After around 40 posts here, I decided to take a look at the whole effort and ask some questions.

Imperial College London

After around 40 posts here, I decided to take a look at the whole effort and ask some questions. For example Should (scientific) blogs be used to report new science, or merely opinion on existing science (see this blog also)? If the former, should they be abstracted in the manner of regular articles (e.g. by CAS etc). Unlike e.g. a journal, a blog is often (and certainly in this case) the effort of an individual.

How long will a blog last?  ArchivePress

The triennial conference is this year located in Munich. With 1500 participants and six parallel sessions, this report can give only a flavour of proceedings.

The triennial conference is this year located in Munich. With 1500 participants and six parallel sessions, this report can give only a flavour of proceedings. Edward Valeev talked about the scaling problem in coupled cluster theories, the so-called gold standard for computing the energy and properties of small molecules.

WATOC 2017 report.

In the previous post, 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.

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.

Short B-H&#8230;H-O Interactions in crystal structures &#8211; a short DFT Exploration using B3LYP+D4 and r2scan-3c

The WATOC congresses occur every three years.

The 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.

WATOC25 and its (Dr Who like) regeneration to Young WATOC25.

I should start by saying that the server on which this blog is posted was set up in June 1993. Although the physical object has been replaced a few times, and had been “virtualised” about 15 years ago, a small number of the underlying software base components may well date way back, perhaps even to 1993.

A peak behind the (hosting) scenes of this blog.

Two years ago, I posted on the topic “Internet Archeology: reviving a 2001 article published in the Internet Journal of Chemistry (IJC)”. The IJC had been founded in 1998,  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 […]

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

The even more mysterious N≡N triple bond in a nitric oxide dimer.

In the previous post, 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.

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.

Energy decomposition analysis of hindered alkenes: Tetra t-butylethene and others.

In the previous post I followed up on an article published on the theme “Physical Organic Chemistry: Never Out of Style“. 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 […]

In 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

Why an Electron-Withdrawing Group is an o, m-Director rather than m-Director in Electrophilic Aromatic Substitution: The example of CN vs NC.

I 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 as an illustration of why nitrosobenzene undergoes electrophilic bromination in the para position of the benzene ring.

I 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.

Mechanism of the dimerisation of Nitrosobenzene.

Tom recently emailed me this question: Do you know how to find out how many of the compounds that appear in the chemical literature are mentioned just once? Intrigued, I first set out to find out how many substances, as Chemical Abstracts refers to the them, there were as of 5 June, 2025.

Tom recently emailed me this question:

 Do you know how to find out how many of the compounds that appear in the chemical literature are mentioned just once?

Intrigued, I first set out to find out how many

 substances

, as Chemical Abstracts refers to the them, there were as of

 5 June, 2025

. There is a static estimate here (219 million), but to get the most up to date information, I asked CAS directly.

How many of the compounds that appear in the chemical literature are mentioned just once?

Last year I reminisced on the occasion of the 40th Anniversary of the Macintosh computer.

Last year I reminisced on the occasion of the 40th Anniversary of the Macintosh computer.[1] Four decades of advances in technology now mean I can do a fair amount of computational quantum modelling on a recent Mac (one from 2022 with M1 processor), and since then they have only got even (~2 or 3 times) faster with the M4 processor. Many of the recent calculations done for these blogs have included at least one or two that were done on the Mac.

Forty (one) years on &#8211; The pico-mac-nano and Chemdraw.

Way back in 1977, the crystal structure of the sulfur ring S7 was reported.

Way back in 1977, the crystal structure of the sulfur ring S

 7

was reported.[1] The authors noted that “

 The δ modification of S
 
 7
 
 contains bonds of widely differing length: this has never been observed before in an unsubstituted molecule.

” No explanation was offered, although they note that similar effects have been observed in S

 8

O, S

 7

I

 +

and S

 7

O. The S

 7

molecule

Cyclo-Heptasulfur, S7 – a classic anomeric effect discovered during a pub lunch!

The two previous  posts, on the topic of anomeric effects in 7-membered sulfur rings illustrated how orbital interactions between the lone pairs in the molecules and S-S bonds produced widely varying S-S bond lengths in the molecules, some are shorter than normal (which is ~2.05Å for e.g. the S8 ring) by ~ 0.1Å and some […]

The two previous  posts[1],[2] on the topic of anomeric effects in 7-membered sulfur rings illustrated how orbital interactions between the lone pairs in the molecules and S-S bonds produced widely varying S-S bond lengths in the molecules, some are shorter than normal (which is ~2.05Å for

 e.g.

the S

 8

ring) by ~ 0.1Å and some are longer by ~0.24Å. Here we extend this to the unknown molecule shown below.

5-Imino-5λ4-heptathiepane 3-oxide. More exuberent anomeric effects.

Starting around 2016, journal publishers started including mandatory “Data Availability” statements as part of research articles; a typical (dated) example is linked here, including guidelines for how to cite the data itself.

Starting around 2016, journal publishers started including mandatory “Data Availability” statements as part of research articles; a typical (dated) example is linked here, including guidelines for how to cite the data itself. I wrote about these aspects last year in a blog post for the RSC journal Digital Discovery[1] and here I follow up with more news.

Finding and Discovery Aids as part of data availability statements for research articles.

This is another in the C&amp;E News list of candidates for the Molecule of the Year, Molecular shuttle in a box

This is another in the C&amp;E News list of candidates for the Molecule of the Year,

 Molecular shuttle in a box

[1] Mirror-image cyclodextrin [2]

 Molecular shuttle in a box

[1] Rule-bending strained alkene [3] First soluble promethium complex [4] Single-electron carbon-carbon bond [5] Hot MOF for capturing carbon[6] The molecule shown below inside the cavity is coronene.

Molecules of the Year 2024: Molecular shuttle in a box.

The idea of so-called FAIR (Findable, Accessible, Interoperable and Reusable) data is that each object has an associated metadata record which serves to enable the four aspects of FAIR. Each such record is itself identified by a persistent identifier known as a DOI.

The secrets of FAIR Metadata: optimisation for Chemical Compounds.

Each year C&amp;E News publishes a list of candidates for the Molecule of the Year.

Molecules of the Year 2024: A crystal structure perspective on anti-Bredt olefins.

More than 100 years ago, before the quantum mechanical treatment of molecules had been formulated, G. N. Lewis proposed a simple model for chemical bonding that is still taught today.

More than 100 years ago, before the quantum mechanical treatment of molecules had been formulated, G. N. Lewis proposed[1] a simple model for chemical bonding that is still taught today. This is the idea of the three categories of bond we know as single, double and triple, comprising respectively two, four and six shared electrons each, at least for the very common carbon-carbon bond.

A carbon-carbon one-electron bond!  Or a weak carbon-carbon interaction?

Calicheamicin was noted in the previous post as a natural product with antitumour properties and having many weird structural features such as  an unusual “enedidyne” motif. The representation is shown below.

Calicheamicin was noted in the previous post as a natural product with antitumour properties and having many weird structural features such as  an unusual “enedidyne” motif. The representation is shown below. A partial structure shown below for Calicheamicin replaces the -(CH

 2

)4- substructure with a four carbon chain that includes two sp

 2

centres instead of two sp

 3

centres.

Mechanism of the Masamune-Bergman reaction. Part 3: The transition state for Calicheamicin models.

The Masamune-Bergman reaction, is an example of  a highly unusual class of chemical mechanism involving the presumed formation of the biradical species shown as Int1 below by cyclisation of a cycloenediyne reactant. Such a species is  so reactive that it will be quickly trapped, as for example by dihydrobenzene to form the final product.

The Masamune-Bergman reaction[1],[2] is an example of  a highly unusual class of chemical mechanism[3] involving the presumed formation of the biradical species shown as

 Int1

below by cyclisation of a cycloenediyne reactant. Such a species is  so reactive that it will be quickly trapped, as for example by dihydrobenzene to form the final product.

Mechanism of the Masamune-Bergman reaction. Part 1.

Calicheamicin is a natural product with antitumour properties discovered in the 1980s, with the structure shown below. As noted elsewhere, this structure has many weird properties, including amongst other features an unusual “enedidyne” motif and the presence of an iodo group on an aromatic ring.

Mechanism of the Masamune-Bergman reaction. Part 2: a possible 3D Model  for Calicheamicin revealing the non-covalent-interactions (NCI) present.

In the previous post, I explored the so-called “impossible” molecule methanetriol. It is regarded as such because the equilbrium resulting in loss of water is very facile, being exoenergic by ~14 kcal/mol in free energy. Here I explore whether changing the substituent R could result in suppressing the loss of water and stabilising the triol.

Possible  Formation of an Impossible Molecule?

Back in 2017, I was asked to peer review an article and its author asked if I would like the review to be “open” – that is that my name would be shown as a reviewer; 10.1073/pnas.1709586114[/cite/] indeed it was!

Back in 2017, I was asked to peer review an article and its author asked if I would like the review to be “open” – that is that my name would be shown as a reviewer; [1] Replication in Science was – and still is – a hot topic and I had taken the opportunity with this article to try to (successfully I might add) replicate its main (computational) findings.

Revisiting open/transparent peer review.

Metadata is something that goes on behind the scenes and is rarely of concern to either author or readers of scientific articles. Here I tell a story where it has rather greater exposure.

Metadata is something that goes on behind the scenes and is rarely of concern to either author or readers of scientific articles. Here I tell a story where it has rather greater exposure. For journals in science and chemistry, each article published has a corresponding metadata record, associated with the persistent identifier of the article and known to most as its DOI.

How should data  be cited in journal articles?  A Crossref request for public comment!

Chemists now use the term “curly arrows” as a language to describe the electronic rearrangements that occur when a (predominately organic) molecule transforms to another – the so called chemical reaction. It is also used to infer, via valence bond or resonance theory, what the mechanistic implications of that reaction are.

Chemists now use the term “curly arrows” as a language to describe the electronic rearrangements that occur when a (predominately organic) molecule transforms to another – the so called chemical reaction. It is also used to infer,

 via

valence bond or resonance theory, what the mechanistic implications of that reaction are.

The 100th Anniversary year of Curly Arrows.

The recent release of the DataCite Data Citation corpus, which has the stated aim of providing “a trusted central aggregate of all data citations to further our understanding of data usage and advance meaningful data metrics” made me want to investigate what the current state of citing data in the area of chemistry might be. […]

The recent release of the DataCite Data Citation corpus, which has the stated aim of providing “a trusted central aggregate of all data citations to further our understanding of data usage and advance meaningful data metrics” made me want to investigate what the current state of citing data in the area of chemistry might be. Chemistry is known to be a “data rich” science (as most of the physical sciences are) and  here on this very blog I

Data Citation &#8211; a snapshot of the chemical landscape.

What constitutes an “impossible molecule”? Well, here are two, the first being the topic of a recent article. The second is a favourite of organic chemistry tutors, to see if their students recognise it as an unusual (= impossible) form of a much better known molecule.

What constitutes an “impossible molecule”? Well, here are two, the first being the topic of a recent article[1]. The second is a favourite of organic chemistry tutors, to see if their students recognise it as an unusual (= impossible) form of a much better known molecule. Perhaps we could define impossible molecules into two slightly different classes.

Exploring Methanetriol &#8211; &#8220;the Formation of an Impossible Molecule&#8221;

In the late 1980s, as I recollected here the equipment needed for real time molecular visualisation as it became known as was still expensive, requiring custom systems such as Evans and Sutherland PS390 workstations.

In the late 1980s, as I recollected here[1] the equipment needed for real time molecular visualisation as it became known as was still expensive, requiring custom systems such as Evans and Sutherland PS390 workstations.

3D Molecular model visualisation: 3 Million atoms +

Previously, a mechanism with a reasonable predicted energy was modelled for the isomerisation of an oxetane carboxylic acid to a lactone by using two further molecules of acid to transfer the proton and in the process encouraging an Sn2 reaction with inversion to open the oxetane ring.

Previously, a mechanism with a reasonable predicted energy was modelled for the isomerisation of an oxetane carboxylic acid to a lactone by using two further molecules of acid to transfer the proton and in the process encouraging an Sn2 reaction with inversion to open the oxetane ring. We are now ready to explore variations to this mechanism to see what happens.

Unexpected Isomerization of Oxetane-Carboxylic Acids – catalyst design.

In the previous post, I looked at the intramolecular rearrangement of the oxetane carboxylic acid to a lactone, finding the barrier to the Sn2 reaction with retention was unfeasibly high. Here I explore alternatives.

In the previous post, I looked at the intramolecular rearrangement of the oxetane carboxylic acid to a lactone, finding the barrier to the Sn2 reaction with retention was unfeasibly high. Here I explore alternatives. This first attempt uses a second molecule of a carboxylic acid (modelled as formic acid for simplicity) to see if it can catalyse the reaction.

Unexpected Isomerization of Oxetane-Carboxylic Acids – a viable mechanism

When you talk π-aromaticity, benzene is the first molecule that springs to mind. But there are smaller molecules that can carry this property; cyclopropenylidene (five atoms) is the smallest in terms of atom count I could think of until now, apart that is from H3+ which is the smallest possible molecule that carries σ-aromaticity.

When you talk π-aromaticity, benzene is the first molecule that springs to mind. But there are smaller molecules that can carry this property; cyclopropenylidene (five atoms) is the smallest in terms of atom count I could think of until now, apart that is from H

 3


 +

which is the smallest possible molecule that carries σ-aromaticity.

An unusually small (doubly) aromatic molecule: C4.

Sometimes a (scientific) thought just pops into one’s mind. Most are probably best not shared with anyone, but since its the summer silly season, I thought I might with this one.

Sometimes a (scientific) thought just pops into one’s mind. Most are probably best not shared with anyone, but since its the summer silly season, I thought I might with this one. Famously, according to Einstein, m  = E/c^^2, the equivalence of energy to mass. Consider a typical exoenergic chemical reaction:   A → B, ΔG -100 kJ/mol.

Question for the day &#8211; Einstein, special relativity and atomic weights.

In the previous post, I showed that carbon can act as a hydrogen bond acceptor (of a proton) to form strong hydrogen bond complexes. Which brings me to a conceptual connection: can singlet dicarbon form such a hydrogen bond?

In the previous post, I showed that carbon can act as a hydrogen bond acceptor (of a proton) to form strong hydrogen bond complexes. Which brings me to a conceptual connection: can singlet dicarbon form such a hydrogen bond?  Dicarbon can be variously represented as above. The first form shows it as a bis-carbene, with an unbonded lone pair of electrons at each end of a carbon double bond.

Carbon as a hydrogen bond acceptor: can dicarbon (C2) act in this manner?

I occasionally notice that posts that first appeared here many years ago suddenly attract attention.

The strongest bond in the universe: revisited ten years on.

In the previous post, I looked at the so-called Kekulé vibration of cyclo[18]carbon using various quantum methods and basis sets.

In the previous post, I looked at the so-called Kekulé vibration of cyclo[18]carbon using various quantum methods and basis sets.  Because some of these procedures can take a very long time,  I could not compare them using the same high-quality consistent atom basis set for the carbon (Def2-TZVPP). Here I try to start to do this using the smaller six and ten carbon rings to see what trends might emerge.

Cyclo[6]  and [10]carbon. The Kekulé vibrations compared.

Click on diagram to see model. The reaction above is ostensibly a very simple pericyclic ring opening  of a cyclopropyl carbocation to an allyl cation, preceeded by a preparatory step involving SN-1 solvolysis. As a 2-electron thermal process, the second step proceeds with disrotation of the terminii. Can this stereochemistry be illustrated with a computed model for the transition state for this process?

Pericyclic assistance for SN-1 solvolysis

It was about a year ago that I came across a profusion of colour in my local Park. Although colour in fact was the topic that sparked my interest in chemistry many years ago (the fantastic reds produced by diazocoupling reactions), I had never really tracked down the origin of colours in many flowers.

It was about a year ago that I came across a profusion of colour in my local Park. Although colour in fact was the topic that sparked my interest in chemistry many years ago (the fantastic reds produced by diazocoupling reactions), I had never really tracked down the origin of colours in many flowers. It is of course a vast field.

Why do flowers such as roses, peonies, dahlias, delphiniums (etc), exhibit so many shades of colours?

The title of this post comes from an article published in a special virtual issue on the theme “Physical Organic Chemistry: Never Out of Style” 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 […]

The 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

“Typical Electron-Withdrawing Groups Are o, m-Directors Rather than m-Directors in Electrophilic Aromatic Substitution”

In an earlier blog, I discussed 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.

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.

The mysterious N=N double bond in nitrosobenzene dimer.

This 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.

This 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. Frank Neese talked about his Bubblepole approximation for large molecules.[1] And he was not kidding – large.

WATOC 2025 report &#8211; extending the limits of computation (accuracy).

In this series of posts about the electronic effects in small sulfur rings I have explored increasingly large induced geometric effects.

In this series of posts about the electronic effects in small sulfur rings[1] I have explored increasingly large induced geometric effects. Here is the largest so far, for the compound S

 7

I

 1+

[2] The calculated geometry[3] is shown below, with the crystallographic values in parentheses – the two matching very well.

S7I1+: The largest anomeric effect exhibited by sulfur.

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.

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. I show the results for the previous blog[1] here. Martin Fenner has just added some interesting new features[2] which I thought would be useful to share with you here.

The spin-offs from adding citations to blog posts.

I thought I was done with exploring anomeric effects in small sulfur rings. However, I then realised that all the systems that I had described had an odd number of atoms and that I had not looked at any even numbered rings.

I thought I was done with exploring anomeric effects in small sulfur rings. However, I then realised that all the systems that I had described had an odd number of atoms and that I had not looked at any even numbered rings. Thus hexasulfur is a smaller (known) ring version of S

 8

, the latter by far the best known allotrope of this element of course.

Cyclo-S6 (Hexathiane) &#8211; anomeric effects again!

Derek Lowe tells the story of “carbyne”, a potential further allotrope of carbon, comprising linear chains of carbon atoms, C-C≡C-C≡C-C. Whether such a molecule can exist on its own has long been the the topic of speculation. Now a report has appeared of a “pseudocarbyne”, stabilised by gold atoms.

Derek Lowe tells the story of “carbyne”, a potential further allotrope of carbon, comprising linear chains of carbon atoms, C-C≡C-C≡C-C. Whether such a molecule can exist on its own has long been the the topic of speculation.

Au-pseudocarbyne &#8211;  a unusual example of a twelve coordination by carbon.

Following on from my template exploration of the Wilkinson hydrogenation catalyst, I now repeat this for the Grubbs variant of the Alkene metathesis reaction. As with the Wilkinson, here I focus on the stereochemistry of the mechanism as first suggested by Chauvin, an aspect lacking in eg the Wikipedia entry.

Following on from my template exploration of the Wilkinson hydrogenation catalyst, I now repeat this for the Grubbs variant of the Alkene metathesis reaction. As with the Wilkinson, here I focus on the stereochemistry of the mechanism as first suggested by Chauvin[1], an aspect lacking in eg the Wikipedia entry.

Mechanistic templates computed for the Grubbs alkene-metathesis reaction.

First, a very brief history of scholarly publishing, starting in 1665 when scientific journals started to be published by learned societies.

First, a very brief history of scholarly publishing, starting in 1665[1] when scientific journals started to be published by learned societies. This model continued until the 1950s, when commercial publishers such as Pergamon Press started with their USP (unique selling point) of rapid time to publication of ~3 months,[2] compared to typical times for many learned society publishers of 2 years or longer.

Scholarly journals vs Scholarly Blogs.

The Science education unit at the ACS publication C&amp;EN publishes its list of molecules of the year (as selected by the editors and voted upon by the readers) in December. Here are some observations about three of this year’s batch.

The Science education unit at the ACS publication C&amp;EN publishes its list of molecules of the year (as selected by the editors and voted upon by the readers) in December. Here are some observations about three of this year’s batch. Diberyllocene[1] with its unusual Be-Be bond has already beeen covered on this blog.[2], where I commented that lithioborocene should be possible to make as well.

Molecules of the year: 2023

In 2023, we very much take for granted that everyone and pretty much everything is online. But it was not always so and when I came across an old plan indicating how the chemistry department at Imperial College was connected in 1989, I was struck by how much has happened in the 34 years since.

In 2023, we very much take for granted that everyone and pretty much everything is online. But it was not always so and when I came across an old plan indicating how the chemistry department at Imperial College was connected in 1989, I was struck by how much has happened in the 34 years since. Nowadays all the infrastructures needed are effectively “built in” to the building when it is constructed and few are even aware of them.

A trip down memory lane: An online departmental connection map from 1989.

What’s a Journal For? This debate has been raging ever since preprint servers were introduced as far back as 1991!

Derek Lowe asks &#8220;What&#8217;s a Journal For?&#8221; &#8211; Knowledge graphs?

I am a member of the  Royal Society of  Chemistry’s Historical group. Amongst other activities, it publishes two editions of a newsletter each year for its members.

Two influential textbooks &#8211; &#8220;Mee&#8221;  and &#8220;Mellor&#8221;.

The Swern oxidation is a class of “activated” dimethyl sulfoxide (DMSO) reaction in which the active species is a chlorodimethylsulfonium chloride salt.

The Swern oxidation[1] is a class of “activated” dimethyl sulfoxide (DMSO) reaction in which the active species is a chlorodimethylsulfonium chloride salt.

Pre-mechanism for the Swern Oxidation: formation of chlorodimethylsulfonium chloride.

Some time ago in 2010, I showed a chemical problem I used to set during university entrance interviews. It was all about pattern recognition and how one can develop a hypothesis based on this.

Some time ago in 2010, I showed a chemical problem I used to set during university entrance interviews. It was all about pattern recognition and how one can develop a hypothesis based on this. In that instance, it involved recognising that a cyclic molecule which appeared to have the cyclohexatriene benzene-aromatic pattern

 1

was in fact a trimer of carbon dioxide.

Tunable aromaticity?  An unrecognized new aromatic molecule?

In an earlier post on this topic,‡ I described how the curly-arrows describing the mechanism of a nucleophilic addition at a carbonyl group choreograph in two distinct ways, as seen in red or blue below.

In an earlier post on this topic,[1]

 ‡

I described how the curly-arrows describing the mechanism of a nucleophilic addition at a carbonyl group choreograph in two distinct ways, as seen in red or blue below. The arrows in red can be described as firstly addition to the carbonyl group to form either a transient intermediate (a two-step process) or instead a formal transition state state as a concerted single-step mechanism.

More examples of &#8220;double-headed&#8221; curly arrows: S and C Nucleophiles attacking acetyl chloride

This editorial from Nature is a timely reminder of the importance of data.

This editorial from Nature[1] is a timely reminder of the importance of data.

&#8220;For chemists, the AI revolution has yet to happen&#8221;.

Science frequently works by people making connections between related (or even apparently unrelated) concepts or data. There are many ways of helping people make these connections – attending a conference or seminar, searching journals for published articles and nowadays also searching for data are just a few examples.

A ROR Persistent Identifier for the WATOC organisation &#8211; helping to make scientific connections.

The topic of dicarbon, C2, has been discussed here for a few years now. It undoubtedly would be a gas!

The topic of dicarbon, C

 2

, has been discussed here for a few years now. It undoubtedly would be a gas!

Gaseous carbon: The energetics of two forms of tetracarbon, C4 and a challenge!

In the previous post, I discussed how data associated with two of the candidates for molecules of the year – 2022 could be retrieved and then used to inspect their three dimensional structures. Here I focus on the ultra large cavitands recently reported.

In the previous post, I discussed how data associated with two of the candidates for molecules of the year – 2022 could be retrieved and then used to inspect their three dimensional structures. Here I focus on the ultra large cavitands recently reported[1]. As I noted, these have an associated data coordinate archive published on Zenodo (DOI: 10.5281/zenodo.6953961) although this is not cited in the article itself.

Molecules of the year -2022. A closer look at the Megalo-Cavitands.

The term bispericyclic reaction was famously coined by Caramella et al in 2002 to describe the unusual features of the apparently innocuous dimerisation of cyclopentadiene.

The term bispericyclic reaction was famously coined by Caramella

 et a

l in 2002[1] to describe the unusual features of the apparently innocuous dimerisation of cyclopentadiene. It shows features of two paths for different pericyclic reactions, comprising a 2+4 cycloaddition in the early stages, but evolving into a (degenerate) pair of [3,3] sigmatropic reactions in the latter stages.

A new type of bispericyclic reaction: Cyclopropanone + butadiene.

The recently reported synthesis of octafluorocubane established a sublimation point as 168.1–177.1°C (a melting point was not observed). In contrast, the heavier perfluoro-octane has an m.p. of -25°C. Why the difference? Firstly, the crystal structure is shown below, albeit as a dimer rather than a periodic lattice (click on image to obtain 3D coordinates).

The recently reported synthesis[1] of octafluorocubane established a sublimation point as 168.1–177.1°C (a melting point was not observed). In contrast, the heavier perfluoro-octane has an m.p. of -25°C. Why the difference?

Why does octafluorocubane have such a high sublimation point?

In previously asking what the largest angle subtended at four-coordinate carbon might be, I noted that as the angle increases beyond 180°, the carbon becomes inverted, or hemispherical (all four ligands in one hemisphere). So what does a search for this situation reveal in the CSD?

Examples of inverted or hemispherical carbon?

Four-coordinate carbon normally adopts a tetrahedral shape, where the four angles at the carbon are all 109.47°. But how large can that angle get, and can it even get to be 180°?

Four-coordinate carbon normally adopts a tetrahedral shape, where the four angles at the carbon are all 109.47°. But how large can that angle get, and can it even get to be 180°?    A search of the CSD (crystal structure database) reveals a spiropentane as having the largest such angle, VAJHAP with 164°[1]    Because crystal structures might have artefacts such as disorder etc, it is always good to check this with a calculation;

What is the largest angle possible at 4-coordinate carbon &#8211; 180°?

Previously, I looked at autocatalytic mechanisms where the carboxyl group of an oxetane-carboxylic acid could catalyse its transformation to a lactone, finding that a chain of two such groups were required to achieve the result.

Previously, I looked at autocatalytic mechanisms where the carboxyl group of an oxetane-carboxylic acid could catalyse its transformation to a lactone, finding that a chain of two such groups were required to achieve the result. Here I look at an alternative mode where the oxetane-carboxylate itself acts as the transfer chain, via a H-bonded dimer shown below.

Unexpected Isomerization of Oxetane-Carboxylic Acids – an alternative autocatalytic mechanism evaluated.

Proton transfers are amongst the most common of all chemical reactions.

Geometries of proton transfers: modelled using total energy or free energy?

Minds (and memories) can work in wonderful ways. In 1987 we were looking at the properties of “stable” tetrahedral intermediates formed in carbonyl group reactions. The reaction involved adding phenylhydroxylamine to acetyl cyanide.

Minds (and memories) can work in wonderful ways. In 1987[1] we were looking at the properties of “stable” tetrahedral intermediates formed in carbonyl group reactions. The reaction involved adding phenylhydroxylamine to acetyl cyanide. NMR signals for two new species were detected, and we surmised one was due to N-attack on the carbonyl and one was due to O-attack, in each case to form a stable tetrahedral intermediate.

Checking a conclusion we made in 1987:  Tetrahedral intermediates formed by nitrogen and oxygen attack of aromatic hydroxylamines on acetyl cyanide

I have long been fascinated by polymers of either carbon dioxide,† or carbon monoxide, or combinations of both. One such molecule, referred to as dioxane tetraketone when it was featured on the ACS molecule-of-the-week site and also known as the anhydride of oxalic acid, or more formally 1,4-dioxane-2,3,5,6-tetraone, has been speculated upon for more than a […]

I have long been fascinated by polymers of either carbon dioxide,

 †

or carbon monoxide, or combinations of both. One such molecule, referred to as dioxane tetraketone when it was featured on the ACS molecule-of-the-week site and also known as the anhydride of oxalic acid, or more formally 1,4-dioxane-2,3,5,6-tetraone, has been speculated upon for more than a century.[1] The history of chemistry has many molecules whose

Dioxane tetraketone &#8211; an ACS molecule of the week with a mystery.

I discussed in the previous post the small molecule C4 and how of the sixteen valence electrons, eight were left over after forming C-C σ-bonds which partitioned into six σ and two π. So now to consider B4. This has four electrons less, and now the partitioning is two σ and two π (CCSD(T)/Def2-TZVPPD calculation, […]

I discussed in the previous post the small molecule C

 4

and how of the sixteen valence electrons, eight were left over after forming C-C σ-bonds which partitioned into six σ and two π. So now to consider B

 4

. This has four electrons less, and now the partitioning is two σ and two π (CCSD(T)/Def2-TZVPPD calculation, FAIR DOI: 10.14469/hpc/10157). Again both these sets fit the Hückel 4n+2 rule (n=0). Since B

 4

has

More aromatic species with four atoms. B4 and N4.

Ever since the concept of a shared two-electron bond was conjured by Gilbert N. Lewis in 1916, chemists have been fascinated by the related concept of a bond order (the number of such bonds that two atoms can participate in, however a bond is defined) and pushing it ever higher for pairs of like-atoms.

Ever since the concept of a shared two-electron bond was conjured by Gilbert N. Lewis in 1916,[1] chemists have been fascinated by the related concept of a bond order (the number of such bonds that two atoms can participate in, however a bond is defined) and pushing it ever higher for pairs of like-atoms. Lewis first showed in 1916[1] how two carbon atoms could share two, four or six electrons to achieve a bond order of up to three.

Chasing ever higher bond orders; the strange case of beryllium.

Way back in the late 1980s or so, research groups in chemistry started to replace the filing of their paper-based research data by storing it in an easily retrievable digital form. This required a computer database and initially these were accessible only on specific dedicated computers in the laboratory.

Data base or Data repository? &#8211; A brief and very selective history of data management in chemistry.

An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom.

An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom. A variation is to replace one oxygen by a nitrogen atom, as in N-C-O. Shown below is a scatter plot of the two distances to the common carbon atom derived from crystal structures. You can see some entries for which the C-O bond length is shorter than normal and the C-N distance very much longer than normal;

More record breakers for the anomeric effect involving C-N bonds.

In the previous post, I showed some of the diverse “non-classical”interactions between Biotin and a protein where it binds very strongly. Here I take a look at two of these interactions to discover how common they are in small molecule structures.

Protein-Biotin complexes. Crystal structure mining.

Earlier this year, Molnupiravir hit the headlines as a promising antiviral drug.

Earlier this year, Molnupiravir hit the headlines as a promising antiviral drug. This is now followed by Paxlovid, which is the first small molecule to be aimed by design at the SAR-CoV-2 protein and which is reported as reducing greatly the risk of hospitalization or death when given within three days of symptoms appearing in high risk patients.      The Wikipedia page (first created in 2021)  will display a pretty good JSmol 3D model of this;

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