Henry Rzepa's Blog

In the previous post,[1] I was commenting that the transition state for borohydride reduction of a ketone contained some close contacts between the hydrogen of the borohydride and the hydrogen of water. A systematic search of the CSD reveals a modest number of such contacts have been observed in crystal structures (Table).  Since it is always good to have a reality check for constructed transition states, here I take a look at some of compounds showing the closest H…H contacts in the experimental database of structures.

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References

1. H. Rzepa, "The mechanism of borohydride reductions. Part 2: 4-t-butyl-cyclohexanone – Dispersion induced stereochemistry.", 2025. https://doi.org/10.59350/x5k75-t2m40

Part one of this topic was posted more than ten years ago.[1] I clearly forgot about it, so belatedly, here is part 2 – dealing with the stereochemistry of the reduction of tert-butyl-cyclohexanone by borohydride in water. The known stereochemistry is nicely summarised in this article, along with an extensive  history of possible explanations of the reasons for the stereochemical preference.[2] Put simply, the hydride nucleophile attacks the carbonyl from an axial rather than equation direction with a ratio of 10:1 (ΔΔG 1.37 kcal/mol). So does the model I previously proposed[1] support this and give any indication of why the stereochemistry is axial?

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References

1. H. Rzepa, "Part 1: ethanal.", 2015. https://doi.org/10.59350/aqrgh-jw887
2. R. Kobetić, V. Petrović-Peroković, V. Ključarić, B. Juršić, and D.E. Sunko, "Selective Reduction of Cyclohexanones with NaBH₄ in β-Cyclodextrin, PEG-400, and Micelles", Supramolecular Chemistry, vol. 20, pp. 379-385, 2008. https://doi.org/10.1080/10610270701268815

In the previous post[1] I mooted the possibility that a high energy form of the dimer of nitric oxide 1 might nonetheless be able to be detected using suitable traps (such as hydrogenation or cycloaddition). However, an interesting alternative is that this species could be trapped by nitric oxide itself. According to [2] in an article entitled “Decomposition of nitric oxide at elevated pressures” the rate of this termolecular reaction 3NO → N₂O + NO₂ are said to obey third order kinetics. One plausible mechanism for this process is shown below.

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References

1. H. Rzepa, "Hydrogenating the even more mysterious N≡N triple bond in a nitric oxide dimer.", 2025. https://doi.org/10.59350/rzepa.29626
2. T. Melia, "Decomposition of nitric oxide at elevated pressures", Journal of Inorganic and Nuclear Chemistry, vol. 27, pp. 95-98, 1965. https://doi.org/10.1016/0022-1902(65)80196-8

Previously[1] I looked at some of the properties of the mysterious dimer of nitric oxide  1 – not the known weak dimer but a higher energy form with a “triple” N≡N bond. This valence bond isomer of the weak dimer was some 24 kcal/mol higher in free energy than the two nitric oxide molecules it would be formed from. An energy decomposition analysis (NEDA) of 1 revealed an interaction energy[2] of +4.5 kcal/mol for the two radical fragments, compared to eg -27 kcal/mol for the equivalent analysis of the N=N double bond in nitrosobenzene dimer[3] So here I take a look at another property of N≡N bonds via their hydrogenation energy (Scheme), mindful that the dinitrogen molecule requires forcing conditions to hydrogenate, in part because of the unfavourable entropy terms (See Wiki and also here^‡ for a calculation of ΔG₂₉₈).

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References

1. H. Rzepa, "The even more mysterious N≡N triple bond in a nitric oxide dimer.", 2025. https://doi.org/10.59350/rzepa.29429
2. H. Rzepa, "N2O2 as strong dimer? bent NEDA 0 1 0 2 0 -2 Total Interaction (E) : 4.520 Wiberg NN bond index 1.0072 NN stretch 2604 cm-1", 2025. https://doi.org/10.14469/hpc/15468
3. H. Rzepa, "Nitrosobenzene dimer NEDA=2, 0,1 0,1 0,1 Total Interaction (E) : -27.564", 2025. https://doi.org/10.14469/hpc/15444

I started adding citations to my blog posts around 2012 using the Kcite plugin.^‡ Rogue Scholar is a service that monitors registered blog sources and adds all sorts of value to the original post, including identifying such citations and creating a list of them.

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Two years ago, I posted on the topic “Internet Archeology: reviving a 2001 article published in the Internet Journal of Chemistry (IJC)”.[1] The IJC had been founded in 1998,[2]  in part at least to “re-invent” the scholarly journal by elevating research data to being a more integrated part of the overall article, rather than as the previously conventional addendum of SI (Supporting Information)^‡. IJC was in one sense following on from an earlier such project dating from 1995[3] by taking it to the next level. Sadly, the pioneering IJC journal had gone off-line in 2004 and the content for around 100 articles was thought lost. It happened that I still retained the original source and associated data for one article of mine and my post[1] described how I managed to get it back into more or less full working order. Now Egon Willighagen[4] has cleverly found a way of rescuing many more of these lost articles, thanks to various Web-based infrastructures: Read the rest of this entry »

References

1. H. Rzepa, "Internet Archeology: reviving a 2001 article published in the Internet Journal of Chemistry.", 2024. https://doi.org/10.59350/xqerh-wam97
2. S.M. Bachrach, and S.R. Heller, "The<i>Internet Journal of Chemistry:</i>A Case Study of an Electronic Chemistry Journal", Serials Review, vol. 26, pp. 3-14, 2000. https://doi.org/10.1080/00987913.2000.10764578
3. D. James, B.J. Whitaker, C. Hildyard, H.S. Rzepa, O. Casher, J.M. Goodman, D. Riddick, and P. Murray‐Rust, "The case for content integrity in electronic chemistry journals: The CLIC project", New Review of Information Networking, vol. 1, pp. 61-69, 1995. https://doi.org/10.1080/13614579509516846
4. E. Willighagen, "The Internet Journal of Chemistry", 2025. https://doi.org/10.59350/2ss5b-jpr33

Previously, I pondered about the strange N=N double bond in nitrosobenzene dimer[1] as a follow up to commenting on the curly arrow mechanism of the dimerisation.[2] By the same curly arrow method, one can produce the below, showing how the simpler nitric oxide radical could potentially dimerise to a species with a N≡N triple bond!^† This involves a total of six electrons entering the N-N region, and hence raises the question of whether these all move in a single concerted/synchronous bond forming reaction, or whether they might go in (asynchronous) stages. Here are some calculations[3]) which might shed some light on this aspect.

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References

1. H. Rzepa, "The mysterious N=N double bond in nitrosobenzene dimer.", 2025. https://doi.org/10.59350/rzepa.29383
2. H. Rzepa, "Mechanism of the dimerisation of Nitrosobenzene.", 2025. https://doi.org/10.59350/rzepa.28849
3. H. Rzepa, "N2O2 as strong dimer TS as biradical cis, G = -259.785500", 2025. https://doi.org/10.14469/hpc/15483

In the previous post,[1] I introduced the N=N double bond in nitrosobenzene dimer, arguing that even though it was a formal double bond, its bond dissociation energy made it nonetheless a very weak double bond! This was backed up by a technique known as energy decomposition analysis or EDA. Here I use a variant of this method  known as  NEDA to look at some other strained alkenes, including the famously non-existent tetra t-Butyl ethene.

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References

1. H. Rzepa, "The mysterious N=N double bond in nitrosobenzene dimer.", 2025. https://doi.org/10.59350/rzepa.29383

In an earlier blog, I discussed[1] the curly arrows associated with the known dimerisation of nitrosobenzene, and how the N=N double bond (shown in red below) forms in a single concerted process.

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References

1. H. Rzepa, "Mechanism of the dimerisation of Nitrosobenzene.", 2025. https://doi.org/10.59350/rzepa.28849