Archive for the 'Uncategorized' Category

SpnF revisited

Medvedev, et al. have examined the cyclization step in the formation of Spinosyn A, which is catalyzed by the putative Diels-Alderase enzyme SpnF.1 This work follows on the computational study done by Houk, Singleton and co-workers,2 which I have discussed in this post (Dynamics in a reaction where a [6+4] and [4+2] cycloadditons compete). In fact, I recommend that you read the previous post before continuing on with this one. In summary, Houk, et al. found that a single transition state connects reactant 1 to both 2 and 3. The experimental product with the enzyme SpnF is 3. In the absence of enzyme, Houk, et al. suggest that reactions will cross the bispericyclic transition state TS-BPC (TS1 in the previous post) leading primarily to 2, which then undergoes a Cope rearrangement to get to product 3. Some molecules will follow pathways that go directly to 3.

The PCM(water)/M06-2x/6-31+G(d) study by Medvedev, et al. first identifies 560 conformations of 3. Next, they identified 384 TSs lying within 30 kcal mol-1 from the lowest TS. These can be classified as either TS-DA (leading directly to 3) or TS-BPC (which may lead to 2 by steepest descent, but can bifurcate towards 3). They opt to utilize the Atoms-in-Molecules theory to identify bond critical points to categorize these TS, and find that 144 are TS-BPC and 240 are TS-DA. (The transition state found by Houk, et al. is the second lowest energy TS found in this study, 0.29 kcal mol-1 higher in energy that the lowest TS and also of TS-BPC type.)

They also examined two alternative routes. First, they propose a path that first takes 1 to 4 via an alternative Diels-Alder reaction, and a second Cope rearrangement (TS-Cope2) takes this to 2, which can then convert to 3 via TS-Cope1. The other route involves a biradical pathway to either A or B. These alternatives prove to be non-competitive, with transition state energies significantly higher than either TS-DA or TS-BPC.

Returning to the set of TS-DA and TS-BPC transition states, while the former are more numerous, the latter are lower in energy. In summary, this study further complicates the complex situation presented by Houk, et. al. In the absence of catalyst, 1 can undergo either a Diels-Alder reaction to 3, or pass through a bispericyclic transition state that can lead to 3, but principally to 2 and then undergo a Cope rearrangement to get to 3. The question that ends my previous post on this subject — “ just what role does the enzyme SpnF play?” — remains to be answered.


1) Medvedev, M. G.; Zeifman, A. A.; Novikov, F. N.; Bushmarinov, I. S.; Stroganov, O. V.; Titov, I. Y.; Chilov, G. G.; Svitanko, I. V., "Quantifying Possible Routes for SpnF-Catalyzed Formal Diels–Alder Cycloaddition." J. Am. Chem. Soc. 2017, 139, 3942-3945, DOI: 10.1021/jacs.6b13243.

2) Patel, A.; Chen, Z.; Yang, Z.; Gutiérrez, O.; Liu, H.-w.; Houk, K. N.; Singleton, D. A., "Dynamically Complex [6+4] and [4+2] Cycloadditions in the Biosynthesis of Spinosyn A." J. Am. Chem. Soc. 2016, 138, 3631-3634, DOI: 10.1021/jacs.6b00017.


1: InChI=1S/C24H34O5/c1-3-21-15-12-17-23(27)19(2)22(26)16-10-7-9-14-20(25)13-8-5-4-6-11-18-24(28)29-21/h4-11,16,18-21,23,25,27H,3,12-15,17H2,1-2H3/b6-4+,8-5+,9-7+,16-10+,18-11+/t19-,20+,21-,23-/m0/s1

2: InChI=1S/C24H34O5/c1-3-19-8-6-10-22(26)15(2)23(27)20-12-11-17-14-18(25)13-16(17)7-4-5-9-21(20)24(28)29-19/h4-5,7,9,11-12,15-22,25-26H,3,6,8,10,13-14H2,1-2H3/b7-4-,9-5+,12-11+/t15-,16-,17-,18-,19+,20+,21-,22+/m1/s1

3: InChI=1S/C24H34O5/c1-3-19-5-4-6-22(26)15(2)23(27)11-10-20-16(9-12-24(28)29-19)7-8-17-13-18(25)14-21(17)20/h7-12,15-22,25-26H,3-6,13-14H2,1-2H3/b11-10+,12-9+/t15-,16+,17-,18-,19+,20-,21-,22+/m1/s1

Uncategorized Steven Bachrach 11 Apr 2017 1 Comment

Automated chemical drawings

Making a good drawing of a chemical structure can be a difficult task. One wants to prepare a drawing that provides a variety of different information in a clean and clear way. We tend to want equal bond lengths, angles that are representative of the atom’s hybridization, symmetrical rings, avoided bond crossings, and the absence of overlapping groups. These ideals may be difficult to manage. Sometimes we might also want to represent something about the actual 3-dimensional shape. So for example, the drawing on the left of Figure 1 properly represents the atom connectivity with no bond crossing, but the figure on the right is probably the image all organic chemists would want to see for cubane.

Figure 1. Two drawing of cubane

For another example, the drawing on the left of Figure 2 nicely captures the relative stereo relationships within D-glucose, but the drawing on the right adds in the fact that the cyclohexyl ring is in a chair conformation. Which drawing is better? Well, it likely is in the eye of the beholder, and the context of the chemistry at hand.

Figure 2. Two drawings of D-glucose.

Frączek has reported on an automated procedure for creating aesthetically pleasing 2-D drawings of chemical structures.1 The method involves optimizing distances between atoms projected onto a 2-D plane, along with rules to try to keep atom lengths and angles similar, and symmetrical rings, and minimize overlapping bonds. He shows a number of nice examples, especially of natural products, where his automated procedure PSM (physical simulation method) provides some very nice drawings, often noticeably superior to those generated by previously proposed schemes for preparing drawings.

Using the web site he has developed (, I recreated the structures of some of the molecules I have discussed in this blog. In Figure 3, these are shown side-by-side to my drawings. My drawings were generally done with MDL/Isis/Accelrys/Biovia Draw (available for free for academic users) with an eye towards representing what I think is a suitable view of the molecule based on what I am discussing in the blog post. For many molecules, PSM does a very nice job, sometimes better than what I have drawn, but in some cases PSM produces an inferior drawing. Nonetheless, creating nice chemical drawings can be tedious and PSM offers a rapid option, worthy of at least trying out. Ultimately, what we decide to draw and publish is often an aesthetic choice and each individual must decide on one’s own how best to present one’s work.

My Drawing


Figure 3. Comparison of my drawings vs. drawing made by PSM.


1) Frączek, T., "Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram Generation of Complex Molecules and Ligand–Protein Interactions." J. Chem. Inform. Model. 2016, 56, 2320-2335, DOI: 10.1021/acs.jcim.6b00391.

Uncategorized Steven Bachrach 21 Mar 2017 5 Comments

Nitrogen substituted buckybowl fragment

Higashibayashi and co-workers prepared the hydrazine-substituted Buckyball fragment 1a and also its mono- and deoxidized analogues.1 To interpret their results, they also computed the parent structure 1b at ωB97Xd/6-311+G(d,p).

1a R = tBut
1b R = H

The optimized structure of 1b is a bowl, but a twisted geometry, where the lone pair on each
nitrogen is on the opposite face of the molecule, lies only 1.6 kcal mol-1 higher in energy. The barrier for moving from the bowl to the twist form is 2.0 kcal mol-1. The completely planar structure, which is also a transition state for inversion of the bowl, lies 5.1 kcal mol-1 above the lowest energy bowl structure. The geometries and energies of the conformations are shown in Figure 1.

1b bowl (0.0)

1b twist (1.6)

1b TS (2.0)

1b planar TS (5.11)

Figure 1. ωB97Xd/6-311+G(d,p) optimized
geometry and relative energy (kcal mol-1) of the conformations of 1b.

The mono oxidized 1b.+ structure is also a bowl, but there is no twist form and inversion takes place through a planar structure that is only 0.5 kcal mol-1 above the bowl ground state. The structures and energies of these conformations of 1b.+ are shown in Figure 2.

1b.+ bowl (0.0)

1b.+ planar TS (0.5)

Figure 2. ωB97Xd/6-311+G(d,p) optimized geometry and relative energy (kcal mol-1) of the conformations of 1b.+.

Lastly, the di-oxidized 1b2+ is planar, and its structure is shown in Figure 3.

1b2+ planar

Figure 2. ωB97Xd/6-311+G(d,p) optimized geometry of 1b2+.

These computations corroborate all of the experimental data observed with 1a. What is particularly of note is the fact that the potential energy surface is so dependent on charge state: a three-well potential for the neutral, and two-well potential for the monocation, and a single-well potential for the dication.


(1) Higashibayashi, S.; Pandit, P.; Haruki, R.; Adachi, S.-I.; Kumai, R. “Redox-Dependent
Transformation of a Hydrazinobuckybowl between Curved and Planar Geometries,” Angew. Chem. Int. Ed. 2016, 55, 10830-10834, DOI: 10.1002/anie.201605340.


1a: InChI=1S/C40H44N2/c1-37(2,3)21-13-25-26-14-22(38(4,5)6)19-31-32-20-24(40(10,11)12)16-28-27-15-23(39(7,8)9)18-30-29(17-21)33(25)41(34(26)31)42(35(27)30)36(28)32/h13-20H,1-12H3


Uncategorized Steven Bachrach 06 Sep 2016 No Comments

Identifying the n→π* interaction

The weak n→π* interaction has been proposed to explain some conformational structure. Singh, Mishra, Sharma, and Das have now provided the first spectroscopic evidence of this interactions.1 They examined the structure of phenylformate 1. This compound can exist as two conformational isomers, having the carbonyl oxygen pointing towards (cis) or away (trans) from the phenyl ring. They optimized the structures of these two conformers at M05-2X/aug-cc-pVDZ and find that the cis isomer is lower in energy by 1.32 kcal mol-1. Unfortunately, the authors do not provide the structures of these isomers, but since they are so small, I reoptimized them at ωB97XD/6-311g(d) and they are displayed in Figure 1. At this computational level, the cis isomer is lower in enthalpy than the trans isomer by 1.35 kcal mol-1.



Figure 1. ωB97XD/6-311g(d) optimized structures of the cis and trans conformations of 1.

One-color resonant 2-photon ionization (1C-R2PI) spectroscopy followed by UV-VIS hole burning spectroscopy identified two isomers of 1, one present in greater amount that the other. The IR spectra of the dominant isomer showed a carbonyl stretch at 1766 cm-1, in nice agreement with the predicted frequency of 1cis (1770 cm-1). The carbonyl stretch for the minor isomer is at 1797 cm-1, again in nice agreement with the computed frequency for 1trans (1800 cm-1). The cis isomer has the lower carbonyl frequency due to partial donation of the carbonyl oxygen electrons to the π* orbital of the phenyl ring.


(1) Singh, S. K.; Mishra, K. K.; Sharma, N.; Das, A. "Direct Spectroscopic Evidence for an n→π* Interaction," Angew. Chem. Int. Ed. 2016, 55, 7801-7805, DOI: 10.1002/anie.201511925.


1: InChI=1S/C7H6O2/c8-6-9-7-4-2-1-3-5-7/h1-6H

Uncategorized Steven Bachrach 18 Jul 2016 1 Comment

Changes to the blog

I have been posting regularly on this blog for over nine years, beginning in July 2007. I have used this blog as a way to keep my book Computational Organic Chemistry current for its readers. I have also used it as a way for me to keep current with the literature.

It has been a terrific adventure for me, but an important change will be taking place in my life that will have an impact on the blog. Starting on August 1, 2016 I will become the Dean of the School of Science at Monmouth University in West Long Branch, NJ. (See the announcement.) I am extraordinarily excited to take on the challenges of leading the School. I suspect that my duties as Dean will keep me from finding the time to post as often as I have been for this past years. I will try to occasionally write a post as I intend to keep connected to the computational chemistry community. I have a few posts backlogged but expect a more infrequent posting schedule come August.

I fully intend to maintain the blog so that past posts remain accessible.

I want to thank all of the readers of this blog, those who read me through the Computational Chemistry Highlights blog, and especially those of you who have posted comments.

Uncategorized Steven Bachrach 11 Jul 2016 5 Comments

Interesting chemistry of biphenalenylidene

Uchida and co-workers reported on the preparation of biphenalenylidene 1 and its interesting electrocyclization to dihydroperopyrene 2.1 The experimental barrier they find by experiment for the conversion of 1-Z to 1-E is only 4.3 kcal mol-1. Secondly, the photochemical electrocyclization of 2-anti to 1-Z proceeds rapidly, through an (expected) allowed conrotatory pathway. However, the reverse reaction did not occur photochemically, but rather did occur thermally, even though this is formally forbidden by the Woodward-Hoffman rules.

To address these issues, they performed a number of computations, with geometries optimized at UB3LYP(BS)/6-31G**. First, CASSCF computations indicated considerable singlet diradical character for 1-Z. Both 1-Z and 1-E show significant twisting about the central double bond, consistent with the singlet diradical character. 1-Z is 1.8 kcal mol-1 lower in energy than 1-E, and the barrier for rotation interconverting these isomers is computed to be 7.0 kcal mol-1, in reasonable agreement with the experiment. These geometries are shown in Figure 1.



TS (Z→E)

Figure 1. UB3LYP(BS)/6-31G** optimized geometries of 1-Z and 1- and the transition state to interconvert these two isomers.

The conrotatory electrocyclization that takes 1-Z into 2-anti has a barrier of 26.0 kcal mol-1 and is exothermic by 3.4 kcal mol-1. The disrotatory process has a higher barrier (34.2 kcal mol-1) and is endothermic by 8.4 kcal mol-1. These transition states and products are shown in Figure 2. So, despite being orbital symmetry forbidden, the conrotatory path is preferred, and this agrees with their experiments.

TS (con)

TS (dis)



Figure 2. UB3LYP(BS)/6-31G** optimized geometries of 2-anti and 2-syn and the transition states leading to them.

The authors argue that the large diradical character of 1 leads to both its low Z→E rotational barrier, and the low barrer for electrocyclization. The Woodward-Hoffmann allowed disrotatory barrier is inhibited by its highly strained geometry, making the conrotatory path the favored route.


(1) Uchida, K.; Ito, S.; Nakano, M.; Abe, M.; Kubo, T. "Biphenalenylidene: Isolation and Characterization of the Reactive Intermediate on the Decomposition Pathway of Phenalenyl Radical," J. Am. Chem. Soc. 2016, 138, 2399-2410, DOI: 10.1021/jacs.5b13033.


1-E: InChI=1S/C26H16/c1-5-17-9-3-11-23-21(15-13-19(7-1)25(17)23)22-16-14-20-8-2-6-18-10-4-12-24(22)26(18)20/h1-16H/b22-21+

1-Z: InChI=1S/C26H16/c1-5-17-9-3-11-23-21(15-13-19(7-1)25(17)23)22-16-14-20-8-2-6-18-10-4-12-24(22)26(18)20/h1-16H/b22-21-

2-anti: InChI=1S/C26H18/c1-3-15-7-11-19-21-13-9-17-5-2-6-18-10-14-22(26(21)24(17)18)20-12-8-16(4-1)23(15)25(19)20/h1-14,19,21,25-26H/t19-,21-,25?,26?/m0/s1

2-syn: InChI=1S/C26H18/c1-3-15-7-11-19-21-13-9-17-5-2-6-18-10-14-22(26(21)24(17)18)20-12-8-16(4-1)23(15)25(19)20/h1-14,19,21,25-26H/t19-,21+,25?,26?

Uncategorized Steven Bachrach 19 Apr 2016 No Comments


Reid, Rathore and colleagues report on the attempted preparation of the interesting molecule 1,3,5-trifluorenylcyclohexane (TFC) 1.1 They had hoped to prepare it by subjecting the precursor 2 to acid, which might then undergo a Friedel-Crafts reaction to prepare the last fluorenyl group, and subsequent loss of a proton would give 1. Unfortunately, they could not get this step to occur, even at high temperature and for long reaction times. What made it particularly frustrating was that they could get 3 to react under these conditions to give 1,4-difluorenylcyclohexane (14-DFC) 4, and convert 5 into 1,4-difluorenylcyclohexane (13-DFC) 6.

To get at why 1 could not be formed they utilized PCM(CH2Cl2)/M06-2X/6-31G(d) calculations. The lowest energy conformations of 1 and 4 are shown in Figure 1. While 4 is in a chair conformation, 1 is not in a chair conformation since this would bring the three fluorenyl groups into very close contact. Instead, the cyclohexyl ring of 1 adopts a twist-boat conformation, with a much flattened ring. They estimate that 1 is strained by about 17 kcal mol-1, with 10 kcal mol-1 coming from strain in the twist-boat conformation and another 7 kcal mol-1 of strain due to steric crowding of the fluorenyl groups.

They next optimized the structures of the intermediates and transition states on the path taking 2 into 1 and 3 into 4. The transition states of the Friedel-Crafts reaction are the highest points on these paths, and their geometries are shown in Figure 1. The barrier through the TS for the Friedel-Crafts step forming 1 is about 17 kcal mol-1 higher than for the barrier to form 4. This very large increase in activation barrier, due to the strains imposed by that third fluorenyl group, explains the lack of reaction. Furthermore, since the reaction 21 is 2.0 kcal mol-1 endothermic, at high temperature the reaction is likely to be reversible and favors 2.



TS to 1

TS to 4

Figure 1. PCM(CH2Cl2)/M06-2X/6-31G(d) optimized geometries.


(1) Talipov, M. R.; Abdelwahed, S. H.; Thakur, K.; Reid, S. A.; Rathore, R. "From Wires to Cables: Attempted Synthesis of 1,3,5-Trifluorenylcyclohexane as a Platform for Molecular Cables," J. Org. Chem. 2016, DOI: 10.1021/acs.joc.5b02792.


1 (TFC): InChI=1S/C42H30/c1-7-19-34-28(13-1)29-14-2-8-20-35(29)40(34)25-41(36-21-9-3-15-30(36)31-16-4-10-22-37(31)41)27-42(26-40)38-23-11-5-17-32(38)33-18-6-12-24-39(33)42/h1-24H,25-27H2

4 (14-DFC): InChI=1S/C30H24/c1-5-13-25-21(9-1)22-10-2-6-14-26(22)29(25)17-19-30(20-18-29)27-15-7-3-11-23(27)24-12-4-8-16-28(24)30/h1-16H,17-20H2

6 (13-DFC):InChI=1S/C30H24/c1-2-11-22(12-3-1)24-14-4-5-15-25(24)23-13-10-20-30(21-23)28-18-8-6-16-26(28)27-17-7-9-19-29(27)30/h1-9,11-19H,10,20-21H2

Uncategorized Steven Bachrach 28 Mar 2016 No Comments

Really short non-bonded HH distances

Setting the record for the shortest non-bonded HH contact has become an active contest. Following on the report of a contact distance of only 1.47 Å that I blogged about here, Firouzi and Shahbazian propose a series of related cage molecules with C-H bonds pointed into their interior.1 The compounds were optimized with a variety of computational methods, and many of them have HH distances well below that of the previous record. The shortest distance is found in 1, shown in Figure 1. The HH distance in 1 is predicted to be less than 1.2 Å with a variety of density functionals and moderate basis sets.


Figure 1. Optimized geometry of 1 at ωB97X-D/cc-pVDZ.


(1) Firouzi, R.; Shahbazian, S. "Seeking Extremes in Molecular Design: To What Extent May Two “Non-Bonded” Hydrogen Atoms be Squeezed in a Hydrocarbon?," ChemPhysChem 2016, 17, 51-54, DOI: 10.1002/cphc.201501002.


1: InChI=1S/C41H44/c1-7-13-25-17-9-3-40-5-11-19(35(17)40)27-15-8-2-39(1,33(13)15)34-14(7)26-18-10-4-41-6-12-20(36(18)41)28(16(8)34)32(27)30-23(11)37(40)21(9)29(31(25)26)22(10)38(41)24(12)30/h7-38H,1-6H2

Uncategorized Steven Bachrach 26 Jan 2016 6 Comments

An amazing barrel structure

I don’t really have anything to say about this recent paper by Anderson, et al.1 They have simply prepared a very beautiful structure, an aryllated analogue of 1. They even optimized the structure of 1 at BLYP/6-31G(d) and it’s shown in Figure 1. That must have taken some time!

Figure 1. BLYP/6-31G(d) optimized structure of 1.
(Remember that you can manipulate this structure by simply clicking on in, which will launch the JMol app.)


(1) Neuhaus, P.; Cnossen, A.; Gong, J. Q.; Herz, L. M.; Anderson, H. L. "A Molecular Nanotube with Three-Dimensional π-Conjugation," Angew. Chem. Int. Ed. 2015, 54, 7344-7348, DOI: 10.1002/anie.201502735.

Uncategorized Steven Bachrach 04 Aug 2015 2 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.



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.



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!


(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.


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

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

Uncategorized Steven Bachrach 15 Dec 2014 2 Comments

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