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.
The spin-offs from adding citations to blog posts.
August 19th, 2025More on rescuing articles from a now defunct early pioneering example of an Internet journal.
August 19th, 2025Two 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
- H. Rzepa, "Internet Archeology: reviving a 2001 article published in the Internet Journal of Chemistry.", 2024. https://doi.org/10.59350/xqerh-wam97
- S.M. Bachrach, and S.R. Heller, "TheInternet Journal of Chemistry:A Case Study of an Electronic Chemistry Journal", Serials Review, vol. 26, pp. 3-14, 2000. https://doi.org/10.1080/00987913.2000.10764578
- 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
- E. Willighagen, "The Internet Journal of Chemistry", 2025. https://doi.org/10.59350/2ss5b-jpr33
The even more mysterious N≡N triple bond in a nitric oxide dimer.
August 18th, 2025Previously, 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 (FAIR data DOI: 10.14469/hpc/15483) which might shed some light on this aspect.
References
- H. Rzepa, "The mysterious N=N double bond in nitrosobenzene dimer.", 2025. https://doi.org/10.59350/rzepa.29383
- H. Rzepa, "Mechanism of the dimerisation of Nitrosobenzene.", 2025. https://doi.org/10.59350/rzepa.28849
Energy decomposition analysis of hindered alkenes: Tetra t-butylethene and others.
August 13th, 2025In 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.
References
- H. Rzepa, "The mysterious N=N double bond in nitrosobenzene dimer.", 2025. https://doi.org/10.59350/rzepa.29383
The mysterious N=N double bond in nitrosobenzene dimer.
August 11th, 2025In 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.
References
- H. Rzepa, "Mechanism of the dimerisation of Nitrosobenzene.", 2025. https://doi.org/10.59350/rzepa.28849
Why an Electron-Withdrawing Group is an o, m-Director rather than m-Director in Electrophilic Aromatic Substitution: The example of CN vs NC.
July 22nd, 2025In the previous post[1] I followed up on an article published on the theme “Physical Organic Chemistry: Never Out of Style“.[2] Paul Rablen presented the case that the amount of o (ortho) product in electrophilic substitution of a phenyl ring bearing an EWG (electron withdrawing group) is often large enough to merit changing the long held rule-of-thumb for EWGs from being just meta directors into being ortho and meta-directors, with a preference for meta. I showed how Paul’s elegant insight could be complemented by an NBO7 analysis of the donor-acceptor interactions in the σ-complex formed by protonating the phenyl ring bearing the EWG. Both the o– and m– isomers showed similar NBO orbital patterns and associated E(2) donor/acceptor interaction energies and also matched the observation that the proportion of meta is modestly greater than ortho substitution (steric effects not modelled). These interactions were both very different from those calculated for the para isomer.
References
- H. Rzepa, "“Typical Electron-Withdrawing Groups Are o, m-Directors Rather than m-Directors in Electrophilic Aromatic Substitution”", 2025. https://doi.org/10.59350/rzepa.28993
- P.R. Rablen, "Typical Electron-Withdrawing Groups Are ortho, meta-Directors Rather than meta-Directors in Electrophilic Aromatic Substitution", The Journal of Organic Chemistry, vol. 90, pp. 6090-6093, 2025. https://doi.org/10.1021/acs.joc.5c00426
“Typical Electron-Withdrawing Groups Are o, m-Directors Rather than m-Directors in Electrophilic Aromatic Substitution”
July 17th, 2025The title of this post comes from an article published in a special virtual issue on the theme “Physical Organic Chemistry: Never Out of Style“[1] There, Paul Rablen presents the case that the amount of o (ortho) product in electrophilic substitution of a phenyl ring bearing an EWG (electron withdrawing group) is often large enough to merit changing the long held rule-of-thumb for EWGs from being just meta directors into these substituents are best understood as ortho, meta-directors, with a preference for meta. I cannot help but add here a citation[2] to the earliest publication I can find showing tables of both o,p and m-directing groups and dating from 1887, so this rule is 138 years old (at least).
References
- P.R. Rablen, "Typical Electron-Withdrawing Groups Are ortho, meta-Directors Rather than meta-Directors in Electrophilic Aromatic Substitution", The Journal of Organic Chemistry, vol. 90, pp. 6090-6093, 2025. https://doi.org/10.1021/acs.joc.5c00426
- H.E. Armstrong, "XXVIII.—An explanation of the laws which govern substitution in the case of benzenoid compounds", J. Chem. Soc., Trans., vol. 51, pp. 258-268, 1887. https://doi.org/10.1039/ct8875100258
WATOC 2025 report – extending the limits of computation (accuracy).
June 25th, 2025This are just a few insights I have got from some of the talks I attended. As usual, this does not represent a report on the WATOC congress itself, but simply some aspects that caught my personal eye. Read the rest of this entry »
WATOC25 and its (Dr Who like) regeneration to Young WATOC25.
June 21st, 2025The WATOC congresses occur every three years. WATOC25, the 13th in a series which started in 1987 takes places tomorrow in Oslo, Norway, The day before the main event there is something new – a session just for early career researchers or “Young WATOC”. As an “old” WATOCer, I dropped into the opening session and was delighted to find a packed auditorium, with literally standing room only comprising mostly young researchers in their 20s.
Mechanism of the dimerisation of Nitrosobenzene.
June 14th, 2025I am in the process of revising my annual lecture to first year university students on the topic of “curly arrows”. I like to start my story in 1924, when Robert Robinson published the very first example[1] as an illustration of why nitrosobenzene undergoes electrophilic bromination in the para position of the benzene ring. I follow this up by showing how “data mining” can be used to see if this supports his assertion. I have used the very latest version of the CSD crystal structure database to update the version originally posted here in 2020.[2]
References
- "Forthcoming events", Journal of the Society of Chemical Industry, vol. 43, pp. 1295-1298, 1924. https://doi.org/10.1002/jctb.5000435208
- H. Rzepa, "The first ever curly arrows. Revisited with some crystal structure mining.", 2020. https://doi.org/10.59350/c6thp-wqe69