)29-17-21-22-18-30(40(4,5)6)37-27(22)15-16-28-24(20-32(38(28,33)34)42(10,11)12)23-19-31(41(7,8)9)36-26(23)14-13-25(21)35-29/h17-20H,1-12H3/b22-21-,24-23-

4: InChI=1S/C32H40O2S4Si4/c1-39(2,3)21-13-17-18-14-22(40(4,5)6)36-30(18)26-25(29(17)35-21)27-28(26)32-20(16-24(38(32,33)34)42(10,11)12)19-15-23(37-31(19)27)41(7,8)9/h13-16H,1-12H3

5: InChI=1S/C32H40O8S4Si4/c1-45(2,3)29-17-21-22-18-30(46(4,5)6)42(35,36)26(22)15-16-28-24(20-32(44(28,39)40)48(10,11)12)23-19-31(47(7,8)9)43(37,38)27(23)14-13-25(21)41(29,33)34/h17-20H,1-12H3/b22-21-,24-23-

6: InChI=1S/C32H40O8S4Si4/c1-45(2,3)21-13-17-18-14-22(46(4,5)6)42(35,36)30(18)26-25(29(17)41(21,33)34)27-28(26)32-20(16-24(44(32,39)40)48(10,11)12)19-15-23(47(7,8)9)43(37,38)31(19)27/h13-16H,1-12H3


Aromaticity Steven Bachrach 09 Jul 2014 No Comments

Macrocycles composed of aromatic subunits, like polycycloparaphenylenes, are of interest as components of nanotubes and for possible interesting optical properties. Tremendous advances have occurred over the past decade in preparing these rings ; see for examples these posts. Yamago now reports on the synthesis, optical properties and structure of [4]cyclo-2,7-pyrenylene 1, made by joining four pyrene units together.1

B3LYP/6-31G(d) optimization of the structure of 1 reveals a D2 geometry (Figure 1). This structure shows a very distorted pyrene unit. The strain energy of 1 is estimated as 392 kJ mol-1 (though how this was arrived at is not mentioned!), which is much larger than the strain energy of [8]-cycloparaphenylene.

Figure 1. B3LYP/6-31G(d) optimized structure of 1
This is another molecule to be sure to click on and rotate using JMol.

The nature of the HOMO and LUMO of 1 is very different than that of linear tetra-2,7-pyrene. The degenerate HOMOs and degenerate LUMOs of the linear compound have a node at the 2 and 7 positions and are localized to the terminal and central pyrene units, respectively. The HOMO and LUMO of 1 are fully delocalized. The implications of this are seen in the spectroscopy and electrochemistry of 1.


(1) Iwamoto, T.; Kayahara, E.; Yasuda, N.; Suzuki, T.; Yamago, S. "Synthesis, Characterization, and Properties of [4]Cyclo-2,7-pyrenylene: Effects of Cyclic Structure on the Electronic Properties of Pyrene Oligomers," Angew. Chem. Int. Ed. 2014, 53, 6430-6434, DOI:


1: InChI=1S/C64H32/c1-2-34-18-50-20-36-4-3-35-19-49(17-33(1)57(35)58(34)36)51-21-37-5-7-41-25-53(26-42-8-6-38(22-51)59(37)61(41)42)55-29-45-13-15-47-31-56(32-48-16-14-46(30-55)63(45)64(47)48)54-27-43-11-9-39-23-52(50)24-40-10-12-44(28-54)62(43)60(39)40/h1-32H/b51-49-,52-50-,55-53-,56-54-

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